Medical Biochemistry-Exam 3 (Everything)

In which human organ is myoglobin (Mb) most impt?
heart b/c rapid O2 supply needed
Explain causes and importance of right shift in Hb/O2 binding curve

right shift caused by:

 

decreased pH (increased [H+])

 

increased [CO2]

 

increased [2,3-BPG]

 

increased temperature

 

all factors lead to increased O2 unloading which means that a higher percentage of O2 is delivered to tissues

In Hb, how does binding of first oxygen molecule affect binding of next ones?

Deoxy Hb is usually in taut (T) form where heme groups restricted and hard for O2 to bind

 

When O2 binds to 1st heme group, the Fe of that heme will shift and pull attached his along.

 

Movement breaks salt bridges pushing Hb into relaxed (R) state and allow more O2 binding sites to become available

 

 

What is Bohr effect?

A right shift when pH decreases (increase in H+ conc.)

 

O2 release from Hb will increase when pH is lowered or [CO2] is high

 

Hb has decreased O2 affinity

 

Raising pH or decreasing [CO2]-shift curve to left

Physiological importance of cooperativity in Hb function
Hb has 4 subunits where binding of O2 at one heme group increases the affinity for O2 of the other heme groups in the same molecule
Compare behavior of Mb and Hb with respect to O2, CO2, and H+

Mb has a greater affinity at lower [O2] than Hb

 

Hb can transport more molecules of O2 b/c of cooperative effect of multiple binding sites

 

Hb can’t readily bind 1st O2, but once it does has higher affinity for O2 at other sites

;

Hb-sigmoidal curve

;

Mb-hyperbolic

;

Hb responds more readily to small changes in partial pressures of O2

;

Mb saturated quicker than Hb at low partial pressure of O2 (doesn’t have much flexibility)

How does protein (globin) portion of Mb or Hb affect reactivity of heme?

weaken strength of heme-O2 interaction. Heme binds O2 so stronglyit can convert it to a superoxide anion, which can be an unwanted oxidizing agent

 

prevents interaction of oxy-heme groups with other oxy-heme groups

How and where does 2,3-BPG interact with Hb?

2,3-BPG binds to deoxy Hb-makes it more stable and resistant to oxygenation after O2 delivery

 

negative charge allows BPG to bind to a site between two alpha chains

 

causes right shift in O2-dissociation curve (lower O2 release)

Where does 2,3-BPG come from?
product of glycolytic pathway
How does fetal Hb (HbF) differ from HbA?

Fetal Hb has two gamma chains instead of beta chains.

 

2,3-BPG can’t bind to fetal Hb and it has greater affinity fo O2 and takes O2 from maternal Hb

;

HbF is left shifted on O2-dissociation curve compared to maternal Hb

;

;

What does Hill Eqn describe?
importance of cooperativity
How does NO interact w/ Hb and what is physiological significance of that interaction?

Hb binds NO at heme Fe and cys residues in globin chain.

;

NO relaxant for vascular smooth muscle

;

Hb can pick up NO, stiffen vascular tissues, and increase BP

;

NO is strong vasodilator so Hb can be used to mediate vascular tone

What is difference btwn HbS and HbA?
HbA has normal beta chain while HbS has sickly cell hemoglobin. 6th AA for normal beta globin would be a glutamic residue but in HbS that Glu is replaced with a Val. Val is uncharged and allows hydrophobic pockets. The chains bind together and crystallize
Physiochemical/Pathological Basis for All Clinical Manifestations of Sickle Cell Disease

crystallization and stiffening of Hbs causes them to adhere to the endothelium and often obstruct small vessels (capillaries) or cause hemolysis

;

hemolysis can cause anemia and hyperbilirubinemia, causing pallor and jaundice

;

Complete vasocclusion can cause ishemia or infarction resulting in organ damage

;

Stroke, infection and excrutiating pain can result

How is Sickle Cell Disease Inherited?
recessive disorder. Only homozygous HbS cause the disease to become expressed.
What is an enzyme?

a protein catalyst for specific biochem rxns.

;

It will not undergo chem rxnitself and can be reused for other rxns

What does enzyme effect and not effect in rxn?

;

;

Enzymes reduce activation energy.

;

Keq and delta G are not affected by enzymes.

Name and describe 2 models used to describe enzyme specificity and/or catalytic activity

lock and key model

;

describes an enzyme active sites (lock) being specific for binding substrate (key)

describe specificity

;

induced fit model

;

active site will conform to fit substrate

describes specificity and catalytic activity

What is prosthetic group?

non-protein organic molecule that is tightly bound to enzyme active site

;

ex-heme, biotin, or flavin

;

holoenzyme-prosthetic group attached

;

apoenzyme-prosthetic group NOT attached

Name 6 Classes of Enzymes

oxidoreductases-catalyze RED/OX reactions

Ex-H+ donor to substrate


transferases-transfer group from one molecule to another

Ex-phosphoylases


hydrolases-hydrolytic cleavage of bond

Ex-peptide bond cleavage


lyases-cleave bonds w/o water to leave double bond or addition of other groups to double bond

Ex-decarboxylase


isomerases-change geometry of molecule

Ex-cis-trans isomerase


ligases-join 2 molecules together though hydrolysis of high energy bond

Ex-carboxylase

What is Michaelis-Menton Eqn and what do terms mean?

V = Vmax[S]/(Km+[S])

;

V – velocity of rxn

Vmax – max rxn velocity

[S] – substrate concentration

Km – constant value for a specific substrate

;

In a Michaelis-Menton plot, where is Vmax and how do you find Km?

Vmax – when [S] is very high

;

Km – [S] when V = 1/2(Vmax)

A Lineweaver-Burk plot is also called a ———
Double-reciprocal plot
What is plotted on Lineweaker-Burk plot and what are the x- and y-intercepts of the plot?

The LB graph plots the inverse of the Michaelis-Menten plot, which is 1/V on the y-axis and 1/[S] on the x-axis

 

x-intercept – 1/Km

 

y-intercept – 1/Vmax

What are advantages of the Eadie-Hofstee plot?
The E-H plot gives more evenly spaced data points than the  L-B plot.
What characteristics distinguish a competitive inhibitor from the other types of inhibitors?

bind directly to the active site and can be overcome by increased [substrate].

 

Other inhibitors bind to other sites on enzyme

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for competitively inhibited rxns?

same y-intercept

 

different x-intercepts

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for non-competitively inhibited rxns?

different y-intercepts

 

same x-intercepts

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for uncompetitively inhibited rxns?

different y-intercepts

 

different x-intercepts

What does inhibitor react with for competitive inhibition?
active site of the enzyme
What does inhibitor react with for non-competitive inhibition?
react with enzyme to reduce its effectiveness to bind w/ substrate
What does inhibitor react with for uncompetitive inhibition?

bind with ES complex.

 

irreversible inhibitors.

Sigmoid V versus [S] plot and curved Lineweaver-Burk plots indicate
allostery and positive cooperativity of the enzyme (n = 2)
What factors determine the amount of enzyme activity in serum?

amount of tissue producing enzyme

 

rate of enzyme released

 

rate of enzyme inactivation/elimination from plasma

Define: Standard International Unit (SIU)
1 standard international unit of enzyme activity converts 1 μM of substrate/minute
2 most commonly measured serum aminotransferases and describe rxns they catalyze

Aspartate aminotransferase (AST) – catalyzes exhange of amino group between alpha amino acids (aspartate) and alpha keto acids

 

Alanine aminotransferase (ALT) – catalyzes exchange of amino group between alpha amino acids (alanine) and alpha keto acids

In which pathological states are the two most commonly measured serum aminotransferases elevated?

AST – liver damage and myocardial cells,hemolysed blood

 

ALT – liver damage

Reaction catalyzed by γ-glutamyltranspeptidase and how it is used diagnostically?

Glutathione + amino acids → γ-glutamyl-amino acid + cys-gly

 

γ-glutamyltranspeptidase found in kidney, intestine, liver, and fetal tissue

 

GGT levels are elevated and very sensitive in liver damage

 

2 commonly measured phosphatases and how are they used diagnostically?

Alkaline phosphatase (ALP)

 

Hydrolyzez phosphate groups from organic monophosphate at pH~9

Found in liver, bone, intestine, and placental tissue

Elevation of ALP means damage to liver and bone tissue

Elevated in gowing children, bone fractures, and pregnant women

 

Acid Phosphatase

 

hydrolyzes phosphate groups from organic monophosphates at pH~5

 

found in prostate, platelets, and erythrocytes

Elevation found in metastatic prostate cancer and hemolysed blood samples

 

 

Diagnostic utility of LDH
Used to detect MI and hemolysis
“flipped” LDH

Most common form is LDH2 (HHHM)

 

After MI or hemolysis, LDH1 (HHHH) predominates causing a “flipped” LDH b/c LDH1>LDH2

What reaction does LDH catalyze?

Lactate + NAD → pyruvate + NADH + H

 

interconversion of pyruvate and lactate

Another name for alpha hydroxybutyrate dehydrogenase (HBD)?

 

 

LDH1
What does elevated serum HBD mean?
damage to myocardial cells due to recent MI
Reaction catalyzed by CK (CPK)
creatine phosphate + ADP → Creatine + ATP
Diagnostic meaning of elevated serum CK

has 2 subunits, M and B

 

MB-MI or brief ischemia

 

MM-vigorous exercise, injection, convulsions

 

BB-neural tissue damage

Diagnostic significance of elevated serum amylase

pancreatitis

 

morphine

Reaction catalyzed by serum amylase

starch + H2O → maltose, maltotriose & limit dextrins

 

digest starch

Elevated serum lipase means

pancreatic pathology

 

morphine

Reaction catalyzed by serum lipase

trigylceride + H2O → fatty acids + glycerol

 

fat digestion

What are troponins and how are they used in diagnosis?

proteins that function in the contractile apparatus of the muscle

 

Cardiac troponin I is increased in plasma 3-6 hours after MI

Serum Enzyme Levels in crush injury

mildly elevated alkaline phosphatase (healing bone)

 

elevated creatine kinase MM (skeletal muscle)

Serum Enzyme Levels in vigorous exercise
elevated creatine kinase MM (skeletal muscle)
Serum Enzyme levels in morphine injection
elevation of serum amylase and lipase
Serum Enzyme Levels in pregnancy

mildly elevated alkaline phosphatase (bone growth)

 

elevated GGT

Four Categories of Cell Adhesion Molecules

integrins

 

immunoglobulin superfamily

 

cadherins

 

selectins

Which of the CAM categories would be actively involved in transmitting signals from the inside to the outisde of the cells and vice versa?
integrins
What CAM category is involved in adherens junction between cell?
cadherins
Abbreviations for 3 types of adhesion molecules of Ig suberfamily and tell their origins

NCAM – neural cell adhesion molecule

 

PECAM – platelet-endothelial cell adhesion molecule

 

VCAM – vascular cell adhesion molecule

 

Named for their similarity in structure to the Igs

4 Diseases in which CAMS are involved

Rheumatoid arthritis – overexpression of VCAMs

 

Psoriasis – form of an integrin

 

Pemphigus vulgaris – autoantibodies interacting with desmoglein

 

von Willebrand disease – expression of P-selectin

Describe alpha-helix
tightly coiled, stabilized by H bonding btwn imido groups and oxygen of carbony groups, many helices (3.6 AA/turn)
Beta sheet

regions of same chain or neighboring chains bond to each other w/ H bonds, the H bonds are perependicular to the long axis of the chain

 

most stable conformation – antiparallel sheets (one side N→C other side C→N

Beta turns

H bonding of AA 3 sequences apart in same chain

 

results in U turn bend of chain

What AA usually phosphoylated in proteins?

ser

 

thr

 

tyr

Commonly occurring modification of AA found in some proteins

acetylation of N terminus

 

carboxylation – add COOH

 

hydroylation – add OH

 

glycosylation – add glucose

 

phosphorylation – add phosphate group

 

disulfide linkages

Primary Structure
AA sequence
Secondary Structure

alpha helix

 

beta-pleated sheets

 

beta-turns

 

random coiling

 

results from free roation of bonds besides peptide bonds

Tertiary Structure

secondary structures fold on each other

 

hydrophobic – inside

hydrophilic – outside

Quarternary Structure
multiple polypeptide chains interact by noncovalent bonds to form single structure
General Solubility Prop. of Proteins

fibrous and insoluble

 

globular and soluble

 

firbrous and soluble

Functions of Proteins

structural roles

 

enzymes

 

role in contractile structures

 

transport (Hb)

 

hormones

 

receptors

 

Abs

What are proteins and peptides made of?

peptides – moderate chain length polymers of amino acids joined by peptide bonds

 

proteins – polymeric compounds composed of AA joined by peptide bonds

What is unique about peptide bond?
it is rigid b/c tautomerism
In ABO blood group, where is difference in oligosaccharide located and how sugars different?

due to presence or absence of N-acetyl-galactosamine or galactose linked to penultimate galactose by C1-C3 linkage

 

1 sugar difference

Glycosaminoglycans and 2 Ex

unbranched polysacc w/ repeating disacc – one is AA, other is uronic acid

 

Ex – hyaluronic acid and heparin

3 Impt Disacc and which alpha or beta linked?

maltose – alpha linked

 

sucrose – alpha linked

 

lactose – beta linked

3 Most Impt polysacc and what are linkages? Why is linkage impt?

starch – alpha linked (spiral)

 

glycogen – 2 types – alpha C1-C4 (linear)

                                 alpha C1-C6 (branched)

 

cellulose – beta linked (linear)

 

alpha and beta linkage affects the shape of the compound and humans can’t digest cellulose b/c beta linkages

What is glycoside?

anomeric -OH group of sugar reacts w/ another -OH compound

 

 

aglycone
compound that attaches to anomeric C of sugar
Name and describe 2 commonly found mod. of sugars

amino sugar – -OH group replaced by amino group

Ex – glucosamine, galactosamine

 

deoxy sugar – 1 OH group replaced by H

Ex – 2-deoxyribose

2 conformation of 6-membered rings
boat and chair
What is mutarotation and where does it take place?

configuration changes in molecule by ring opening and closing

 

occurs at anomeric C

Pyran and furan are named after which sugar structures and how many Cs are in each?

pyranose – 6 C ring

 

furanose – 5 C ring

Most Impt Monosacc and Polysacc made up of this monosacc

glucose – most impt monosacc

 

Polysacc made up of glucose – starch

                                             cellulose

                                             glycogen

What are aldoses?
monosaccharides w/ aldehyde group
What are ketoses?
monosaccharides w/ ketone group
What are carbohydrates?
polyhydroxy aldehydes or ketones or compounts that can by hydrolyzed to these
4 Types of Compounds of which AAs are precursors

hormones

 

nucleotides

 

neurotransmitters

 

AAs

Essential AA

Pvt. Tim Hall

 

Phe

Val

Thr

 

Trp

Ile

Met

 

His

Arg

Leu

Lys

What is nucleotide not found in DNA or RNA that has role in energy metabolism?
NAD+
Patient given adenosine during cardiac arrythmia. EKG during adenosine txt show AV block. If adenosine discontinuation does work, what will?
theophylline
Nucleoside more useful that nucleotide as a drug b/c
nucleoside does not have phosphate group, which restricts movement inside body
Biochemical mechanism that enables coffee-drinking college student to stay awake

caffeine is competitive antagonist of adenosine receptor.

 

Blocks depressant action of adenosine-R and is therefore a stimulant

What is the modification of a normal base found in mRNA?
methylated guanine
What is mod of a normal DNA base that affects gene expression?
methylated cytosine
What happens when DNA exposed to 94 degrees C temperature during PCR?
denaturation and 2 strands separate
What does it mean that DNA strands are “antiparallel”?

strands run in opposite directions

 

one strand goes 3’5′

 

other strand goes 5’3′

Number of H bonds between A and T

 

Number of H bonds between G and C

A-T : 2 bonds

 

G-C: 3 bonds

Difference between nucleotide and nucleic acid

nucleotide – 1 molecule w/ phosphate group, base, and sugar

 

nucleic acid-several nucleotides connected w/ phosphodiester bonds

What 4 bases in DNA

adenine

 

thymine

 

cystosine

 

guanine

4 bases in RNa

adenine

 

uracil

 

cytosine

 

guanine

Diff in chemical structure of nucleotide and nucleoside
no phosphate group is attached to a nucleoside
Difference in chemical structure of ribonucleotide and deoxyribonucleotide

ribose has -OH at 2′ C in pentose sugar

 

deoxy doesn’t

What is difference in chemical structure of purine and pyrimidine?

different nitrogenous bases

 

purine: 2 C-rings

 

pyrimidine – 1 C-ring

which bases purines?
adenine and guanine
Which bases pyrimidines?
cytosine, thymine, uracil (CUT)
3 components of nucleotide

nitrogenous base

 

pentose sugar

 

phosphate group

What purpose does enzyme phosphorylation serve?
regulation of activity and turn pathways on/off
After ATP and GTP cyclized to form cAMP and cGMP, what is their role?
regulate cellular processes through enzyme activation/deactivation
Arsenate can substitute for phosphate of ATP. Arsenate undergoes spontaneous hydrolysis w/o enzymes. What property of ATP as ideal storage does this spoil?

stability

 

ability to form high energy phosphate bonds

What are [ ] of conjugate acid/base when pH = pK?
[conjugate acid/base] are equal to each other (50/50) in solution
What is Henderson-Hasselback equation? How would a doctor use it?

pH = pK’ + log [base]/[acid]

 

Doctor could use it to relate [ ] of each of the conjugated acid/base pairs to the pH of its surrounding enviro

How are “acid” + “base” described in biological systems?

acid – proton donor

 

base – proton acceptor

What are pKs of bicarbonate and phosphate systems?

bicarbonate~6.1

 

phosphate~6.7

Two most impt. buffer systems in body?

 

Which buffer system is more impt and why?

phosphate and bicarbonate

 

bicarbonate is more important because there is a greater [bicarbonate] in the body

How does H+ effect biological systems?

rate of rxns

 

membrane permeability

 

molecule stability and native conformations of proteins and macromolecules

 

rate of transport through membranes

 

drug properties

 

hydrophobicity/hydrophilicity of compound

Equilibrium Constant

Keq = [H+][A-]/ [HA}

 

relate [ion] w/ [aqueous compound]

 

measure of dissociation of compound into ionic components

 

What is H3O+?

 

hydronium ion
Characteristics of H2O responsible for behavior

dipolar

 

H bonds

 

↑ than normal bp for mw

 

↑ than normal fp

 

↑ heat capacity

 

density solid < density liquid (ice floats on liquid H2O)

What rxns do proteins containing S- undergo
sulfahydryl groups oxidized to form disulfide linkages (cysteine)
AA-related cause of pellagra
lack of trp
What AAs contain S?

met

 

cys

What AAs have -OH groups on sidechain?

ser

 

thr

 

tyr

Disorders that arise from defects in tyr metabolism?

tyrosinosis

 

albinism

 

alcaptonuria

Disorder that arises from defects in phe metabolism?
phenylketonuria
Defects in metabolism of which AAs leads to maple syrup urine disease?

val

 

leu

 

pro

 

 

Acidic AAs

glu

 

asp

 

asn

 

gln

Basic AAs

lys

 

arg

 

his

AAs w/ aromatic sidechains

phe

 

tyr

 

trp

AAs w/ aliphatic sidechains

pro

 

ile

 

gly

 

val

 

ala

 

leu

Two Ex of Differences Between Identical Twins that Illustrate that Environment plays a role in development and health

fingerprints are different of two twins – different positions in womb

 

type I diabetes – if one gets, less than 1/2 the time other twin gets

What percentage of live births suffer from a disease causing monogenic defect?

 

1/100 or 1% of libe births suffer from a monogenic defect
What percentage of live births suffer from a disease-causing chromosomal abnormality?
1/1000 or 0.1% of live births suffer from a disease-causing chromosomal abnormality
How many of the chromosomes are X chromosomes?

normal female – 2 X chromosomes

 

normal male – 1 X chromosome

How many chromosomes are Y chromosomes?

normal female – 0 Y chromosomes

 

normal male – 1 Y chromosome

How many of the chromosomes are considered autosomes?
44 (22 from father, 22 from mother)
What is an autosome?
a chromosome that is not a sex chromosome
4 trisomies for which live birth are possible

trisomy 13

 

trisomy 18

 

trisomy 21

 

trisomy X

 

XYY

Which of the 4 trisomies produces mild to undetectable symptoms?

trisomy XYY

 

trisomy XXX

Which trisomy is otherwise known as Down’s syndrome?
trisomy 21
What is XYY syndrome?

tall

 

other mild symptoms

What is Klinefelter’s Syndrome?

male

 

testicular failure

 

can’t conceive

What is Turner’s Syndrome?

X-

 

sexually immature

 

short

 

web neck

 

phenotypically female

How does x-linked disease inheritance differ from inheritance of an autosomal disease?

lack of male to male transmission

 

gender-dependent

 

x-linked gene comes from mother on X chromosome only, but can affect both males and females, through mostly males show disease

 

autosomal come from chromosomes other than sex chromosome

How does inheritance of a mitochondrial disease differ from the inheritance of an autosomal disease?

An autosomal disease passes on one allele from the mother and one allele from the father

 

A mitochrondrial disease has only one allele from the female/mother only and all offspring will show some degree of the disease

Which will probably have greatest number of offspring who suffer from an inherited disease (may be more than one):

 

A. parents both heterozygous for autosomal recessive disease

 

B. parents both heterozygous for an autosomal dominant disease

 

C. a father who suffers from an X-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

 

D. a mother who is heterozygous for an x-linked recessive disease and a father who is wild type hemizygous (has the well form of that disease gene)

 

E. a father who suffers from a mitochondrial disease and a mother who does not at all have it

 

 

B. parents both heterozygous for a dominant disease will have greatest # of offspring

Of these, which will probably have the least number of offspring who suffer from an inherited disease (may be more than one):

 

A. parents both heterozygous for autosomal recessive disease

 

B. parents both heterozygous for an autosomal dominant disease

 

C. a father who suffers from an X-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

 

D. a mother who is heterozygous for an x-linked recessive disease and a father who is wild type hemizygous (has the well form of that disease gene)

 

E. a father who suffers from a mitochondrial disease and a mother who does not have it

 

 

E. a male who suffers from mitochondrial disease and a female who does not

 

C. a father who suffers from an x-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

Explain how penetrance might mean that individuals with disease symptoms might not be observed in a pedigree
Just because genotypically the person has the disease doesn’t mean they express it phenotypically

Genotype?

 

Phenotype?

genotype-genetic makeup

 

phenotype-physical manifestation

How does penetrance affect onset of hereditary hemochromatosis?

used to be thought rare

 

now known as the most common hereditary disease in the USA

What environmental factors affect the onset of hereditary hemochromatosis?

gender – females under 50 not have disease (menstrual cycle expels excess iron)

 

blood donations

 

diet – not enough Fe normally and you make most of Fe intake

 

alcohol consumption

 

environment

Why does an X-linked disease such as Duchenne muscular dystrophy seldom cause symptoms in females?

X-inactivation and that males with the defect do not reproduce.

 

Females need both x’s to be defective in order the x-recessive diseases to show

 

females have two x’s

A newly inherited disease has been discovered in which the disease ocuurs only when the defect is inherited from the father. The disease gene has what pattern of genetic inheritance?
imprinted
Which is meant by “a genetic disease is never inherited”?
A defect that if inherited would prevent the survival of the fetus and/or prevent reproduction of the fetus
What disease is a genetic disease in which the mutations that cause it often occur after birth?
cancer
Tay Sachs inheritance type
autosomal recessive
cystic fibrosis inheritance type
autosomal recessive
sickle cell anemia inheritance type
autosomal recessive
Huntington disease inheritance type
autosomal dominant
hereditary hemochromatosis type of inheritance
autosomal recessive
Duchenne muscular dystropy inheritannce type
x-linked (recessive)
familial hypercholesterolemia inheritance type
autosomal dominant
Leber’s hereditary optic neutopathy type of inheritance
mitochondrial
genetic defect in Huntington disease

a triplet repeat of CAG (glutamines) amino acids that encode for polyglutamine tract.

 

Normally – ≤ 34

 

Have Disease – ≥ 37

most common inherited disease in the USA
hereditary hemochromatosis
Is hereditary hemochromatosis fatal w/o txt?
yes
most common lethal inherited disease
cystic fibrosis
What protein in defective in cystic fibrosis?
CFTR (Cl- transporter)
Is what organ is the defect of cystic fibrosis most problematic?
lungs
What problem generally causes death in cystic fibrosis?

lung infections caused by P. aeroginosa

 

accumulates in lungs and destroys lining

What does the protein involved in cystic fibrosis do to promote the eventually fatal action that happens?

CFTR used to clear out bacteria from lungs

 

dysfunctional in CF and can’t remove bacteria anymore

 

lungs get destoyed by inhaled bacteria (P. aeroginosa)

2 inherited diseases that protect against infectious disease and what they protect against

cystic fibrosis – protect from typhoid fever

 

sickle cell anemia – protects from malaria

Enzyme defective in Tay Sachs disease
hexosaminidase A
What builds up and where does it build up in Tay Sachs?
glycosphinogolipids build up in the brain
What are the symptoms of Tay Sachs?

mental retardation

 

blindness

 

paralysis

 

muscle atrophy

 

cherry red spot on retina

Is hexosaminidase A the only enzyme that is involved in trimming sugars off glycosphinolipids that is defective in disease?
no
What is class of diseases that involve defective enzymes involved in trimming sugars off of glycosphingolipids?
sphinogolipid storage disorders
3 monogenic or polygenic diseases

hypertension

 

cardiovascular disease

 

type 2 diabetes

Only polygenic diseases

anencephaly

 

spina bifida

 

cleft lip/palate

 

alchoholism

 

asthma

 

bipolar disorder

 

inherited epilepsy

 

idiopathic gout

 

obesity

 

schizophrenizia

 

type I diabetes

3 inherited monogenic diseases that cause hypertension

glucocorticoid-remediable aldosteronism

 

apparent mineralocorticoid excess

 

Liddle syndrome

polygenic syndrome that is generally considered cause of most hypertension
essential hypertension
3 genes that have been associated with type 1 diabetes
3 HLA genes
Name genes that have been associated with a monogenic disease that may be though of as type 2 diabetes
MODY 1-7
3 genes that have been associated with polygenic type 2 diabetes

PPAR-gamma

 

glucokinase

 

calpain 10

Are all individuals with a defect in one of the genes associated with polygenic type 2 diabetes going to develop the disease?
no
Which of these genes associated with type 2 diabetes has been found in 85% of the world population?
PPAR-gamma

Which of the following infectious diseases is NOT thought to be protected against by an inherited genetic mutation or deletion (may be more than one):

 

A. HIV

B. typhoid fever

C. anthrax

D. malaria

E. leprosy

anthrax

 

leprosy

What is a “snip” and with what frequency are SNPs encountered in human DNA?

single nucleotide polymorphisms

 

1:300 bps

A patient has the form of the gene that cause Huntington’s (20 repeats). The patient asks about a “gray area” in testing and whether the result in certain.

 

What do you say?

some people have an intermediate number of repeats (mid-30s) but for someone with 20 repeats the test is certain.

You are treating a case of erythroblastosis fetalis, a disease of the fetus in pregnancy. This is most often caused by isoimmune reaction to the D antigen, which is one of the antigens responsible for the Rh blood group. Abs developed by the Rh- mother “attack” an Rh+ fetus’s RBCs leading to hemolysis. You want to quickly counsel the expecting couple about the likelihood the offspring will have another Rh+ fetus. The antigen is inherited in autosomal domianant fashion so you know the mother is

homozygous for the genes that make her Rh-. The father knows he is Rh+ so you able to advise them that on avg?

 

AND

 

You ask the father if he has previously fathered an Rh- child and he says YES you are able to advise that on avg?

 

AND

 

if the father says that has  has fathered an Rh- child and he instead says NO you are able to advise that on avg?

the info given you can’t determine the likelihood of the disease for their future offspring

 

the info given you can’t determine the likelihood of the disease for their future offspring

 

50% of their offspring will suffer from the disease

 

autosomal recessive homozygote

 

male and female

 

which get disease?

female and male

autosomal recessive heterozygote

 

male and female

 

which get disease?

neither

autosomal dominant homozygote

 

male and female

 

which get disease?

both

autosomal dominant heterozygote

 

male and female

 

which get disease?

both
x-linked recessive hemizygous

male

 

x-linked recessive heterozygote

 

male and female

 

which get disease?

neither

x-linked recessive homozygote

 

male and female

 

which get disease?

female

Mitochondrial, only father has disease

 

male and female

 

which get disease?

neither

Mitochondrial, only mother has disease

 

male and female

 

which get disease?

Both
What are some ways DNA is obtained from children and adults?

blood

 

saliva

 

cheek swabs

3 forms of prenatal diagnosis of inherited disease that utilized together cover most of period between 10 weeks of gestation through birth and rate of fetal loss associated w/ each?

chorionic villus sampling (CVS) – 0.5-1.0% loss

 

ultrasound – 0% loss

 

cordocentesis- 1-2% loss

What does preimplantation diagnosis of in vitro eggs allow?
embryo selection

How many inherited diseases does FL screen for?

 

What do these diseases have in common that makes them a good idea to screen for?

 

What instrument made possible the recent expansion in the number of diseases screened in FL and does it analyze sequences or metabolites?

35 diseases screened in FL

 

cause early damage and effective txt exists

 

tandem mass spectrometry-analyzes metabolites

Advantages of screening for genetic diseases by DNA sequencing

may catch a patient gives a false – by another method

 

easier, less expensive to do in quantity than biochem assays

 

heritage and fam history of person gives info about what diseases and mutations to look for

 

it is predictive (before symptom onset)

Disadvantages of screening by DNA sequencing

false negatives due to gene mutation being in unexpected location in gene

 

limited coverage of test – only test for specific disease, might miss others

 

may have added expenses due to patented genes

% frequency of two most often occuring mutations in CTFR genes

 

Any high frequency mutations in familial hypercholesterimia genes?

70% and 2.5%

 

no, high freq mutations in FH genes

Gene defect that resulted in fava beans causing health problems in Greece and primaquine causing health problems in WW2
hemolytic anemia

Knowledge of person’s VKORC1 and CYP2C9 seq can help you decide what about a patient?

 

What other seq can be screened?

drug dosage and type

 

P450 screened also

 

 

Pharmacogenomics
use sequence info to make decisions about a drug
A 27 y/o patient’s father has been diagnosed with Huntington disease. It would be important to:
tell the patient there is a test involving DNA seq to show if he will suffer from Huntington disease later in life
Is Cushing syndrome characterized as a cancer b/c it involves overgrowth of cells (a tumor) in the adrenal gland that produces cortisol?
No, it is not metastatic
What can be involved in genesis of cancer and which always involved?

bacteria

 

viruses

 

inherited predispositions

 

gene defects – always involved

 

enviro causes

 

cell cycle genes
Rb and p53
growth signal transduction genes
ras, HER2, PDGF, EGF
DNA repair genes

hMLH1

 

hMSH2

BRCA-1
anti-oncogene
Why can hEGFR be considered a protooncogene and how might become an oncogene?

protooncogene b/c it is a growth-stimulating gene

 

can become oncogene if its activity starts to result in uncontrolled growth

 

 

Gene A loses activity w/ certain mutation.

 

Is the normal gene a tumor suppressor, oncogne, anti-oncogne, or proto-oncogene?

tumor suppressor and anti-oncogene for both normal and mutant genes
characteristics of matrix metalloproteinases and involved in what cancerous process

protein/enzymes that require a metal (Zn or Ca) ion to break down proteins in ECM of cell

 

involved in metastasis

Tumorigenic cells for cancer therapy

only some cells in tumor can generate new tumor

 

if can treat or cut out those cells, then localize tumor and control metastasis

Unique Characteristic of PARs
proteolytically remove N-terminus of receptor itself and new N-terminus is the ligand that activates receptor
Kd

[ligand] for 1/2 max occupancy of receptors

 

measure affinity of ligand for receptor

EC50

[ligand] for 1/2 max response

 

effectiveness in eliciting cellular response

largest superfamily of receptors
GPCRs
What family of receptors facilitates addiction to tobacco?
ionotropic nicotinic Ach-R
Differences and Similarities in Intracellular Receptors

some reside in cytoplasm until encounter ligands-glucocorticoid and aldosterone-Rs

 

most reside full time in nucleus

 

receptor ligand complex acts on nucleus by binds to DNA and affecting expression (turn on/off expression)

concentration of albumin in serum
4 g/dL
4 functions of plasma albumin

fatty acid transport

 

bilirubin transport

 

transport of steroid hormones

 

transport of sulta drugs, penicillin, aspirin

Plasma protein degraded randomly at a rate of 100%/day. What is biological half life?
0.693 days

most abundant alpha-1 globulin?

 

Function?

 

Clinical result of its absence?

alpha-1 antiprotease

 

protease inhibitor on compounds such as elastase and collagenase

 

prevents proteolysis in lungs

 

lung loses ability to recoil after inspiration leading to emphysema and respiratory failure

organ albumin is synthesized in
liver
major class of proteins NOT synthesized in liver
immunoglobulins
most abundant of plasma proteins
albumin
how are fatty acids transported in plasma
bound to albumin
major fetal plasma protein
alpha-1 fetoglobulin
plasma protein that binds and transports iron
transferrin
plasma protein that binds and transports cortisol

cortisol-binding clobulin (alpha-1 globulin)

 

 

plasma protein that binds and transports vitamin A derivitives
retinol-binding protein (alpha-1 globulin)
plasma protein that binds and transports testosterone

sex hormone binding globulin (SHBG)

 

beta-globulin

plasma protein that binds and transports bilirubin
albumin
What ahppens to free hemoglobin in plasma?
degraded by reticulothelial cells
What would happen to hemoglobin in plasma if haptoglobin were absent?

iron would be lost due to Hb breakdown.

 

Hb is lost through the kidney and excreted in urine.

blue protein and what is its function

ceruloplasmin

 

blue b/c of copper

 

oxidize Fe 2+ Fe 3+ in plasma

 

low levels found in Wilson’s disease

In which human organ is myoglobin (Mb) most impt?
heart b/c rapid O2 supply needed
Explain causes and importance of right shift in Hb/O2 binding curve

right shift caused by:

 

decreased pH (increased [H+])

 

increased [CO2]

 

increased [2,3-BPG]

 

increased temperature

 

all factors lead to increased O2 unloading which means that a higher percentage of O2 is delivered to tissues

In Hb, how does binding of first oxygen molecule affect binding of next ones?

Deoxy Hb is usually in taut (T) form where heme groups restricted and hard for O2 to bind

 

When O2 binds to 1st heme group, the Fe of that heme will shift and pull attached his along.

 

Movement breaks salt bridges pushing Hb into relaxed (R) state and allow more O2 binding sites to become available

 

 

What is Bohr effect?

A right shift when pH decreases (increase in H+ conc.)

 

O2 release from Hb will increase when pH is lowered or [CO2] is high

 

Hb has decreased O2 affinity

 

Raising pH or decreasing [CO2]-shift curve to left

Physiological importance of cooperativity in Hb function
Hb has 4 subunits where binding of O2 at one heme group increases the affinity for O2 of the other heme groups in the same molecule
Compare behavior of Mb and Hb with respect to O2, CO2, and H+

Mb has a greater affinity at lower [O2] than Hb

 

Hb can transport more molecules of O2 b/c of cooperative effect of multiple binding sites

 

Hb can’t readily bind 1st O2, but once it does has higher affinity for O2 at other sites

 

Hb-sigmoidal curve

 

Mb-hyperbolic

 

Hb responds more readily to small changes in partial pressures of O2

 

Mb saturated quicker than Hb at low partial pressure of O2 (doesn’t have much flexibility)

How does protein (globin) portion of Mb or Hb affect reactivity of heme?

weaken strength of heme-O2 interaction. Heme binds O2 so stronglyit can convert it to a superoxide anion, which can be an unwanted oxidizing agent

 

prevents interaction of oxy-heme groups with other oxy-heme groups

How and where does 2,3-BPG interact with Hb?

2,3-BPG binds to deoxy Hb-makes it more stable and resistant to oxygenation after O2 delivery

 

negative charge allows BPG to bind to a site between two alpha chains

 

causes right shift in O2-dissociation curve (lower O2 release)

Where does 2,3-BPG come from?
product of glycolytic pathway
How does fetal Hb (HbF) differ from HbA?

Fetal Hb has two gamma chains instead of beta chains.

 

2,3-BPG can’t bind to fetal Hb and it has greater affinity fo O2 and takes O2 from maternal Hb

 

HbF is left shifted on O2-dissociation curve compared to maternal Hb

 

 

What does Hill Eqn describe?
importance of cooperativity
How does NO interact w/ Hb and what is physiological significance of that interaction?

Hb binds NO at heme Fe and cys residues in globin chain.

 

NO relaxant for vascular smooth muscle

 

Hb can pick up NO, stiffen vascular tissues, and increase BP

 

NO is strong vasodilator so Hb can be used to mediate vascular tone

What is difference btwn HbS and HbA?
HbA has normal beta chain while HbS has sickly cell hemoglobin. 6th AA for normal beta globin would be a glutamic residue but in HbS that Glu is replaced with a Val. Val is uncharged and allows hydrophobic pockets. The chains bind together and crystallize
Physiochemical/Pathological Basis for All Clinical Manifestations of Sickle Cell Disease

crystallization and stiffening of Hbs causes them to adhere to the endothelium and often obstruct small vessels (capillaries) or cause hemolysis

 

hemolysis can cause anemia and hyperbilirubinemia, causing pallor and jaundice

 

Complete vasocclusion can cause ishemia or infarction resulting in organ damage

 

Stroke, infection and excrutiating pain can result

How is Sickle Cell Disease Inherited?
recessive disorder. Only homozygous HbS cause the disease to become expressed.
What is an enzyme?

a protein catalyst for specific biochem rxns.

 

It will not undergo chem rxnitself and can be reused for other rxns

What does enzyme effect and not effect in rxn?

 

 

Enzymes reduce activation energy.

 

Keq and delta G are not affected by enzymes.

Name and describe 2 models used to describe enzyme specificity and/or catalytic activity

lock and key model

 

describes an enzyme active sites (lock) being specific for binding substrate (key)

describe specificity

 

induced fit model

 

active site will conform to fit substrate

describes specificity and catalytic activity

What is prosthetic group?

non-protein organic molecule that is tightly bound to enzyme active site

 

ex-heme, biotin, or flavin

 

holoenzyme-prosthetic group attached

 

apoenzyme-prosthetic group NOT attached

Name 6 Classes of Enzymes

oxidoreductases-catalyze RED/OX reactions

Ex-H+ donor to substrate


transferases-transfer group from one molecule to another

Ex-phosphoylases


hydrolases-hydrolytic cleavage of bond

Ex-peptide bond cleavage


lyases-cleave bonds w/o water to leave double bond or addition of other groups to double bond

Ex-decarboxylase


isomerases-change geometry of molecule

Ex-cis-trans isomerase


ligases-join 2 molecules together though hydrolysis of high energy bond

Ex-carboxylase

What is Michaelis-Menton Eqn and what do terms mean?

V = Vmax[S]/(Km+[S])

 

V – velocity of rxn

Vmax – max rxn velocity

[S] – substrate concentration

Km – constant value for a specific substrate

 

In a Michaelis-Menton plot, where is Vmax and how do you find Km?

Vmax – when [S] is very high

 

Km – [S] when V = 1/2(Vmax)

A Lineweaver-Burk plot is also called a ———
Double-reciprocal plot
What is plotted on Lineweaker-Burk plot and what are the x- and y-intercepts of the plot?

The LB graph plots the inverse of the Michaelis-Menten plot, which is 1/V on the y-axis and 1/[S] on the x-axis

 

x-intercept – 1/Km

 

y-intercept – 1/Vmax

What are advantages of the Eadie-Hofstee plot?
The E-H plot gives more evenly spaced data points than the  L-B plot.
What characteristics distinguish a competitive inhibitor from the other types of inhibitors?

bind directly to the active site and can be overcome by increased [substrate].

 

Other inhibitors bind to other sites on enzyme

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for competitively inhibited rxns?

same y-intercept

 

different x-intercepts

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for non-competitively inhibited rxns?

different y-intercepts

 

same x-intercepts

On the Lineweaver-Burk plots are the vertical or horizontal intercepts the same or different for uncompetitively inhibited rxns?

different y-intercepts

 

different x-intercepts

What does inhibitor react with for competitive inhibition?
active site of the enzyme
What does inhibitor react with for non-competitive inhibition?
react with enzyme to reduce its effectiveness to bind w/ substrate
What does inhibitor react with for uncompetitive inhibition?

bind with ES complex.

 

irreversible inhibitors.

Sigmoid V versus [S] plot and curved Lineweaver-Burk plots indicate
allostery and positive cooperativity of the enzyme (n = 2)
What factors determine the amount of enzyme activity in serum?

amount of tissue producing enzyme

 

rate of enzyme released

 

rate of enzyme inactivation/elimination from plasma

Define: Standard International Unit (SIU)
1 standard international unit of enzyme activity converts 1 μM of substrate/minute
2 most commonly measured serum aminotransferases and describe rxns they catalyze

Aspartate aminotransferase (AST) – catalyzes exhange of amino group between alpha amino acids (aspartate) and alpha keto acids

 

Alanine aminotransferase (ALT) – catalyzes exchange of amino group between alpha amino acids (alanine) and alpha keto acids

In which pathological states are the two most commonly measured serum aminotransferases elevated?

AST – liver damage and myocardial cells,hemolysed blood

 

ALT – liver damage

Reaction catalyzed by γ-glutamyltranspeptidase and how it is used diagnostically?

Glutathione + amino acids → γ-glutamyl-amino acid + cys-gly

 

γ-glutamyltranspeptidase found in kidney, intestine, liver, and fetal tissue

 

GGT levels are elevated and very sensitive in liver damage

 

2 commonly measured phosphatases and how are they used diagnostically?

Alkaline phosphatase (ALP)

 

Hydrolyzez phosphate groups from organic monophosphate at pH~9

Found in liver, bone, intestine, and placental tissue

Elevation of ALP means damage to liver and bone tissue

Elevated in gowing children, bone fractures, and pregnant women

 

Acid Phosphatase

 

hydrolyzes phosphate groups from organic monophosphates at pH~5

 

found in prostate, platelets, and erythrocytes

Elevation found in metastatic prostate cancer and hemolysed blood samples

 

 

Diagnostic utility of LDH
Used to detect MI and hemolysis
“flipped” LDH

Most common form is LDH2 (HHHM)

 

After MI or hemolysis, LDH1 (HHHH) predominates causing a “flipped” LDH b/c LDH1>LDH2

What reaction does LDH catalyze?

Lactate + NAD → pyruvate + NADH + H

 

interconversion of pyruvate and lactate

Another name for alpha hydroxybutyrate dehydrogenase (HBD)?

 

 

LDH1
What does elevated serum HBD mean?
damage to myocardial cells due to recent MI
Reaction catalyzed by CK (CPK)
creatine phosphate + ADP → Creatine + ATP
Diagnostic meaning of elevated serum CK

has 2 subunits, M and B

 

MB-MI or brief ischemia

 

MM-vigorous exercise, injection, convulsions

 

BB-neural tissue damage

Diagnostic significance of elevated serum amylase

pancreatitis

 

morphine

Reaction catalyzed by serum amylase

starch + H2O → maltose, maltotriose & limit dextrins

 

digest starch

Elevated serum lipase means

pancreatic pathology

 

morphine

Reaction catalyzed by serum lipase

trigylceride + H2O → fatty acids + glycerol

 

fat digestion

What are troponins and how are they used in diagnosis?

proteins that function in the contractile apparatus of the muscle

 

Cardiac troponin I is increased in plasma 3-6 hours after MI

Serum Enzyme Levels in crush injury

mildly elevated alkaline phosphatase (healing bone)

 

elevated creatine kinase MM (skeletal muscle)

Serum Enzyme Levels in vigorous exercise
elevated creatine kinase MM (skeletal muscle)
Serum Enzyme levels in morphine injection
elevation of serum amylase and lipase
Serum Enzyme Levels in pregnancy

mildly elevated alkaline phosphatase (bone growth)

 

elevated GGT

Four Categories of Cell Adhesion Molecules

integrins

 

immunoglobulin superfamily

 

cadherins

 

selectins

Which of the CAM categories would be actively involved in transmitting signals from the inside to the outisde of the cells and vice versa?
integrins
What CAM category is involved in adherens junction between cell?
cadherins
Abbreviations for 3 types of adhesion molecules of Ig suberfamily and tell their origins

NCAM – neural cell adhesion molecule

 

PECAM – platelet-endothelial cell adhesion molecule

 

VCAM – vascular cell adhesion molecule

 

Named for their similarity in structure to the Igs

4 Diseases in which CAMS are involved

Rheumatoid arthritis – overexpression of VCAMs

 

Psoriasis – form of an integrin

 

Pemphigus vulgaris – autoantibodies interacting with desmoglein

 

von Willebrand disease – expression of P-selectin

Describe alpha-helix
tightly coiled, stabilized by H bonding btwn imido groups and oxygen of carbony groups, many helices (3.6 AA/turn)
Beta sheet

regions of same chain or neighboring chains bond to each other w/ H bonds, the H bonds are perependicular to the long axis of the chain

 

most stable conformation – antiparallel sheets (one side N→C other side C→N

Beta turns

H bonding of AA 3 sequences apart in same chain

 

results in U turn bend of chain

What AA usually phosphoylated in proteins?

ser

 

thr

 

tyr

Commonly occurring modification of AA found in some proteins

acetylation of N terminus

 

carboxylation – add COOH

 

hydroylation – add OH

 

glycosylation – add glucose

 

phosphorylation – add phosphate group

 

disulfide linkages

Primary Structure
AA sequence
Secondary Structure

alpha helix

 

beta-pleated sheets

 

beta-turns

 

random coiling

 

results from free roation of bonds besides peptide bonds

Tertiary Structure

secondary structures fold on each other

 

hydrophobic – inside

hydrophilic – outside

Quarternary Structure
multiple polypeptide chains interact by noncovalent bonds to form single structure
General Solubility Prop. of Proteins

fibrous and insoluble

 

globular and soluble

 

firbrous and soluble

Functions of Proteins

structural roles

 

enzymes

 

role in contractile structures

 

transport (Hb)

 

hormones

 

receptors

 

Abs

What are proteins and peptides made of?

peptides – moderate chain length polymers of amino acids joined by peptide bonds

 

proteins – polymeric compounds composed of AA joined by peptide bonds

What is unique about peptide bond?
it is rigid b/c tautomerism
In ABO blood group, where is difference in oligosaccharide located and how sugars different?

due to presence or absence of N-acetyl-galactosamine or galactose linked to penultimate galactose by C1-C3 linkage

 

1 sugar difference

Glycosaminoglycans and 2 Ex

unbranched polysacc w/ repeating disacc – one is AA, other is uronic acid

 

Ex – hyaluronic acid and heparin

3 Impt Disacc and which alpha or beta linked?

maltose – alpha linked

 

sucrose – alpha linked

 

lactose – beta linked

3 Most Impt polysacc and what are linkages? Why is linkage impt?

starch – alpha linked (spiral)

 

glycogen – 2 types – alpha C1-C4 (linear)

                                 alpha C1-C6 (branched)

 

cellulose – beta linked (linear)

 

alpha and beta linkage affects the shape of the compound and humans can’t digest cellulose b/c beta linkages

What is glycoside?

anomeric -OH group of sugar reacts w/ another -OH compound

 

 

aglycone
compound that attaches to anomeric C of sugar
Name and describe 2 commonly found mod. of sugars

amino sugar – -OH group replaced by amino group

Ex – glucosamine, galactosamine

 

deoxy sugar – 1 OH group replaced by H

Ex – 2-deoxyribose

2 conformation of 6-membered rings
boat and chair
What is mutarotation and where does it take place?

configuration changes in molecule by ring opening and closing

 

occurs at anomeric C

Pyran and furan are named after which sugar structures and how many Cs are in each?

pyranose – 6 C ring

 

furanose – 5 C ring

Most Impt Monosacc and Polysacc made up of this monosacc

glucose – most impt monosacc

 

Polysacc made up of glucose – starch

                                             cellulose

                                             glycogen

What are aldoses?
monosaccharides w/ aldehyde group
What are ketoses?
monosaccharides w/ ketone group
What are carbohydrates?
polyhydroxy aldehydes or ketones or compounts that can by hydrolyzed to these
4 Types of Compounds of which AAs are precursors

hormones

 

nucleotides

 

neurotransmitters

 

AAs

Essential AA

Pvt. Tim Hall

 

Phe

Val

Thr

 

Trp

Ile

Met

 

His

Arg

Leu

Lys

What is nucleotide not found in DNA or RNA that has role in energy metabolism?
NAD+
Patient given adenosine during cardiac arrythmia. EKG during adenosine txt show AV block. If adenosine discontinuation does work, what will?
theophylline
Nucleoside more useful that nucleotide as a drug b/c
nucleoside does not have phosphate group, which restricts movement inside body
Biochemical mechanism that enables coffee-drinking college student to stay awake

caffeine is competitive antagonist of adenosine receptor.

 

Blocks depressant action of adenosine-R and is therefore a stimulant

What is the modification of a normal base found in mRNA?
methylated guanine
What is mod of a normal DNA base that affects gene expression?
methylated cytosine
What happens when DNA exposed to 94 degrees C temperature during PCR?
denaturation and 2 strands separate
What does it mean that DNA strands are “antiparallel”?

strands run in opposite directions

 

one strand goes 3’5′

 

other strand goes 5’3′

Number of H bonds between A and T

 

Number of H bonds between G and C

A-T : 2 bonds

 

G-C: 3 bonds

Difference between nucleotide and nucleic acid

nucleotide – 1 molecule w/ phosphate group, base, and sugar

 

nucleic acid-several nucleotides connected w/ phosphodiester bonds

What 4 bases in DNA

adenine

 

thymine

 

cystosine

 

guanine

4 bases in RNa

adenine

 

uracil

 

cytosine

 

guanine

Diff in chemical structure of nucleotide and nucleoside
no phosphate group is attached to a nucleoside
Difference in chemical structure of ribonucleotide and deoxyribonucleotide

ribose has -OH at 2′ C in pentose sugar

 

deoxy doesn’t

What is difference in chemical structure of purine and pyrimidine?

different nitrogenous bases

 

purine: 2 C-rings

 

pyrimidine – 1 C-ring

which bases purines?
adenine and guanine
Which bases pyrimidines?
cytosine, thymine, uracil (CUT)
3 components of nucleotide

nitrogenous base

 

pentose sugar

 

phosphate group

What purpose does enzyme phosphorylation serve?
regulation of activity and turn pathways on/off
After ATP and GTP cyclized to form cAMP and cGMP, what is their role?
regulate cellular processes through enzyme activation/deactivation
Arsenate can substitute for phosphate of ATP. Arsenate undergoes spontaneous hydrolysis w/o enzymes. What property of ATP as ideal storage does this spoil?

stability

 

ability to form high energy phosphate bonds

What are [ ] of conjugate acid/base when pH = pK?
[conjugate acid/base] are equal to each other (50/50) in solution
What is Henderson-Hasselback equation? How would a doctor use it?

pH = pK’ + log [base]/[acid]

 

Doctor could use it to relate [ ] of each of the conjugated acid/base pairs to the pH of its surrounding enviro

How are “acid” + “base” described in biological systems?

acid – proton donor

 

base – proton acceptor

What are pKs of bicarbonate and phosphate systems?

bicarbonate~6.1

 

phosphate~6.7

Two most impt. buffer systems in body?

 

Which buffer system is more impt and why?

phosphate and bicarbonate

 

bicarbonate is more important because there is a greater [bicarbonate] in the body

How does H+ effect biological systems?

rate of rxns

 

membrane permeability

 

molecule stability and native conformations of proteins and macromolecules

 

rate of transport through membranes

 

drug properties

 

hydrophobicity/hydrophilicity of compound

Equilibrium Constant

Keq = [H+][A-]/ [HA}

 

relate [ion] w/ [aqueous compound]

 

measure of dissociation of compound into ionic components

 

What is H3O+?

 

hydronium ion
Characteristics of H2O responsible for behavior

dipolar

 

H bonds

 

↑ than normal bp for mw

 

↑ than normal fp

 

↑ heat capacity

 

density solid < density liquid (ice floats on liquid H2O)

What rxns do proteins containing S- undergo
sulfahydryl groups oxidized to form disulfide linkages (cysteine)
AA-related cause of pellagra
lack of trp
What AAs contain S?

met

 

cys

What AAs have -OH groups on sidechain?

ser

 

thr

 

tyr

Disorders that arise from defects in tyr metabolism?

tyrosinosis

 

albinism

 

alcaptonuria

Disorder that arises from defects in phe metabolism?
phenylketonuria
Defects in metabolism of which AAs leads to maple syrup urine disease?

val

 

leu

 

pro

 

 

Acidic AAs

glu

 

asp

 

asn

 

gln

Basic AAs

lys

 

arg

 

his

AAs w/ aromatic sidechains

phe

 

tyr

 

trp

AAs w/ aliphatic sidechains

pro

 

ile

 

gly

 

val

 

ala

 

leu

Two Ex of Differences Between Identical Twins that Illustrate that Environment plays a role in development and health

fingerprints are different of two twins – different positions in womb

 

type I diabetes – if one gets, less than 1/2 the time other twin gets

What percentage of live births suffer from a disease causing monogenic defect?

 

1/100 or 1% of libe births suffer from a monogenic defect
What percentage of live births suffer from a disease-causing chromosomal abnormality?
1/1000 or 0.1% of live births suffer from a disease-causing chromosomal abnormality
How many of the chromosomes are X chromosomes?

normal female – 2 X chromosomes

 

normal male – 1 X chromosome

How many chromosomes are Y chromosomes?

normal female – 0 Y chromosomes

 

normal male – 1 Y chromosome

How many of the chromosomes are considered autosomes?
44 (22 from father, 22 from mother)
What is an autosome?
a chromosome that is not a sex chromosome
4 trisomies for which live birth are possible

trisomy 13

 

trisomy 18

 

trisomy 21

 

trisomy X

 

XYY

Which of the 4 trisomies produces mild to undetectable symptoms?

trisomy XYY

 

trisomy XXX

Which trisomy is otherwise known as Down’s syndrome?
trisomy 21
What is XYY syndrome?

tall

 

other mild symptoms

What is Klinefelter’s Syndrome?

male

 

testicular failure

 

can’t conceive

What is Turner’s Syndrome?

X-

 

sexually immature

 

short

 

web neck

 

phenotypically female

How does x-linked disease inheritance differ from inheritance of an autosomal disease?

lack of male to male transmission

 

gender-dependent

 

x-linked gene comes from mother on X chromosome only, but can affect both males and females, through mostly males show disease

 

autosomal come from chromosomes other than sex chromosome

How does inheritance of a mitochondrial disease differ from the inheritance of an autosomal disease?

An autosomal disease passes on one allele from the mother and one allele from the father

 

A mitochrondrial disease has only one allele from the female/mother only and all offspring will show some degree of the disease

Which will probably have greatest number of offspring who suffer from an inherited disease (may be more than one):

 

A. parents both heterozygous for autosomal recessive disease

 

B. parents both heterozygous for an autosomal dominant disease

 

C. a father who suffers from an X-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

 

D. a mother who is heterozygous for an x-linked recessive disease and a father who is wild type hemizygous (has the well form of that disease gene)

 

E. a father who suffers from a mitochondrial disease and a mother who does not at all have it

 

 

B. parents both heterozygous for a dominant disease will have greatest # of offspring

Of these, which will probably have the least number of offspring who suffer from an inherited disease (may be more than one):

 

A. parents both heterozygous for autosomal recessive disease

 

B. parents both heterozygous for an autosomal dominant disease

 

C. a father who suffers from an X-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

 

D. a mother who is heterozygous for an x-linked recessive disease and a father who is wild type hemizygous (has the well form of that disease gene)

 

E. a father who suffers from a mitochondrial disease and a mother who does not have it

 

 

E. a male who suffers from mitochondrial disease and a female who does not

 

C. a father who suffers from an x-linked recessive disease and a mother who is homozygous wild type (has only well type of disease gene)

Explain how penetrance might mean that individuals with disease symptoms might not be observed in a pedigree
Just because genotypically the person has the disease doesn’t mean they express it phenotypically

Genotype?

 

Phenotype?

genotype-genetic makeup

 

phenotype-physical manifestation

How does penetrance affect onset of hereditary hemochromatosis?

used to be thought rare

 

now known as the most common hereditary disease in the USA

What environmental factors affect the onset of hereditary hemochromatosis?

gender – females under 50 not have disease (menstrual cycle expels excess iron)

 

blood donations

 

diet – not enough Fe normally and you make most of Fe intake

 

alcohol consumption

 

environment

Why does an X-linked disease such as Duchenne muscular dystrophy seldom cause symptoms in females?

X-inactivation and that males with the defect do not reproduce.

 

Females need both x’s to be defective in order the x-recessive diseases to show

 

females have two x’s

A newly inherited disease has been discovered in which the disease ocuurs only when the defect is inherited from the father. The disease gene has what pattern of genetic inheritance?
imprinted
Which is meant by “a genetic disease is never inherited”?
A defect that if inherited would prevent the survival of the fetus and/or prevent reproduction of the fetus
What disease is a genetic disease in which the mutations that cause it often occur after birth?
cancer
Tay Sachs inheritance type
autosomal recessive
cystic fibrosis inheritance type
autosomal recessive
sickle cell anemia inheritance type
autosomal recessive
Huntington disease inheritance type
autosomal dominant
hereditary hemochromatosis type of inheritance
autosomal recessive
Duchenne muscular dystropy inheritannce type
x-linked (recessive)
familial hypercholesterolemia inheritance type
autosomal dominant
Leber’s hereditary optic neutopathy type of inheritance
mitochondrial
genetic defect in Huntington disease

a triplet repeat of CAG (glutamines) amino acids that encode for polyglutamine tract.

 

Normally – ≤ 34

 

Have Disease – ≥ 37

most common inherited disease in the USA
hereditary hemochromatosis
Is hereditary hemochromatosis fatal w/o txt?
yes
most common lethal inherited disease
cystic fibrosis
What protein in defective in cystic fibrosis?
CFTR (Cl- transporter)
Is what organ is the defect of cystic fibrosis most problematic?
lungs
What problem generally causes death in cystic fibrosis?

lung infections caused by P. aeroginosa

 

accumulates in lungs and destroys lining

What does the protein involved in cystic fibrosis do to promote the eventually fatal action that happens?

CFTR used to clear out bacteria from lungs

 

dysfunctional in CF and can’t remove bacteria anymore

 

lungs get destoyed by inhaled bacteria (P. aeroginosa)

2 inherited diseases that protect against infectious disease and what they protect against

cystic fibrosis – protect from typhoid fever

 

sickle cell anemia – protects from malaria

Enzyme defective in Tay Sachs disease
hexosaminidase A
What builds up and where does it build up in Tay Sachs?
glycosphinogolipids build up in the brain
What are the symptoms of Tay Sachs?

mental retardation

 

blindness

 

paralysis

 

muscle atrophy

 

cherry red spot on retina

Is hexosaminidase A the only enzyme that is involved in trimming sugars off glycosphinolipids that is defective in disease?
no
What is class of diseases that involve defective enzymes involved in trimming sugars off of glycosphingolipids?
sphinogolipid storage disorders
3 monogenic or polygenic diseases

hypertension

 

cardiovascular disease

 

type 2 diabetes

Only polygenic diseases

anencephaly

 

spina bifida

 

cleft lip/palate

 

alchoholism

 

asthma

 

bipolar disorder

 

inherited epilepsy

 

idiopathic gout

 

obesity

 

schizophrenizia

 

type I diabetes

3 inherited monogenic diseases that cause hypertension

glucocorticoid-remediable aldosteronism

 

apparent mineralocorticoid excess

 

Liddle syndrome

polygenic syndrome that is generally considered cause of most hypertension
essential hypertension
3 genes that have been associated with type 1 diabetes
3 HLA genes
Name genes that have been associated with a monogenic disease that may be though of as type 2 diabetes
MODY 1-7
3 genes that have been associated with polygenic type 2 diabetes

PPAR-gamma

 

glucokinase

 

calpain 10

Are all individuals with a defect in one of the genes associated with polygenic type 2 diabetes going to develop the disease?
no
Which of these genes associated with type 2 diabetes has been found in 85% of the world population?
PPAR-gamma

Which of the following infectious diseases is NOT thought to be protected against by an inherited genetic mutation or deletion (may be more than one):

 

A. HIV

B. typhoid fever

C. anthrax

D. malaria

E. leprosy

anthrax

 

leprosy

What is a “snip” and with what frequency are SNPs encountered in human DNA?

single nucleotide polymorphisms

 

1:300 bps

A patient has the form of the gene that cause Huntington’s (20 repeats). The patient asks about a “gray area” in testing and whether the result in certain.

 

What do you say?

some people have an intermediate number of repeats (mid-30s) but for someone with 20 repeats the test is certain.

You are treating a case of erythroblastosis fetalis, a disease of the fetus in pregnancy. This is most often caused by isoimmune reaction to the D antigen, which is one of the antigens responsible for the Rh blood group. Abs developed by the Rh- mother “attack” an Rh+ fetus’s RBCs leading to hemolysis. You want to quickly counsel the expecting couple about the likelihood the offspring will have another Rh+ fetus. The antigen is inherited in autosomal domianant fashion so you know the mother is

homozygous for the genes that make her Rh-. The father knows he is Rh+ so you able to advise them that on avg?

 

AND

 

You ask the father if he has previously fathered an Rh- child and he says YES you are able to advise that on avg?

 

AND

 

if the father says that has  has fathered an Rh- child and he instead says NO you are able to advise that on avg?

the info given you can’t determine the likelihood of the disease for their future offspring

 

the info given you can’t determine the likelihood of the disease for their future offspring

 

50% of their offspring will suffer from the disease

 

autosomal recessive homozygote

 

male and female

 

which get disease?

female and male

autosomal recessive heterozygote

 

male and female

 

which get disease?

neither

autosomal dominant homozygote

 

male and female

 

which get disease?

both

autosomal dominant heterozygote

 

male and female

 

which get disease?

both
x-linked recessive hemizygous

male

 

x-linked recessive heterozygote

 

male and female

 

which get disease?

neither

x-linked recessive homozygote

 

male and female

 

which get disease?

female

Mitochondrial, only father has disease

 

male and female

 

which get disease?

neither

Mitochondrial, only mother has disease

 

male and female

 

which get disease?

Both
What are some ways DNA is obtained from children and adults?

blood

 

saliva

 

cheek swabs

3 forms of prenatal diagnosis of inherited disease that utilized together cover most of period between 10 weeks of gestation through birth and rate of fetal loss associated w/ each?

chorionic villus sampling (CVS) – 0.5-1.0% loss

 

ultrasound – 0% loss

 

cordocentesis- 1-2% loss

What does preimplantation diagnosis of in vitro eggs allow?
embryo selection

How many inherited diseases does FL screen for?

 

What do these diseases have in common that makes them a good idea to screen for?

 

What instrument made possible the recent expansion in the number of diseases screened in FL and does it analyze sequences or metabolites?

35 diseases screened in FL

 

cause early damage and effective txt exists

 

tandem mass spectrometry-analyzes metabolites

Advantages of screening for genetic diseases by DNA sequencing

may catch a patient gives a false – by another method

 

easier, less expensive to do in quantity than biochem assays

 

heritage and fam history of person gives info about what diseases and mutations to look for

 

it is predictive (before symptom onset)

Disadvantages of screening by DNA sequencing

false negatives due to gene mutation being in unexpected location in gene

 

limited coverage of test – only test for specific disease, might miss others

 

may have added expenses due to patented genes

% frequency of two most often occuring mutations in CTFR genes

 

Any high frequency mutations in familial hypercholesterimia genes?

70% and 2.5%

 

no, high freq mutations in FH genes

Gene defect that resulted in fava beans causing health problems in Greece and primaquine causing health problems in WW2
hemolytic anemia

Knowledge of person’s VKORC1 and CYP2C9 seq can help you decide what about a patient?

 

What other seq can be screened?

drug dosage and type

 

P450 screened also

 

 

Pharmacogenomics
use sequence info to make decisions about a drug
A 27 y/o patient’s father has been diagnosed with Huntington disease. It would be important to:
tell the patient there is a test involving DNA seq to show if he will suffer from Huntington disease later in life
Is Cushing syndrome characterized as a cancer b/c it involves overgrowth of cells (a tumor) in the adrenal gland that produces cortisol?
No, it is not metastatic
What can be involved in genesis of cancer and which always involved?

bacteria

 

viruses

 

inherited predispositions

 

gene defects – always involved

 

enviro causes

 

cell cycle genes
Rb and p53
growth signal transduction genes
ras, HER2, PDGF, EGF
DNA repair genes

hMLH1

 

hMSH2

BRCA-1
anti-oncogene
Why can hEGFR be considered a protooncogene and how might become an oncogene?

protooncogene b/c it is a growth-stimulating gene

 

can become oncogene if its activity starts to result in uncontrolled growth

 

 

Gene A loses activity w/ certain mutation.

 

Is the normal gene a tumor suppressor, oncogne, anti-oncogne, or proto-oncogene?

tumor suppressor and anti-oncogene for both normal and mutant genes
characteristics of matrix metalloproteinases and involved in what cancerous process

protein/enzymes that require a metal (Zn or Ca) ion to break down proteins in ECM of cell

 

involved in metastasis

Tumorigenic cells for cancer therapy

only some cells in tumor can generate new tumor

 

if can treat or cut out those cells, then localize tumor and control metastasis

Unique Characteristic of PARs
proteolytically remove N-terminus of receptor itself and new N-terminus is the ligand that activates receptor
Kd

[ligand] for 1/2 max occupancy of receptors

 

measure affinity of ligand for receptor

EC50

[ligand] for 1/2 max response

 

effectiveness in eliciting cellular response

largest superfamily of receptors
GPCRs
What family of receptors facilitates addiction to tobacco?
ionotropic nicotinic Ach-R
Differences and Similarities in Intracellular Receptors

some reside in cytoplasm until encounter ligands-glucocorticoid and aldosterone-Rs

 

most reside full time in nucleus

 

receptor ligand complex acts on nucleus by binds to DNA and affecting expression (turn on/off expression)

concentration of albumin in serum
4 g/dL
4 functions of plasma albumin

fatty acid transport

 

bilirubin transport

 

transport of steroid hormones

 

transport of sulta drugs, penicillin, aspirin

Plasma protein degraded randomly at a rate of 100%/day. What is biological half life?
0.693 days

most abundant alpha-1 globulin?

 

Function?

 

Clinical result of its absence?

alpha-1 antiprotease

 

protease inhibitor on compounds such as elastase and collagenase

 

prevents proteolysis in lungs

 

lung loses ability to recoil after inspiration leading to emphysema and respiratory failure

organ albumin is synthesized in
liver
major class of proteins NOT synthesized in liver
immunoglobulins
most abundant of plasma proteins
albumin
how are fatty acids transported in plasma
bound to albumin
major fetal plasma protein
alpha-1 fetoglobulin
plasma protein that binds and transports iron
transferrin
plasma protein that binds and transports cortisol

cortisol-binding clobulin (alpha-1 globulin)

 

 

plasma protein that binds and transports vitamin A derivitives
retinol-binding protein (alpha-1 globulin)
plasma protein that binds and transports testosterone

sex hormone binding globulin (SHBG)

 

beta-globulin

plasma protein that binds and transports bilirubin
albumin
What ahppens to free hemoglobin in plasma?
degraded by reticulothelial cells
What would happen to hemoglobin in plasma if haptoglobin were absent?

iron would be lost due to Hb breakdown.

 

Hb is lost through the kidney and excreted in urine.

blue protein and what is its function

ceruloplasmin

 

blue b/c of copper

 

oxidize Fe 2+ Fe 3+ in plasma

 

low levels found in Wilson’s disease

Antiport
molecules transported simultaneously in opposite directions
symport
molecules transported simultaneously in same direction
uniport
one molecule type is transported
primary active transport

driven directly by release of energy

 

ATP hydrolysis

secondary active transport

driven by large favorable gradient but the molecule described moves against a small unfavorable gradient

 

uses energy derived from pumping other ions to fuel its own movement

passive facilitated diffusion
driven by a favorable gradient and uses a transport protein to get across the membrane
simple diffusion
driven by a favorable gradient and does not require a transport protein to get through the membrane
Give an example of a hormone that is released in response to sensing a condition by the same tissue that synthesizes and secretes the hormone
insulin is released by the pancreas in response to low blood sugar
Some hormones involve a complicated stimulation, a cascade involving sensing of the stimulus, release of a factor from one tissue, the hormone stmulates release of another factor from another tissue. Name a hormone that is an example of this, the tissue the hormone is secreted from, and its stimulus.
cortisol is released by the adrenal cortex in response to stress

Two hormones that largely control blood glucose.

 

Which is released in response to high blood glucose?

 

Which is released in response to low blood glucose?

insulin and glucagon

 

insulin is released in response to high blood glucose and brings blood glucose levels down

 

glucagon is released in response to low blood glucose levels and brings blood glucose levels up

What is circulating form of carbs in animals?

 

Storage form of carbs in animals?

 

Aerobic pathway of carb degradation that produces energy?

 

Anaerobic pathway pathway of carb degradation that produces energy?

 

Pathway of glucose synthesis?

glucose

 

glycogen

 

glycolysis accompanied to TCA cycle coupled with oxidative phosphorylation

 

glycolysis diverted to form lactic acid

 

gluconeogenesis

 

Which of the following NOT directly required for synthesis of nucleotides?

 

A. carbohydrate

B. amino acid

C. fatty acid

C. fatty acid
Pathway that is involved in degrading carboxylic acid group group on amino acids?
urea cycle
Chem process by which energy is obtained from biological fuels such as the carbon skeletons of carbs, fatty acids, or amino acids (or any fuel)?
oxidation

Organ that is the “brain” of metabolism

 

Organ that has priority over all others for supply of fuel

 

Why other tissues called extrahepatic tissues with respect to metabolism?

liver

 

brain

 

b/c liver is so impt to metabolism

Organ that is king of metabolism
brain

Fatblox is a drug that cannot be absorbed by cells in dig tract or cells lining blood vessels. Fatblox binds fats, thus preventing their absorption. When Fatblox is taken as a pill, you find that it prevents fats from being absorbed by the intestine, but the adipose tissues of those who take it shrink only a little. When Fatblox is given by IV into the circulation, adipose tissue shrinks drastically.

 

Explain and what are drawbacks to its use in IV form.

Other organs can interconvert molecules to make fats

 

Fatblox can inhibit the transport of lipid signaling molecules by binding to them, preventing them from reaching their targets, could cause problems

Why can’t brain use fatty acids as fuel for energy?
blood brain barrier blocks them
What organ is most responsible for uptake and disposal of glucose from circulation and uses most glucose?
skeletal muscle
What metabolic pathways used for energy skeletal muscles at rest and during contractile activity?

In order of work rate (from high to low):

 

free ATP

 

Creatine Pi

 

glycolysis

 

fatty acids

 

 

Where does glycolysis take place?
cytosol
Where does TCA cycle take place?
mitochondria
Where does urea cycle take place?
cytosol and mitochondria
Where are many components of plasma membrane synthesized?
ER

The Multi-Drug Resistance gene, which encodes a protein known as p-glycoprotein, is often turned on in cancer cells. P-glycoprotein is a transporter that has the capability of pumping certain cancer drugs such as doxorubicin, daunorubicin, vinblastine and vincristine is a process driven by hydrolysis of ATP. Thus, the cancer cell is able to evade being killed by the cancer drug, even when the drug concentation outise the cell are high. This process would best be described as

 

A. primary active transport

B. secondary active transport

C. passive facilitated diffusion

D. simple diffusion

E. cannot be determined from info given

A. primary active transport
What are difficulties in transducing a signal outside cell into cellular response inside cell?
cell must be able to respond to signal and molecules causing the signal generally need to be impermeable to the cell membrane
Two major classifications of signal transduction (due to two major places receptors are found)?

membrane receptors-cause intracellular stimulation

 

intracellular receptors-affect gene regulation

What is a ligand?
extracellular protein that is able to bind to a specific receptor
What is the property of ligands that accounts for two major classifications of signal transduction?
permeability of the ligand
Two differences between three histamine receptors in their response to histamine

H1 located in endothelium and smooth muscle and causes a vasodilation effect when acted upon by an antagonist (Claritin Allegra)

Acts on sinus and allergy

 

H2 receptor is located in the stomach and causes a decrease in gastric acid secretion when acted upon by an antagonist (Zantac)

Ciproxifan is a potent and specific histamine H3 receptor antagonist. Would it be expected that ciprofan would alleviate allergy symtoms or suppress gastric acidity?
It would not be expected to do either because the H3 receptor is located in the brain and neurons
2 major types of molecular switches for intracellular signaling and how is their action reversed?

cAMP formation and phosphorylation

 

cAMP turned on by cyclases

turned off by phosphodiesterases

 

phosphorylation by kinases

turned off by phosphatases

3 ways to make a cell less responsive to adenosine receptor action even when adenosine is present in adequate amounts

receptor inactivation by phosphorylation

 

receptor internalization

 

receptor degradation

Role of proto-oncogene ras in intracellular signal transduction
small GTPase, hydrolyzes GTP

How do cytokines alter gene expression?

bind to cytokine receptors which activate secondary messengers that activate gene expression
The effect of cholera toxin on signal tranduction
the toxin enters the cells by riding in on a ganglioside and enters by endocytosis and inducing ADP ribosylation of G-protein. This K/O the GTPase activity that would have shut off the cyclase. Results in increases secretion, diarrhea, and death.
Molecule that is precursor for lipid involved in signal mediation of inflammation, blood clotting, control of vascular tone, pain, and fever is released from membranes by a phospholipase?
arachidonic acid is cleaved which is a precursor for eicosanoids

Are all signal transduction pathways independent of each other?

 

What do they do or not do to account for this?

No, pathways are independent on each other

 

They inhibit one pathway and pick up slack on other pathway

Where does glycolysis take place?
cytosol
Starting substrate for glycolysis
glucose
Ending products for glycolysis

aerobic – pyruvate

 

anaerobic – lactate

What must every cell that metabolizes glucose do first?

 

What enzymes do this?

phosphorylate glucose to glucose-6-phosphate

 

enzyme – hexokinase (in all tissues)

 

or

 

glucokinase (only in liver)

Enzyme Substrate and Product for Committed Step of glycolysis?

 

Is ATP generated or used in this reaction?

enzyme – phosphofructokinase-1

 

step is phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate

 

ATP is not generated in this step, but is used to transfer Pi to fructose-6-phosphate

Control factors that affect glycolysis?

Phosphofructokinase-1 is committed step and heavily regulated by enzymes.

 

IN MUSCLE

 

In muscle, phosphofructokinase-1 is inhibited by citrate and increased levels of ATP.

 

AMP, ADP, cAMP, and Pi reverse the inhibitory affects of ATP on PFK-1.

 

Another control is from the synthesis of pyruvate and ATP from PEP and ADP. In muscle, pyruvate kinase is feedback inhibited by ATP.

 

IN LIVER

 

fructose-1,6-bisphosphatase will remove phosphate from f-1,6-bisphosphate, converting it backwards into fructose-6-phosphate. Phosphatase is also monitored.

 

Fructose-2,6-Phosphate (vasopressin and phenylephrine promote its synthesis) will inhibit this enzyme from removing the phsophate, thus activating PFK-1 when blood glucose is low. Fructose-2,6-Bisphosphate acts as a competitive inhibitor of fructose-1,6-bisphosphatase, inhibiting it from deposphorylating F-1,6-Bisphosphate and increasing the flux of F-6 Phosphate through PFK-1. Glucagon controls F-2,6-bisphosphate, stopping glycolysis and enhancing gluconeogenesis.

 

Another control is from the synthesis of pyruvate and ATP from PEP and ADP. In liver, pyruvate kinase feedback is inhibited by ATP and positively affected by fructose-1,6-bisphosphate.

 

 

 

 

 

 

In what steps are ATP generated?

2 steps:

 

1) conversion of 1,3-bisphoshoglycerate by phosphoglycerate kinase, 1 ATP produced.

 

 

2) Second ATP generated by conversion of PEP to pyruvate by pyruvate kinase. A total of 4 ATP (2 net ATP are produced) from glycolysis. 2 ATP are used up during the glycolysis process.

What steps of the glycolysis pathway cannot be reversed for use in gluconeogenesis?

3 steps:

 

1) phosphorylation of pyruvate to give phosphoenol pyruvate

 

2) Dephosphorylation of fructose-1,6-bisphosphate to furctose-6-phosphate.

 

3) dephosphorylation of glucose-6-phosphate into glucose.

2 types of approaches that are used to get around barriers encountered in reversing glycolytic pathway

gluconeogenesis uses enzymes specific to glucose synthesis

 

Certain processes are localized to certain cellular compartments

Subcellular organelles involved in gluconeogenesis

mitochondria

 

ER

Malate shuttle and where does it take place?

Mitochondrial matrix.

 

After pyruvate converted to oxaloacetate by pyruvate carboxylase, it must be transported out to cytosol. Mitochondrial membrane doesn’t allow oxaloacetate to pass through membrane so it is converted to malate, by malate dehydrogenase.

 

Malate is then transported across membrane to cytosol.

 

Malale dehydrogenase is both in the cytosol and mitochondrial matrix. The cytosolic enzyme converts malate back into oxaloacete.

 

The shuttle also transports NADH as well as oxaloacetate. Mitochondrial malate dehydrogenase uses up mitochondrial NADH for the conversion. The cytosolic malate dehydrogenase will produce NADH in the reverse reaction, replenishing cytosolic NADH.

 

Aspartate Amino Transferase used as an alternative method for transporting oxaloacetate when cytosolic NADH is high.

How does glucose-6-phosphate get converted into glucose?

conversion of glucose-6-phosphate occurs in the lumen of the ER.

 

There is a series of transporter proteins that play an integral role in the conversion of glucose.

 

1) T1 translocase pumps G-6-Phosphate into the lumen of the ER. The phosphatase for converting G-6-Phosphate lies in the lumen.

 

2) After dephosphorylation, the dissociated Pi is removed from the lumen into the cytosol by T2 translocase. T2 requires Ca to pump out Pi. A separate channel allows Ca to flow in the ER lumen.

 

3) glucose is pumped out of ER to cytosol by T3 translocase.

 

Enzyme used in gluconeogeneis both inside mitochondria and outside cytosol?
malate dehydrogenase
Tissues capable of carrying out ALL STEPS of gluconeogenesis?
liver and cortex of kidney

Is ATP or NADPH utilized or produced in the petose phosphate pathway?

 

What rxns produce/utilize ATP or NADPH?

PPP does not produce or utilize any ATP, but NADPH (reducing agent) is produced which is why PPP occurs requently is tissues where high amounts of oxidative damage can occur (RBCs and leucocytes) or tissues where lipid or catecholamine synthesis occur also involve PPP for NADPH production (liver, adipose, lactating mammary, adrenal cortex, nervous system. Tissues with high nucleotide synthesis (bone marrow, skin, gastric mucosa) depend on PPP too.

 

NADPH produced in oxidative reactions of G6P and 6-phosphogluconate.

What are functions of the pentose phosphate pathway?

1) produce reducing agents, NADPH, for cytosolic rxns

 

2) produce ribulose-5-phosphate for nucleotide synthesis

 

3) provide alternative method for metabolizing glucose

 

4) allow for interconversion of pentoses and hexoses

Possible starting materials for pentose phosphate pathway?
glucose-6-phosphate
Enzymes , substrate, and product for rate limiting step of pentose phosphate pathway?

Rate limiting step

 

glucose-6-phosphate converted to 6-phosphoglucono-δ-lactone by glucose-6-phosphate dehydrogenase.

 

Glucose-6-dehydrgoenase is inhibited by NADPH and activated by ↑ NADP+ (substrate availability)

How can glucose-6-phosphate dehydrogenase deficiency be related to hemolytic anemia?

Reduced glutathione in RBCs react with peroxides to form glutathionedimers. Glutathione can prevent oxidative damage to RBCs. NADPH is used to break up glutathione dimer in the cell and restore glutathione levels to react with other peroxides.

 

A deficiency in glucose-6-phosphate dehydrogenase can’t produce enough NADPH to restore glutathione levels.

 

This has 2 effects:

 

1) peroxides build up and damage RBC membranes

 

2) Heinz bodies (cross linkings of Hb) will reduce Hb flexibility, causing rupture of now fragile hemoglobin that is passed through small vesssels.

 

Weakened membranes and Heinz bodies will lead to acute hemolytic anemia, black urine, and increased urine flow (compensation to reduce renal damage from lysed RBCs)

In what kinds of tissues is this pathway most active?

 

In what part of the cell is it carried out?

Carried out in tissues with high amts of oxidation such as erythrocytes and leukocytes. Essential is nucleotide synthesis (gastric mucosa, bone marrow, and skin). Frequently occurs in tissues heavily involved in lipid and catecholamine synthesis (adipose, liver, lactating mammary, adrenal cortex, nervous system)

 

Takes place in the cytoplasm.

What tissues require ribose phosphate for high rates of nucleotide synthesis?

skin cells

 

bone marrow

 

gastric mucosa

 

generally tissues with a high rate of turnover of cells

What tissues require NADPH for lipid and catecholamine synthesis?

liver

 

adrenal cortex

 

lactating mammary

 

adipose

 

nervous system

What tissues require NADPH for protection against oxidative damage?

erythrocytes

 

leukocytes

What categories of rxns are utilized in the pentose phosphate pathway?

3 categories

 

1) oxidative rxns

 

2) isomerization or epimerization rxns

 

3) rxns that require C-C bonds to be cleaved or formed


 

Fatty acid synthesis occurs in what compartment of the cell?
cytosol
A hormone that stimulates fatty acid synthesis is?
insulin stimulates fatty acid synthesis in the liver
Acetyl CoA carboxylase has a covalently bound prosthetic group called?
biotin
Substrates that are required by acetyl CoA carboxylase to form malonyl CoA

ATP

 

bicarbonate

 

acetyl CoA

Describe how mitochondrial acetyl CoA is made available in the cytosol

acetyl CoA in mitochondrial matrix combined with OAA to form citrate

 

citrate is transported via a transporter from the mitochondria into the cytosl

 

citrate lyase using CoA cleaves citrate, into OAA and acetyl CoA

 

 

Redundant that is required for fatty acid synthesis
NADPH
Substrate and products of malic enzyme
malate catalyzed by malic enzyme into pyruvate and CO2
vitamin derivative that is part of the ACP portion of the fatty acid synthesis complex?
phosphopantetheine
Starting from acetyl CoA and malonyl CoA, describe the steps that are involved in the synthesis of palmitate

1) acetyl CoA + enzyme → acetyl-Enz by acetyl transferase

 

2) malonyl CoA + ACP → Malonyl-ACP by malonyl transferase

 

3) acetyl-enz+malonyl-ACP → acetoacetyl-ACP by keto synthase or condensing enzyme

 

4) acetocetyl-ACP → beta-hydroxybutyryl-ACP by beta-ketoacyl ruductase

 

5) beta-hydroxybutyryl-ACP → crotonyl-ACP by dehydratase

 

6) crotonyl-ACP → butyryl-ACP by enoyl reductase

 

7) butyryl-ACP → palmitoyl-ACP using 6 more malonyl coA in 6 rounds of steps 1-6

 

8) palmitoyl-ACP → palmitic acid by thioesterase

name enzyme domain that releases palmitate from the fatty acid synthase complex
thioesterase I domain
name the enzyme that is expressed during lactation in mammary glands that is relevant to fatty acid synthesis
thioesterase II
Name fatty acids that are released by thioesterase II

capric (C10)

 

lauric (C12)

 

myristic (C14)

 

easier to digest compared to palmitate for sucking infants

Name 2 essential fatty acids

linoleic (18:2)(9,12)

 

linolenic (18:3)(9,12,15)

All naturally occurring double bonds of fatty acids are of cis configuration?

 

true or false

false (I think)
Linoleic acid is the precursor for the biosynthesis of what?
arachidonic acid
Storage form of fatty acid
triglycerides
Triglycerides are stored in what tissue?
adipose tissue
Precursors for the synthesis of triglycerides

fatty acids are acylated by condensing with CoA to form Fatty acyl CoA

 

3 fatty acyl CoAs are then esterified to glycerol-3-phosphate to eventually form triglycerides (also called triacylglycerol)

backbone compound on which fatty acids are esterified to form triglycerides are
glycerol phosphate
Before beta-oxidation, activated fatty acids are esterified to THIS compound so that it can be transported from cytosol to mitochondria
fatty acyl carnitine
Name 3 energy related compounds that are produced upon beta-oxidation of fatty acids

FADH2

 

NADH

 

acetyl CoA

Name enzyme in mitochondrial matrix that cleaves fatty acylc carnitine
carnitine acyltransferase II (CPT II)
Complete oxidation of stearic acid, myristic acid, and lauric acid, leads to the formation of how many moles of ATP
Name a methylated fatty acid that is derived from dairy products
phytanic acid
name an enzyme that uses vitamin B12 derivative as a coenzyme in the enzyme catalysis
methyl malonyl CoA mutase
Name a 3 carbon compound that is formed from the oxidation of odd chain fatty acid
propionyl CoA
Name 2 enzymes that convert propionyl CoA into succinyl CoA

racemase

 

methy malony CoA mutase

Name 2 carboxylases that require biotin as a coenzyme

propionyl CoA carboxylase

 

acetyl CoA carboxylase

Name a compound that is catabolized by alpha-oxidation
phytanic acid
Name an allosteric activator and an inhibitor of acetyl CoA carboxylase?

allosteric activator – citrate

 

inhibitor – fatty acyl CoA

Carnitine acyl-transferase is inhibited by what?
malonyl CoA
A hormone that triggers catabolism of fats
glucagon

Phosphorylation of acetyl CoA carboxylase by protein kinase A inactivates the enzyme

 

True or False?

True

Phosphorylation of acetyl CoA carboxylase by hormone sensitive lipase activates the enzyme?

 

True or False?

True
Name the defect in Refsum’s disease
inability to properly degrade phytanic acid due to deficiency in the alpha hydroxylase enzyme
In Sudden Infant Death Syndrome the enzyme that is defective is?
medium chain fatty acyl CoA dehydrogenase deficiency
Name 2 conditions that would result in methylmalonic acedemia

methylmalonyl CoA mutase is missing

 

conversion of Vitamin B12 into coenzyme is missing

Definition of Obesity
BMI > 30
Name a natural and an artificial compound that inhibits fatty acid synthase

natural inhibitor compound – cerulenin

 

artificial inhibitor compound – C75

Malonyl CoA inhibits production of a neuropeptide compound called?
NPY

Neuropeptide Y signals the inhibition of feeding?

 

True or False?

False
Describe diabetic ketoacidosis?

blood concentrations of acetoacetic acid and beta-hydroxybutyric acid are as high as 20 mM.

 

These compounds are strong acids with a pKa of ~3.5, resulting in acidosis

 

In biochemical terms, the events are very similar to starvation mediated ketosis:

 

a) increased glucagon/insulin ratio results in elevation of liver cAMP

 

b) Elevated liver cAMP leads to decreased malonyl CoA

 

c) decreased malonyl CoA leads to de-inhibition of CPT I

 

d) de-inhibition of CPT I results in activation of fatty acid oxidation (fatty acid degradation) and increased ketone body production

 

 

Name 2 enzymes that convert alcohol into acetate

alcohol dehydrogenase

 

aldehyde dehydrogenase

Name the reductant that is produced during the oxidation of alcohol
NADH
How many moles of ATP are produced upon complete oxidation of ethanol?
12 ATP
Name a few compounds that are metabolized by omega-oxidation pathway

ω-methyl

 

adjacent methylene carbon of fatty acids

 

fatty acids 6-10 Cs long

Upon complete oxidation of capric acid, how many moles of net ATP are produced?

Capric acid = C10   4 NADH + 4 FADH2 + 5 Acetyl CoA = (4×3) + (4×2) + (5×12) = 80 ATP

 

What are advantages of having fatty acid synthase as a multi enzyme complex as seen in mammals as  opposed to individual polypeptides as seen in bacteria?
more control
Why is fat storage energetically better compared to glycogen?

Adipose storage of TAG’s initially uses less energy to produce TAG’s, plus, degradation via ß-oxidation provides

            more energy/ ATP than Glycogen storage

 

Explain how ketone bodies can serve as an energy source in brain during starvation?

ketone bodies are synthesized by liver during starvation to feed the brain

 

acetoacetate is converted to acetoacetyl CoA by thiophorase after cross blood brain barrier

 

acetoacetyl CoA can be converted to 2 acetyl CoA by thiokinase

 

2 acetyl CoA then undergo citric acid cycle to produce energy in the brain

Why can carnitine palmitoyltransferase I deficiency lead to hypoketosis?

defect in transporting fatty acid carnitine

 

don’t have free fatty acids to make acetyl CoA and subsequently don’t get ketone bodies

 

don’t make enough ketone bodies

Why are alcoholics hypoglycemic?
What compound is the source of all carbons in cholesterol?
acetyl CoA
Cholesterol is the precursor for what 4 major types of compounds?

bile salts

 

vitamin D

 

corticosteroids

 

sex hormones

What are the 5 stages in cholesterol biosynthesis that we discussed and their products?

1.)  Mevalonate synthesis → Mevalonate

 

2.) Isoprenoid synthesis → Isoprenoid units

 

3.) Squalene synthesis → Squalene

 

4.)  Lansterol Synthesis → Lansterol


5.)  Synthesis of Cholesterol from Lanosterol → Cholesterol

 

What are substrate, enzyme, and product of the rate-limiting step of cholesterol synthesis?

rate limiting step

 

HMG-CoA + 2 NADPH + 2 H+ → Mevalonate + 2 NADP+ + CoASH

What are different means by which cholesterol synthesis is controlled naturally?

1.)  Bicyclic control system:

      As insulin ↑ ­, cholesterol ­↑

      As glucagon ↑ ­, cholesterol ↓

 

2.)  HMG-Reductase degradation:

As cholesterol ↑ ­HMG-Reducases downregulates.

 

3.)  Genetic controls:  Sterols and mevalonate metabolites inhibit HMG-Reductase RNA synthesis

 

What are the main dietary sources of cholesterol?

meat

 

dairy

 

poultry

How does the body get rid of cholesterol?

The body metabolizes some cholesterol into bile salts and steroids.

 

Rest go to tissues for storage or excreted out of body in feces.

What are bile salts and their use?

modification of cholesterol by ring hydrozylations and side chain oxidation result is cholic acid

 

cholic acid reacts with amino acids to form amides known as bile salts

 

Fxn: released by gall bladder to help solubilize dietary fats

What is the route of circulation for the re-absorption of bile salts?

Liver  → Gall bladder storage Intestine (some to lymphatics)   Bloodstream Liver.

What are 2 ways in which pharmaceutical intervention is used to lower patient cholesterol levels?

1) inhibition of HMG-CoA reductase; Mevacor

 

2) in small intestine removal and excretion of bile salts; Colestipol or Cholestyramine

What types of compounds supply the precursors for the eicosanoids and where are they found?
glycerophospholipids in plasma membrane
What enzyme cleaves the fatty acid off of the starting material?
phospholipase A2
What kinds of compounds activate phospholipase A2?

angiotensin

 

bradykinin

 

epinephrine

 

thrombin

What kinds of compounds inhibit phospholipase A2?
inhibited by anti-inflammatory corticosteroids through induction of protein inhibitor of phospholipase A2 → lipocortin
Where are the general types of eicosanoids and how their names arise?

Eicosanods: Latin for “20” (number of C atoms in the molecules)

 

Prostaglandins:  Thought to be from the prostate gland

 

Thromboxanes:  Isolated from platelets

 

Leukotrienes:  Isolated from leukocytes

 

What enzyme  paths are used for the synthesis of prostaglandins, thromboxanes, and leukotrienes?

glycerophospholipid → arachidonic acid

 

cyclooxygenase reaction of arachidonic acid → thromboxane or prostaglandin

 

lipoxygenase reaction of arachidonic acid → leukotriene

What compounds inhibit cyclooxygenases?

aspirin

 

non-steroidal anti-inflammatory drugs (NSAIDS)

What are some of the effects that prostaglandins can have?

8 EFFECTS

 

stimulate smooth muscle contraction

 

regulate steroid synthesis

 

inhibit gastric secretion

 

inhibit hormone sensitive lipases

 

inhibit platelet aggregation

 

regulate nerve transmissions

 

sensitive to pain

 

mediate inflammatory response

What effects do thromboxanes have?
platelet aggregation and vasoconstriction
Where are leukotrienes found?

leukocytes

 

mast cells

 

vascular tissue

 

platelets

 

macrophages

What pathway is used to synthesize leukotrienes?
leukotrienes are synthesized from arachidonic acid or linolenic acid by the lipoxygenase path
What are the slow reacting substances of anaphylaxis?
leukotrienes
What biological effects do leukotrienes have?

contraction of smooth muscle in pulmonary airway

 

alteration in permeability of microvasculature, resulting in fluids and proteins leaking into tissues

Is the NADH/NAD+ ratio high or low in alcoholics?
high
Why does high NADH production in alcoholics lead to lipid formation?

↑ NADH levels indicate excess energy; therefore, ß-oxidation of triacyglycerols doesn’t occur resulting in high lipid levels

What are ω-3 and ω-6 fatty acids?

ω-3 = Omega-3 Fatty acids = Fatty acids with a double bond 3 carbons away from the last (ω) carbon on the F.A. chain

                   Example = Linolenic acid 18:3 (9,12,15) 


         ω-6 = Omega-6 Fatty acids = Fatty acids with a double bond 6 carbons away from the last (ω) carbon on the F.A. chain

                   Example = Linoleic acid  18:2 (9,12)

 

Describe the citrate lyase catalyzed reaction
Can carbon skelton from C-17 fatty acid oxidation enter gluconeogenic pathway. If yes, explain how
Can a carbon skeleton from C-16 fatty acid oxidation enter the gluconeogenic pathway?
Excretion of higher methylmalonic acid through urine is a sign of what vitamin deficiency?
B12?
What are the biochemical reasons for the peripheral neuropathy in Vitamin B12 deficient individuals?
lack of vitamin B12 inhibits fat beta oxidation which further has negative effects on myelin synthesis and results in peripheral neuropathy?
Describe the pathway of ketogenesis

1) 2 molecules of acetyl CoA → acetoacetyl CoA (thiolase)

 

2) acetoacetyl CoA → HMG CoA

(HMG CoA synthase)

 

3) HMG CoA → Acetoacetate + Acetyl CoA

(HMG CoA lyase)

 

4a) Acetoacetate → Acetone

(Spontaneous)

 

or

 

4b) Acetoacetate → Beta-Hydroxy Butyrate

(dehydrogenase)

 

 

Describe the pathway of ketogenolysis

Ketogenesis occurs before

 

Acetoacetate

 

1) Acetoacetate → Goes Through Blood to Tissue

 

2) Acetoacetate + succinyl CoA → Acetoacetyl CoA

(thiophorase)

 

3) Acetoacetyl CoA → 2 Acetyl CoA

(thiokinase + CoA)

 

4) 2 Acetyl CoA enter TCA cycle to produce energy

 

SEE PAGE 67

Can muscle use ketone bodies as energy source? If yes, explain how ketone bodies enter energy metabolism?

Yes, muscles can use ketone bodies as energy source

 

2) Acetoacetate + succinyl CoA → Acetoacetyl CoA

(thiophorase)

 

3) Acetoacetyl CoA → 2 Acetyl CoA

(thiokinase + CoA)

 

4) 2 Acetyl CoA enter TCA cycle to produce energy

 

Explain the hormonal bases of ketogenesis (in liver) and ketogenolysis (in extrahepatic tissues) in Type I diabetes?

Insulin production = [Glucagon]/[Insulin] ratio, hence, F.A.’s will be mobilized via Hormone sensitive Lipase. 

 

Due to  Insulin, there will be an increase in F.A. ß-oxidation producing an overabundance of Acetyl CoA, which is then converted into Ketone Bodies.  The [Ketone Body] , and because these compounds contain highly acidic protons (pKa = 3.5), the blood pH will become acidic = DKA.

High NADH/NAD+ in alcoholics results in the production of what?
3-hydroxybutyrate (beta-hydroxybutyrate)
A person with a deficiency of vitamin B12 is recommended to avoid what type of food?
fatty food ???
A person with biotin deficiency cannot metabolize what fatty acid?
Name 3 types of sphinogolipids and describe them

sphinogomyelin

 

impt membrane component esp. in nervous sytem

synthesized from 2 routes by ceramide


ceramide

 

immediate precursor of sphinogolipids

second messenger for NGF

 

globoside

 

neutral cerebroside oligosaccharides

 

gangliosides

 

acidic ceramide oligosaccharides that contain N-acetyl neuraminic acid (NANA or sialic acid)

What compounds are the precursors for sphinogosine?
serine and palmitoyl CoA

How is ceramide formed?

 

Sphingosine + acyl CoA  Ceramide + CoASH

                                       (Acyl CoA transferase)

 

How is sphingomyelin synthesized?

ceramide + CDP-choline → sphingomyelin + CMP

 

OR

 

ceramide + phosphatidyl choline → sphingomyelin + DAG

What are the 4 types of glycosphinogolipids?

cerebrosides

 

sulfatides

 

globosides

 

gangliosides

How are cerebrosides synthesized?
ceramide + UDP sugar → cerebroside + UDP
What is PAPS and what is it used for?

3’-phosphoadenosine-5’-phosphosulfate

 

It is an activated sulfate which converts galactocerebroside to sulfatide

 

What defect exists in Gaucher’s disease?
Deficiency of glucocerebrosidase, preventing degradative path of Glucocerebroside to Ceramide.  This is the most common sphingolipidoses (lipid storage disease)
What defect exists in Tay-Sachs disease?
deficiency of hexoaminidase A
What are the structural features of gangliosides?
acidic ceramide oligosaccharides that contain N-acetyl neuraminic acid (NANA or sialic acid)
What does semiconservative replication mean?
the 2 daughter double-stranded DNA molecules each contain 1 strand of parent DNA
What 3 observations have been made for all DNA polymerases?

Incoming base paring is selected by complementary base pairing with a template strand.

 

Chain growth is in the 5’ to 3’ direction

 

All DNA polymerases require a primer strand to add bases to.

 

What is the function of DNA polymerase I?

prokaryotic DNA elongation and repair

 

5′-3′ polymerization activity (synthesis)

 

5′-3′ exonuclease activity (repair and removal)

 

3′-5′ activity (proofreading)

What is the Klenow fragment?
larger subunit of DNA polymerase I that contains 5′-3′ synthesis activity and 3′-5′ proofreading activity
What is the function of DNA polymerase III?

prokaryotic DNA elongation and repair enzyme

 

complex structure; 10 subunits

 

forms a sliding clamp on the DNA strand

 

has a higher processivity than DNA polymerase I

What is the function of a topoisomerase?

enzyme that changes the topography of DNA molecules by cutting strands; allows the amount of supercoiling to be adjusted and re-ligating the strands

 

relieves supercoiling

What is the function of a helicase?
enzyme that catalyzes the unwinding of double stranded DNA by disrupting base-pair H-bonding
In replication, what is the leading strand and what is the lagging strand?

leading strand – DNA continuously synthesized in 5′-3′ direction

 

lagging strand – DNA discontinuously synthesized in 3′-5′ direction (Okazaki fragments)

How is RNA used in DNA replication?
RNA sequences serve as the primer sequences for DNA polymerase in the discontinuous synthesis of the lagging strand
What are Okazaki fragments?

pieces of DNA that are replicated on the 3’-5’ (lagging) strand that will eventually be joined by ligases to make a complete DNA replicate strand.

 

Where is E. coli DNA replication initiated and where is it terminated?

initiated at oriC

 

terminated at the tau or ter site

What are the processivities of DNA polymerases I and III?

DNA polymerase I has a low processivity (20 bases before it disassociates)

 

DNA polymerase III has a high processivity (5 million bases before it dissociates)

 

 

 

Where is DNA found in eukaryotes?
in the nucleus
How is DNA packaged in eukaryotes?
the double stranded DNA moleculed are wrapped with their negatively charged phosphate groups around octamers of positively charged proteins called histones
What are some contrasts between features of prokaryotic and eukaryotic DNA replication?

Eukaryotic DNA is much longer, the synthesis is much slower and occurs in accordance with the cell cycle.

 

Eukaryotic cells use a large number of DNA polymerase molecules and begin replication at multiple sites.

 

What DNA polymerase is believed to be responsible for leading strand synthesis and which for lagging strand synthesis in eukaryotes?

leading strand synthesis – DNA polymerase delta

 

lagging strand synthesis – DNA polymerase alpha

What proteins are in nucleosomes and why do they bind to DNA?

nucleosomes contain positively charged histone proteins

 

these + charged histones are attracted to the – charged  phosphate groups of DNA

What is PCNA and what role does it play?

Proliferating cell Nuclear Antigen (PCNA) is a cyclin that forms a clamp around the template DNA strand to dramatically increase the processivity of DNA polymerase delta.

 

What is the arrangement of nucleosomes after DNA replication?

Nucleosomes are cooperatively distributed after DNA replication

 

The new histones end up along one daughter stand near each replication fork

 

The histones from the original nucleosomes are found in the nucleosomes reformed along the other new strand

 

How might nucleosomes affect eukaryotic DNA replication?

The presence of these histones (specifically the original ones, that remain associated with one strand of the replication fork) (may be why DNA polymerization is so much slower in eukaryotes)

 

What is the model used to describe DNA replication in mitochondria?
displacement loop replication
What are the overall anabolic and catabolic pathways involved in nucleotide metabolism?

anabolic – purine and pyrimidine de novo synthesis and salvage pathways

 

 

catabolic – purine and pyrimidine degradation pathways

What major difference is there between purine and pyrimidine synthesis in terms of when and how the ring is added?

purines – the ring is built as the pathway progresses.

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pyrimidines, the ring is built 1st, then added to the PRPP.

 

Both purine and pyrimidine synthesis have a molecule in common. What is that molecule?
PRPP
What molecule is used at the start of the purine synthesis pathway?
PRPP
What molecule is formed by the purine synthesis pathway?
IMP
What is the name of the enzyme that catalyzes the addition of the first component of the purine ring?
PRPP synthetase
What nitrogen-containing amino acid donates this first part of the ring?
glutamine
How many enzymatic steps are required to synthesize IMP from PRPP in humans?
10 steps
What is the cellular localization of all the enzymes that carry out these steps (many of the steps are carried out by enzymatic activities contained on a single polypeptide chain).
the cytosol
What carrier is utilized in two different steps to add to the ring?
N10 formyl tetrahydrofolate
What vitamin is N10 formyl THF derived from?
folate
What atom does N10 formyl THF donate? Hint- the class of enzymes known as transformylases catalyze these steps.
C atom
What are glial cells?
supporting neuronal cells that maintain the normal physiology of the nervous system
What are some of the biochemical functions of microglia, astrocytes, and oligodendocytes?

MICROGLIA

 

fight infections; release inflammatory substances that could damage neurons

 

ASTROCYTES

 

regulate molecules necessary for inter-neuron communication

 

clear glutamate in the synapse to stop the neurotransmission mediated by glutamate

 

release neural growth factors

 

take up monoamine transmitters like serotonin or dopamine

 

OLIGODENDROCYTES

 

provide fatty myelin sheaths that insulate axons in the CNS

 

multiple sclerosis results when axonal connections die off

 

Acetycholine is not metabolized by reuptake process. Explain which cells would catabolize acetylcholine after action potential?
astrocytes
Explain the differences between endogenous proteolysis (protein degradation) VS digestion related protein degradation.
What are normal blood creatinine values?
< 1.5 mg/dl
Describe the metabolism of glucogenic and ketogenic amino acids in relation to TCA cycle.

different amino acids (both ketogenic and glucogenic) synthesize different components of the TCA cycle.

 

For example, both aspartate and asparagine synthesize oxaloacetate

 

SEE PG. 71 IN DR. VENK’S LECTURE #1

Describe the lactate dehydrogenase catalyzed reaction.

(1) pyruvate→lactate (LDH M)

 

(2) lactate→pyruvate (LDH L)

 

Prolonged muscle activity results in pyruvate being converted into lactate by LDH M

 

lactate then moves from the muscle into blood and enters the liver

 

In the liver, LDH L converts lactate back into pyruvate

 

pyruvate is further metabolized to form glucose to gluconeogenesis

 

This entire process is known as Cori’s cycle.

When lactate accumulates in the blood it is a problem. Why?

accumulation of lactate in the blood leads to lactate acidosis

 

indicative of tissue hypoxia, hypoperfusion, and possible damage

Describe the catecholamine synthesis pathway.

(1) tyrosine→DOPA (tyrosine hydroxylase)

 

(2) DOPA→dopamine (DOPA decarboxylase)

 

(3) dopamine→norepinephrine (hydroxylase)

 

(4) norepinephrine→epinephrine

(methyl transferase)

 

Rate limiting step = tyrosine hydroxylase catalyzed reaction (step 1)

 

Step 1 requires molecular oxygen and tetrahydrobiopterin (THB)

 

Explain why vitamin B6 deficiency can cause brain related problem.

GABA is found in high concentrations in the brain where it serves as an inhibitory neurotransmitter.

 

glutamate→GABA (glutamate decarboxylase)

 

The enzyme requires the vitamin B6 derivate pyridoxal phosphate as a coenzyme so deficieny of vitamin B6 would impair activity of the decarboxylase and production of GABA.

Describe the biosynthesis of serotonin and melatonin.

Synthesis of Serotonin

 

1) Tryptophan→5-hydroxy tryptophan

(tryptophan hydroxylase)

 

2) 5-hydroxy tryptophan→serotonin

(decarboxylase)

 

Synthesis of Melatonin

 

1) serotonin→N-acetyl serotonin

(NAT)

 

2) N-acetyl serotonin→melatonin

(methyl transferase)

 

 

Describe the biosynthesis of histamine and its functions.

histidine→histamine

(histidine decarboxylase)

 

Functions: 1) mediate allergic and inflammatory reactions

 

2) powerful vasodilator

 

3) causes constriction of bronchioles in lungs

 

4) stimulates secretion of HCl in stomach

Describe the biosynthesis of creatine phosphate and its degradation.

Synthesis

 

1) arginine + glycine→guanido acetate + ornithine

(transamidase)

 

2) guanidino acetate→creatine

(SAM-dependent methylation)

 

3) creatine→creatine phosphate

(creatine kinase)

 

Degradation

 

1) phosphocreatine→creatinine

(non-enzymatic conversion)

 

creatinine is excreted through the urine

Which vitamin derivative is required as a cofactor for many of the decarboxylases?

pyridoxal phosphate

 

derived from vitamin B6

Describe the three nitric oxide synthases and the respective functions of the nitric oxides in different tissues.

Endothelium-derived NO

 

NO diffuses out of endothelial cells and into vascular smooth muscle cells.

 

Activates cytosolic guanylate cyclase→increases cGMP

 

Activation of cGMP dependent protein kinase→phosphorylation of smooth muscle contractile proteins and relaxation

 

Brain-derived NO

 

receptors for NO in neurons

 

stimulation of guanylate cyclase→increased cGMP synthesis

 

Proteins that are phosphorylated and activated not well understood

 

Macrophage-derived NO

 

due to infections by bacteria, NO synthesis stimulated

 

NO toxic to bacteria

Biochemical basis for Parkinson’s

degeneration of the substantia nigra leads to reduced dopamine production

 

treated by: administration of L-DOPA which is precursor of dopamine that can cross blood brain barrier

Biochemical basis for depression

Serotonin from synaptic cleft is taken up by presynaptic cells for catabolism

 

Treated with: Prozac which inhibits the serotonin reuptake process and enables prolonged serotonin presence in synaptic cleft

Biochemical basis of pheochromocytomas

tumors of chromaffin tissue that produce large amounts of catecholamines

 

leads to hypertension

Biochemical basis of Huntington’s
Now thought to be a polyglutamine trinucleotide repeat problem rather than a problem with low GABA levels
What is the definition of biopharmaceutical? What is the definition of recombinant DNA?

biopharmaceutical – drug produced in living cells

 

recombinant DNA – taking a given DNA sequence and putting it together in a different arrangment

Describe how one “recombines” DNA including cutting, hybridizing, and ligating it. What enzymes are utilized for cutting DNA?

cutting – use restriction enzymes

 

hybridizing – complementary base pairing of strands in test tube; GC and AT pairs (H bonds)

 

ligation – covalent bonds btwn base in each strand; ligases make covalent bonds; permanently put DNA strand back together; make sequence functional

 

 

What is a plasmid? Give an example of a gene found on a plasmid that is naturally occurring.

small DNA circle in bacteria that can be cut with restriction enzymes and recombinant DNA can be replicated by ligating the recombinant sequence into the bacterial chromosome and allowing the bacteria to produce many copies of the DNA sequence

 

gene on a plasmid that is naturally occurring – Bacillacis anthracis toxins in DNA

What about insulin causes difficulty in producing it be recombinant DNA means (2 things)?

not 1 polypeptide chain but 2 (A and B chains)

 

3 disulfide linkages and bacteria don’t have disulfide linkages

What are the advantages of producing insulin in bacteria?

bacteria produces more product than yeast

 

bacteria easier to set up and maintain than yeast

What are the advantages of producing insulin in yeast?

insulin is already folded and disulfide bonds are linked correctly

 

more like mammalian cells

What do we mean by calling Enbrel (etanercept) a fusion protein? Why does it involve fusing 2 proteins, i.e. what properties are due to each part? What do we mean by calling Enbrel a decoy?

block TNF alpha signal transduction pathway

 

fusion protein b/c it binds to the TNF alpha receptor with a receptor domain and a immunogammaglobulin to pull TNF alpha away from cell and float in circulation (decoy)

 

 

It might be quicker to go from the idea of inhibiting TNF to a drug by making the drug as a biopharmaceutical than it would be to go from the idea of making a conventional drug. Why? What might be an advantage of a small molecule conventional drug?

it can take a lot of time in the lab to grow small molecule drugs and see what blocks signal transduction pathway

 

This small molecule conventional drug might have a more specific effect???

What are the advantages of producing Enbrel in Chinese Hamster Ovary cells?

folding is more like a human than yeast

 

additions of sugars and other modifications are required for some proteins that can be done by the hamster ovary cells

Are drugs on the market more likely to be polyclonal antibodies, or are they more likely to be monoclonal antibodies, or are they more likely to be recombinant DNA molecules based on monoclonal antibody sequence information? Why? What is meant be humanized antibody?

recombinant DNA molecule based on moloclonal antibody sequence information b/c eliminate human immune response to mouse antibody

 

humanized antibody – monoclonal antibody exposed to  humans and those humans who don’t have an immune response have their DNA substituted for the mouse DNA to prevent an immune reaction

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