Medical Biochemistry-Exam 3 (Everything) – Flashcards
Unlock all answers in this set
Unlock answers| 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 = (4x3) + (4x2) + (5x12) = 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. <
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 |
