Final Exam

Combustion

Alkane reacting with Oxygen

 

-results most of the time CO2 and H2O

Halogenation

The replacement of an alkane hydrogen by a chlorine or bromine atom in a process initiated by heat or light

(mixture of products)

Cyclic alkanes [cycloalkanes]

 

 

 

contain a ring of carbon atoms

 

 

Alkene

A hydrocarbon that contains a carbon double bond

 

C=C

Alkyne

a hydrocarbon that contains a carbon triple bond

 

 –

C=C

Nonpolar

Alkenes and alkynes

-insoluble in water, soluble in nonpolar organic solvents; less dense than water

 

Cis-trans isomerism 

each double-bond carbon atom has different

substituents  

Reaction type 1: addition 

substance x-y adds to the multiple bond of an unsaturated reactant to yield a saturated product that has only single bonds.  

 

[[slide 15 chpt 13 ]]

Reaction 2: Elimination

 

a saturated reactant yields an unsaturated product by losing groups from two adjacent carbons.  

 

[slide 16 chpt 13]]

Reaction 3: Substitution 

an atom or group of atoms in a molecule is replaced by another atom or group of atoms 

-switcheroooo! 

 

[[slide 17 chpt 13]]

Reaction 4: rearrangement 

 

a molecule undergoes bond reorganization to yield an isomer. 

-cis-trans

 

[[slide 18 chpt 13]]

Addition 1: Hydrogenation
addition of H2 to a multiple bond to give a saturated product.  
Addition 2: Halogenation 
addition of Cl2 or Br2 to a multiple bond to give a dihalide product.  
Addition 3: Hydrohalogenation
Alkenees react with hydrogen bromide (HBr) to yield alkyl bromides and with hydrogen chloride (HCl) to yield alkyl chlorides in what are called hydrohalogenation reactions. 
Markovnikov’s Rule;
in the addition of HX to an alkene, the H attaches to the carbon that already has the most H’s, and the X attaches to the carbon that has fewer H’s.;
Addition 4: Hydration
the addition of water in the presence of a strong acid catalyst, to a multiple bond to give an alcohol product. ;
Aromatic Substitution 1: Nitration
the substitution of a nitro group for one of the ring hydrogens.;
Aromatic Substitution 2: Halogenation;
the substation of a halogen atom, usually bromine or chlorine, for one of the ring hydrogens;
Aromatic substitution 3: sulfonation;
the substitution of a sulfuric acid group for one of the ring hydrogens;
isomer
the same formula and connections between atoms, but different structures.;
Carbohydrate

a member of a large class of naturally occurring polyhydroxy ketones and aldehydes.;

ending in -ose

Monosaccharide;
a carbohydrate with 3-7 carbon atoms
Disaccharide
a carbohydrate composed of two monosaccharides;
Polysaccharide
a carbohydrate that is a polymer of monosaccharides.
Aldose
a monosaccharide that contains an aldehyde carbonyl group.;
Ketose
a monosaccharide that contains a ketone carbonyl group.
Chiral Carbons
carbons that are bonded to four different groups;
enantiomer

-lacking a plane of symmetry and exist as a pair of non-superimposable mirror image

-“right-handed” or “left-handed”

Diastereomers;
stereoisomers, but not mirror images of each other.;
Fischer Projection;

a way of drawing stereoisomers on a flat page so that we can tell one from another.;

-aldehyde or ketone is always located at the top.

D-sugar
monosaccharide with the -OH group on the chiral carbon atom farthest from the carbonyl group pointing to the right in a Fischer projection. ;
L-Sugar
Monosaccharide with the -OH group on the chiral carbon atom farthest from the carbonyl group pointing to the left in a Fischer projection.;
anomer

cyclic sugars that differ only in positions of substituents at the hemiacetal carbon; the alpha form has the -OH on the opposite side from the -CH2OH;

the beta form has the -OH on the same side as the -CH2OH

Anomeric Carbon atom:
the hemiacetal C atom in a cyclic sugar; the C atom bonded to an -OH group and an O in the ring. ;
Reducing Sugar
a carbohydrate that reacts in basic solution with a mild oxidizing agent.
glycoside;
a cyclic acetal formed by reaction of a monosaccharide with an alcohol, accompanied by loss of H2O
Glycosidic bond
Bond between the anomeric carbon atom of a monosaccharide and an -OR group. ;
Disaccharide formation
reaction of the anomeric carbon of one monosaccharide with an -OH group of a second monosaccharide
alpha 1,4 link
when the O is in the middle and both sides are up
Beta 1,4 link
when the O is in the middle and the first monosaccharide is down and the second monosaccharide is up
Glycoproteins
proteins that contain short carbohydrate chains
Chitin
a hard, structural polymer
enzyme
a protein or other molecule that acts as a catalyst for a biological reaction.;
active site;
a pocket in an enzyme with the specific shape and chemical makeup necessary;
Substrate
a reactant in an enzyme-catalyzed reaction
Specificity
the limitation of the activity of an enzyme to a specific substrate, specific reaction, or specific type of reaction
Cofactor
a nonprotein part of an enzyme that is essential to the enzyme’s catalytic activity; a metal ion or a coenzyme 
Coenzyme 
an organic molecule that acts as an enzyme cofactor
Six main classes of enzymes 

1. oxidoreductase 

2. Transferase

3. Hydrolase

4. Lyase

5. Isomerase

6. Ligase

Oxidoreductase

catalyze redox reactions of substrates, most commonly addition or removal of oxygen or hydrogen

-require coenzymes that are reduced or oxidized as the substrate is oxidized or reduced.  

Transferases
-catalyze transfer of a group from one molecule to another. Kinases transfer a phosphate group from ATP to give ADP and phosphorylated product.  
hydrolases 
catalyze the breaking of bonds with addition of water. The digestion of carbohydrates and proteins by hydrolysis requires these enzymes.
ligases
catalyze the bonding together of two substrates. Such reactions are generally not favorable and require energy from ATP hydrolysis
Isomerases 
catalyze the isomerization (rearrangement of atoms) of a substrate in reactions that have but one substrate and one product.  
lyases 
catalyze the addition of a molecules to a double bond or the reverse reaction in which a molecule is eliminated from a double bond.  
induced-fit model 
has a flexible active site that changes shape to best fit the substrate and catalyze the reaction
Low substrate concentration

the reaction rate is directly proportional to the substrate concentration.  

-when the substrate concentration increases, the rate drops off as more of the active sites are occupied 

-when all the active sites are occupied the rate reaches a maximum 

presence of excess substrate 

-the concentration of an enzyme can vary according to our metabolic needs. 

-if the substrate does not become a limitation, the reaction rate varies directly with the enzyme concentration 

Enzyme catalytic activity dependencies 
-dependent on pH and temperature. 
reaction rate dependencies 

-rate increases with increasing temperature until the protein begins to denature then the rate decreases rapidly

-the optimum activity for an enzyme occurs at pH where it acts. 

activation 
any process that starts or increases the action of an enzyme 
inhibition
any process that slows or stops the action of an enzyme 
Feedback control:
the regulation of an enzyme’s activity by the product of a reaction later in a pathway;
allosteric control:;
an interaction in which the binding of a regulator at one site on a protein affects the proteins ability to bind to another molecule at a different site. ;
positive regulator;
changes the active sites so that the enzyme becomes a better catalyst and the rate accelerates. ;
negative regulator;
changes the active sites so that the enzyme is a less effective catalyst and the rate slows down;
reversible inhibition;
the inhibitor can leave restoring the enzyme to its uninhibited level of activity;
irreversible inhibition;
the inhibitor remains permanently bound and the enzyme is permanently inhibited;
competitive inhibition;
makes it so the substrate cannot enter the active site;
noncompetitive inhibition;
there is not an active site where the substrate can enter.;
Genetic control:
regulation of enzyme activity by hormonal control of the synthesis of enzymes is especially useful for enzymes needed only at certain times. ;
vitamins;
an organic molecule, essential in trace amounts that must be obtained in the diet because it is not synthesized in the body.;
antioxidant;
a substance that prevents oxidation;
free radicals;
highly reactive molecular fragments with unpaired electrons;
esters;

have an -OR group bonded to the carbonyl C atom. ;-boil at much lower temps than carboxylic groups because there is no hydrogen bonding. ;

-easier to break;

esterification;
-warming a carboxylic acid with an alcohol in the presence of a strong-acid catalyst.;
amide formation;
– carboxylic acid + amine yields an amide;

acid-catalyzed hydrolysis

;

-the reverse of esterification;

-ester is treated with water in the presence of a strong acid and hydrolysis (add water) takes place. ;

saponification;

-the product of saponification is a carboxylate anion rather than a free carboxylic acid. ;

-ester hydrolysis by reaction with a base [[NaOH or KOH]]

amide hydrolysis;
-acidic conditions – adds H30 but under basic conditions adds OH-
Phosphate ester;
compound formed by reaction of an alcohol with phosphoric acid
phosphorylation;
the transferring of a phosphoric group from one molecule to another;
amine
a compound that has one or more organic groups bonded to nitrogen;
heterocycle;
a ring that contains nitrogen or some other atom in addition to carbon. ;
Protein
a large biological molecule made of many amino acids linked together through peptide bonds;
Alpha-amino acid
compound with an amino group bonded to the C atom next to the -COOH group;
peptide bond
an amide bond linking 2 amino acids;
zwitterions;
neutral dipolar ions;
Acidic conditions for zwitterions;
accept protons on their basic -COO- groups to leave only the positively charged NH3+ groups
basic conditions for zwitterions;
lose protons from their acidic NH3+ groups to leave only the negatively charged COO- groups;
achiral
opposite of chiral, having superimposable mirror images and thus no right- or left handedness.;
enantiomers or optical isomers

the mirror-image forms of a chiral molecule like alanine

-enantiomers are one kind of stereoisomer compounds that have the same formula and atomic connections but different spatial arrangements;

primary protein structure
the sequence in which amino acids are linked by peptide bonds in a protein
salt bridge;
the attraction between the positive and negative charges in ionized acidic and basic side chains.;
disulfide bonds;
side chains of thiol functional groups that react
secondary protein structure
the spatial arrangement of the polypeptide backbones of proteins;
fibrous proteins
-tough insoluble proteins in which the chains form long fibers or sheets. ;
globular proteins;
water-soluble proteins whose chains are folded into compact, globe-like shapes.;
tertiary protein structure;

the overall three-dimensional shape that results from the folding of a protein chain

-depends mainly on interactions of amino acid side chains that are far apart along the same backbone;

quaternary protein structure;
the way in which two or more polypeptide subunits associate to foam a single three-dimensional protein unit;
protein hydrolysis;
the reverse of protein formation, peptide bonds are hydrolyzed to yield amino acids;
denaturation;
the loss of secondary, tertiary, or quaternary protein structure due to disruption of noncovalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.;
mechanical agitation;

-denaturation

-denaturation of proteins at the surface of the air bubbles stiffens the protein and causes the bubbles to be held in place. ;

Detergents
very low concentrations of detergents can cause denaturation by disrupting the association of hydrophobic side chains. ;
Chromosomes;

chromatin organizes itself here;

-contains a different DNA molecule, and the DNA is duplicated so that each new cell receives a complete copy;

genes

;

individual segments of DNA that contain the instructions that direct the syntheses of a single polypeptide;
Nucleic acid;
a polymer of nucleotides;
nucleotide;
5-carbon sugar bonded to a cyclic amine base and a phosphate group;
nucleoside;
a 5-carbon sugar bonded to a cyclic amine base, a nucleotide with no phosphate group;
ribonucleotides;
nucleotides that contain ribose;
deoxyribonucleotides;

contain 2-deoxy-D-ribose, designated by leading their abbreviations with a lower case;

“d”

double helix

heterocyclic bases are on the inside, so that a base on one strand points directly toward a base on the second strand. ;

-sugar-phosphate backbone making up the sides and the hydrogen-bonded base paris (the ladder part)

replication;
process by which copies of DNA are made when cell divides;
transcription;
process by which the information in DNA is read and used to synthesize RNA;
translation;
the process by which RNA directs protein synthesis.;
helicases;
enzymes that begins unwinding of the double helix;
Okazaki Fragments;
the short segments replicate from 5′ to 3′
semiconservative replication;
the newly synthesized strand in the new double helix during replication;
ribosomal RNA;
outside the nucleus but within the cytoplasm of a cell[ribosomes], small granular organelles where protein synthesis takes place;
transfer RNA;

smaller RNA’s that deliver amino acids one by one to protein chains growing at ribosomes 

-each one carries only one amino acid 

messenger RNA

carry information transcribed from DNA

-formed in the cell nucleus and transported out to the ribosomes, where proteins will be synthesized 

exon
the code for a gene is contained in one or more small sections of DNA 
intron 
the code for a gene may be interrupted by a sequence of bases 
heterogeneous nuclear RNA 
the initial mRNA strand contains both exons and introns 
Codon 

a sequence of three ribonucleotides in the messenger RNA chain that codes for a specific amino acid 

-also a three-nucleotide sequence that is a stop codon and stops translation 

genetic code 
the sequence of nucleotides, coded in triplets (codons) in mRNA, that determines the sequence of amino acids in protein synthesis 
initiation 
-protein synthesis begins when an mRNA, the first tRNA, and the small subunit of a ribosome come together.  
termination 
a “stop” codon signals the end of translation. 
lipid
a naturally occurring molecule from a plant or animal soluble in nonpolar organic solvents 
Waxes 

carboxylic acid esters, with long, straight hydrocarbon chains in both R groups

-they are secreted by sebaceous glands in the skin of animals and perform mostly external protective functions.  

-carboxylic acid and alcohol combine to form an ester

fatty acid 
a long-chain carboxylic acid; those in animal fats and vegetable oils often have 12-22 carbon atoms 
tryacylglycerols 

carboxylic acid trimesters of glycerol, a three-carbon trialcohol. they make up the fats stored in our bodies and most dietary fats and oils. 

-triester 

glycerophospholipids 

trimesters of glycerols that contain charged phosphate dieter groups and are abundant in cell membranes 

-polar head and non-polar tail 

sphingomyelins 

amides derived from an amino alcohol, also contain charged phosphate dieter groups

-amide, phosphate diester 

glycolipids 

different amides derived from sphingosine, contain polar carbohydrate groups

-carbohydrate and lipid 

steriods

are tetracyclic molecules that act as hormones and contribute to the structure of cell membranes 

-all ring molecules

Eicosanoids 

carboxylic acids that are a special type of intracellular chemical messenger 

-ring with 2 side chains (bobby pin)

saturated fatty acid 
a long-chain carboxylic acid containing one or more carbon-carbon single  bonds 
unsaturated fatty acids 
a long-chain carboxylic acid containing one or more carbon-carbon double bonds 
polyunsaturated fatty acids 
have more than one carbon-carbon double bond. 
oil
a mixture of triacylglycerols that is liquid because it contains a high proportion of unsaturated fatty acids 
fat
a mixture of triacylglycerols that is sold because it contains a high proportion of saturated fatty acids 
phospholipid 
a lipid that has an ester link between phosphoric acid and an alcohol 
lipid bilayer 
formed by 2 parallel layers of lipids oriented so that their ionic head groups protrude into the aqueous environments on either side of the bilayer their nonpolar tails cluster together in the middle of the bilayer where they can interact and avoid water.  
liposomes 
small spherical vesicles with a lipid bilayer surrounding an aqueous center.  
fluid-mosaic model 
the membrane is described as fluid because it is not rigid and molecules can move around within it, and as a mosaic because it contains many kinds of molecules 
active transport 
movement of substances across a cell membrane using energy 
passive transport 
movement of a substance across a cell membrane without the use of energy, from a region of higher concentration to a region of lower concentration 
simple diffusion 
passive transport by the random motion of diffusion through the cell membrane or through channel proteins. 
Facilitated diffusion 
passive transport across a cell membrane with the assistance of a protein that changes shape 
hemiketal 
ketone + alcohol 
Ketal
ketone + 2 alcohol 
Acetal 
aldehyde + 2 Alcohol

Alanine 

Ala

 

A

Arginine 

Arg 

 

Asparagine 

Asn

 

N

Aspartate 

Asp

 

Cysteine 

Cys

 

C

Glutamate 

Glu

 

Glutamine 

Gln

 

Q

Glycine

Gly

 

G

Histidine 

His

 

H

Isoleucine

ile

 

I

Leucine

 

Leu

 

L

Lysine

Lys

 

K

Methionine 

Met

 

M

Phenylalanine 

Phe

 

Proline 

 

Pro

 

P

Serine

 

 

Ser

 

S

Threonine

Thr

 

Tryptophan 

Trp

 

W

Tyrosine 

Tyr

 

Y

x

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