Biochemistry test 2

1. enymes
2. hormones
3. transport functions
4. storage function
5. structure function
6. motor protein (actin in muscle movement)
7. antibodies
8. Transcription factors
9. signaling molecules (function in signal transduction )

peptide

polypeptide

protein

1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. proline
7. asparagine
8. Glutamine
9. aspartate
10. glutamate
11. Phenalalanine
12. Tyrosine
13. Tryptophan
14. lysine
15. histidine
16. arginine
17. threonine
18. serine
19. methinonie
20. Cystine

it is the isoelectric point, it is the pH where the net charge of a molecule is zero.

the chinral carbon indicates that there are four different groups attached to that carbon. Since the Calpha is chiral, there are 2 possible non-superimposable and mirror images of the amino acid; enantiomers are the nonsuperimposable & miror images ; every amino acid has a chiral carbon except Glycine

1. Globular proteins
2. Fibrous proteins
3. Membrane proteins

globular protein

fibrous protein

membrane proteins

1. each protein has its unique amino acid sequence (25,000 protein sequences)
2. amino acid sequence determines its 3D structure
3. 3D structures determine protein functions
4. each protein has its own unique function

1. primary
2. secondary
3. tertiary
4. quatnary

primary structure

secondary structure

Teritary strucuture

quatnary structure

Phi

psi

Phi and Psi

1. alpha helix- right handed helix
2. Beta pleated sheets
3.beta turn

Alpha helix - right handed helix

phi = -60 and psi = -47
degrees

beta pleated sheets

phi = -120 and psi = 120
degrees

beta turns

phi = 60 and psi= 45
degrees

1. alpha keratin
2. Collagen

alpha-keratin

quatnary structure (4th degree) --> start for alpha keratine --> coiled-coiled structure --> protofillamint --> filamint = alpha-keratin ;

coiled-coiled = 2 alpha helices
protofillament = 4 alpha helices
Filament = Alpha keratin (16 alpha helices)

Collagen

start with 4th degree(quatnary strucutre) --> amino acids --> tropocollagen (3amino acids) --> fibrils ( 8 tropocolalgen) --> fibers (13 fibrils) --> 1 collagen protein

4 polypeptides; it trasports oxygen from the lungs to the tissues ; alpha2beta2

myoglobin; alpha

2,3-bis phosphoglycerate : function is to decrease O2 binding to hemoglobin -[2,3-BPG]

molecular chaperons

Neuron problems: Alzheimers and Huntington (HTT)

Disulfide bonds of proteins

1. size
2. charge
3. specificity
4. polarity
5. density
6. solubility

ionic analytes display reversible electrostatic interactions with a charged stationary phase; classified as a cation or anion. strength of binding can be affected by pH and salt concentration of the buffer; The ionic species "stuck" to the column can be eluted and collected by changing one or both of these conditions

seperates proteins based on size; stationary phase = insoluble and prous carbohydrate beads
mobile phase = liquid
The larger proteins cant fit in pores so flow is faster
The medium proteins get trapped int he pores
The small proteins stay trapped in the pores longer

SDS page serpates based on size; SDS binds to proteins and a number of SDS molecules bound by a protein is proportional to its length; use to determine purity and also molecular weight; 2-D gel (IEF-SDS-page) seperates protein based on pI and size ;

enzymes

1. high catalytic power
2. high specificity
3. highly regualted

1. enzymes may speed up reactions without changing ( 10^14th faster- high catalytic power ) the termodynamics of the reaction

S --(E)--> P
2. Enzymes do not alter equilibrium constant (Keq)
3. Ezymes lower activiation energy
4. enzymes are not destroyed and consumed during the reaction

1. oxidoreductase
2. transferase
3. lyase
4. hydrolase
5. isomerase
6. ligase

redox reactions (oxidative reduction)
ex: enzyme = alcohol dehydrogenase

involed in transfer of functional groups ; ex: enzyme = hexikinase

Glucose has 6 carbons and the phosphate attaches to that carbon becomming Glucose 6-phosphate and ADP

catalist of a substrate, generating a double bond
ex: enzyme = pyruvate decarboxylase

involved in hydrolysis reactions ; ex: enzyme = chymotripsin ;
chymotripsin is in the digestive tract (dietary proteins) --> requires F,Y,W (aromatics ) as R groups

isomerization reactions ; ex: enzyme = alanine racemase

formation of bonds with ATP cleavage ;
Ex: enzyme = pyruvate carboxylase

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

enzyme kinetics

reverse inhibitor

irreversible inhibitor

as an antibiotic is an inhibitor of glycopeptide transpeptidase ; Penicillin binds to glycopeptide transpeptidase and kills it so cell wall cannot be made; glycopeptide transpeptidase is required to make bacterial cell wall

Reversible inhibitors (competitive , uncompetitive, and non competitive) and irreversible inhibitors

reversible inhibition

competitive, uncompetitive, and noncompetitive

competitive

uncompetitive

noncompetitive inhibition

irreversible inhibitor

1.a sequential bisubstrate reaction : random or ordered
2. a ping pong bisubstrate reaction

A+B --> P + Q

catalytic mechanisms

1. covalent catalysis
2. acid-base catalysis
3. H bond catalysis
4. electrostatic catalysis
5. Metal ion catalysis
6. proximity and orientation catalysis

active site

Chymotrypsin is in the human digestive system, its main function is to cleave peptide bonds of dietary proteins; can cleave c-side of F,Y,W ;
specificity

Vitamins

trace amounts

B1, B2, B3, B6, B12, niacin, and vitamin C

Vitamin A, D, E, and K

Vitamin C

some enzymes but not all require cofactors, with cofactors those enzymes have functions, without cofactors the enzymes have no functions ; cofactors could be metal oins or coenzymes

complex organic molecules; cosubstrates - loosely bound and prosthetic groups - tightly bound

niacin

nicotinamide adenine diculeotide

NAD+ and NADP+ = oxidized
NADH and NADPH = reduced

two electron transferred reactions by the 2 coenzymes as two electron carriers ; they transfer hydride anion (H:-) to and from substrates

Pellegra - not enough Niacin; mental , skin problems, and diarrhea

B2 (riboflavin) is a precursor of FAD and FMN; FAD and FMN are the coenzyme form of B2 ; the biochemical function : one or two electron transfer reactions (redox rxn) ; disease is growth retardation if theres a shortage

B3 =pantothenate
B3 is a precursor of Coenzyme-A (CoA) ; Biochemical function: 1. acetyl group transfer reation by nucleophilic attack 2. activation of the alpha-hydrogen of the aceyl group for abstraction as a proton ; the disease is dermatitis

1. a strong reducing agent ( antioxidant)
2. electron carrier
3. required for enzyme function
disease : Scurvy, bruised skin, muscle fatigue, swollen gums

1. temperature, pH, buffer
2. [substrate] , [product]
3. Genetic control ( DNA --> {transcription} mRNA --> {translation} protein)
4. Covalent regulation

protein kinase

protein phosphatase

kinase

phosphatase

allosteric enzyme

allosteric transition

allostery

allosteric effectors

allosteric effectors

allosteric enzymes

allosteric activators and allosteric inhibitors

T(taut) states = no activity
R(relaxed) states = has activity

catalytic (active) and regulatory (binds CTP) ; 12 and 6

binding of substrate promotes formation of the active R states; binding CTP stabilizes the inactive T state; Activity of ATCase will depend upon relative concentrations of substrates versus CTP

concerted transition

equillibrium

substrate induced (homotropic) and ATP/CTP-induced (heterotropic)

opposite

CTP inhibition

ATP activation

the cleavage of the peptide bond between arginine 15 and isoleucine 16 by the protease Trypsin results in the enzyme pi-chymotrypsin, which cleaves other pi-chymotrypsin molecules to form alpha-chymotrypsin; the 3 chains of alpha-chymotrysin are connected by two disulfide bonds