protein classification

Question 1

2 ways that you can classify a protein

Answer 1

shape or composition

Question 2

what are the 2 shapes of proteins

Answer 2

fibrous protein or globular protein

Question 3

fibrous protein

Answer 3

long, rod, provides strength, insoluble in water i.e. keratin and collagen

Question 4

globular protein

Answer 4

compact, spherical, dynamic function (i.e. enzymes, carrier proteins), soluble in water
i.e. enzymes, albumin, hemoglobin

Question 5

what are the 2 compositions of protein and explain

Answer 5

simple: composed only of amino acids

conjugated: composed of protein portion (amino acids only) and non-protein portion (prosthetic group)

-conjugated protein without prosthetic group= apoprotein

Question 6

protein structures 1,2,3,4,

Answer 6

1: polypeptide chain, linear amino acid sequence (synthesized via translation from mRNA), held together via peptide bon

2: repeating backbone formed by hydrogen bonds between carboxyl and amino groups
–> alpha helix: each carboxyl group hydrogen bonds with amino group 4 amino acids away (curled ribbon)
–> beta pleated sheet: 2+ polypeptide segments line up side by side- held together by hydrogen bonds between distant carboxyl and amino groups (i.e. N–> C terminal) (parallel or antiparallel)
-can combine i.e. beta alpha beta

3: 3D structure created by side chain interactions (i.e. hydrogen bonds, salt bridges, hydrophobic interactions, disulfide bridges
–> disulfide bridge: strong, protect from denaturation in blood pH or salt [ ] changes (i.e. insulin)

4: multiple protein subunits i.e. hemoglobin, 2 alpha and 2 beta subunits
-2 subunits= dimer
-several subunits= oligomer
-many subunits= multimer

Question 7

strongest bond in tertiary structure

Answer 7

disulfide bridges

Question 8

protein folding; which proteins help do this?

Answer 8

chaperone proteins for correct 2,3,4 shape and cellular location

i.e. heat shock protein (hsp): bind and stabilize portions of the protein not yet folded –> chaperones released via ATP hydrolysis

Question 9

protein denaturation

what are the 4 things that can cause denaturation?

Answer 9

-lose protein structure (i.e. disrupt folding/ shape), when bonds are disrupted (i.e. hydrogen bond, disulfide bond, salt bridge, hydrophobic)

1. strong acid or base: remove or add hydrogen
2. organic solvents, detergents: disrupt hydrophobic, polar and charged interactions
3. salts: disrupt polar and charged interactions
4. heavy metal ions (i.e. mercury Hg2+, lead Pb2+), bind to negative amino acid side chains, disrupt salt bridges
   –> also bind sulfhydryl (SH groups)- alters shape =poison

Question 10

enzymes: what type of protein, what do they lower

Answer 10

-globular protein
-protein catalysts, speed up rxn and remain unchanged (not used up)
-lower activation energy (Ea)
-dont change standard free energy (G) of rxn or equilibrium of rxn

Question 11

activation energy (Ea)

Answer 11

-free energy of activation G
-minimal amount of energy needed to make/break bonds necessary for rxn to occur
-amount of energy needed to reach transition state (highest energy configuration formed when go from reactants to products)

Question 12

enzyme specificity

Answer 12

-active site (4* structure) (specific substrate with shape and size) –> substrate binds and forms enzyme-substrate (ES) complex –> induces conformational change (induced fit model)
-amino acids in active site participate in substrate binding and catalysis

-electrostatic interactions
-correct positioning of catalytic groups in the enzyme
-catalytic groups speed up the rxn in 2 ways:
1. acid-base catalysis
2. covalent catalysis

Question 13

what are the two ways that enzymes use catalytic groups

Answer 13

1. acid-base catalysis
2. covalent catalysis

Question 14

what is the model in which enzymes form a complex with a substrate and induce a conformational change

Answer 14

induced fit model

Question 15

acid base effects of enzymes

Answer 15

add or remove protein makes substrate more reactive
-amino acid side chains can add or remove hydrogens by acting as acids or bases
i.e. histidine pKa~6

Question 16

what amino acid can act as an acid or base to catalyse a rxn

Answer 16

histidine pKa~6

Question 17

covalent catalysis via enzymes

Answer 17

nucleophilic side group in the enzyme active site forms a temporary covalent bond with the substrate
i.e Asp and Glu (R-COO-_
i.e. Ser (R-OH) and Cls (R-SH) [weak nucleophiles, but increase when other amino acids remove hydrogen]

Question 18

what are the 3 ways that cofactors/ coenzymes help

Answer 18

1. position substrate in active site of enzymes
2. stabilize negative charges on substrate or TS to make nucleophilic attack easier
3. attack/ donate electrons in redox reactions

Question 19

cofactors and coenzymes

Answer 19

-typically metal cations (i.e. Mg2+, Zn2+ - cofactors) to help enzymes
-Mg2+ positions ATP to enzyme active site and stabilize negative charges (from phosphate) on ATP
-coenzymes: vitamin derivatives (i.e. B3: NAD+ <–> NADH + H+) accept or donate electrons in reduce rxns

Question 20

temperature effect on proteins

Answer 20

too hot= denature proteins

Question 21

effect of pH on enzymes and substrates

Answer 21

-change protonation state of enzyme and/ or substrate
-ES bonds disrupted by pH:
–> hydrogen bonds (if hydrogen removed, no hydrogen bond can form. if added, lower pH, form unusual bonds)
–> electrostatic interactions: COO- –> COOH, NH3+ –> NH2
-i.e. lysosome low pH so only specific enzymes can function

Question 22

4 ways to regulate enzymes

Answer 22

1. genetic
2. covalent modification (reversible or irreversible)
3. allosteric regulation
4. compartmentalization

Question 23

genetic regulation of enzymes

and give insulin example

Answer 23

-repress or induce enzyme transcription based on needs

regular consumption of a meal rich in carbs –> high insulin –> increased transcription of genes for glucokinase, PFK-1, and pyruvate kinase –> increased translation –> higher amount of glucokinase, PFK-1, and pyruvate kinase in the cytosol –> more efficient conversion of glucose to pyruvate

Question 24

covalent modification of enzymes (reversible and irreversible)

Answer 24

alter enzyme or proenzyme structure by making or breaking bonds

a) reversible: add or remove group to / from enzyme to cause it to convert to active/ inactive form –> i.e. kinase add phosphate, add or remove methyl or acetyl groups
–> i.e. glycogenesis: deactivate by phosphorylation
–> i.e. glycogenolysis: activate by phosphorylation
——-> both use PKA, so both pathways dont run at same time

b) irreversible: cleave peptide bonds in proenzymes or zymogens
-make sure enzyme not used until in correct location or until needed
i.e. proinsulin –> insulin

Question 25

allosteric regulation of enzymes

Answer 25

-allosteric modification of allosteric enzymes
-bind to enzymes allosteric site –> change confirmation –> change enzyme activity
-changes binding affinity of substrate at the active site
-commonly used to control regulatory enzymes

-allosteric enzymes have >1 subunit (active site on other subunit)
-binding of effector molecule to allosteric enzyme can:
–> increase binding or substrate to enzyme (effector= activator)
–> decrease binding of substrate to enzyme (effector = inhibitor)

i.e. PFK1 enzyme –> irreversible rxn
-inhibited allosterically by high levels of ATP (dont need to do glycolysis to make more ATP)
-activated allosterically by high levels of AMP (high AMP= cells are starved and need glycolysis to replenish ATP)

Question 26

compartmentalization of enzymes

Answer 26

-via membrane bound organelles

1. separation of enzymes from opposing pathways into different cellular compartments and selective transportation of substrates (i.e. mitochondria- CAC, ETC)
2. create unique microenvironment (lysosome @ pH~4.5, other cellular enzymes function at pH of ~7)

Question 27

high AMP vs high ATP: inhibit or activate glycolysis? at which enzyme?

Answer 27

i.e. PFK1 enzyme –> irreversible rxn
-inhibited allosterically by high levels of ATP (dont need to do glycolysis to make more ATP)
-activated allosterically by high levels of AMP (high AMP= cells are starved and need glycolysis to replenish ATP)