protein classification Flashcards
2 ways that you can classify a protein
shape or composition
what are the 2 shapes of proteins
fibrous protein or globular protein
fibrous protein
long, rod, provides strength, insoluble in water i.e. keratin and collagen
globular protein
compact, spherical, dynamic function (i.e. enzymes, carrier proteins), soluble in water
i.e. enzymes, albumin, hemoglobin
what are the 2 compositions of protein and explain
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
protein structures 1,2,3,4,
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
strongest bond in tertiary structure
disulfide bridges
protein folding; which proteins help do this?
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
protein denaturation
what are the 4 things that can cause denaturation?
-lose protein structure (i.e. disrupt folding/ shape), when bonds are disrupted (i.e. hydrogen bond, disulfide bond, salt bridge, hydrophobic)
- strong acid or base: remove or add hydrogen
- organic solvents, detergents: disrupt hydrophobic, polar and charged interactions
- salts: disrupt polar and charged interactions
- 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
enzymes: what type of protein, what do they lower
-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
activation energy (Ea)
-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)
enzyme specificity
-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
what are the two ways that enzymes use catalytic groups
- acid-base catalysis
- covalent catalysis
what is the model in which enzymes form a complex with a substrate and induce a conformational change
induced fit model
acid base effects of enzymes
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
what amino acid can act as an acid or base to catalyse a rxn
histidine pKa~6
covalent catalysis via enzymes
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]
what are the 3 ways that cofactors/ coenzymes help
- position substrate in active site of enzymes
- stabilize negative charges on substrate or TS to make nucleophilic attack easier
- attack/ donate electrons in redox reactions
cofactors and coenzymes
-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
temperature effect on proteins
too hot= denature proteins
effect of pH on enzymes and substrates
-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
4 ways to regulate enzymes
- genetic
- covalent modification (reversible or irreversible)
- allosteric regulation
- compartmentalization
genetic regulation of enzymes
and give insulin example
-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
covalent modification of enzymes (reversible and irreversible)
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
allosteric regulation of enzymes
-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)
compartmentalization of enzymes
-via membrane bound organelles
- separation of enzymes from opposing pathways into different cellular compartments and selective transportation of substrates (i.e. mitochondria- CAC, ETC)
- create unique microenvironment (lysosome @ pH~4.5, other cellular enzymes function at pH of ~7)
high AMP vs high ATP: inhibit or activate glycolysis? at which enzyme?
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)
