chap 3 (protein structure and function)

components of an amino acid

central carbon, carboxyl group, amino group, R side chain

ph 7: both amino and carboxyl groups are ionized —> neutral charge

basic side chains

positive charge at physiological pH

histidine, arginine, lysine (HRK)

acidic side chains

negative charge at physiological pH

aspartic acid, glutamic acid (DE)

nonpolar side chains

alanine, valine, methionine, tryptophan, leucine, isoleucine, glycine, cysteine, proline, phenylalanine

(AVMWLIGCPF)

2 cysteine side chains form disulfide bonds

uncharged polar side chains

neutral charge at physiological pH

asparagine, glutamine, serine, threonine, tyrosine (NQSTY)

where are there steric limitations?

on the bond angles in a protein

there is flexibility, but there is also steric hinderance

3 types of NONcovalent bonds to help proteins fold

electrostatic attractions - b/w positive and negative charges of side chains

hydrogen bonds - between H to N,O,F of side chains

van der Waals - b/w nonpolar side chains

protein 3D conformation

hydrophobic core (nonpolar side chains) + hydrophilic exterior (polar side chains form bonds with water)

denature + renature (reversible) based on temperature, pH, ionic solvents

what kind of structure (1, 2, 3, 4) involved R-group bonding?

tertiary

beta sheet structures

anti-parallel

parallel

coiled coil

multiple alpha helices

proline + glycine common

protein domains

modular units from which larger proteins are built

• form from a singular polypeptide domain

a conserved part of a given protein sequence (w/ its own tertiary structure)

• can function independently from the rest of the protein

*can live on its own if separate domains broken apart*

domain shuffling

some protein domains found in many different proteins

—> even with different function (evolutionary history)

three common protein domains

immunoglobulin module

fibronectin type 3 module

kringle module

increasing complexity… (in terms of number of domains)

= increasing domains

≠ increasing genome size

quarternary structure

larger protein molecule often have MORE THAN ONE polypeptide chain

each subunit = individual polypeptide chain

example: heme

some globular proteins form long helical filaments

dimer —> tetramers —> octamers

ex: vementin, actin

many protein molecules have what kind of shape?

elongated, fibrous shapes

covalent cross-linkages stabilize extracellular proteins

interchain disulfide bond = b/w 2 chains

intrachain disulfide bond = w/in 1 chain

oxidation —> 2 cysteines bond —> a disulfide bond

reduction —> a disulfide bond breaks into 2 cysteines

individual protein molecules often serve as subunits for the assembly of larger structures

ex: protein coat of virus, tubes (microtubules), sheets

proinsulin (inactive form) —> insulin (active form

1. specific folding stabilized by INTRAchain disulfide bonds

2. connecting peptide removed —> 2 chain insulin molecule

3. reduction irreversibly separates 2 chains

amyloid fibrils

form from many proteins —> lead to disease

many copies of the protein stack together (beta strand of each line up) held together by hydrogen bonds —> hydrophobic zipper —> amyloid fibril

2 monomers of alpha-synnuclei pair up

prion diseases

neurodegenerative diseases

sheep: scrapie

humans: creutzfeld jacob, kuru

cattle: bovine spongiform encephalopathy (mad cow disease)

—> can lead to alzheimer’s disease

amyloid structures can perform useful functions in cells

help in release of soluble peptide hormones (glucagon + calcitonin) in mammals

create bacteria biofilms (protection from attacks) to protect individual bacteria

cAMP is…

a ligand

—> has to bind to an active site

surface conformation of a protein determines its chemistry and binding

3 ways a protein can find to each other:

surface-string

helix-helix

surface-surface

equilibrium constant (K)

measures binding strength

depending on how well the surfaces of 2 molecules match, it will change the strength of the bonds that they can form

dissociation rate, association rate, and equilibrium constant equations

relationship b/w standard free-energy differences (°ΔG) and equilibrium constants (37°C)

larger value = stronger binding b/w A and B = binding more favorable

for every ↓ 5.9kJ °ΔG = ↑ K * 10

general enzymes

enzyme kinetics graph + value definitions

Vmax = maximum value that can be reached

• all substrate binding sites on enzyme are occupied

Km = substrate concentration at which reaction is 0.5Vmax

• measures how tightly substrate binds to enzyme

enzymes speed up chemical reactions by lowering the activation energy (graph)

enzymes can use simultaneous acid and base catalysis

reaction catalyzed by lysozyme

catalyzes cutting of a polysaccharide chain

vitamin derivatives function as…

coenzymes

tightly bound small molecules…

add extra functions to proteins

ex: retinal - light sensitive molecule attached to rhodopsin in the eye

ex: heme - tightly bound to each of the 4 polypeptides of hemoglobin

the cell regulates the catalytic activities of its enzymes through…

positive and negative feedback

positive feedback - the binding of one molecule affects binding of another by changing the 3D structure of the enzyme

negative feedback - binding of either ligand interferes with binding of the other through change in 3D structure

enzyme activity vs. conc. inhibitory ligand (graph)

↑ complexity = ↓ inhibitor concentration needed

cooperative allosteric transition…

enzyme that has 2 identical subunits

disrupting an already disrupted enzyme = easier

kinases and phosphatases

kinases - phosphorylate —> usually activate

phosphatases - dephosphorylate —> usually inactivate

plays a big role in signal transduction pathways

—> regulates acitivation of genes —> regulates proteins being made

^^similar —> descended from a common ancestor

a protein can function as a microprocessor

ex: regulation of the src protein kinase

how does src protein kinase act as a signal integrating device?

integrates several inputs to decide whether its kinase activity should fully turn on

GTP-binding proteins (GTPases)…

act as molecular switches that activate (P) + inactivate (de-P)

ex: ras protein

2 major signaling intracellular pathways in eukaryotic cells

GEF - guanine nucleotide exchange factor

GAP - GTPase activating protein

ubiquitilation

when proteins can be regulated by the covalent addition of other proteins

ubiquitin - small 76aa protein that is added to other proteins by ubiquitin ligases

—> regulates their activity

ubiquitinylated proteins are often marked for… which amino acid does ubiquitin bind to…

proteosomal degradation

lysine side chain of target protein

names of ubiquitination enzymes (E1-E3)

E1 (ubiquitin-activating enzyme)

—> ubiquitin binds

—> E2 (ubiquitin-conjugating enzyme) binds

—> ubiquitin transfers from E1 to E2

—> E2 + E3 (ubiquitin ligase) moves ubiquitin from E2 to amino group of lysine side chain on target protein

motor proteins produce large movements in cells (image)

intrinsically disordered protein sequences = versatile binding sites

bringing molecules close together helps them interact more efficiently

1. scaffold proteins - a platform that holds proteins near each other

2. multienzyme complexes - an assembly line

   1. biomolecular condensates - concentrated gathering of moelcules

computationally designed proteins

designed so that each protein would move into a specific 3D conformation in its lowest energy state