BIO chem exam 2

ligand

a molecule that is reversibly bound

binding site

specific location on a protein

substrate

is a ligand

cataylistic site

the active site where the binding happens

Native fold

when proteins adapt a specific three dimensional conformation and fulfil specific biological functions

hydrophobic effect

non polar side chains cluster inside the molecule avoiding the aqueos enviroment

molecular forces

• hydrogen bonds

• van der waals forces

• disulfide bonds

hydrogen bonding

responsible for 2nd structures of proteins

• N-H and C=O bonds lead to alpha helixs and B-sheets

• occur between the backbone and R-groups

amide functional groups

carbon-carbon bonds can rotate while carbon-nitrogen (peptide) bonds cannot

• this helps create the rigidy and limits the amount of protein conformations

steric hinderence

will prevent some angles from occurring

apha helix

the helical backbone held together by hydrogen bonds between the backbone amide and carbonyl group

• right handed

• stabilized by hydrogen bonds within polypeptide chain

• side chains point outward perpindicular and can interact with other chains

• can fit into the grooves of DNA

alpha helix breakers

• proline: the rigid ring disrupts the helix

• glyicine: helix cannot form bond the the H R-group

alpha helix formers

• alinine

• leucine

types of 2nd structures

• alpha helixs

• B-sheets (parallel and anti-parallel

B-sheets

planarity of the peptide bond and tetrahedra geometry of alpha carbon create a pleated sheet like structure

• backbone is held together by hydrogen bonds between amids and carbonyl groups in differnet strands

• side chains protrude from sheets alternating in up and down directions (perpendicular)

AAs found in B-sheets

• tryptophan (W)

• tyrosine (Y)

• phenylalanine (F)

branched

• valine (V)

• isoleucine (I)

• threonine (T)

AAs not found in B-sheets

• glycine (G)

• proline (P)

parallel B-sheets

the H bonds run in the same direction which means the H bonds are bent (weaker)

• indiviual strands can be either close or far apart

anti-parallel B-sheets

H bond runs in the opposite directions creating linear H bonds (stronger bonds)

2nd structure characteristics

• most proteins are globular → have frequnet turns and loops (1/3 of AAs here) that connect beta strand and alpha helices

B-sheet turns

• 180 degree turns accomplished by 4 AA and stabilized by H-bonds

tertiary (3) structures

overall 3D arrangment of all atoms in a protein

• stabilized by numerous weak interactions between amino acids and side chains (mostly hydrophobic/philic interactions)

• disulfide bonds

• high percentage of hydrophobic AAs

main groups in tertiary structures

• alpha keratin

• collagen

• silk fibroin

alpha keratin

fibrous, strong and provide tensile strength

• made from right handed alpha helixs form a left handed super helix (strenghtened by disulfide bonds in cross links)

• found in hair and nails

• coiled coils

collagen

fibrous, strong, and provide tensile strength

• each protein folds into left handed helix (alpha-chains NOT a-helixs)

• 3 seperate a-chains supertwisted in right handed manner (think rope)

AAs found in collagen

• glycine

• aline

special to collagen

• HyLys and HyPro (hydroxylysine) → form corss links

a-karatin characteristics

• a-helixs

• tough, strong

• Insoluble protective structure

• flexible

collagen characteristcis

• a-chains super twisted around each other right handed manner

• high tensile strength (no stretch)

• Found in tendons and bone matrix

silk fibroin characteristics

anti-parallel b-sheets H bonded

• extended sheets

• soft flexible filaments

• NO cross-links

• van der waals and hydrogen bonding

AAs in silk fibroins

• alanine (A)

• glycine (G)

myoglobin

a globular protein that has high affinity for oxygen (storing it in muscles)

• heme prostehetic group with an iron atom

• mostly a-helixs

• buried hydrophobic group in interior

motifs

a recurring arrangement of 2nd structures

• sometimes considered supersecondary structures

• proteins made up of different motifs folded together

recongnized by a pattern of helixs and sheets

domain

a compact region of a protein that can often fold relatively independently within tertiary structures and may encompass one or more motiffs

• Proteins can have several domains that perform different functions

• Recognized by a distinct region within a chain

quarternary (4) structures

results from the association of two or more polypeptide subunits into larger functional clusters

• Subunits associate into larger functional clusters via side chain

quarternary association

• driven by stability → reduction of surface to volume ratio

• bringing catalytic sites together

hemoglobin

a quartaernary structure made of four subunits two a and two b

• each subunit contains a heme group

• transports oxygen in the blood

• cooperative binding

what cause protein to denature

• heat

• pH change

• detergents

• misfolding: adopts an incorrect structure

• aggregation: misfolded proteins stick together

• organic solvents

• reducing agents

• salt concentration

• heavy metal ions

• mechanical stress

instrinsically disorded proteins/segments

protein may remain in primary form or has domain that interacts with others while the rest of it remain disorganized

• 1/3 of all human proteins disordered

• composed of Lys, Arg, Glu, and Pro and lack hydrophobic core

• disordered regions conform to interact with many different proteins

diseases associated with denatured proteins

• alzheimers

• parkinsons

• sicklecell disease

proteostasis

the constant level of the active set of proteins in a cell

chaperonis

promote correct protein folding

isomerases

make sure of the correct stereochemistry

• PDI: protein disulfide isomerase

• PPI: peptide proyl cis-trans isomerase

Kd

the free ligands at which half of the avalible ligand-binding sites are occupied

(the dissociation constant)

• lower Kd = higher affinity

• higher Kd = lower affinity

Ka

how tightly a protein holds on to its partner molecule

• higher Ka = higher affinity

• lower Ka = lower affinity

\(\theta\) (0 with a slash)

the fraction of binding site, so at Kd it equals 50% or 0.5

catalyst

change rate of rxn without a net change of itself

• increase rxns rates without being used up and do not ulter equilibrium

enzyme

a subtance produced by a living organisim that acts as a cataylst to bring about a specific biochemcial rxn

substrate

a substance acted upon = ligand

product

results

active site

location in the enzyme where the rxn occurs = binding site

holoenzyme

apoenzyme + prosthetic group

• when an inactive protein (apoenzyme) binds with required non-protein helper (cofactor)

traintrack G

lower train track G = slower rxn

Kd

the substrate concentration at which an enzyme-cataylzed rxn runs at half of its max velocity

• when km is small affinity is high and the curve is to the left

• when km is large affinity is low and the curve is shifted to the right

competitive inhibitor type

Km increases and Vmax remains unchanged

uncompetitive inhibitor type

Km is decreased and Vmax is decreased (has parallel lines)

mixed inhibitor type

Km increases/decrease Vmax decreases (not parallel lines)

non-competitive inhibitor

Km stay the same and Vmax is decreased

Why is the Vmax decreased from an inhibitor

because the inhibitor blocks the enzyme substrate turning into enzyme products

equation for the slope of a line (m)

Km/Vmax

y-intercept equation

1/Vmax

x-intercept equation

-1/Km

Vmax is equal to what

1/y-intercept

the Km is equal to

-1/x-intercept

is [S] is doubled what happens to Km and Vmax

Km remains unchanged

Vmax remains unchanged

when E doubles what happens to Vmax and Km

Km remains unchanged

Vmax changes