biochem exam 1

strucutre tutorials

general strucutre of amino acid

sp3 hydrid, carboxyl group, alpha amino group, r group, H+

non polar AA specifics

each R group is hydrophobic

Glycine, Gly, G imporants

not chiral, simplest R group, most conf. flexible

Pro, P, Proline important

least conf flexible, R group covalent bond with its alpha amino group

Met, M, Methionine

aliphatic chain with sulfur, hydrophobic and flexible

Polar R groups

dipole-dipole, hydrogen bonding, exterior of globular proteins

Cys, C, cystine

Sulfhydryl, R-group covalent bond are disulfide bonds

when oxidized htefulrhydrl bonds for covalent bonds with toher sulfhydryls

Lys, Lys, K, Arginine, Arg, R basic quliaties

R groups can ahve protonated amine groups, gives them positive charge that can from ionic interaction with adjacent negative charges

His, Histidine basic quality

does not form ionic bonds like K & R, pKr=6.01 and is 10% protonated at a PH of 7.0 and has neutral characteristic

what has a negative charge at a PH of 7.0?

Aspartate, it is acidic

which of the following as a positive charge at a pH 7.0?

Lys, it is basic a

what does the red highlight show

peptide bond which

what does this show

the dipole-dipole moment. the negative is oxygen and will be a hydrogen bond acceptor, the postive end is the hydrogen which will be the hydrogen bond donor

trans geometric isomer

observed in 99% of all peptides

cis configuration

beta carbons are overlapping

trans pro

small steric clash between beta carbon of serine which destabilizes the trans configuration (relative to trans configuration that lack a proline side chain)

cis pro

carbonyl carbon clases with beta carbon

phi angle

alpha carbon and c-N

psi angle

covalent bond between alpha carbon to carbonyl carbon

disallowed angle

physically impossible conformations due to steric clashes

rotamer changes

conformation changes of R groups between beta and g-carbons pr alpha and beta carbons

primary strucutre

all covalent bonds linking among acids together in a protein

3 major classes of proteins found in organisms

globular, membrane, filamentous proteins

secondary strucutre

recurring backbone strucutral patterns found in protein strucuture

globular proteins

soluble in aqueous environment of the cell,

number of peptide bonds

one less than the number of AA

first residue in an AA

N-terminus

membranous proteins

tightly associated with bio membranes

filamentus proteins

long filament strucutres with both extracellular and intracellular compartments

ramachandran plot

visualizing the phi/psi angle combination of very AA in a protein, the more concentrated areas means more aAA with that bond angle

favorable angles

+-180

why are angle unfavorable?

steric clashing- think 120 example

given what you have seen of the tertiary structure which wou;d you expect ot be true

configurations

change by breaking bonds

conformation

change by twisting- not breaking bonds

bond enthalpy depends on

geometry, distance, nature of surroundings,

bond enthalpy

a measure of the polarizability of the solvent, low for nonpolar solvents, high for polar solvents

hydrophobic effect

tendency of nonpolar solutes to come together when placed in a polar solvent

low entropy

high degree of order and concentration of energy

clathrate cage

molecular interaction water molecules will adopt when surrounding a molecule, resulting in an like structure of water

ionic bond

electrostatic interaction betwee two atoms with formal charges

acid v base

proton donors, proton acceptors

conjugate base

formed when an acid loses its proton

buffer

solution consisting of a conjugate acid/base pair that resist large changes in ph

transcriptome

total number of gene products that can be produced from the genome including products of alternative splicing

proteonome

entire collection of proteins that van be produced and is encoded for by an organisms genome

N terminus

1st amino group in the protein and the only amnio acid with a free alpha amino group

C terminus

last amnio acid, alpha carboxyl group

side chain stability delta dleta G meaning

larger the number the more unlikely it will b found in a alpha helix