Cell Biology Ch. 3

nine major classes of proteins

enzymes, structural, motility, regulatory, transport, signaling, receptor, defensive, storage

2 structural classes of proteins

globular and fibrous

how many amino acids used in protein synthesis and biologically relevant? are there more than that existing?

20 / yes

explain and draw basic structure of amino acid

carboxyl group, amino group, hydrogen, and side chain R group attached to alpha carbon

different for each amino acid and gives each amino acid its distinctive properties.

R group

what is glycine R group and how does that make it different from other AA

just hydrogen / not enantiomeric

are amino acids for proteins d or l

l

where are hydrophobic amino acids found

interior of proteins when the proteins are in an aqueous environment or in cell membrane

where are hydrophilic amino acids found and why

surface of proteins in solution to maximize interactions with water and other polar or charged substances

function of enzyme proteins

catalysts, increasing rate of chemical reaction

function of structural proteins

physical support and shape

function of motility proteins

contraction and movement

function of regulatory proteins

control and coordinate cell function

function of transport proteins

move substances into and out of cells

function of signaling proteins

communication between cells, made by cell and sent to cell surface

function of receptor proteins

enable cells to respond to signaling proteins and chemical stimuli from environment

function of defensive proteins

protect against disease

function of storage proteins

reservoirs of AA

what are the 3 types of R groups and subsection

hydrophobic, polar uncharged, polar charged (acidic negative charge, basic positive charge)

what is found in R group of nonpolar amino acids

hydrocarbons

what is found in polar uncharged amino acid R groups

lot of O, N, and SH

what is found in acidic polar charged amino acid R groups

negative charged terminal carboxyl

what is found in basic polar charged amino acid R groups

positive amine

each amino acid has what names

name, 3 letter abbreviation, 1 letter abbreviation

single chain of amino acids

polypeptide

two or more polypeptide chains that have a function

protein

t or f: all polypeptides are proteins

f (all proteins are made of polypeptides but not all polypeptides are proteins)

protein that consists of a single, polypeptide chain

monomeric protein

protein that consists of more than one polypeptide chain

multimeric protein

composed of 2 polypeptide chains is (__). 3 is (___). 4 is (__)

dimer / trimer / tetramer

single chain of a multimeric protein

subunit

describe a peptide bond and what kind of reaction it is

covalent bond between the C of a carboxyl group of one amino acid and the nitrogen of the amino group of the next amino acid / dehydration synthesis condensation

what do the n- and c-terminus ends of polypeptide have

n-terminus has unbound amine group. c-terminus has unbound carboxyl group

how is sequence of polypeptide read and synthesized

both N to C

describe what is happening. what are the starting molecules and what do they form? what kind of bond is formed? what kind of reaction?

2 amino acids forming a polypeptide / peptide bond / dehydration synthesis or condensation

final folded, functional shape of a protein is (__) which is NOT (__) and can be manipulated to regulate protein (__).

conformation / static / function

t or f: amino acids of protein held together by polar covalent bonds, but the folded shape of protein help together by noncovalent bonds and interactions (and covalent disulfide)

t

core structure of polypeptide is the (__) and (__) project out in alternating arrangement

polypeptide backbone / R groups

noncovalent bonds form between (__) of protein. disulfide bonds form between (__) by (__) reaction

R groups, R groups and backbone, and just backbone / cysteine R groups terminal SH / redox

if the wild type was ASN and the mutation GLY on number 232, how would you write the amino acid

ASN232GLY

what is the primary structure? kind of bonds and interactions involved?

amino acid sequence / covalent peptide bonds

what is the secondary structure? kind of bonds and interactions involved?

folding into alpha helix, beta sheets, and random coils / hydrogen bonds between NH and CO groups of peptide bonds in backbone

what is the tertiary structure? kind of bonds and interactions involved?

3-D folding of single polypeptide chain / disulfide bonds, all types of noncovalent bonds

what is the quaternary structure? what kind of bonds and interactions invovled?

multiple polypeptides forming multimeric protein / disulfide bonds and all types of noncovalent bonds

how is primary structure determined

order of nucleotides in DNA determines order of nucleotides in mRNA which in turn gives amino acid sequence

what is at the N-terminus

NH3+

t or f: R groups participate in the bonding of secondary structure

f

explain the backbone model of protein structure

traces backbone

describe the wire model of protein structure

outlines R groups with backbone

describe the ribbon model of protein structure

has arrows and coils that highlight secondary structure beta sheets and alpha helices

describe the space-filling model of protein structure

shows 3-D shape, distance, and size. good for finding binding sites

what are the 4 protein structure models

backbone, ribbon, wire, and space-filling

what does the arrow of beta sheets mean in ribbon model

arrow points to C-terminus

alpha helices are (__) structure. (__) bonds between (__) and (__) groups about (__) carbons away. only between atoms of (__). what do amino acid R groups look like

spiral / hydrogen / carboxyl / amino / 4 / polypeptide backbone / project out from spiralled backbone

beta sheets are (__) structure. (__) bonds between atoms of (__). made up of (__) that are connected by (__). what do R groups look like?

pleated sheet / hydrogen / polypeptide backbone / strands / random coils / alternating above and below sheet

t or f: the secondary/tertiary structure may lump beta sheets together and be in a different order than the primary structure even if the primary structure is not continuous beta sheet

t

what are the two beta sheet forms

parallel (strands fun in same direction) and antiparallel (strands run in opposite directions)

small secondary structures with common shape and function

motif

identify the motif

beta-alpha-beta

identify the motif

hairpin loop

identify the motif

helix-turn-helix

identify the motif

coiled coils

identify the motif

leucine zipper

which motif is commonly found binding to DNA

leucine zipper

tertiary structure contains bonds between atoms of

R groups and polypeptide backbone

structures in single polypeptide chain, discrete, locally folded unit of tertiary structure folding and functioning independently

protein domains

domains act (__) with specific (__). what useful experiments can you do?

modularly / jobs / can take off DNA binding domain to see if still binds to DNA. then could but DNA binding domain on non binding molecule to see if will bind to DNA

t or f: all proteins achieve quarternary structure

f

t or f: some proteins function as a single polypeptide chain

t

individual peptide of quaternary protein

subunit

subunits can be either (__) like in (__) or (__) like in (__)

identical / p53 / different / hemoglobin

are subunits of quaternary structure functional in isolation

no