Proteins, structure and function Flashcards
What monomer are proteins composed of?
amino acids
structure of an amino acid?
purpose/function of proteins? why are they called the workhorses of cell bio?
Structural, signaling, enzymes.
Muscle, fibers, regulators, hormones, etc
which enantiomeric form do amino acids exist in in living things: D or L?
amino acids (except glycine) are in L form
Lysine : structure (don’t worry about R group) , category (basic/acidic?) abbreviation
Lysine. Lys/K. Basic.
R
NH3+-C-COO
H
tyrosine- special solubility properties, group it belongs to, unique name
tyrosine nonpolar uncharged-In water, it is very insoluble .
aromatic
real world application: infant formula has to be shaken up, because the tryosine protein in it always settles to the bottom.
what is a peptide bond, and point out the peptide bond in the following diagram
link between O, C, N and H.
peptide bond is the covalent bond that links two amino acids.
structural ramifications of peptide bonds?
limit rotation: amino acids are not free to rotate around the N-C linkage because the peptide bond has a partial double bond character. This makes peptide bonds really stiff, gives rise to protein structure
How do you name a peptide chain that has 4 peptides?
tetrapeptide
How do you name a peptide chain with 5-18 peptides?
oligopeptide
How do you name peptide chains? Which end do you start on, and what is the primary structure?
Start with amino terminus. Give name of each amino acid in the chain. If 2 amino acids, di-peptide. if 3, tripeptide. if 4 tetrapeptide.
How do you determine solubility of a peptide chain?
Look at the R groups of the amino acids- if they mostly have CH2 or CH3’s, non polar. Lots of OH’s or O’s usually mean polar.
What types of bonds determine a protein’s shape?
Hydrogen bonds, ionic bonds, van der waals forces. Hydrophobic exclusions can also bend it inwards
What is a disulfide bridge?
covalent disulfide bridges can form between the S’s in two cystein side chains
What 3 types of hydrogen bonds exist in proteins?
hydrogen bonds between atoms of 2 peptide chains. H bond between atom of a peptide bond and amino acid side chain. H bond between 2 amino acid side chains.
name the 3 basic amino acids
arginine (arg) lysine (lys) histidine
name the 2 acidic amino acids
glutamic acid (glu) aspartic acid (asp)
name the polar uncharged amino acids
Serine (ser), threonine (thr), tyrosine (tyr)
nonpolar amino acids
leucine (leu) alanine (ala)
draw proline
anfinson experiment
can break disulfide bonds with reducing agent. can denature a protein with urea/heat- renature it with cooling, remove urea.
function of ribonuclease
chops up RNA
native conformation
a protein in its normal structure
T/F: can you regain enzyme activity in a previously denatured protein?
yes! anfinson- nobel prize
where is all the information about the shape a protein is supposed to take stored?
right in the amino acid chains
how long does it take to denature a protein?
not long ! can do it in 15 mins
what are some ways to denaute a protein?
heat. changes in PH. detergent. changes in ionic condition. changes in REDOX state.
describe the levels of protein structure and what each contains
primary- amino acid sequence
secondary- folding shapes (alpha, beta) arising from backbone H-bond interactions
tertiary- the final 3d shape of molecule
quaternary- when 2 tertiary molecules fold into each other
where do hydrogen bonds form in an alpha helix?
in the peptide backbone NH and CO, every 4th residue
in which direction do beta sheets point?
from N terminus to C terminus
what forces are interacting in a tertiary bond?
vand der waals, hydrogen bonds, ionic bonds, disulfide bonds
what do you call a polypeptide with 4 subunits
a tetramer
in which type of structure is there interactions between the side chains?
tertiary structure
what are embellishments in protein structure?
prosthetic groups and covalent modifications
what is a prosthetic group?
non protein groups, either inorganic or organic, bound tightly to proteins to help them do a function. ex: heme group, hemoglobin, transports oxygen.
give an example of covalent modification
protein phosphorylation; putting on phosphate group to activate enzyme, removing it to inactivate enzyme
what is a metal co-factor? give an example of one
something a protein uses to help it get a job done- in this case, uses a metal to help it attain the structure it wants. carbonic anhydrase uses zinc for structure, and DNA uses magnesium.
what is a zwitter ion?
an amino acid in its charged form; NH3+ on one end, COO- on the other
Asp: full name and one letter symbol?
aspartic acid. D. acidic
cys: full name and one letter symbol?
cysteine, cys, c
E: full name and 3 letter name
glutamic acid, glu. acidic
K: 3 letter and full name and property
basic lysine lys
proline: 3 and 1 letter name
pro, P
threonine: 3 and 1 letter abbreviation and property
nonpolar uncharged. thr. T.
tyrosine
Y, tyr. non polar uncharged
serine
ser , S, nonpolar uncharged
arginine
R, arg, basic
