Proteins, structure and function

Question 1

What monomer are proteins composed of?

Answer 1

amino acids

Question 2

structure of an amino acid?

Answer 2

Question 3

purpose/function of proteins? why are they called the workhorses of cell bio?

Answer 3

Structural, signaling, enzymes.

Muscle, fibers, regulators, hormones, etc

Question 4

which enantiomeric form do amino acids exist in in living things: D or L?

Answer 4

amino acids (except glycine) are in L form

Question 5

Lysine : structure (don’t worry about R group) , category (basic/acidic?) abbreviation

Answer 5

Lysine. Lys/K. Basic.

R

NH3+-C-COO

H

Question 6

tyrosine- special solubility properties, group it belongs to, unique name

Answer 6

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.

Question 7

what is a peptide bond, and point out the peptide bond in the following diagram

Answer 7

link between O, C, N and H.

peptide bond is the covalent bond that links two amino acids.

Question 8

structural ramifications of peptide bonds?

Answer 8

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

Question 9

How do you name a peptide chain that has 4 peptides?

Answer 9

tetrapeptide

Question 10

How do you name a peptide chain with 5-18 peptides?

Answer 10

oligopeptide

Question 11

How do you name peptide chains? Which end do you start on, and what is the primary structure?

Answer 11

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.

Question 12

How do you determine solubility of a peptide chain?

Answer 12

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.

Question 13

What types of bonds determine a protein’s shape?

Answer 13

Hydrogen bonds, ionic bonds, van der waals forces. Hydrophobic exclusions can also bend it inwards

Question 14

What is a disulfide bridge?

Answer 14

covalent disulfide bridges can form between the S’s in two cystein side chains

Question 15

What 3 types of hydrogen bonds exist in proteins?

Answer 15

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.

Question 16

name the 3 basic amino acids

Answer 16

arginine (arg) lysine (lys) histidine

Question 17

name the 2 acidic amino acids

Answer 17

glutamic acid (glu) aspartic acid (asp)

Question 18

name the polar uncharged amino acids

Answer 18

Serine (ser), threonine (thr), tyrosine (tyr)

Question 19

nonpolar amino acids

Answer 19

leucine (leu) alanine (ala)

Question 20

draw proline

Answer 20

Question 21

anfinson experiment

Answer 21

can break disulfide bonds with reducing agent. can denature a protein with urea/heat- renature it with cooling, remove urea.

Question 22

function of ribonuclease

Answer 22

chops up RNA

Question 23

native conformation

Answer 23

a protein in its normal structure

Question 24

T/F: can you regain enzyme activity in a previously denatured protein?

Answer 24

yes! anfinson- nobel prize

Question 25

where is all the information about the shape a protein is supposed to take stored?

Answer 25

right in the amino acid chains

Question 26

how long does it take to denature a protein?

Answer 26

not long ! can do it in 15 mins

Question 27

what are some ways to denaute a protein?

Answer 27

heat. changes in PH. detergent. changes in ionic condition. changes in REDOX state.

Question 28

describe the levels of protein structure and what each contains

Answer 28

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

Question 29

where do hydrogen bonds form in an alpha helix?

Answer 29

in the peptide backbone NH and CO, every 4th residue

Question 30

in which direction do beta sheets point?

Answer 30

from N terminus to C terminus

Question 31

what forces are interacting in a tertiary bond?

Answer 31

vand der waals, hydrogen bonds, ionic bonds, disulfide bonds

Question 32

what do you call a polypeptide with 4 subunits

Answer 32

a tetramer

Question 33

in which type of structure is there interactions between the side chains?

Answer 33

tertiary structure

Question 34

what are embellishments in protein structure?

Answer 34

prosthetic groups and covalent modifications

Question 35

what is a prosthetic group?

Answer 35

non protein groups, either inorganic or organic, bound tightly to proteins to help them do a function. ex: heme group, hemoglobin, transports oxygen.

Question 36

give an example of covalent modification

Answer 36

protein phosphorylation; putting on phosphate group to activate enzyme, removing it to inactivate enzyme

Question 37

what is a metal co-factor? give an example of one

Answer 37

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.

Question 38

what is a zwitter ion?

Answer 38

an amino acid in its charged form; NH3+ on one end, COO- on the other

Question 39

Asp: full name and one letter symbol?

Answer 39

aspartic acid. D. acidic

Question 40

cys: full name and one letter symbol?

Answer 40

cysteine, cys, c

Question 41

E: full name and 3 letter name

Answer 41

glutamic acid, glu. acidic

Question 42

K: 3 letter and full name and property

Answer 42

basic lysine lys

Question 43

proline: 3 and 1 letter name

Answer 43

pro, P

Question 44

threonine: 3 and 1 letter abbreviation and property

Answer 44

nonpolar uncharged. thr. T.

Question 45

tyrosine

Answer 45

Y, tyr. non polar uncharged

Question 46

serine

Answer 46

ser , S, nonpolar uncharged

Question 47

arginine

Answer 47

R, arg, basic