Lecture 1

Question 1

what are the general functions of proteins?

Answer 1

Enzymes, plasma membrane proteins, signaling, structural proteins, motor proteins, anitbodies, hormones

Question 2

who coined the term protein?

Answer 2

Jons J Berzelius

Question 3

which amino acids have sulfur groups?

Answer 3

cysteine and methionine

Question 4

which amino acids have -OH groups?

Answer 4

tyrosine, serine, threonine

Question 5

how are peptide bonds formed?

Answer 5

a-carboxyl group joined to a-amino group
includes a loss of water molecule

Question 6

what kind of bond is a peptide bond?

Answer 6

planar bond

Question 7

how many bonds do amino acids contribute to protein backbone?

Answer 7

3

Question 8

steric (spatial) effect

Answer 8

effect in which the shape of a molecule influences its reactions

Question 9

why are peptide bonds rigid?

Answer 9

carbonyl carbon atom and nitrogen atom has partial double-bond character

Question 10

which end of a polypeptide chain is the beginning?
(amino end or carboxyl end)

Answer 10

amino end (N terminal)

Question 11

polypeptide backbone

Answer 11

repeating atoms along the core of the polypeptide chain

Question 12

what bonds constrain protein folding? what type of bonds are they?

Answer 12

weak non covalent bonds
hydrogen bonds, ionic bonds, van der waals

Question 13

hydrophobic interactions

Answer 13

minimize disruption of hydrogen bonding between water molecules

Question 14

where are non-polar side chains of amino acids? (in terms of hydrophobic interactions)

Answer 14

cluster in the interior of proteins

Question 15

where are polar side chains of amino acids? (in terms of hydrophobic interactions)

Answer 15

outside of the proteins
hydrogen bonded to other polar amino acids or to polypeptide backbone

Question 16

disulfide bonds

Answer 16

covalent links between the sulfur atoms in the side chains of cysteins

Question 17

what is the function of disulfide bonds?

Answer 17

stabilize protein structure (folding or mediate attachment of protein subunits)

Question 18

intrachain disulfide bonds

Answer 18

joining two parts of the same polypeptide

Question 19

interchain disulfide bonds

Answer 19

joining two different polypeptide chains

Question 20

where do disulfide bonds form?

Answer 20

ER

Question 21

why can’t disulfide bonds be formed in the cytosol?

Answer 21

high concentration of reducing agents in the cytosol

Question 22

what are the four levels of protein structure?

Answer 22

primary, secondary, tertiary and quaternary

Question 23

primary protein structure

Answer 23

order/sequence of covalently linked amino acids

Question 24

tertiary protein structure

Answer 24

3D organization of polypeptide chain
- steric relationship of amino acids that are far apart in linear sequence

Question 24

secondary protein structure

Answer 24

folding of polypeptide chains (maintained by repetitive hydrogen bonding) - steric (spatial) relationship of amino acids that are close to one another in the linear sequence -a-helix and b-pleated sheets

Question 24

quaternary protein structure

Answer 24

complete 3D structure of multi-subunit protein complexes (the way protein chains are packed together)

Question 24

who sequenced the first protein? what kind of protein?

Answer 24

Frederick Sanger; bovine insulin

Question 25

how are a-helix and b-pleated sheets bonded?

Answer 25

hydrogen bonding of amino and carbonyl groups in polypeptide backbone **no bonding between side chains of amino acids**

Question 25

what determines the conformation of a protein?

Answer 25

amino acid sequence

Question 25

how many possible primary protein sequences can exist?

Answer 25

20^n

Question 25

how many protein sequences are known?

Answer 25

500,000

Question 25

where does the H-bond occur in a-helix?

Answer 25

every fourth peptide (3.6 amino acids)

Question 25

coiled- coil

Answer 25

a-helices when they wrap around each other (triple helix)

Question 25

how do colied-coils form?

Answer 25

two or three a-helices have their nonpolar side chains on one side -> wraps around each other with side chains facing inward

Question 25

what proteins contain a-helices?

Answer 25

cell membrane proteins (transport proteins and receptor) -nonpolar side chains -rich in areas that cross lipid bilayer

Question 26

what factors destabilize a-helices?

Answer 26

- electrostatic repulsion between similarly charged R groups - steric hinderance due to bulky substitutions on the B- carbons of R group

Question 26

what amino acid is incompatible with the a-helix?

Answer 26

proline

Question 26

what protein was b-pleated sheets first identified in?

Answer 26

fibroin (silk)

Question 26

why is a amino acid incompatible with the a-helix?

Answer 26

proline b/c it causes bends in the polypeptide backbone - proline amino group cannot participate in H bonding - rotation around the bond between nitrogen of proline is restricted

Question 27

similarities of B-sheet and a-helix

Answer 27

both involve H bonding between carbonyl and amino groups of peptide bonds

Question 28

differences of B-sheet and a-helix

Answer 28

- H bonds form between different parts of single chain (intrachain vs interchain) - bonds are perpendicular on b-sheet vs parallel in a-helix

Question 29

parallel pleated sheet

Answer 29

h bonded peptide chains run in same direction

Question 30

antiparallel pleated sheet

Answer 30

H bonded peptide chain run in opposite directions

Question 31

reverse turns

Answer 31

regions of secondary structure where the chains change direction or fold back

Question 32

supersecondary structure

Answer 32

secondary structures that combine (BaB, aa, B-meander unit, greek key)

Question 33

motifs

Answer 33

repeated combinations of supersecondary structure within a protein (usually short repetitive units)

Question 34

domain (module)

Answer 34

- specific region of protein that can fold independently of the rest of the protein into a discrete stable structure that has its own function - modular units that construct larger proteins - smaller proteins = single domain - larger proteins = several dozen domains connected by unstructured polypeptide chains

Question 35

domain shuffling (multidomain proteins)

Answer 35

DNA sequences encoding each domain accidentally joined, creating new gene

Question 36

how many domains does fibronectin have?

Answer 36

four of fibronectin type 3 domains