exam 2 protein shape and structure

Question 1

what is protein structure determined by

Answer 1

the sequence of amino acids

Question 2

what can proteins be divided into

Answer 2

functional and structural domains

Question 3

what are function and structural domains

Answer 3

independently folding subregions within the protein sequence

Question 4

what determines a protein’s function

Answer 4

the 3D structure of it

Question 5

what is primary structure of proteins

Answer 5

linear sequence of amino acid residues determined by the mRNA code

Question 6

what is primary structure held together by

Answer 6

peptide bonds between amino acids

Question 7

what determines higher order structures

Answer 7

protein structure in combination with a protein’s environment

Question 8

what is the sequence of proteins different from

Answer 8

the sequence that initiates folding process

Question 9

what is the secondary structure of a protein

Answer 9

the folding and twisting of peptide backbone

Question 10

what is the secondary structure held together by

Answer 10

weak H-bonds between C=O (carbonyl) and N-H (amine) groups in the backbone

Question 11

what do the two bonds of every amino acid have

Answer 11

the two bonds have freedom of rotation

Question 12

what is the purpose of side chains in the secondary structure

Answer 12

they make it more or less difficult for structure to form, but don’t hold secondary structure together

Question 13

what are the two secondary structures

Answer 13

alpha helices and beta sheets

Question 14

what is the structure of the alpha helix

Answer 14

rigid cylindrical structure

Question 15

when does an alpha helix form

Answer 15

forms when H-bonding occurs between a carbonyl and amine group that are 4 amino acids apart on the polypeptide backbone

Question 16

what makes one turn of the helix

Answer 16

four amino acids

Question 17

what direction does coiling of the alpha helix happen in

Answer 17

a clockwise direction down the length of the chain

Question 18

what is the beta sheet

Answer 18

a flat, folded, sheet-like structure

Question 19

when does a beta sheet form

Answer 19

when H-bonding occurs between a carbonyl and amine group on adjacent polypeptide chains

Question 20

what does it mean for an adjacent beta sheet chain to be parallel

Answer 20

adjacent chains run N-terminal to C-terminal

Question 21

what does it mean for an adjacent beta sheet chain to be antiparallel

Answer 21

adjacent chains run in opposite directions

Question 22

what do rigid proline residues do

Answer 22

insert a kink in a protein’s backbone and disrupt secondary structures

Question 23

what is tertiary structure of proteins

Answer 23

3D arrangement of secondary structures to assume the lowest possible energy state

Question 24

what is tertiary structure (detailed)

Answer 24

stretches of proteins that serve as links between secondary structures to allow them to fold up

Question 25

what is tertiary structure held together by

Answer 25

non-covalent attractions between R-groups along with R-groups + the surrounding environment

Question 26

what links secondary structures together to form tertiary structures

Answer 26

unstructured loops (aka random coils)

Question 27

what can tertiary structure stabilized by

Answer 27

covalent interactions - most important are disulfide bonds

Question 28

where can covalent disulfide bonds form to stabilize tertiary structures

Answer 28

between cysteine residues to cross-link parts of the polypeptide backbones

Question 29

what does stabilizing tertiary structures do

Answer 29

makes it more difficult to unfold once it’s in the shape

Question 30

what is the difference is the energy of unfolded and folded proteins

Answer 30

unfolded proteins have a higher free energy than when it’s folded due to entropy

Question 31

what does protein stability depend on

Answer 31

the free energy change between the folded and unfolded states

Question 32

what is delta G

Answer 32

G(folded) - G(unfolded) : products minus reactants

Question 33

what charge creates the most stable folded protein

Answer 33

the most negative the change in free energy

Question 34

what are molecular chaperones (chaperonins)

Answer 34

provide an isolated chemical environment in which they can fold, which proteins require to 3D fold

Question 35

what is a prion

Answer 35

an infectious protein

Question 36

what are prions evidence of

Answer 36

that some unusual contagious neurological diseases are caused by proteins alone

Question 37

what happens when a prion protein interacts with a correctly folded protein

Answer 37

it recruits it to also fold incorrectly (ex: mad cow, kuru)

Question 38

what is a protein domain

Answer 38

a region of the protein that folds essentially independently of other regions

Question 39

how many protein domains can a protein have

Answer 39

single or multiple

Question 40

what does a domain represent

Answer 40

a functional region of the protein - different domains have different function

Question 41

what do catalytic protein domains do

Answer 41

inhibit host cell protein synthesis

Question 42

what do hydrophobic protein domains do

Answer 42

inserts into the membrane

Question 43

what do receptor binding protein domains do

Answer 43

attach to cell surface

Question 44

what are motifs

Answer 44

similar domains that occur in many related proteins

Question 45

what is quaternary protein structure

Answer 45

arrangement of multiple tertiary structures

Question 46

what are quaternary structures held together by

Answer 46

weak bonds and some disulphide bonds

Question 47

what are homomers of quaternary structures

Answer 47

identical subunit polypeptides

Question 48

what are heteromers of quaternary structures

Answer 48

different subunit polypeptides

Question 49

what is the final structure of a protein after quaternary structure

Answer 49

mature protein

Question 50

what does a higher order structure increase

Answer 50

efficiency