BSCI330 protein shape and structure

Question 1

how can ribosomes synthesizing peptide chains move quicker

Answer 1

each ribosome binds to the cap after the prior one has moved far enough along and begins translating

a single mRNA may thus have several ribosomes translating simultaneously - this is called a polyribosome

Question 2

what do protein synthesis inhibitors do

Answer 2

cause premature termination

Question 3

what is protein structure determined by

Answer 3

sequence of amino acids

Question 4

what are proteins divided into

Answer 4

functional or structural domains, which are independently folding sub-regions within the protein sequence

Question 5

what determines a protein’s function

Answer 5

its 3D structure

Question 6

what is the primary structure

Answer 6

linear sequence of amino acid residues

determined by mRNA code

in combination with protein’s environment, it determines secondary, tertiary, quaternary structures

Question 7

what is secondary structure

Answer 7

folding and twisting of peptide backbone around alpha carbon

Question 8

how is the secondary structure held together

Answer 8

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

R-groups stick out from backbone

Question 9

what are the two well-known secondary structures

Answer 9

alpha helices and beta sheets

Question 10

what are alpha helices

Answer 10

makes rigid cylindrical structure

forms when hydrogen bonding between carbonyl and amine groups that are 4 amino acids apart on backbone

Question 11

what are beta sheets

Answer 11

folded, sheet-like structure

adjacent chains can be parallel (adjacent chains run N terminal to C terminal) or antiparallel chain (adjacent chains run in opposite directions)

Question 12

what disrupts secondary structure

Answer 12

rigid proline residues insert a kink in a protein’s backbone

Question 13

what is tertiary structure

Answer 13

3D arrangement of secondary structure held together by non-covalent attractions between R groups and surrounding environment

Question 14

what can R group interactions lead to

Answer 14

the folding of secondary structures into 3D structures

Question 15

why do proteins require chaperonins

Answer 15

they provide an isolated chemical environment in which they can fold, which is spontaneous

Question 16

what are prions

Answer 16

proteins synthesized by neurons that create diseases of protein folding (folding the wrong way is disruptive to the cell)

Question 17

what are protein domains

Answer 17

a protein domain is a region of the tertiary structure of a protein that folds independently of other regions

• a domain represents a functional region of the protein (different domains have different functions)

Question 18

what is quaternary structure

Answer 18

arrangement of multiple tertiary structures - multiple independent polypeptide chains folded up in 3D interacting with each other

Question 19

what are quaternary structures held together by

Answer 19

weak bonds and disulphide bonds

Question 20

what identify quaternary structures

Answer 20

interactions of side chains

Question 21

what are homomers

Answer 21

repeating identical subunit polypeptides of quaternary structure

Question 22

what are heteromers

Answer 22

different subunit polypeptides of quaternary structure

Question 23

what do covalent modifications of amino acid side chains do

Answer 23

controls function of folded proteins, changing their chemical properties

Question 24

what does proteolytic cleavage do

Answer 24

removes amino acids from the original translated sequence

Question 25

what is phosphorylation

Answer 25

covalent modification to protein - adds a negatively charged phosphate group to the side chain of serine, threonine, or tyrosine

Question 26

what do kinases do to phosphate normally

Answer 26

remove a phosphate from ATP and transfer it to serine, threonine, or tyrosine, leaving an ADP

Question 27

what do kinases do in relation to phosphatases

Answer 27

kinases add a phosphate, phosphatases remove one

Question 28

what does addition or subtraction of phosphate do

Answer 28

major structural changes, activity changes, or changes in protein solubility because each phosphate group adds two negative charges to a protein

the added phosphate group can create a new recognition site that allows other proteins to bind to the phosphorylated protein

Question 29

what is ubiquitylation

Answer 29

covalent modification to proteins - the addition of the small, cytosolic protein ubiquitin

Question 30

what does ubiquitin do

Answer 30

serves as a tag that can either mark a protein for degradation or direct proteins to specific locations in the cell

Question 31

what are ligands

Answer 31

molecules that bind to proteins

Question 32

what determines a protein’s biological properties

Answer 32

its interactions with other molecules

Question 33

what is binding strength achieved through

Answer 33

3D complementarity of bonding and the formation of several noncovalent bonds

Question 34

what are equilibrium constants

Answer 34

Ka = Kon/Koff

Kon and Koff are the rates of the forward (association) and backward (disassociation) reactions that create or breakdown the protein-ligand complex

if the association constant is >1 = spontaneous, <1 = non-spontaneous

Question 35

what is the dissociation constant

Answer 35

Kd = 1/Ka

the smaller the dissociation constant, the stronger the binding is

Question 36

whats are GEFs

Answer 36

Guanine nucleotide exchange factors, which allows GDP to be released and GTP to be bound

Question 37

what are GAPs

Answer 37

GTPase activating proteins, which allow for hydrolysis of GTP to GDP and turns the system off again