chapter 3

Question 1

what is the sequence of protein structure

Answer 1

primary –> secondary –> tertiary –> quaternary –> function or supramolecule (large scale assembly)

Question 2

what are some of the functions that a quaternary protein can perform

Answer 2

regulation (giving signal to turn on/off), structure, movement (in/out of the cell+chromosome separation), catalysis, transport, signaling

Question 3

where does peptide bond formation happen

Answer 3

in the cytoplasm

Question 4

how is a peptide bond formed

Answer 4

amino acid + amino acid = peptide bond + water (water is released in the process)

Question 5

what is the primary structure of a protein

Answer 5

the linear sequence of amino acids linked together by peptide bonds (methionine is always first but it is VERY often cleaved)

Question 6

what are the two common secondary structures that proteins adopt

Answer 6

alpha helix and beta sheets

Question 7

what is the backbone of an alpha helix made out of

Answer 7

polypeptides (CCN - peptide bond - CCN, etc)

Question 8

how does an alpha helix form

Answer 8

the polypeptide backbone is folded into a spiral that is held in place by hydrogen bonds between BACKBONE oxygen and hydrogen atoms

Question 9

in alpha helix, R groups determine what

Answer 9

HOW spiral takes place (hydrophobic/hydrophilic quality) but they are NOT actively involved in the structure (bonds between R groups do not occur/do not form the helix)

Question 10

how does a beta sheet form

Answer 10

hydrogen bonds form between the carbonyl oxygen atoms of each residue(amino acid) in one B strand and the amide hydrogen atom of a residue(amino acid) in a separate, BUT ADJACENT, B strand

Question 11

what are the two structures of beta sheets

Answer 11

anti-parallel and parallel

Question 12

what is the structure of a beta sheet turn

Answer 12

four residues (amino acids) reverse the direction of the chain

Question 13

what are the two common amino acids in beta sheet turns

Answer 13

glycine, proline

Question 14

what is the oil drop effect in protein folding

Answer 14

proteins will fold so hydrophilic side chains will be outwards to cell (bc the cell is an aqueous environment) and hydrophobic side chains will go to the core away from the cell

NOTE: membrane proteins and channel proteins will be vice versa bc the inside of these are hydrophobic so the hydrophobic side chains will be outwards

Question 15

what is the hand in glove fit in the quaternary structure of a protein

Answer 15

molecular complementarity between the molecule in question and the site to which it binds (epitope)

Question 16

how are the light chains and heavy chains of an antibody linked together

Answer 16

by disulfide bonds

Question 17

what are structural motifs of secondary structure

Answer 17

regular combinations of secondary structures usually with a specific type of function

NOTE: can be encoded by a highly conserved sequence motif

Question 18

what are three common motifs

Answer 18

coiled-coil motif, EFhand/helix-loop motif, Zinc-finger motif

Question 19

what is a motif (for dummies)

Answer 19

a combination of secondary structures (alpha helix, beta sheets) that is regularly observed and used by the cell when making proteins that is associated with a particular function

proteins will take on certain motifs when being created because the motifs are associated with a certain function

basic: small regions of protein sequences that are shared between different proteins

NOTE: secondary structure only

Question 20

what is a domain (for dummies)

Answer 20

domains are distinct functional and/or structural units in a protein

usually they are responsible for a particular function or interaction, contributing to the overall role of a protein

NOTE: domains can be made up of motifs

Question 21

what is EGF

Answer 21

a small, soluble peptide hormone that binds to cells and promotes their cell division

Question 22

EGF domains

Answer 22

EGF precursor: epidermal growth factor precursor - generated by cleavage and generates multiple EFGs

Neu: EGF domain + other domains

TPA: tissue plasminogen activator - EGF domain + other domains

NOTE: ~75% of eukaryotic proteins have multiple structural domains

Question 23

what are supramolecule complexes

Answer 23

can contain tens ot hundreds of polypeptide chains and sometimes other biopolymers such as nucleic acids

Question 24

what is an example of a supramolecule

Answer 24

transcription initiation complex

Question 25

what are the two things that assist in protein folding

Answer 25

1. molecular chaperone
2. chaperonins

Question 26

what is molecular chaperone-mediated protein folding

Answer 26

molecular chaperones bind to a short segment of a protein substrate and stabilize unfolded or partly folded proteins, preventing aggregation or degradation

Question 27

what is chaperonin-mediated protein folding

Answer 27

chaperonins are folding chambers into which all or part of an unfolded protein can be found in an appropriate environment, giving it time to fold properly

Question 28

what is molecular chaperone-mediated protein folding common

Answer 28

during stress and mitochondrial functions

commonly functioning during normal processes