MVU2 PROTEIN FOLDING IN THE CELL-1

Question 1

what are some of the functions of proteins?

Answer 1

cell building blocks: provide shape and structure
undertake most functions: enzymes catalyse cell chemical reactions
membrane proteins form communication channels
transport of cargo and mechanical forces

Question 2

what does protein folding provide?

Answer 2

provides physical stability and functional surfaces (interactions with other molecules)

Question 3

what does the sequence of amino acids determine?

Answer 3

determines its structure function and localisation

Question 4

what are the four groups around the alpha carbon of an amino acid?

Answer 4

side chain
hydrogen
amino group
carboxyl group

Question 5

how many different side chains are there?

Answer 5

20

Question 6

what is the charge of an amino acid at pH7?

Answer 6

the amino and carboxyl groups are both ionised, the charge is 0
the charge depends on the side chain

Question 7

what are the different chemical characteristics of the different side chains?

Answer 7

1. hydrophobic, polar or charged (basic or acidic)
2. small or large
3. covalently linked to polypeptides

Question 8

how many polar amino acids are there?

Answer 8

5

Question 9

what are the characteristics of polar amino acids?

Answer 9

the R groups form hydrogen bonds with other amino acids or water

Question 10

what are the 5 polar amino acids? their 3 letter codes and 1 letter codes? (goodnotes flashcards for notes)

Answer 10

asparagine (Asn or N)
glutamine (Gln or Q)
serine (Ser or S)
threonine (Thr or T)
Tyrosine (Tyr or Y)

Question 11

how many acidic and basic amino acids are there?

Answer 11

3 basic (positively charged)
and 2 acidic (negatively charged)

Question 12

what are the 3 basic amino acids? (positive)

Answer 12

lysine (Lys or K)
arginine (Arg or R)
histidine (His or H)

Question 13

what are the 2 acidic amino acids? (negative)

Answer 13

asparate (Asp or D)
glutamate (Glu or E)

Question 14

what do the R groups of acidic and basic allow for?

Answer 14

allow for electrostatic/ionic interactions (non covalent interactions)

Question 15

what are the 10 hydrophobic nonpolar amino acids?

Answer 15

alanine (Ala or A)
valine (Val or V)
proline (Pro or P)
phenylalanine (Phe or F)
Glycine (Gly or G)
Cysteine (cys or c)
leucine (Leu or L)
isoleucine (Ile or I)
methionine (Met or M)
tryptophan (Trp or W)

Question 16

what are the characteristics of the hydrophobic amino acids?

Answer 16

they interact through the hydrophobic interactions (exclusion of water molecules)

Question 17

what is special about proline?

Answer 17

it is the only one with the lock conformation

Question 18

what is special about glycine?

Answer 18

very small, fits everywhere

Question 19

what is special about cysteine?

Answer 19

can ave covalent bonding with another cysteine
can make disulfide bonds (very strong covalent bond)
intra and inter chain bond
only happens in the exterior of the cell or in the ER lumen

Question 20

what is special about tryptophan?

Answer 20

has a little bit of a polar hydrogen, can do some hydrogen bonding

Question 21

what is the bond between two amino acids called?

Answer 21

amide linkage, called a peptide bond
uncharged but polar bond

Question 22

what determines the charge and hydrophobicity of a polypeptide?

Answer 22

determined by the side chains

Question 23

what is able to do non covalent bonds with other AA?

Answer 23

side chains and the backbone

Question 24

what can and cannot rotate in a polypeptide?

Answer 24

the peptide bond is planar and cannot rotate (it has partial double bond character)
rotations around the alpha carbon is possible
the polypeptide backbone has limited freedom of rotation

Question 25

what isomers of amino acids do proteins contain?

Answer 25

L amino acids (amino group goes first)

Question 26

in what configuration do peptide bonds occur in? and why?

Answer 26

occur in a trans configuration (to reduce steric hindrance) in all amino acids except P (proline)
proline can be both trans and cis

Question 27

what are the different non covalent interactions that stabilise the polypeptide?

Answer 27

hydrogen bonds
van der waals interactions (transient dipoles)
ionic bonds
hydrophobic interactions

Question 28

what is the hydrophobic effect?

Answer 28

water molecules cage around the hydrophobic molecule
need less water molecules for a larger cage
if you use too much water it creates disorder

Question 29

what kind of proteins do and do not have disulfide bonds?

Answer 29

secretory proteins have disulfide bonds
extracellular proteins in secretory organelles, disulfides reinforce structure
cytosolic proteins do not have disulfide bonds

Question 30

what do secondary structures result from?

Answer 30

hydrogen bonding between N-H and C=O groups in polypeptide backbone

Question 31

what are characteristics of the alpha helix?

Answer 31

backbone is coiled
hydrogen bonds between amine and carbonyl
formed every 4 peptide bonds in each turn of the helix (one helix is 3.6 AA long)
side chains point outward

Question 32

what are characteristics of beta sheets?

Answer 32

bakbone is extended almost straight
several strands pack sideways into a beta sheet
hydrogen bonds between the backbone strands
side chains on alternate sides
very rigid structure
two types (parallel and antiparallel)

Question 33

why are disulfide bonds not formed in the cytoplasm?

Answer 33

it is a reducing environment which doesn’t allow for disulfide bonds

Question 34

what are characteristics of the tertiary structure?

Answer 34

secondary structure elements are packed together to form the tertiary structure
hydrophobic contacts between secondary elements
long range contacts between residues that are far apart in primary sequence

Question 35

what are the loops in the tertiary structure?

Answer 35

have no regular secondary structure and can be flexible
intrinsically disordered and receive post translational modification

Question 36

what are characteristics of quaternary structure?

Answer 36

multiple polypeptide subunits into a final proteins
non covalent interactions between subunits are very stable
oligomer: many subunits

Question 37

what is a domain?

Answer 37

an independently folded unit within a protein
proteins can have one or multiple domains
different domains have different functions

Question 38

what is special about conserved domains?

Answer 38

found in different proteins in combination with other domains
these “modular” domains form reversible, specific, non covalent contacts with other molecules

Question 39

what makes histidine different from the other basic positively charged amino acids?

Answer 39

has a ring, doesn’t have as big of a positive charge, not as easy to have ionic interactions