Amino acids and proteins

Question 1

peptide bonds

Answer 1

joins amino acids together

Question 2

insulin

Answer 2

cell signaling

binds to the insulin receptor to signal cells to take up glucose

Question 3

trypsin

Answer 3

digestion

an enzyme that breaks down proteins during digestion

Question 4

amylase

Answer 4

digestion
an enzyme that breaks down starch into sugars
found in saliva as well as pancreatic juices

Question 5

alcohol dehydrogenase

Answer 5

metabolism

an enzyme that helps to metabolise ethanol

Question 6

1cza hexokinase

Answer 6

metabolism

an enzyme that adds a phosphate to glucose, after glucose is taken up by the cell

Question 7

haemoglobin

Answer 7

oxygen transport and metabolism

binds oxygen in the lungs and carries it in the blood to tissues for use in metabolism

Question 8

ATP synthase

Answer 8

metabolism and energetics (membrane proteins

membrane protein that generates ATP for use in cellular functions

Question 9

antibody

Answer 9

immune protection

bind to cellular invaders like bacteria and viruses to help protect the body from infection

Question 10

DNA polymerase

Answer 10

replication and maintenance

binds to one strand of DNA and adds the complementary strand to it

Question 11

RNA polymerase

Answer 11

replication and maintenance

creates a single strand of RNA that is complementary to one of the strands of duplex DNA

Question 12

amino acid 4 main properties

Answer 12

amino acids are chiral
amino acids in solution are zwitterions
amino acids have a common backbone but vary in their side chains

Question 13

Imino acid

Answer 13

the side chain bonds back to the main chain e.g. a CH3 bonds to the NH to make CH2 bonded to NH2+

Question 14

4 groups of amino acids

Answer 14

non-polar side chains
negatively charged side chains (acidic)
positively charged side chains (basic)
polar side chains

Question 15

one letter abbreviations

describing mutations

Answer 15

first letter = original or native amino acid
number = location of mutation in the protein
second letter = new or mutated residue

Question 16

pKa

Answer 16

the pKa value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised

Question 17

pl

Answer 17

the pl, or isoelectric point, is the pH at which the net charge on an amino acid (or protein) is zero

Question 18

disulfide bond

Answer 18

a bond between two S functional groups

e.g. cysteine forming a covalent bond with another cysteine

Question 19

amino acid modifications can be

Answer 19

phosphorylation
hydroxylation
carboxylation
metal binding
iodination
glycosylation
many more

Question 20

phosphorylation

Answer 20

often used to control enzyme activity, acts as a chemical on/off switch

Question 21

hydroxylation

Answer 21

needed to prevent connective tissue diseases and scurvy, often proline and lysine involved

Question 22

carboxylation

Answer 22

needed for blood clotting, often glutamate involved

Question 23

peptide

Answer 23

a short stretch of amino acids joined together by peptide bonds

Question 24

protein

Answer 24

a longer chain of amino acids joined together, usually with a defined biological function

Question 25

amino acid residue

Answer 25

when amino acids are covalently joined together in a peptide or protein they are referred to as amino acid residues as they are no longer complete, individual, amino acids
their location by residue number is often referred to as well

Question 26

how are amino acid residues in a polypeptide chain numbered

Answer 26

starting from the amino terminus to the carboxy terminus

Question 27

globular proteins turn out to be comprised of primarily…

Answer 27

α-helix
β-structure
turns

Question 28

levels of protein structure

Answer 28

primary
secondary
tertiary
quaternary

Question 29

primary protein structure

Answer 29

amino acid sequences of a protein

Question 30

secondary protein structure

Answer 30

local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

Question 31

tertiary protein structures

Answer 31

3D structure of a complete protein chain

Question 32

quaternary protein structure

Answer 32

interchain packing and structure for a protein that contains multiple protein chains

Question 33

main chain atoms in a protein

Answer 33

N
Cα
C’

Question 34

phi bond angle

Φ

Answer 34

bond angle between N and Cα

ranging from 0 to +/- 180˚

Question 35

psi bond angle

Ψ

Answer 35

bond angle between Cα and C’

ranging from 0 to +/- 180˚

Question 36

omega bond angle

ω

Answer 36

rotation angle around the peptide bond

usually very close to either 0 or 180˚

Question 37

phi-psi restrictions caused by steric hindrance

Answer 37

• phi rotation can lead to O-O collisions

- psi rotation can lead to NH-NH collisions

Question 38

steric hindrance

Answer 38

hindrance of chemical action ascribed to the arrangement of atoms in a molecule

Question 39

peptide bonds can be either…

Answer 39

trans or cis

Question 40

trans peptide bonds

Answer 40

• most common for peptide bonds
• ω is about 180˚
• Cα atoms are found on opposite sides of the peptide bond

Question 41

cis peptide bonds

Answer 41

• less common for peptide bonds
• ω is about 0˚
• Cα atoms are found on the same side of the peptide bond
• steric crowding is increased
• once formed, the peptide bond angle usually doesn’t rotate very much

Question 42

how does the structure of a protein lead to it’s function

Answer 42

combination of all the rotations and twists around all the bonds in a protein –> overall 3D structure –> arrangement of all the side chains in the protein –> function (different for every protein)

Question 43

protein secondary structure

two canonical structures

Answer 43

β-strand

β-sheet

Question 44

right handed spiral

Answer 44

in the α-helix, the main chain spirals around the central axis like a spiral staircase