protein structure function

Question 1

primary structure

Answer 1

linear sequence of amino acids linked together by peptide bonds

= non-covalent interactions

Question 2

secondary structure

Answer 2

folding of the polypeptide chain into local alpha helices or beta sheets (&b turns)

Question 3

tertiary structure

Answer 3

structure of a peptide composed of secondary structural elements & various loops & turns
- main form distinct, independently stable domains

Question 4

quaternary structure

Answer 4

multiple polypeptides

Question 5

exception amino acid in secondary structure

Answer 5

prolines can’t participate in hydrogen bonding & thus excluded from alpha helix

Question 6

alpha helix bonds in secondary structure

Answer 6

= held together by hydrogen bonds b/w backbone aminde & carbonyl groups

Question 7

beta strand bonds in secondary structure

Answer 7

= stabilised by hydrogen bonds b/w backbone oxygen & hydrogen atoms in amino acids on different strands

Question 8

beta turn bonds in secondary structure

Answer 8

= composed of 4 residues
= reverses direction of polypeptide chain
= facilitate the folding of long polypeptides into compact structures
= glycine (smallest R group) & proline (built in bend) are commonly found

Question 9

IDPs

Answer 9

= intrinsically disordered polypeptide regions
= have no particular structure
= change structure to adapt to function

• binding
• signalling
• tethering
• diffusion barrier

Question 10

ways to visualise tertiary structure & what can see x5

Answer 10

1. backbone trace = depicts how the polypeptide is tightly packed into a small volume
2. ball and stick model = reveals locations of all the atoms
3. ribbon diagram = highlights beta strands & alpha helices
4. water-accessible surface = protein surface topology with positive charge & neg charge regions
5. hybrid model

Question 11

what is a structural motif & what protein level

Answer 11

= combination of different protein secondary structures with specific type function

• coiled-coil motif = transcription factors
• helix-loop-helix motif = calcium-binding & DNA- binding regulatory proteins
• zinc-finger motif = DNA binding proteins that help regulate transcription

Question 12

define protein domains & what protein level

Answer 12

molecular units from which larger proteins are built

= repeated in a number of different proteins

Question 13

example of protein domain types x2

Answer 13

1. protein molecules that have elongated, fibrous shapes
   - collagen found in extracellular space, tendons, ligaments, cartilage, skin
   - crosslinks formed by hydroxylation of lysine = allow stretch & relax
2. globular proteins form long helical filaments example
   - cytoskeleton protein F-actin formed from G-actin

Question 14

what structure do multiple protein domains make

Answer 14

tertiary structure & multiple of them make quaternary

Question 15

what are supramolecular complexes & example

Answer 15

• can contain hundreds of polypeptide chains & sometimes other biopolymers such as nucleic acid
  e. g., transcription initiation complex = core RNA polymerase & general transcription factors containing about 20 subunits = transcribes DNA into mRNA

Question 16

where are motifs found

Answer 16

secondary structure

Question 17

where are domains found

Answer 17

tertiary structure

Question 18

what can missfolded/denatured proteins form

Answer 18

well-organised amyloid fibril aggregates that can cause diseases e.g., alzheimer’s disease & parkinson’s disease

• structures accumulate inside, or outside of cells in various organs including joints, b/w bones, liver, brain = damage

Question 19

how are tertiary structures stabilised

Answer 19

hydrophobic interactions between non-polar side chains & hydrogen bonds involving polar side chains & backbone amino & carboxyl groups

Question 20

role of hydrophobic residues in tertiary structure folding

Answer 20

cluster together like drops of oil in folded protein core, driven away from the aqueous surroundings by the hydrophobic effect

Question 21

charged & uncharged polar side chains role in tertiary structure folding

Answer 21

form stabilising interactions with surrounding water & ions on the protein surface

Question 22

what interactions hold together tertiary structures

Answer 22

• hydrogen bonds (more interior)
• electrostatic attractions (more surface)
• van der waals attractions (more interior)

Question 23

native state

Answer 23

= goal of folding = the most stable structure for prime functioning

usually the conformation with the lowest free energy

Question 24

summary folding

Answer 24

1. motif
2. domains
3. multiple domains = tertiary or could be one domain
4. native state

Question 25

molecular chaperones

Answer 25

bind to a short segment of a protein substrate & stabilise unfolded or partly folded proteins, preventing aggregation or degradation

Question 26

chaperonins

Answer 26

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

= exclude outward solvent to help folding without disruption

Question 27

result of aggregate folding

Answer 27

cytotoxic effects

Question 28

how are missfolded proteins recycled

Answer 28

ubiquitin chops up the proteins allowing it to be recycled

Question 29

how does an enzyme folding work

Answer 29

folds so the amino acid side chains contribute to the formation of a pocket and the side chains contribute to a binding of a substrate within the pocket

Question 30

what is acid & base catalysis

Answer 30

molecule besides water that acts as a protein doner or accepter during the enzymatic reaction

Question 31

enzyme functions

Answer 31

= make or break covalent bonds

• lowers the energy input/activation energy required for a chemical reaction to proceed
• remain unchanged
• can facilitate reversible reactions
• can be denatured due to temp or pH change

Question 32

does enzyme binding change the equilibrium constant of the reaction

Answer 32

no

Question 33

what is the catalytic site

Answer 33

composed of side chains and catalytic triad that works to break the peptide bonds = by acid & base catalysis

Question 34

what is lysozome and where is it found

Answer 34

an enzyme found in tears, saliva, sweat & other bodily fluids

Question 35

what type of enzyme is a lysozome

Answer 35

glycoside hydrolase

Question 36

what is peptidoglycan a major component of

Answer 36

gram-positive (thick peptidoglycan wall) bacterial cell wall

Question 37

lysosome reaction that is catalyses

Answer 37

the hydrolysis of 1,4-beta linkages between N-acetylmuramic acid & N-acetyl-D-glucosamine (breaks the bonds) residues in peptidoglycan = antimicrobial agent

Question 38

what is a reaction pathway

Answer 38

converts substrate into final products by the sequential action enzymes A,B, C

Question 39

action of enzymes free in solution (reaction pathway)

Answer 39

reaction intermediates diffuse from one enzyme to the next, which may be inherently slow

Question 40

multi-subunit enzyme complex

Answer 40

formed by a scaffold protein minimises or eliminates substrate diffusion time

Question 41

enzymes fused at a genetic level

Answer 41

= becoming domains in a single polypeptide chain - also minimises or eliminates substrate diffusion time

Question 42

3 types of reaction pathway enzymes

Answer 42

1. in a free solution
2. multi-subunit
3. fused at a genetic level

Question 43

can all enzymes recognise multiple substrates

Answer 43

no

Question 44

competitive compared to non-competitive enzyme and an example of non-competitive

Answer 44

competitive - inhibition involves the binding of a molecule at the active site of the enzyme

non-competitive - inhibition involves binding of a molecule at a site other than the active site e.g., allosteric regulation

Question 45

explain the two types of allosteric regulation

Answer 45

1. allosteric inhibition

= mediate a conformation change which translates to the active site and it may not be able to bind to the substrate = alter action

2. allosteric activation = alter the conformation = enhance binding of the substrate = increasing enzyme activity

Question 46

coenzyme

Answer 46

helps to facilitate the activity of an enzyme e.g., vitamins

Question 47

ubiquitintins

Answer 47

small polypeptide added to proteins to target then for degradation

Question 48

what enzyme:

1. breaks down proteins
2. add a phosphate group to molecules
3. remove a phosphate group from molecules
4. join two molecules together
5. break down nucleic acids

Answer 48

1. proteases
2. kinases
3. phosphatase
4. ligases
5. nucleases