amino acids and proteins

Question 1

what is the primary structure of an amino acid determined by?

Answer 1

the linear order of residues in the chain

Question 2

describe the folding process

Answer 2

initial formations of sections of secondary structure at certain point along the poly chain.
packing together of these secondary structures to form stable domains.
docking together of the domains and the other subunits.

Question 3

bond between amide links in an alpha helix

Answer 3

hydrogen

Question 4

what direction do the sidechains point in an alpha helix?

Answer 4

outwards

Question 5

who discovered the structure of the alpha helix?

Answer 5

linus pauling

Question 6

what is the structure of a beta strand?

Answer 6

two anti-parallel/parallel strands, with hydrogen bonds between linkages

Question 7

what direction do the side chains point in a beta strand?

Answer 7

in front and behind

Question 8

what is silk?

Answer 8

an almost pure beta sheet

Question 9

what determines whether the structure is a helix, sheet, or turn?

Answer 9

the local sequence of side chains

Question 10

what amino acids occur more frequently in each type of structure?

Answer 10

helix - glutamine (E)
sheet - valine (V)
turns - proline and glycine (P) (G)

Question 11

describe the tertiary structure

Answer 11

hydrophobic core and hydrophilic residues located at the surface.
charged residues rarely buried unless a complementary charge is buried alongside (help with stability)
hydrogen bonding between side chains is not involved in helix, sheet or turn
disulphide bridges formed

Question 12

what are disulphide bridges?

Answer 12

covalent links between the sulphur atom of two cysteine amino acids

Question 13

prosthetic groups

Answer 13

metal ions
nucleotides
flavins
phosphates
porphyrins

Question 14

describe the quaternary structure

Answer 14

5 subunits arranged to form a transmembrane channel.
This refers to the assembly of two or more independently folded protein chains to create a larger complex. This often serves to link several processes together (e.g. a chain of enzyme reactions) or creates co-operative effects in which each subunit regulates the action of the other to achieve greater efficiency (e.g. in allosteric mechanisms). The same forces that stabilise tertiary structures can be responsible for holding protein subunits together. Subunits can be identical or different, and arranged in variety of different ways (with different axes of symmetry).

Question 15

why are they called secondary structures?

Answer 15

defined by hydrogen bonding

Question 16

why are proline and glycine not easily accommodated into alpha helix and beta strands?

Answer 16

atypical structures have non-complementary geometrics

Question 17

alpha helix

Answer 17

3.6 amino acid residues per turn and is stabilised by H bonding in the amide backbone, further stabilised/destabilised by the attraction/repulsions between the side chains that are oriented outwards from the helix. 10 residues long (15 angstroms), and are quite stable.

Question 18

what are the end to end dipoles in alpha helixes created by?

Answer 18

cumulative alignment of all the amide bonds in the same direction

Question 19

why is antiparallel the most common form of beta sheet?

Answer 19

H bonds are better aligned and stronger

Question 20

beta sheets description

Answer 20

20-40 residues, 4-6 strands, often twisted into a propeller shape(twist is right handed when viewed edge on). =variations on the theme are H bond stabilised beta turns and bulges which can allow the chain to turn 90 or 180 degrees. beta turns are usually found near the surface of a protein molecule.

Question 21

how have the preferences of all amino acids been calculated?

Answer 21

by taking an average across 4/5/6 residues can give a reasonable prediction of which will be favoured

Question 22

why are P and G suited to forming tight turns?

Answer 22

atypical structures, often coupled together - P forces the chain to turn and G continues a tight chain reversal because it has no side chain to cause obstruction.

Question 23

how does the tertiary structure arise?

Answer 23

formed by the chain folding up against itself, with the preformed helix and sheet sections packing together to form a closely packed structure that excludes solvents from the interior. occurs in a defined way because of the physical fit of helices and sheets.

Question 24

final chain folding patterns

Answer 24

motifs/topologies

Question 25

more tertiary structure and domains

Answer 25

Larger proteins have several domains within their tertiary structures. These are compact, locally folded, regions connected by the continuous polypeptide chain that could maintain their structural integrity if excised from the protein

Question 26

fibrous

Answer 26

Fibrous proteins are long, elongated, usually of regular secondary structure and mainly perform structural roles in cells and organisms. e.g. keratin (helix, hair and nails) fibroins (sheet, silk) collagen (triple helix) and elastin (cross-linked random coils).

Question 27

globular

Answer 27

Where there is a mixture of short helix and/or sheet segments and these regular secondary structures only account for about 60% of the molecule, the protein is termed “globular” (i.e. it is usually water soluble, rounded and has a defined hydrophobic core).

Question 28

collagen

Answer 28

this is a structural protein found in skin, bone, cartilage, tendon, etc. It is fibrous, rigid and inextensible. In mammals it comprises 25% of the total protein.

Question 29

haemoglobin structure

Answer 29

haemoglobin is a tetramer of 4 polypeptide chains; 2 α chains and 2 β chains. The α and β chains are very similar in primary sequence and shape (i.e. they are genetically related). Each polypeptide chain consists of around 150 residues and is folded into 8 α helical sections

Question 30

carboxypeptidase

Answer 30

digestive enzyme that can be found in the mammalian gut as part of the complement of enzymes that digest food protein. carboxypeptidase A, which prefers to remove aromatic amino acids residues from the C-terminal ends of proteins, and carboxypeptidase B, which prefers to remove amino acids with positively charged side chains.

Question 31

kinetic information

Answer 31

predicting how a given enzyme will behave and respond in various situations and conditions, and thus how much product it will produce. diagnosing the mechanisms of inhibitor and effector actions

Question 32

enzyme reaction rates

Answer 32

when measured experimentally, velocity is directly proportional to the starting conc.