13 Amino Acids and Proteins Flashcards

Question

What is the tertiary structure of a protein?

Answer 1

proteins fold into compact three-dimensional structures | generally, the most stable structures in terms of intra-molecular bonds and a minimum surface area accessible to water

Answer 2

It is a simple repeat sequence (G X Y)n where X is any amino acid and Y is Proline or 4-Hydroxyproline.

Answer 3

20 amino acids | referred to by either their full names or a 3-letter code

Answer 4

from the amino terminus at the (top) left to carboxyl terminus at the (bottom) right

Answer 5

if the sequence is known

Answer 6

a) are basic and accept H⁺ as pH decreases NH₂ + H⁺ ⇌ NH₃ b) a group that readily loses H⁺ as pH increases COOH ⇌ COO- + H⁺

Answer 7

a) see document 4 AAs per turn b) see document c) see document

Answer 8

Hydrogen bonds parallel to the axis of the helix | Sidechains project outwards from the helix – can accommodate large groups

Answer 9

a) between oppositely charged side-chains, called an ion pair or salt bridge e.g. Glu + Lys b) stabilise tertiary structure by H-bonding between side-chains. Most polar residues can H-bond eg Ser, Thr. c) non-covalent forces of attraction between neutral molecules. All amino acids form these eg Leu, Tyr. d) the most important effect in stabilising protein 3D shapes and involves burying the hydrophobic residues eg Ala, Val e) forms between 2 cysteine residues as [methionine cannot form] (-SH + -SH → S-S)

Answer 10

G in the middle (red) – small, no sidechain

Answer 11

Interior of the protein contains hydrophobic amino acids Exterior of the protein contains hydrophilic amino acids

Answer 12

often bigger: simple protein united with a non-protein factor – Prosthetic group, Cofactor, Lipids or Carbohydrates e.g. Glycoproteins (protein + carbohydrate)

Answer 13

See table on document

Answer 14

the average of the 2 pKas | pI = (pK1 + pK2)/2

Answer 15

non-covalent bonding | results in α-helices and β-sheets

Answer 16

essential in certain physiologic conditions Conditionally essential: Cysteine, Glutamine, Tyrosine

Answer 17

the pH of the surroundings

Answer 18

see document

Answer 19

the structure as pH varies

Answer 20

Many proteins exist as oligomers. | These are assemblies of two or more separate folded monomer subunits (single peptide chains).

Answer 21

the pH at which there is no charge and an equal amount of positive and negative charges present so the amino acid is neutral

Answer 22

Determined by the gene encoding the protein | Changes to gene result in different amino acids in a protein

Answer 23

see document for structure equations and net charges pI = average of pKas of functional groups that are involved in equilibria with the neutral form = (9.0+10.5)/2 = 9.75

Answer 24

see document for structures Small protein MW ~ 6000 Daltons. Two chains held together by disulfide bonds

Answer 25

often smaller: chains of amino acid units joined by peptide bonds e.g. Albumins, globulins etc.

Answer 26

(see document for drawings) Sidechains alternate above and below sheet. Sheets can form from multiple chains side by side or a single chain parallel: N-C repeated anti-parallel: N-C and C-N alternating repeated

Answer 27

Permanent trans configuration in the –CO-NH- system because of the absence of free rotation Partial double bond character Trans configuration

Answer 28

a) as enzymes e.g. catalase b) as hormones e.g insulin or receptors, e.g. 7-transmembrane receptors c) e.g haemoglobin and myoglobin d) as contractile proteins e.g. myosin e) as structural proteins e.g. actin f) as immunity proteins e.g. γ globulin antibodies

Answer 29

Subdivided into elastic (coiled) and inelastic (extended – sheet structures) Elastic – e.g. keratin, elastin, myosin Inelastic – e.g. fibroin, collagen

Answer 30

ionisable groups

Answer 31

L α-amino acids

Answer 32

Highly elongated fibre-like structure. | Polypeptide chains are held together by inter-chain hydrogen bonds

Answer 33

see document for structure equations and net charges ``` k = [products]/reactants] K1 = [H₃N⁺CH₂CO₂-][H⁺]/[H₃N⁺CH₂CO₂H] K2 = [H₂NCH₂CO₂-][H⁺]/[H₃N⁺CH₂CO₂-] ``` At the isoelectric point [H₃N⁺CH₂CO₂H] = [H₃N⁺CH₂CO₂-] Therefore: K1 x K2 = [H⁺]^2 and: pI = (pK1 + pK2)/2

Answer 34

``` can destabilise collagen fibres osteogenesis imperfecta (brittle bone disease) ```

Answer 35

Compact and spheroidal shape. Contain α-helices and β-sheets. Polypeptide chains are held together by intra-chain hydrogen bonds maintaining a compact shape

Answer 36

different 3D shapes

Answer 37

non-covalent bonding | multisubunit protein

Answer 38

residues | are numbered in sequence

Answer 39

First a positive net charge to the most negative possible

Answer 40

Size (large / small) Shape (aliphatic / aromatic) Hydrophobicity (polar / non-polar) Charge at physiological pH (acidic / basic) Sulphur-containing (cysteine & methionine) Imino

Answer 41

(see document for drawings) α-helices β-sheets

Answer 42

Non-covalent bonds, as listed for tertiary structure, hold the monomers together

Answer 43

None in a globular protein | Yes, usually one in a fibrous protein

Answer 44

The interior of proteins is hydrophobic i.e. contains Leu, Val, Met, Phe etc. amino acid residues The exterior of proteins is mostly hydrophilic i.e. contains Lys, Arg, Asp, Glu etc. amino acid residues – although most proteins do have small exposed hydrophobic regions

Answer 45

see document

Answer 46

see document

Answer 47

see document

Answer 48

as neutral

Answer 49

Water soluble | Usually found in solution, e.g. in the cytosol and blood. Functional uses rather than structural eg enzymes

Answer 50

can be produced in the body. synthesised from essential amino acids or simpler precursors uses and functions in the body are equally as important as the essential amino acids Non-essential: Alanine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine

13 Amino Acids and Proteins Flashcards

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