Week 2

Question 1

parts of an amino acid

Answer 1

• alpha carbon to which all other atoms and groups are attached
• amino group (NH2)
• carboxyl group (COOH)
• R group - side chain

Question 2

how is a peptide bond formed?

Answer 2

• there is a reaction between the carboxyl group on one amino acid and the amino group on the other.
• the OH group on the carboxyl end of one amino acid reacts with the hydrogen atom on the amino group of the other to eliminate a molecule of water

Question 3

what two features are always present in polypeptides, even in short chains?

Answer 3

an amino end (N-terminus) and a carboxyl end (C-terminus)

Question 4

residues

Answer 4

what amino acids are referred to as once they have joined together into a polypeptide chain

Question 5

in an alpha helix, where does hydrogen bonding occur between residues?

Answer 5

• there is hydrogen bonding between an oxygen atom of the carbonyl group of residue ‘n’ and the hydrogen atom of the amide group of the residue ‘n+4’ on the same polypeptide chain
• this is repeated in a regular fashion (1 and 5, 2 and 6, 3 and 7)
• the peptide chain thus twists around on itself and forms a cylindrical structure (a stable alpha helix)

Question 6

are R-groups involved in the formation of alpha helices?

Answer 6

no

Question 7

give the hierarchy of protein structure and examples for each

Answer 7

1. primary; AA sequence
2. secondary; local folding, like alpha helix and beta sheet
3. tertiary; long-range folding, essentially 3D structure
4. quaternary; multimeric organisation (the organization of multiple polypeptide chains with respect to each other)
5. multiprotein complexes

Question 8

major categories of amino acids

Answer 8

• acidic: negatively charged
• basic: positively charged
• uncharged polar: tends to form H=bonds, interact with h2o on the outside of proteins
• non polar: on the inside of proteins, ‘hydrophobic core’ due to hydrophobic interactions. found in lipid bilayer

Question 9

what type of amino acids usually have enzymatic functions?

Answer 9

polar amino acids

Question 10

what is unique about the structure of cysteine?

Answer 10

• contains interchain disulphide bonds
• whether these occur can be controlled by the cell based on redox conditions
• helps the protein hold its shape with physical or chemical stress

Question 11

how is the primary structure of a protein numbered?

Answer 11

from the amino group (N-terminus)

Question 12

give an example of how differences in primary amino acid sequence matter

Answer 12

• vasopressin and oxytocin
• both are 9AA long neuropeptide hormones
• AA sequence is identical except at 2 positions
• vasopressin controls urine production rates and oxytocin is involved in birth, lactation, and pair bonding

Question 13

give an example of how the order of AA’s is important too

Answer 13

• Leu-Enkephalin (pentapeptide N-Tyr-Gly-Gly-Phe-Leu-C) is a natural opioid peptide which down modulates the perception of pain
• the pentapeptide N-Leu-Phe-Gly-Gly-Tyr-C, basically a reversal, has no pharmacological effects
• the NH2-COOH orientation of the peptide is essential for function

Question 14

describe the structure of the beta sheet

Answer 14

• H-bonding between carbonyl oxygen (C=O) of 1aa and amide hydrogen (N-H) of aa in neighbouring strand
• R groups not involved but alternately project up and down
• beta sheets typically contains 4-5 beta strands but can have more than 10

Question 15

types of beta sheets

Answer 15

• anti-parallel
• parallel

Question 16

where are beta sheets found

Answer 16

strong, rigid structure found in silk

Question 17

compare and contrast hydrogen bonding in alpha helices and beta sheets

Answer 17

• H bonds formed between carbonyl oxygen, amide hydrogen in peptide backbone
  Alpha:
• 4 AA’s apart and within the same segment of
  pp chain
  Beta:
• Between AA’s in different segments or
  strands of pp chain

Question 18

coiled coil

Answer 18

• when alpha helices are twisting together
• amphipathic alpha helix
• these are found in alpha-keratin of skin, hair, and also myosin motor proteins
• helices wrap around each other to minimise exposure of hydrophobic amino acid side chains to aqueous environment

Question 19

tertiary structure

Answer 19

• 3D overall structure of a protein
• held together by hydrophobic interactions, non-covalent bonds (hydrogen bonds, dipole-dipole and van der Waals), and covalent disulphide bonds

Question 20

What determines the confirmations into which proteins fold?

Answer 20

proteins generally fold into the conformation that is the most energetically favourable

Question 21

what helps fold proteins?

Answer 21

Proteins will fold into the shape dictated by their
amino acid sequence, but chaperone proteins help make the process more efficient and reliable
in living cells.

Question 22

3 types of hydrogen bonding within tertiary structure of a protein

Answer 22

backbone to backbone: hydrogen bond between atoms of two peptide bonds
backbone to side chain: hydrogen bond between atoms of a peptide bond and an amino acid side chain
side chain to side chain: hydrogen bond between atoms of two amino acid side chains

Question 23

What are protein domains?

Answer 23

• portion of a protein that has its own tertiary structure, often functioning in a semi-independent manner
• eukaryotic proteins often have 2 or more domains connected by intrinsically disordered sequences
• domains are important for the evolution of proteins

Question 24

domains are often specialised for

Answer 24

different functions

Question 25

Src protein kinase

Answer 25

- contains SH3 domain, SH2 domain, and kinase domain with 2 lobes - phosphorylates amino acids to change the activity of proteins - SH2 regulates kinase domain - SH3 regulates kinase domain in a different way - kinase domain phosphorylates the amino acids

Question 26

protein families

Answer 26

- have similar amino acid sequences and tertiary structures - however, members have often evolved to have different functions - most proteins belong to families with similar structural domains

Question 27

quaternary structure

Answer 27

proteins that have more than one polypeptide chain

Question 28

describe haemoglobin

Answer 28

- 4 separate polypeptide chains - 2 alpha subunits and 2 beta subunits - each subunit is a separate polypeptide - sickle cell anaemia is caused by a mutation in the beta subunit

Question 29

give 3 types of multi protein complexes

Answer 29

- many identical subunits (eg actin filaments) - mixtures of different proteins and DNA/RNA (eg viruses and ribosomes) - very dynamic assemblies of proteins to form molecular machines (eg machines for DNA replication initiation or for transcription)

Question 30

scaffold proteins

Answer 30

assemble other proteins needed for a particular process, getting them close together so work can be carried out

Question 31

how are proteins studied?

Answer 31

- first purify protein/proteins of interest via various types of electrophoresis and affinity chromatography - then determine amino acid sequence (eg mass spectrometry) - discover precise 3D structure using techniques such as x ray crystallography, nuclear magnetic resonance spectroscopy or cry-electron microscopy

Question 32

what properties can be exploited to separate proteins from one another so they can be studied individually?

Answer 32

- size, shape, charge, hydrophobicity, and their affinity for other molecules.

Question 33

AI used to predict protein structure

Answer 33

alphafold to predict protein structure from linear amino acid sequences

Question 34

proteomics

Answer 34

large scale study of proteins - identity and structure of proteins - protein-protein interactions, regulation of these interactions and their position within a pathway - abundance and turnover of proteins - location within a cell or tissue - bioinformatics, statistics, and artificial intelligence often in combination with other 'omics' data