W5.4_Primary Structure of Proteins

Question 1

What are the major functions of proteins?

Answer 1

• Catalysis in enzymes (ex. protease breaks protein, ATPase hydrolyses ATP, kinase adds phosphate, nuclease breaks nucleic acid)
• Movement in muscle proteins (ex. myosin, actin, flagella)
• Cellular control in hormones (ex. insulin, growth and sex hormones) and receptors (gives specific ligand recognition to induce response)
• Transport in respiratory proteins (ex. haemoglobin, cytochromes) and storage (ex. ferritin stores iron in soluble and non-toxic form)
• Structural like collagen in skin/bones and keratin in hair/fingernails
• Defence against toxins/pathogens in the immune system (ex. antibodies, complement system, T-cell receptors)

Question 2

Describe the process of protein production. What is the general rule in amino acids and how is the function of proteins determined?

Answer 2

• DNA -transcription-> RNA -translation-> polypeptide -fold&interact-> proteins
• General rule: <50 amino acid chain -> peptide (ex. oxytocin, melittin)
• Function of protein is dependent on amino acid sequence, structure (size&shape), chemical properties, post-translational modification (ex. phosphorylation, glycosylation), co-factors, metal ions, ligands

Question 3

State the general composition of an amino acid. How many types of R groups are there? What is their usual configuration?

Answer 3

• α-amino group, α-carbon, α-carboxylic acid, side group
• 20 types of R groups:
  asymmetric/chiral for 19 amino acids
• Achiral when R≡H
• Only L-isomer (CORN) exists naturally (H must stick out instead of popping backwards in R/S categorisation), while D-isomer does not

Question 4

How is a polypeptide formed from amino acids? What is a peptide backbone and why is its rotation restricted?

Answer 4

• Primary sequence: condensation between α-COOH and α-NH2 groups, water removed to form CONH-link peptide bond
• Polypeptide: N-terminus (left) <- -> C-terminus (right)
• Amount of peptides: amino acid residues
• Peptide backbone: planar peptide bond with restricted rotation
• ∵ Resonance stabilisation

Question 5

Where can a polypeptide freely rotates? Which configuration do they prefer and why? Define primary structure and residue of amino acids.

Answer 5

• Free rotation are possible on either side of α-carbon
• with torsion angles of Φ(Cα-N) and ψ(Cα-CO)
• trans configuration is favoured (R groups opposite to each other to avoid steric contratint)
• Apart from proline that prefers cis (∵ cyclic structure without double bonds reduce steric constraint)
• Amino acid sequence = primary structure
• Amino acid = residue

Question 6

Classify the amino side chains into different groups. How does its pI affects its net charge?

Answer 6

• Polar (serineS, threonineT, asparagineN, glutamineQ)
• Acidic (aspartic acidD, glutamic acidE)
• Basic (lysineK, arginineR, histidineH)
• Non-polar (alanineA, valineV, isoleucineI, leucineL, methionineM)
• Aromatic (phenylalanineF, tyrosineY, tryptophanW)
• Achiral/Thiol/Cyclic(glycineG, cysteineC, prolineP)
• 7 polar, 8 non-polar, 2 acidic, 3 basic, 12 has H-bonding
• Amino & acid group linked to α-carbon: ionisable
• ∵ low pKa of acid/high pKa of amino -> zwitterionic
• If pH > pI:-ve net charge
• If pI > pH: +ve net charge

Question 7

Explain the different classifications of amino side groups.

Answer 7

• Aliphatic side chains (glycine + yellow + proline): size increases -> more bulky and hydrophobic, less flexible, Gly is the only achiral, Ile has 2 chiral centres
• Basic side chains (red): Arg has highest pKa and is always protonated, His has pKa ≈ 7, useful in proton transfer
• Acidic side chains (green)
• Aromatic side chains (purple): Tyr has acidic ionisable phenol, Phe most hydrophobic, can weakly absorb UV, Trp absorbs most UV
• Neutral side chains (blue + cysteine): Ser (-OH), Thr (-OH), Asn (-CONH2), Gln (-CONH2), Cys (-SH)
• Ionisable: Glu, Asp (usually -ve), Lys (usually +ve), Arg (always +ve), His (usually neutral)
• Cys: strongest in direction, where disulfide bridge contributes to overall shape of protein (can fold back) (ex. insulin contains intrachain and interchain molecular bonds (-SH HS- -O2-> -S-S-) to maintain structure)