Learning Objectives

FC 1: What is biochemistry?

The study of chemical processes within and relating to living organisms

FC 2: What are the major macromolecules in cells?

Proteins, phospholipids, polysaccharides, RNA and DNA

FC 3: What percentage of cellular macromolecules are proteins?

Approximately 50% of cellular macromolecules are proteins

FC 4: What are proteins?

Biological macromolecules made from amino acids linked by peptide bonds that perform structural, catalytic, transport and regulatory functions

FC 5: What are examples of protein functions?

Enzymes catalyse reactions

antibodies neutralise pathogens

haemoglobin transports oxygen

keratin provides structural support

insulin regulates blood glucose

FC 6: What is translation?

The process where ribosomes synthesise proteins from mRNA sequences

FC 7: What occurs during initiation of translation?

Small ribosomal subunit binds mRNA

AUG start codon recognised

methionine tRNA binds

large ribosomal subunit joins

FC 8: What occurs during elongation of translation?

tRNAs bring amino acids

peptide bonds form

ribosome moves along mRNA codons

FC 9: What occurs during termination of translation?

Stop codon reached

ribosome dissociates

protein released

FC 10: What are amino acids?

Organic molecules that are the building blocks of proteins

FC 11: How many standard amino acids are used in proteins?

20 standard amino acids

FC 12: What are essential amino acids?

Amino acids that must be obtained from the diet

FC 13: What are nonessential amino acids?

Amino acids that can be synthesised by the body

FC 14: What is the general structure of an amino acid?

Central α-carbon attached to amino group, carboxyl group, hydrogen atom and variable R-group

FC 15: Which amino acid lacks a chiral centre?

Glycine

FC 16: What determines amino acid properties?

The chemical nature of the side chain (R-group)

FC 17: What are the five major amino acid classes?

Non-polar aliphatic

polar uncharged

polar positively charged

polar negatively charged

aromatic

FC 18: Which amino acids are non-polar aliphatic?

Glycine, alanine, valine, leucine, isoleucine, methionine and proline

FC 19: Which amino acids are polar uncharged?

Serine, threonine, asparagine, glutamine and cysteine

FC 20: Which amino acids are positively charged?

Lysine, arginine and histidine

FC 21: Which amino acids are negatively charged?

Aspartate and glutamate

FC 22: Which amino acids are aromatic?

Phenylalanine, tyrosine and tryptophan

FC 23: Which amino acid contains sulfur and always initiates protein synthesis?

Methionine

FC 24: Which amino acid forms disulfide bridges?

Cysteine

FC 25: Which amino acid is cyclic and disrupts α-helices?

Proline

FC 26: What is a covalent bond?

A bond involving sharing of electron pairs between atoms

FC 27: What is a hydrogen bond?

Attraction between hydrogen attached to N or O and another nearby N or O atom

FC 28: What is a salt bridge?

Electrostatic interaction between oppositely charged amino acid side chains

FC 29: What is a hydrophobic interaction?

Association between non-polar molecules to avoid water

FC 30: What is electronegativity?

Tendency of an atom to attract bonding electrons

FC 31: What does hydrophilic mean?

Able to interact with water and form hydrogen bonds

FC 32: What does hydrophobic mean?

Non-polar and unable to interact favourably with water

FC 33: What is a chiral centre?

A carbon atom attached to four different groups

FC 34: What are stereoisomers?

Molecules with same molecular formula but different 3D arrangement

FC 35: What are enantiomers?

Non-superimposable mirror-image stereoisomers

FC 36: What is a racemic mixture?

Equal mixture of both enantiomers

FC 37: What distinguishes D and L amino acids?

Different arrangement around the chiral α-carbon

FC 38: Which amino acid configuration is used in proteins?

L-amino acids

FC 39: What is pH?

Negative logarithm of hydrogen ion concentration

FC 40: What is the equation for pH?

pH = -log[H+]

FC 41: What is neutral pH?

pH 7 where [H+] equals [OH−]

FC 42: What is an acid according to Brønsted-Lowry theory?

A proton donor

FC 43: What is a base according to Brønsted-Lowry theory?

A proton acceptor

FC 44: What is Ka?

Acid dissociation constant describing tendency of an acid to donate protons

FC 45: What does a low pKa indicate?

Strong acid with high tendency to dissociate

FC 46: What is the Henderson-Hasselbalch equation?

Equation relating pH, pKa and ratio of conjugate base to acid

FC 47: What is the Henderson-Hasselbalch equation formula?

pH = pKa + log([A−]/[HA])

FC 48: What is a buffer?

Mixture of weak acid and conjugate base that resists pH changes

FC 49: What is buffer capacity?

Efficiency of a buffer at resisting pH changes

FC 50: When is buffer capacity greatest?

When pH equals pKa

FC 51: What principle explains buffering?

Le Chatelier’s principle

FC 52: What ionisable groups occur in amino acids?

α-carboxyl group, α-amino group and some ionisable side chains

FC 53: What is the isoelectric point (pI)?

pH at which a molecule has zero net charge

FC 54: How is pI calculated for amino acids with two ionisable groups?

Average of the two pKa values

FC 55: What is the equation for pI?

pI = (pK1 + pK2) / 2

FC 56: What is a zwitterion?

Molecule containing both positive and negative charges with overall net charge zero

FC 57: At pH below pI, what charge does a protein have?

Net positive charge

FC 58: At pH above pI, what charge does a protein have?

Net negative charge

FC 59: What is primary protein structure?

Linear amino acid sequence of a protein

FC 60: What is secondary protein structure?

Local spatial arrangement of the polypeptide backbone

FC 61: What is tertiary protein structure?

Overall 3D structure of a polypeptide including side chains

FC 62: What is quaternary protein structure?

Association of multiple polypeptide subunits

FC 63: What is a peptide bond?

Covalent CO-NH bond linking amino acids

FC 64: How are peptide bonds formed?

Condensation reaction between amino and carboxyl groups releasing water

FC 65: Why is the peptide bond rigid?

Resonance gives partial double-bond character

FC 66: What peptide bond conformation is favoured?

Trans configuration

FC 67: What are phi (ϕ) and psi (ψ) angles?

Rotatable backbone torsion angles around Cα-N and Cα-C bonds

FC 68: What stabilises α-helices?

Hydrogen bonds between C=O and N-H groups every fourth residue (i to i+4)

FC 69: What are the characteristics of an α-helix?

Right-handed helix

3.6 residues per turn

5.4 Å pitch

side chains project outward

FC 70: Which amino acids favour α-helix formation?

Alanine and leucine

FC 71: Which amino acids disrupt α-helices?

Proline and glycine

FC 72: What stabilises β-sheets?

Hydrogen bonds between adjacent β-strands

FC 73: Difference between parallel and antiparallel β-sheets?

Parallel strands run same direction

antiparallel run opposite directions and are more stable

FC 74: What is a β-turn?

Four-residue turn reversing polypeptide chain direction

FC 75: Which amino acids commonly occur in β-turns?

Proline and glycine

FC 76: What are fibrous proteins?

Structural elongated proteins composed mainly of one secondary structure type

FC 77: Examples of fibrous proteins?

Keratin and collagen

FC 78: What is α-keratin?

Coiled-coil fibrous protein composed of α-helices

FC 79: What stabilises keratin?

Hydrophobic interactions and disulfide bonds

FC 80: How do disulfide bridges form?

Oxidation of two cysteine thiol groups

FC 81: What enzyme assists disulfide bond formation in ER?

Protein disulfide isomerase