BGM1002/L02 Protein Structure Flashcards
What are proteins?
Complex polymers made of amino acid monomers joined by peptide bonds
How many levels of complexity do proteins exhibit?
4
What type of isomer are amino acids (in proteins)?
L-isomers
How many covalent bonds can carbon form?
4
What formation do electron shells form with 4 bonds in carbon?
sp3 hybridisation
How many possible configurations does carbon have with 4 different substituent groups?
2 stereoisomers
What do chiral enantiomers affect? And how?
Polarised light
Rotation of plane of light clockwise (+) or anticlockwise (-)
How is a chiral enantiomer indicated?
L-/D- or S/R
What does L-/D- mean?
Configuration relative to D-glyceradehyde
What does S/R mean?
Absolute configuration
How is absolute configuration determined?
Based on priority of substituent groups around chiral centre according to Cahn-Ingold-Prelog sequence
Give 2 examples of where D-amino acids are found in nature.
Bacterial cell walls
Non-ribosomal peptides
What handedness do alpha-helices have?
Right-handedness
How are interactions between proteins and other molecules specific?
They display a preference for specific chiral forms
What 3 uses does Thalidomide have?
Anti-cancer
Leprosy treatment
Graft-versus host disease treatment
What effect did Thalidomide have when given as anti-nausea to pregnant women?
Development arrest of limbs in foetuses
Which enantiomer of Thalidomide causes complications?
S-enantiomer
Which enantiomer of Thalidomide is therapeutic?
R-enantiomer
Why is there no safe way to administer R-Thalidomide?
Body converts R- to S-Thalidomide
What charge do acidic amino acids have?
Negative
What charge do basic amino acids have?
Positive
What is minimised when a protein folds?
Hydrophobic residue on its surface
What amino acid do most proteins start with?
Methionine
What type of bonding can uncharged side chains be involved with?
Hydrogen bonding
What 4 enzymes is Selenocysteine an essential component of?
Glutathione peroxidase
Thioredoxin reductase
De-ionase
Formate dehydrogenase
How is Selenocysteine encoded?
With a modified stop codon which forms an mRNA structure allowing U to be accepted
How is Hydroxyproline produced?
Post-translational modification of proline (hydrogenation)
What vitamin is required for synthesis of Hydroxyproline?
Vitamin C
What is the purpose of Hydroxyproline in collagen?
Attachment point for glycans
What 2 things does vitamin C deficiency cause?
Scurvy
Breakdown of cell walls
What is each amino acid in sequence called?
Residue
What is vital for a proteinās function?
Charge of protein at given pH
Why are peptide bonds rigid and planar?
Partial double bond character
What does the polypeptide bond link?
2 alpha carbon atoms from neighbouring amino acids
What 3 ways can a phosphate backbone spin?
š½-phi
šæ-psi
š-omega
What is a phi rotation?
Cā-NāCš-C
What is a psi rotation?
N-Cš-Cā-N
What is an omega rotation?
Cš-Cā-N-Cš
What 2 rotations do proteins fold into structure around?
Phi and Psi
Are most peptides Cis or Trans?
Trans
Why does attraction of different elements for electrons vary? (2)
Atomic number
Distance from nucleus of valence electrons
What is the electronegativity series for peptides?
O>N>C=H
Which group in amino acids is slightly negative?
Carbonyl group
Which group in amino acids is slightly positive?
Amide group
How does the strength of a Hydrogen bond compare to a covalent bond?
H-bond is 0.1x strength of covalent bond
Why is hydrogen bonding vital for protein structure? (2)
Backbone hydrogen bonding in secondary structure
Higher level structures have larger H-bonding contributions
What does an alpha helix consist of?
A-helix
B-strand
What degree of repeat does an alpha helix have?
100 degrees - 3.6 residues per turn
How long is a pitch in DNA?
5.4Ć
Which way do side chains point in DNA?
Outwards
How many residues point the same way in DNA?
3-4
Which amino acid is a Cis isomer and cannot be in alpha-helices?
Proline
What is the average number of residues in DNA?
11
How many residues form a repeat in beta-strands?
2
How long are residue repeats in beta-strands?
7Ć
Name the 3 preferred amino acids for beta-strands.
Ile, Tyr, Val
What is the average length of a beta-strand?
6 amino acids
Why are parallel strands weaker than antiparallel strands?
Geometric imperfections
Why are most sheets right-handed?
To accommodate L-amino acid side chains
How much of DNA structure do alpha-helices and beta-strands comprise?
50%
What 3 structures does DNA consist of?
Alpha-helices, beta-strands, loops & turns etc.
What determines the secondary structure of proteins?
Hydrogen bonds between peptide bond carbonyls and amides
