Proteins Flashcards
Describe the general structure of an amino acid
Tetrahedral and chiral molecule
alpha-carbon in the centre, bonded to an amine group (NH2 or NH3+), a carboxylic acid (COOH or COO-), a hydrogen and an R-group
Which amino acid enantiomer is present in mammals, and where can the other be found?
L-amino acid
The D-amino acid can be found in the peptidoglycan bacterial cell wall and mimicked in some antibiotics to interfere with bacterial metabolism
What are the different side chain groupings for amino acids? Give examples for each.
Positively charged: arginine, lysine, histidine (can be uncharged)
Negatively charged: aspartate/aspartic acid, glutamate/glutamic acid
Polar uncharged: asparagine, glutamine, serine, threonine
Hydrophobic aromatic: phenylalanine, tyrosine, tryptophan
Hydrophobic aliphatic: glycine, alanine, valine, leucine, isoleucine, methionine, cysteine, *proline
*Structural: proline, because its aliphatic side chain bonds back onto the amine side group, and so it creates a kink in the pp chain
Which is the only amino acid that cannot form stereoisomers and why?
Glycine, as its R-group is just a hydrogen, and so, due to the presence of two of the same side groups, the molecule is symmetric and superimposable on its mirror image
Describe the peptide bond and its formation
Formed by condensation reaction
Between alpha-amine and alpha-carboxylic acid groups of different amino acids
Planar and rigid, as the bond exhibits partial double bond character
Almost always in trans configuration, where hydrogen of the NH is on opposite side of double bond to the oxygen on CO
How does the polypeptide chain form 3D shapes if the peptide bond is rigid?
Free rotation around the alpha-C to N and C atoms respectively
Explain the stability and structure of alpha helices
Most stable helical secondary structural arrangement as there is minimal strain on the inter-amino acid hydrogen bonding
R groups point outwards from helix
Hydrogen bond formed between every 4 amino acids, between the carbonyl O and the amino H
Periodicity of 3.6 residues
Explain the stability, structure and characteristics of beta sheets
Fully extended pp chain
Adjacent chains can run parallel or antiparallel
Planarity causes protrusion of R groups above and below the sheets
Hydrogen bonds formed between the carbonyl O and amino H of aligned sheets
Strong and rigid
Explain the stability, structure and function of loop regions
Stabilized by hydrogen bonding between carbonyl O of residue 1 and amino H of residue 4 on the other side of the turn
The second and third residues are often proline (due to lack of amino H for hydrogen bonding) or glycine, as they can’t contribute any stabilizing bonds
Define primary, secondary, tertiary and quaternary structure
P - the linear sequence of amino acids in the pp chain
S - the local interactions and folding of the amino acid chain
T - the overall structures formed and spatial arrangement of amino acids in the pp chain
Q - the complex formed by interactions between multiple polypeptide chains
What is a domain?
A specific region of a polypeptide chain which has an independent function (e.g. ATP-binding site, zinc finger, immunoglobulin fold etc.) that may be common to other polypeptide chains with an overall different tertiary structure
What reaction forms a disulphide bridge? Between which two residues can it be formed, and what residue does it generate?
Oxidation (SH SH –> S-S + 2H+)
Occurs between the R groups of two cysteine residues, and forms one cystine residue
What is the difference between a homo-oligomeric protein and a hetero-oligomeric multi-subunit protein?
Both have quaternary structure, and are thus complexes of multiple pp chains, however homo-O contains same pp subunits whereas hetero-O contains different pp subunits.
What is cooperativity? Give an example of it in action
When an enzyme has more than one active site, and the binding of one substrate to an active site will influence the binding of another substrate to another active site.
In haemoglobin, the O2 affinity curve is sigmoidal because the binding of the first O2 to one of the haem groups causes an allosteric change in the protein making binding to the other binding sites easier, and so on.
What is an allosteric change?
A conformational change occurring in an enzyme that influences the shape of one binding site due to the binding of a ligand at another, distant binding site
Describe the post-translational modifications below:
- Disulphide bonding
- Crosslinking
- Peptidolysis
- Glycosylation
- Phosphorylation
- Adenylation
- Farnesylation
- Oxidation reaction removing 2H+ from two cysteine residues to form an S-S covalent bond, creating a new, single cystine residue
- Covalent crosslinks between molecules
- Removal of parts of the protein after synthesis
- Addition of carb groups
- Addition of phosphate groups to specific residues
- Addition of adenosine monophosphate
- Attachment of an unsaturated C15 hydrocarbon group called a farnesyl anchor which can insert into the plasma membrane
What general roles can post translational modifications have, using an example for each?
Regulation - phosphorylation by PKA, for example, can turn a protein on or off
Targeting - glycosylation, for example, can act as a signal to intracellular targeting or sorting machinery
Turnover - labelling with ubiquitin protein, for example, can mark proteins out for degradation by proteosomes
Structural - crosslinking between collagen molecules, for example, can greatly increase the strength of the resulting fibril
What is collagen, where is it found and what is the structure of collagen type 1?
Structural, fibrous protein
Found in tendons, ligaments and other connective tissues
A triple helix of two alpha 1 chains and one alpha 2 chain
Describe the collagen polypeptide sequence and the helix/triple helix it forms
A glycine occurs every third residue as it is the only residue small enough that it can be positioned at the centre of the triple helix
There are repeats of the sequence -gly-X-Y, with X usually being pro and Y usually being OHpro
The helix of each chain is left handed, but the triple helix itself is right handed
Two amino acids, OHpro and OHlys, are formed post-translationally and are a key feature of the molecule
Outline the stabilizing features of tropocollagen
Interchain hydrogen bonding between peptidyl amino and carbonyl groups of the gly, and the hydroxyl groups of the OHpro
What are the different stages in collagen fibril formation, and note where each stage occurs?
Pre-procollagen = individual chains (nucleus to RER)
Procollagen = triple helix formed, but with C and N terminal propeptides (RER to Golgi)
Tropocollagen = only the triple helix, terminal propeptides cleaved (extracellular)
Collagen fibril = tropocollagen molecules align parallel in a staggered arrangement, covalently crosslinked via lys and OHlys residues’ side chains (extracellular)
What are the two causes, and symptoms, of Ehler-Danlos syndrome?
Causes: Defective enzyme that cross links hydroxylysine residues, and defective enzymes that cleave terminal propeptides of procollagen to form tropocollagen
Symptoms: Hyperextensible skin, recurrent joint dislocation
What are the two causes of osteogenesis imperfecta? What are the symptoms?
Broadly speaking, OI is caused by an inability to form the triple helix. This can occur due to gene defects producing an abnormally short alpha 1 chain which cannot form a stable helix and therefore fibre, or the substitution of gly for arg or cys which are two big, and therefore destabilise the centre of the helix
Symptoms: brittle bones, repeated fractures, bone deformities in infancy
What is the function of histone proteins?
To package DNA in order to make it more space efficient, but also to regulate gene expression
