Amino acids and proteins Flashcards
What is the inside of a cell like?
Packed with macromolecules (proteins/RNA/DNA)
Give some roles of proteins.
- enzymatic catalysis e.g. rubisco
- transport and storage of small molecules
and ions e.g. myoglobin in muscle and
ferritin in blood - coordinated motion e.g. myosin is a major
component of muscle, flagella and
cytoskeleton - mechanical support e.g. collagen in high
tensive strength of skin and bone - Immune protection e.g. immunoglobin in
antibodies to combine with invading
substances - generation and transmission of nerve
impulses e.g. ACh receptor proteins
mediate nerve responses to specific
stimuli - control of growth and differentiation e.g.
hormones and growth factors control gene
expression
What do polymers of amino acids spontaneously do?
Fold into 3D structures.
What do proteins interact with?
One another and other biological macromolecules.
Some proteins are rigid and others…
flexible
What is the primary structure of a protein?
The sequence of amino acids in the polypeptide chain, held by peptide bonds.
What is the secondary structure of a protein?
Formed when the chain folds into alpha helices/beta sheets.
What is the tertiary structure of a protein?
3D structure of a protein.
What are amino acids?
Monomeric unit of a protein.
What is the quaternary structure of a protein?
Exhibited by proteins with more than one polypeptide chain.
What groups does the amino acid have?
Alpha carbon attached to an R-group, carboxylic acid group and an amino group.
What does the property of an amino acid depend on?
The nature of its R-group.
Why is the alpha carbon chiral?
It has 4 different substituents.
Substituent = atom/group of atoms occupying place in a molecule.
How do chiral molecules exist?
In two different forms (isomers) that are mirror images.
All amino acids except glycine have mirror images.
How do you label each image?
L (laevus, left) and D (dexter, right).
Which form (L or D) are amino acids in when they are part of a protein?
L form, only in D form in bacterial cell walls.
What is pKa?
dissociation constant
What is pH?
A measure of the concentration of hydrogen ions in solution.
What is the pH of most bodily fluids?
6.5-7.5 = physiological range.
Give the equation for pH.
pH = -log10[H+]
so [H+] = 10^-pH
How is H+ released into solution?
Acid molecules dissociate.
HA ⇌ H+ + A-
What is the strength of an acid given by?
Ka = ([H+][A-])/[HA]
What does the pKa of an acid tell us?
The pH at which half the acid present is dissociated.
e.g.
pKa of weak acetic acid = 4.8
pKa of strong hydrochloric acid = -7
Give the equation for pKa.
pKa = -log10 Ka
At neutral pH, amino acids in solution exist predominantly as…
dipolar ions/zwitterions.
Describe the amino and carboxyl groups of an amino acid in dipolar form.
Amino group: protonated (+ve charge) and pKa = 8.0.
Carboxyl group: deprotonated (-ve charge) and pKa = 3.1.
What is the overall charge of an amino acid at pH 0?
Positive - both groups protonated.
At pH 12, what is the overall charge of the amino acid?
Negative - both groups deprotonated.
Glycine (Gly, G) is hydro…
philic.
What is the R group of glycine?
Is it polar?
A hydrogen atom.
Non-polar.
What does glycine provide for proteins?
Provides flexibility to proteins where other side chains would be too bulky.
What is the R-group of alanine? How does this affect its size? Is it polar?
A methyl (aliphatic) side chain.
Non-polar
Small size.
Aliphatic = organic compounds which carbon atoms form open chains.
Alanine (Ala, A) is hydro…
phobic.
Why is proline (Pro, P) an unusual amino acid?
The aliphatic side chain bonds to nitrogen atom of amino group.
Proline is hydro…
phobic.
Is the side chain on proline polar?
Non-polar.
Why are there tight restraints on the conformation/shape of the protein?
Due to the rigidity of the pyrrolidine ring.
Where is proline found?
In proteins that need to be rigid (collagen and turns of globular proteins).
What is the R-group of serine?
-CH2-OH
What does the hydroxyl functional group mean for the amino acid Ser, S?
Polar due to difference in electronegativity between O and H.
Hydrophilic.
Can participate in hydrogen bonding interactions.
Where is Serine often found?
In the active sites of enzymes because the OH group is reactive (nucleophilic) and can form a covalent bond to the substrate during an enzyme-catalysed reaction.
What is the R group on histidine (His, H) and is it polar?
Imidazole ring (5 membered aromatic ring).
Polar.
Histidine is hydro…
philic.
Depending on the local environment (protein and solvent), how can histidine be found?
Can be neutral or positively charged. Only amino acid with a pKa of side chain of near neutral pH (6.7).
Where is histidine found?
In the active site of many enzymes because the imidazole ring can bind and release protons during the course of an enzymatic reaction.
What is the R-group of cysteine?
-CH2SH (thiol functional group).
Cysteine (Cys, C) is hydro…
phobic.
What is pKa of the cysteine side chain? What does this mean?
8.4 - often found in active sites because this pKa is close to physiological pH.
Is a thiol or hydroxyl group more reactive?
Thiol.
Cysteine’s side chain is weakly…
polar.
What is the functional group of phenylalanine (Phe, F)?
Benzene.
Phenylalanine is hydro…
phobic.
What is the R group of phenylalanine, tyrosine (Tyr, Y) and tryptophan (Trp, W)? Is it polar?
Methylene (CH2) linked to aromatic ring.
Non-polar for phenylalanine and tryptophan but polar for tyrosine.
How can phenylalanine, tyrosine and tryptophan help to determine the concentration of proteins in solution?
Absorb UV radiation (280nm).
What does the hydroxyl group mean on Tyrosine’s phenol side chain?
It is less hydrophobic and more reactive.
What functional group does tryptophan have?
Indole functional group (six membered benzene ring fused to five membered pyrrole ring - 4C, 1N).
Tryptophan is hydro…
phobic.
What do glutamate (Glu, E) and lysine (Lys, K) have in common? What does this mean for them?
Charged amino acid side chains. They have highly polar side chains, so can participate in hydrogen bonding and ionic interactions.
What is the R-group and functional group of glutamate?
What is the pKa of the functional group?
R-group = -CH2-CH2-COO-
Functional group = acidic carboxyl with pKa of 4.1.
What is the R-group and functional group of lysine?
What is the pKa of the functional group?
R-group = -CH2-CH2-CH2-CH2-NH3+
Functional group = basic amine with pKa of 10.8.
Any pKa value higher than pH7 in solution will be…
protonated.
Any pKa value lower than pH7 in solution will be…
deprotonated.
Why can cysteine and histidine switch between charges depending on the reaction?
Their values for pKa are close to physiological pH.
What does a pair of cysteines form when they approach each other in the 3D structure?
A covalent bond = disulphide bond.
What is special about the disulphide bond?
It is the only covalent bond that stabilises the tertiary structure.
Write the oxidation-reduction (redox) reaction for the formation of a disulphide bond.
2R-SH
⇌
R-S-S-R + 2H+ + 2e-
What is a polypeptide?
Chains of series of amino acids joined by peptide bonds.
Linking 2 amino acids forms a peptide bond and involves a water molecule being…
eliminated.
What is the name of each amino acid within a polypeptide?
A residue.
Why do polypeptide chains have different direction?
Their ends are different.
What do polypeptide chains start with?
N-terminal = amino terminal residue.
What do polypeptide chains end with?
C-terminal = carboxyl terminal residue.
Give 2 reasons as to why its important to know the primary structure of a protein.
- Determines the 3D structure of the
protein so is essential to elucidating
(making it clear) to the protein’s function. - Alterations in sequence can lead to
abnormal protein function and disease.
