Amino acids and proteins Flashcards
What are some biological roles of proteins?
TRANSPORT (e.g. membrane proteins, Hb), STORAGE (e.g. ferritin stores Fe2+ in liver), ENZYMES (reactions can occur at 37C), MOTION (e.g. muscles, intestinal flagellae), SKELETAL SUPPORT (e.g. collagen), IMMUNE PROTECTION (e.g. antibodies, opsonins, cytokines), NERVE IMPULSE TRANSMISSION, control of METABOLISM, growth and differentiation (e.g insulin, gene repressors, EGF)
Polypeptide definition
polymer of amino acids linked by peptide bonds
What is the smallest functional protein?
A tripeptide called thyrotropin-releasing hormone
How many amino acids are there?
20
What is the structure of amino acids?
alpha carbon which is bonded to a carboxyl group, amine group, H and R group
How does an amino acid act as a proton donor (acidic)?
COOH –> H+ + COO-
How does an amino acid act as a proton acceptor (basic)?
NH2 + H+ –> NH3+
Why can amino acids form D and L isomers?
The alpha carbon has 4 different groups attached so the amino acid is asymmetric (chiral centre, optical isomers)
Which amino acid cannot form D and L isomers and why?
Glycine - the R group is a H so the alpha carbon is not bonded to 4 different groups (2 Hs)
How do you distinguish between D and L amino acids?
L amino acids (laevorotatory) have the amino group on the left whereas D amino acids (dextrorotatory) have the amino group on the right
Which amino acids isomer is found in proteins?
Only L amino acids
What is the ionisation of amino acids at pH 1, pH 7.4 and pH 11?
At pH 1 the amino acid is fully protonated with a cationic (+1) charge - NH3+. At pH 7.4, the amino acid is Dipolar (zwitterion = 0) - NH3+ and COO-. At pH 11 the amino acid is anionic (-1) - NH2 and COO-.
Where to D isomers occur?
Bacterial cell walls
How do amino acids act as buffers?
As pH increases, amino acids donate H+ ions to counteract the increasing alkalinity. When pH decreases, amino acids mop up H+ ions to counteract the increasing acidity.
How are amino acids classified?
Split into 7 groups based on chemical composition of R groups
What are the 7 classification groups of amino acids?
Aliphatic, Hydroxyl, Sulfur, Aromatic, Acidic (with corresponding neutral amide), Basic, Imino
What characteristic is common to aliphatic amino acids?
R groups contain C and H only.
What characteristic is common to hydroxyl amino acids?
OH in R group
What characteristic is common to sulfur amino acids?
Contain S in R group e.g. cysteine has sulfur hydryl / thiol, methionine has thioether / methyl sulfide
What feature is common to all aromatic amino acids?
Contain a benzene ring in R group
What feature is common to all acidic amino acids?
Have a carboxyl group in R group (COO-)
What is the corresponding neutral compound to all acidic amino acids?
Amide (-ine). e.g. aspartic acid -> asparagine. glutamic acid -> glutamine
What feature is common to all basic amino acids?
Have an amino group (or N) in R chain that can accept protons to become positively charged.
What feature is present in an imino amino acid?
5 membered ring containing a secondary amine group (imine). Only proline (could also be aliphatic)
What are the alternate categories for classifying amino acids based on the ionisation character of the R group?
Neutral
Basic - R ionises. Accepts H+ to form a +ve charge.
Acidic - R ionises. Donates H+ to form a -ve charge
What does it mean if an amino acid is neutral?
R group doesn’t ionise. Cannot donate/accept H+
Which amino acids are neutral?
Aliphatic amino acids, hydroxyl amino acids, methionine (S), Proline, Phenylalanine and tryptophan, asparagine and glutamine (amides)
Which amino acids are basic?
Arginine, histidine (weakly), lysine. Same group as other classification.
Which amino acids are acidic?
Aspartic acid and glutamic acid (acidic group), cysteine (S bonded to H), tyrosine (aromatic - phenol group)
Electronegativity definition
an atom’s ability to attract electrons towards itself in a covalent bond
What is the order of electronegativity?
F>O>Cl = N>Br>C = S>H
What influences whether an R group is hydrophobic or hydrophilic?
If the R group is polar, it is hydrophilic. If an R group is non-polar, it is hydrophobic.
What are the characteristics of polar R groups?
Hydrophilic. Either there is a full positive or negative charge in the R group at pH 7, or there are partial charges in permanent dipole bonds in non-ionisable R groups (polar, uncharged)
What are the characteristic of non-polar R groups?
Hydrophobic. No full or partial charges due to many C-C and C-H bonds (similar electronegativity).
Why is glycine often classed as polar?
R group is a single H atom. Gly is hydrophilic
How is a peptide bond formed?
Condensation reaction between -COO- and +H3N-
What is the name of the left terminus / amino acid end terminal in a polypeptide chain?
N-terminal residue (-NH3+)
What is the name of the right terminus/carboxylic acid terminal? (-COO- is on the right due to L-amino acid)
C-terminal residue
How are R groups arranged in a polypeptide chain?
Alternate and protrude from both sides of the chain.
Why do R groups alternate?
Ensures steric stability of polypeptide
Example of post synthetic modification of proline
Proline is hydroxylated to form hydroxyproline - OH group stabilises collagen fibre. Insufficient hydroxylation leads to scurvy
Example of post-synthetic modifications of glutamic acid
glutamic acid is carboxylated to form gamma-carboxyglutamate in prothrombin. Lack of carboxylation leads to haemorrhage
Example of post-synthetic modification of serine
Serine is phosphorylated to form O-phosphoserine, which is a common way of regulating protein activity.
Primary structure definition
amino acid sequence
secondary structure definition
arrangement in space of amino acids close to one another in the polypeptide chain e.g. a-helix, B-sheet
tertiary structure definition
3D structure of all the atoms in a single polypeptide chain. interactions between R groups fold protein.
Quaternary structure definition
3D interaction of protein subunits in proteins with more than one polypeptide chain
