Lecture 1 Flashcards
What are proteins? What is the relationship between structure and function?
Proteins are the workhouses of the cell, they carry out many processes (including structural) within our body. They are non branching polymers that form macromolecules about 50-100 Ångström long and are composed of a specific amino acid sequence. Protein function is determined by structure.
What is an angstrom? What is the unit?
A unit of measurement used to measure the size of macromolecules like proteins the size is 1 angstrom = 10^-10 m (the unit is a capital A with a small circle above it).
What is the basic structure for every amino acid?
An amino, Hydrogen, carboxyl and side chain group attached to a central (alpha) carbon.
What are zwitterions? Why can amino acids be this?
A zwitterion is a molecule with both a positive and negative charge but is overall neutral. In solution amino acids can have their amino group protonated and their carboxyl group deprotonated, this will mean a positive and negative charge respectively with an overall neutrality.
What are the nonpolar amino acids? give a unique feature of the side chain and the name, 3 letter and one letter name.
Alanine (Ala, A methyl side chain),
Valine (Val, V, isopropyl side chain),
Leucine (Leu, L, like valine, but with a methyl group before the isopropyl group)
Isoleucine (ile, I, side chain is a 3 carbon chain with a methyl group off carbon 1)
Glycine (Gly, G, H for the side chain)
Cysteine (Cys, C, C-S)
Phenylalanine (Phe, F, C-aromatic ring)
Tryptophan (Trp, W, contains aromatic ring bonded with a nitrogen and carbon)
Methionine (Met, M, C-C-S-C)
Proline (Pro, P, side chain merges with amino group).
What are the charged polar amino acids? What charge? Give a unique feature also.
Aspartic acid (Asp, D, negatively charged C-COO) Glutamic acid (Glu, E, C-C-CO, negatively charged) Lysine (lys, K, C-C-C-C-NH3, positively charged ) Arginine (Arg, R, C-C-C-N-C=N, positively charged) Histidine (His, H, positively charged, cyclic component with C=C-N=C-N)
What are the uncharged polar amino acids? Give a unique feature?
Serine (Ser, S, C-OH) Threonine (Thr, T, OH on first carbon of a two carbon chain) Tyrosine ( Tyr, Y, C-aromatic-OH) Asparagine (Asn, N, C-CON) Glutamine (Gln, Q, C-C-CON)
Why are amino acids normally ionisable? What can be used to classify them?
The amino and carboxyl ends can become charged by donating a proton (COOH) or recieving one (amino group), some side chains can also become charged. They can be categorised by pKa value.
What do pKa and pl refer to?
pKa value is the pH of an ionizable group on an amino acid or protein at which 50% of the group is ionized. The pl is the isoelectric point, it is the pH at which the net charge on an amino acid or protein is zero.
What is a post translational modification? What are some examples? How does the name change?
This refers to when an amino acid is modified after it is added to a protein, examples are disulfide bonds formed between cysteines or: phosphorylation, glycosylation, methylation, adenylation, iodination, metal binding. The name of the amino acid is given a prefix based on what change occured.
What is the typical form for notating mutations?
First letter is the wild type or native amino acid, the number in between is the location of the mutation in the chain, numbered from the N terminus, the second letter is the mutated residue.
What is a residue with regards to proteins?
This refers to the remaining part of the amino acids which make up the protein after they have been merged.
What bonds join amino acids, what odd features does it have? Where does a protein start by convention?
peptide bonds, these have a 40% double bond character, they are planar to maximise pi bond overlap and can’t be easily rotated, they have a dipole and are predominantly trans. Starts from the N terminus.
What amino acid can break the exclusively trans rule? What dihedral angle is each type?
all amino acids can break the rule, but proline is the biggest offender with apporximately 10% of peptide bonds before it being cis.
By definition a trans bond has dihedral angle 180 degrees and a cis has a dihedral angle of 0 degrees.
