Week 8 (Proteins I) Flashcards
What are proteins?
A linear polymer of amino acids (Amino acids joined together to form long chains)
How many different amino acids are there?
20
How do amino acids differ?
Amino acids all have the same basic structure, but with one side chain that differs
Which isomers are found in proteins?
Only L-amino acids are found in proteins
How to amino acid side chains vary?
Side chains vary in size, shape, charge, polarity and chemical reactivity
Which amino acid isn’t chiral?
Glycines variable group is ‘H’ so does not have 4 different groups attached to the central carbon atom
Which amino acid links to itself?
Proline
what is the 1 letter code for Glycine?
G (Gly)
what is the 1 letter code for Alanine?
A (Ala)
what is the 1 letter code for Valine?
V (Val)
what is the 1 letter code for Leucine?
L (Leu)
what is the 1 letter code for Isoleucine?
I (Ile)
what is the 1 letter code for Methionine?
M (Met)
what is the 1 letter code for Proline?
P (Pro)
what is the 1 letter code for Phenylalanine?
F (Phe)
what is the 1 letter code for Tryptophan?
W (Trp)
what is the 1 letter code for Serine?
S (Ser)
what is the 1 letter code for Threonine?
T (Thr)
what is the 1 letter code for Cysteine?
C (Cys)
what is the 1 letter code for Tyrosine?
Y (Tyr)
what is the 1 letter code for Asparagine?
N (Asn)
what is the 1 letter code for Glutamine?
E (Gln)
what is the 1 letter code for Aspartic Acid?
D (Asp)
what is the 1 letter code for Glutamic Acid?
E (Glu)
what is the 1 letter code for Lysine?
K (Lys)
what is the 1 letter code for Arginine?
R (Arg)
what is the 1 letter code for Histidine?
H (His)
What is each amino acid within a polypeptide chain called?
A residue
How do you know which is residue number 1?
- Chain has an amino or N – terminus and a carboxyl or C – terminus.
- Always go from amino to carboxyl
- the N-terminal residue is numbered 1.
What is the primary structure?
The primary structure of a protein is simply the amino acid sequence in the polypeptide chain Every protein has a unique, precisely defined sequence
The function of a protein is dependent upon its amino acid sequence
What determines the 3D structure of a protein?
Proteins fold up into complex 3-D shapes/structures which are essential for their function, and the structure is determined by the amino acid sequence.
Describe folding of the polypeptide chain
- The polypeptide chain is quite flexible and can fold up to form structures
- 3 types of non-covalent bond help to stabilise the folded structure
What is the secondary structure?
Secondary structure is when the sequence of amino acids are linked by hydrogen bonds (between the amino hydrogen N-H and carboxyl oxygen C=O atoms in the peptide backbone) to form repeating structures:
- α-helices
- β-sheets
-Turns & loops
Describe an alpha helix
- The polypeptide chain forms a helical coil
- Hydrogen bonding stabilises the structure
- Amino acid side chains protrude on the outside of the helix
What are important measurements characteristic of alpha helices?
Right-handed helix
- you go from left to right as you go up the helix 36 amino acids per 10 turns = 3.6 amino acids per turn Pitch
- distance along the long axis for one turn of the helix = 0.54 nm
- Rise per amino acid = 0.15 nm
- The C=O group of a residue i hydrogen bonds with the N-H group of residue i+4 along the sequence
Describe the properties of beta sheets
- Comprised of 2 or more polypeptide β-strands
- Hydrogen bonding between the strands holds them together in a sheet
- Strands can be parallel or anti-parallel
- Amino acid side chains are alternately above and below the plane of the β-sheet
- Sometimes referred to as β-pleated sheet
What are beta turns?
- Many amino acids are found in turns or loops
- Particularly common are β-turns or hairpin turns, which connect the ends of two adjacent segments of an antiparallel β-sheet
- Commonly contain proline residues (its unique structure allows a tighter turn) and glycine (small and flexible)
What is the single letter code for each amino acid?
