BIOL 4070U Study Guide - Midterm Guide: Alternative Splicing, Sequence Motif, Ammonium Sulfate
Midterm I biol 4070: Advanced Biochemistry Notes
LECTURER 1
Peptide: has less than 50 Amino acid residue
Protein: has more than 50 amino acid residue
Amino acid residue: means an amino acid within a polypeptide chain that has been dehydrated
Anatomy of an amino acid: -amin group, R-group (side chain), -carboxyl group and -carbon
(chiral center)
Most amino acids are L conformation not D
Non-polar amino acids:
- Aliphatic: carbon chains that are open
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Polar amino acids
- Easily interact with water
- Serine, threonine and tyrosine participate in kinase reactions, can be phosphorylate
Acidic Amino Acids:
- Their side chains are negatively charged at physiological pH, they are often referred to
aspartic acid and glutamic acid
Basic amino Acids:
- Positive charge at physiological pH
There are three amino acids that have an aromatic group: phenylalanine (F), Tryptophan (W)
and Tyrosine(Y). At the wavelength 280 nm absorption can be used to measure protein
concentration, this is non-destructive.
- This is important for determination of protein chain folding (hydrophobic side chains cluser
in the interior; hydrophilic are on the surface)
7 amino acids have ionizable groups: histidine, glutamate, aspartate, lysine, arginine, tyrosine,
cysteine.
- Henderson-Hasselbalch equation
Zwitter ion: is a charged compound who has a net charge of zero
Peptide bond formation:
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- -carboxyl of one amino acid is joined to -amino of a second amino acid (with removal of
water)
- No R groups participate in bond formation
- N-terminus is the beginning of the polypeptide chain and C-terminus is the end
- The backbone of the polypeptide chain is determined by the value of 3 dihedral angles:
(between N4 -carbon), psi (between -carbon and carboxyl group and omega.
- Clusters of conserved residue are called “motifs”. Motifs carry out a particular function or
form a particular structure that is important for conserved proteins
Ramachandran Plot
Primary structure: order of amino acids in protein chain
Secondary structure: local folding of residues into regular patterns. Ex -helix and -sheets
Loops & Turns:
- Connect -helix and -strands
- Allow peptide to fold back on itself, compact 3D shape
- Loops: hydrophilic residues, surface of protein (exposed to solvent; form H-bond with
water), up to 5 residues = turn (if cause abrupt change is polypeptide chain direction)
- -turns (reverse turns): connect different antiparallel -strands
- type I: 4 aa residue, stabilized by H-bonding, abrupt (180) changes in direction
3
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Document Summary
Peptide: has less than 50 amino acid residue. Protein: has more than 50 amino acid residue. Amino acid residue: means an amino acid within a polypeptide chain that has been dehydrated. Anatomy of an amino acid: -amin group, r-group (side chain), -carboxyl group and -carbon (chiral center) Most amino acids are l conformation not d. Serine, threonine and tyrosine participate in kinase reactions, can be phosphorylate. Their side chains are negatively charged at physiological ph, they are often referred to aspartic acid and glutamic acid. There are three amino acids that have an aromatic group: phenylalanine (f), tryptophan (w) and tyrosine(y). At the wavelength 280 nm absorption can be used to measure protein concentration, this is non-destructive. This is important for determination of protein chain folding (hydrophobic side chains cluser in the interior; hydrophilic are on the surface) 7 amino acids have ionizable groups: histidine, glutamate, aspartate, lysine, arginine, tyrosine, cysteine.
