Lecture 4 - Building Blovks Flashcards
What is similar between amino acids and what makes them different
- same common back bone
- differ by their Side chains
- varied chemical properties, mostly due to their side chains
In proteins, which part carry’s out the biochemical reactions for which proteins are known
- side chains of amino acids
Properties of amino acids
- amino group
- carboxyl group
- side chain
Amino acids are chiral / not chiral
Chiral
- most naturally occurring amino acids are L in natures - D form doesn’t really allow formation of a polypeptide bond
Amino acids in solutions are…
Zwitterions
Non polar amino acids - how to figure them out
Non-polar: • Only C or H at the end of their
side chain. • Hydrophobic.
3 prominent non polar amino acids
Glycine:
- R=H
- non chiral
- flexible
- almost on a group by itself
Proline:
- R-group bonds back to main chain N
- Imino acid
- rigid
- almost in a group by itself
Cysteine:
- not really non-polar
- but not polar either
Charged polar side chains - what does the positive and basic mean ? Acidic? Basic?
- positively charged - basic
- negatively charged - acidic
Polar side chains uncharged
How to figure out if an amino acid is polar
Polar:
- Also have –OH, –NH2, or –O in their side chain.
- Able to form bonds with other atoms.
- Hydrophilic.
How to know if an amino acid is positively charged polar
- Also have –OH, –NH2, or –O in their side chain.
- Able to form bonds with other atoms.
- Hydrophilic.
- has a +ve charge at ph 7
How to know if an amino acid is negatively charged polar
- Also have –OH, –NH2, or –O in their side chain.
- Able to form bonds with other atoms.
- Hydrophilic.
- has a negative charge at ph 7
Some amino acids have ionisable side groups
- this contributes to the net charge of the protein
- their charge can change, depending on the pH of the environment
- the ionisable side chains can be classified by their pka value
What is a pka
The pka value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised
What is the pI
The pI is the pH at which the net charge on an amino acid (or protein) in zero
How can you tell is something is ionisable ?
- it is polar
- it has an H-atom that can participate in acid-base reactions
- donates and accepts electrons
What is a post-translational modification (PTM)
- almost all amino acids start out as one of the standard 20
- they are ‘translated’ from RNA into proteins at the ribosome
- a chemical group can be added to an amino acid residue after translation has occurred (PTM)
- added via covalent attachment (usually enzyme-mediated)
- modify the protein is a way that switches it on or off, directs cellular location, targets degration etc
How does a disulfide bond form
Cysteine can sometimes form a covealonet bond with nearby cysteine
Possible amino acid modifications
- phosporylation
- hydroxylation
- carboxylation
- metal binding
- iodination
- glycosylation
What is phosphorylation used for
- often used to control enzyme activity - like a chemical ON/OFF switch
What is hydroxylation used for ?
Needed to prevent connective tissues diseases and scurvy, often proline and lysine involved
What is carbovylation needed for
- needed for blood clotting, often glutamate is involved
Phopholation
- addition of a phosphate group
Glycosylation of threonine
Glycosylated haemoglobin, know as HbA1c, is used to diagnose and follow patients with diabetes
Asparagiine often glycosylated as well
What are peptide bonds
- a covalent bond
Rotations of peptide bonds
- planar, trans, dipole
- flat, a-carbons go on opposite sides, ends have opposite charges
- partial double bond character (40%)
- formed via dehydration reaction between C-terminal of one amino acid and N-terminal of another.
What is a peptide
A short stretch of amino acids joined together by peptide bonds
What is a protein
- a longer chain of amino acids joined together, usually with a defined biological function
What are amino acid residues
- when amino acids are covalently joined together in a peptide or protein
- they are no longer complete, individual amino acids
- their location by residual number e.g met184 refers to a methionine residue at position 184 in a protein or peptide
When linked together in a protein,
___ ___ side chains perform the _____ needed to carry out the proteins biochemical reactions
When they are linked together in a protein, amino acid side chains perform the chemistry needed to carry out the proteins biochemical reactions
