Week 1 (protein) Flashcards
Name the three parts making up an amino acid
Carboxyl group
Amino group
Side chain (R group)
How do you classify amino acids?
By their R groups
Name the classifications of amino acids R groups
Aromatic R groups
Positively charged R groups
Polar uncharged R groups
Nonpolar aliphatic R groups
Negatively charged R groups
How are amino acids linked in a polypeptide chain?
They are linked covalently by a peptide bind.
How does a peptide bond form?
It is formed via a condensation reaction between the amino group of one amino acid and the hydroxyl group of another.
A water molecule is released.
Name the chains of amino acids form in order of size/complexity
Dipeptides/tripeptides
Oligopeptides
Polypeptides
Proteins
In what order are amino acid sequences written in?
Written from the first amino group to the last carboxyl group.
Define oligomeric
If at least two polypeptide chains in the protein are identical
Define protomers
An identical unit in a protein
What do simple proteins contain?
Only amino acids
What doe conjugated proteins contain?
Additional permanently associated chemical components.
What is a prosthetic group?
The non-amino acid part of a protein.
Some proteins have more than one prosthetic group.
How do we classify conjugated proteins?
On the basis of their prosthetic group
Describe the primary protein structure
Sequence of a chain of amino acids
Describe the secondary protein structure
Local folding of the polypeptide chain into helices or sheets
Describe the tertiary protein structure
3D folding pattern of a protein due to side chain interactions
Describe the quaternary protein structure
Protein consisting of more than one amino acid chain.
Describe the structure of an alpha helix (secondary structure)
Amino acids and carboxyl groups of amino acids go into the middle of the helix whilst the R groups stick out.
Describe the hydrogen bonding that occurs in an alpha helix
Hydrogen bonds occur every three residues.
They continue all the way up the alpha helix and will occur inside the helix.
The binding that occurs gives the protein its secondary structure.
What does delta delta G angle show?
How likely it is going to form an appropriate hydrogen bond and help with the formation of an alpha helix.
The higher the number the more difficult it will be take up the alpha helical structure.
Describe the structure of beta strands and beta sheets (secondary structure)
zigzag or ‘pleated’ structure
Several beta-strands can pack together to form a beta-sheet.
Describe the hydrogen bonding between the beta sheets/strands
Bonding occurs between the beta strands to create a beta street.
Why is hydrogen bonding between strands stronger in antiparallel beta sheets?
The C=O and N-H groups are better aligned.
What does circular dichroism identify?
Secondary structures of a protein
How does circular dichroism work?
Circularly polarised UV light is absorbed differently by alpha-helices, beta-sheets and unstructured regions of proteins.
Name and describe the 5 bond types in tertiary structure
Hydrophobic interactions: these amino acids orient themselves towards the centre of the polypeptide to avoid the water.
Disulphide bridge: the amino acid cysteine forms a bond with another cysteine through its R group.
Hydrogen bonds: polar ‘R’ groups on the amino acids form bonds with other polar R group.
Hydrophilic interactions: these amino acids orient themselves outward to be close to the water.
Ionic bonds: positively charged R groups bond together.
Describe fibrous proteins
- long sheets
- extensive regions of a single type of secondary structure
- insoluble (rich in hydrophobic residues)
- most proteins that provide support, shape, and external protection to vertebrates.
Describe globular proteins
- roughly spherical shape
- often soluble (hydrophobic residues burrow inside, hydrophilic residues stick outside
- most enzymes and regulatory proteins
What can the accumulation of misfolded proteins lead to?
Alzheimer’s
Parkinson’s
Name the 4 common ways to denature proteins
Heat: breaks weak interaction, including hydrogen bonds.
Change pH: disrupts electrostatic interactions
Detergents: disrupts hydrophobic effect
Chaotropic agents: disrupts hydrogen bonds and hydrophobic effect.
What is a ligand?
A molecule that reversibly binds to a protein.
Proteins are specific for their ligands.
Where do ligands bind to proteins?
At its binding site (complements the ligand’s size, shape and charge)
Describe the process of ligand association and ligand disassociation
Association: when a protein binds a ligand
Disassociation: when the ligand is released
What is Kd?
Disassociation constant
What does Kd measure?
The level of affinity.
A protein that binds a ligand very tightly will have a low Kd so have high affinity. A lower concentration of ligand is needed to occupy half of the binding sites.
Describe the structure of haemoglobin
A red protein which is responsible for transporting oxygen in the blood of vertebrae.
Composed of four polypeptide chains.
A tetramer composed of two alpha and two beta subunits.
Binds with 4 oxygen molecules.
Exhibits cooperative binding with oxygen.
Has a low affinity to bind with oxygen.
Takes oxygen from lungs and transports to the rest of the body.
Describe the structure of myoglobin
A red protein with haem which carries and stores oxygen in the muscle cells.
Composed of a single polypeptide chain.
A monomer and lacks quaternary structure.
Binds with a single oxygen molecule.
Does not exhibit cooperative binding with oxygen.
Has a high affinity to bind with oxygen (does not depend in the oxygen concentration).
Stores oxygen in the muscle cells and releases it when needed.
How does haemoglobin bind and release to oxygen?
Binding: Hb binds to oxygen in the lungs where partial pressure of oxygen is high.
Release: Hb releases oxygen in tissues where the partial pressure of oxygen is lower.
How does haemoglobin bind and release to carbon dioixide?
Binding: carbon dioxide directly binds to amino acid residues on the haemoglobin molecule.
Release: Carbon dioxide is release from Hb in the lungs where the partial pressure of carbon dioxide is lower.
How does haemoglobin bind and release to hydrogen?
Binding: Hb binds to hydrogen ions which are released during the conversion of carbon dioxide to bicarbonate ions.
Release: hydrogen ions are released when Hb binds with oxygen.
