Lecture 3.5 (Proteins) Flashcards
Describe the formation of a peptide bond
A hydrogen atom from an AMINE GROUP from one amino acid is combined with an OH from a CARBOXYL GROUP of another amino acid to form WATER and leaves behind a PEPTIDE BOND
What does an amino acid consist of?
- Central carbon atom
- Carboxyl group
- Amine group
- Variable group
- Hydrogen atom
What is the difference between Primary, Secondary, Tertiary and Quaternary protein structure?
PRIMARY STRUCTURE = sequence of a chain of amino acids
SECONDARY STRUCTURE = Local folding of the polypeptide chain into a-helices or b-pleated sheets
TERTIARY STRUCTURE = three-dimensional folding pattern of a protein due to side chain interactions
QUATERNARY STRUCTURE = protein consisting of more than one amino acid chain
What does “self assembly” mean?
The forces driving the molecules to assemble in the appropriate configuration or quaternary structure exist in the molecules themselves and in their interactions with solvent molecules
How can proteins be denatured?
- pH changes
- Temperature
- Chemical changes
How can folding moderators/chaperones help with protein assembly?
- Catalyse a step in the folding process
- Temporarily bind to peptide chain and bring certain parts of the molecule closer together
- Provide sequestered environment that foster’s protein’s native state
How many major amino acids are commonly found in proteins?
20
List the Non-polar, hydrophobic amino acids
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Proline
- Phenylalanine
- Tryptophan
What is significant about Tryptophan?
Large which creates the STERIC FORCES that limit the possible conformations available to the peptide chain
What is significant about Glycine and Alanine?
Small which allows the possibility of tightly packed configurations
Which amino acids are aromatic?
- Phenylalanine (hydrophobic)
- Tryptophan (hydrophobic)
- Tyrosine (polar)
List the Uncharged, Polar amino acids
- Serine
- Threonine
- Asparagine
- Glutamine
- Tyrosine
- Cysteine
- Lysine
- Arginine
List the charged, polar amino acids
- Histidine
- Aspartate
- Glutamate
How do charges occur in proteins?
- Ionisation of the amine and carboxyl groups of amino acids at the ends of the polypeptide chain
- Ionisation of various amino acid side chains
What do the charges cause the protein to do?
Fold in a way that maximises the distance between like charges while bringing opposite charges as close together as possible -> minimises FREE ENERGY and STABILISES the protein structure
What is a Zwitterion?
An ionised molecule that has both a positive and negative charge on it but a net charge of zero
[formed by adding a proton to the amine group + the carboxyl group losing a proton]
What is the difference between a Primary, Secondary and Tertiary amine?
PRIMARY AMINE = has only one connection to the rest of the molecule
SECONDARY AMINE = has only one H atom attached and two covalent bonds to the rest of the molecule
TERTIARY AMINE = three connections to the rest of the molecule
What are the properties of Amines?
- Slightly -ve on nitrogen atom and +ve on hydrogen atom
- Participate in H bonding on either +ve or -ve side of bond
- One amine group can participate in up to 3 H bonds at once
Describe the Hydrophobic effect
Hydrophobic functional groups create a FREE-ENERGY PENALTY by forcing water molecules adjacent to the hydrophobic molecule into a more ORDERED STATE -> Lowering ENTROPY -> FREE-ENERGY benefit to moving these functional groups away from water, into the center of the protein
What decreases the hydrophobic effect?
- Hydrophobic solvents
- Cooler temperatures
[order all of the H2O molecules so the cost of ordering the H2O molecules adjacent to a hydrophobic functional group becomes negligible]
Disulphide bonds between _____________ residues help stabilise and add rigidity to protein structure
Cysteine
Describe a Disulphide bond
When a sulphur atom attached to one amino acid forms a covalent bond with another sulphur atom on another amino acid
Describe dipoles
Lined up in parallel will repel each other while those lined up antiparallel will attract one another. HOWEVER, dipoles lined up end to end with the +ve end of one dipole facing the -ve end of another dipole will be more favourable than other configurations
Why cannot the bond between the carbonyl carbon and the amide nitrogen not rotate?
The pair of non-bonded electrons on the nitrogen spends a portion of its time within that bond -> gives bond double-bond characteristic -> Prevents free rotation around the bond
What are the two biggest contributors to the limits on bond between amide nitrogen & a-carbon and a-carbon & carbonyl carbon?
- Steric hindrances
- Dipole-dipole interactions from adjacent peptide bonds
What is Sickle Cell Anaemia?
One of the polypeptide chains that make up haemoglobin has a slight change with GLUTAMIC ACID (the sixth amino acid of haemoglobin B) is replaced by VALINE.
CAUSES:
Glutamic acid-to-valine amino acid change makes the haemoglobin molecules assemble into long fibers -> Distort disc-shaped red blood cells into crescent shapes -> Sickled cells get stuck as they pass through blood vessels impairing blood flow
SYMPTOMS:
- Breathlessness
- Dizziness
- Headaches
- Abdominal pain
- Extreme tiredness
Describe an a-helix
The carbonyl of one amino acid is hydrogen bonded to the amino of an amino acid FOUR down the chain -> HELICAL STRUCTURE with each turn of the helix containing 3.6 amino acids
Describe b-pleated sheets
Hydrogen bonds form between CARBONYL and AMINO GROUPS of backbone while the R GROUPS extend above and below the plane of the sheet -> Strands may be PARALLEL or ANTIPARALLEL
Why is proline called a “helix breaker”?
- Unusual R group creates a bend in chain
- Not compatible with helix formation
[hence why proline is typically found in bends and unstructured regions between secondary structures]
Which R group interactions contribute to the tertiary structure?
- Hydrogen bonding
- Ionic bonding
- Dipole-dipole interactions
- London dispersion forces
- Hydrophobic interactions
- Disulphide bonds
What is the difference between Peripheral membrane proteins and Integral membrane proteins?
Peripheral membrane proteins = attach to integral membrane proteins or penetrate the peripheral regions of the lipid bilayer
Integral membrane proteins = embedded through the whole lipid bilayer cross-section
What are the major functions of membrane proteins?
- Transport
- Enzymatic activity
- Signal transduction
- Cell-cell recognition
- Intercellular joining
- Attachment to the cytoskeleton and extracellular matrix (ECM)
