Protein Structure and Function Flashcards
What makes cytosolic proteins and what makes secreted proteins and membrane proteins?
Ribosomes make cytosolic proteins. RER makes secreted and membrane proteins.
Examples of structural proteins
Actin, microtubules, intermediate filaments
Example of secreted protein
Hormones e.g. insulin
Examples of molecular motors
DNA helicase, actin, myosin
Example of secreted structural proteins
Collagen
Example of intracellular protein, giving its function
Cytosolic signalling molecule- transfers signals from plasma membrane to the nucleus
How to make all the different proteins from relatively limited number of genes?
SNPs, Post-translational modifications
What are the two functional groups of amino acid?
Amino group, carboxylic acid group
Why is the polypeptide backbone flexible?
So that it can bend and fold into many shapes for the secondary and tertiary structures.
What determines folding of a protein?
Polarity (hydrophobic/hydrophilic) of side chains of amino acids
What kind of bond do polar side chains form with water molecules
Hydrogen bonds
What is the direction of an amino acid sequence?
Amino terminus to carboxyl terminus
What directions can beta-pleated sheets go in?
Anti-parallel and parallel
What two types of alpha helix are there?
Left-handed and right-handed
Alpha helix
Polypeptide backbone folded into spiral. Shape forms due to hydrogen bonds between carbonyl groups and amine groups along chain. Side chains stick out at sides.
Where are alpha helices abundant? How are they suited to this?
Abundant in membrane proteins. Hydrophobic side chains shield the hydrophilic backbone/alpha helix from lipid environment. Hydrophobic side chains interact with hydrophobic phospholipid tails. Hydrophilic parts of backbone form hydrogen bonds.
Beta pleated sheet
Flat sheet made of laterally packed strands. Shape forms due to hydrogen bonds between carbonyl and amine groups of adjacent chains. Side chains above and below sheet. Strands antiparallel.
Turn
Sharp bend redirecting polypeptide backbone
Loop
A longer turn of the polypeptide backbone. Have hydrophilic residues and are found on surface of proteins
Random coils
Polypeptide chains with random configuration
Name 3 other secondary structures, other than beta or alpha.
Loops, turns, random coils
Side chain interactions
VdW, Electrostatic attractions, hydrogen bonds (non covalent bonds). Spontaneous.
Myoglobin secondary structure
Mainly alpha helices
Tumour necrosis factor- secondary structure and what is it?
Mainly beta pleated sheet and it is an inflammatory cytokine
What are barrels?
A tertiary structure formed by beta sheets that allow ions to pass through them
Coiled coils, giving examples
Made of 2 or 3 alpha helices wound around each other. Hydrophobic amino acids line up where helices meet. Coiled coils give structural strength. Keratin and collagen
Proteolytic cleavage
The process of breaking the peptide bonds between amino acids in proteins
Post translational modifications. Name two examples.
A covalent processing event resulting from a proteolytic cleavage or additon of modifying group. Modulate the function of eukaryote proteins by altering activity state, localization, turnover, interactions with other proteins. Phosphorylation and Glycosylation.
Phosphorylation
Addition of phosphate to amino acids
Glycosylation
Addition of carbohydrates to specific sites on protein
Disulphide bonds
A PTM. Stabilises tertiary structure. Formed between cysteines next to each other in folded structure. Do not alter shape. Generally found in excreted proteins, not cytosolic, because it’s a strong bond so gives secreted proteins strength for extracellular environment
Reversible denaturation
Add solvent (acids or bases etc.) to disrupt non-covalent interactions. Protein loses secondary and tertiary structure and unfolds. If solvent is removed, protein refolds/renatures.
Irreversible denaturation
Heat
Why is protein folding possible naturally?
Because proteins always fold to lowest free energy. The process of folding is energetically favourable as it releases energy and increases entropy.
Molecular chaperones. Name the two classes.
Proteins that bind to the partially folded polypeptide chains and assist them in folding. Two classes are chaperonins and heat shock proteins. Chaperones do not change 3D structure but speed up the process of folding and prevent aggregation and formation of non-productive intermediates.
Aggregation
Different proteins all collecting up in one big group
Why are molecular chaperones needed?
Because not all proteins fold simultaneously
What is the charge of proteins dependent on?
Amino acid side chains
Protein domains
Any segment of a polypeptide chain that can fold independently into a compact, stable structure. It is the modular unit from which larger proteins are made. Some proteins can form more than one domain. Each domain has different functions.
Signal sequence
Part of the amino acid sequence that provides info as to where a protein should go after translation. Proteins without signal sequence remain in cytosol.
Examples of diseases due to mutated/modified/misfolded
Cystic Fibrosis, Creutzfeldt-Jakob disease, Huntington’s, Alzheimer’s
Cystic fibrosis
Inherited disease of secretory glands. DNA mutation (3 base pairs deleted) alters shape of a transmembrane protein which is involved in chloride transport. Impaired chloride transport leads to abnormal mucus which can cause recurrent bacterial infections and make it hard to breathe due to pulmonary obstruction.
Creutzfeldt-Jakob disease
Misfolded prion proteins promote refolding of other prions into a disease conformation. The misfolded proteins form tightly packed beta-sheets. These build up in brain, forming amyloid plaques that cause death of nerves in death.
Name one process in the cell to get rid of misfolding
Chaperones
