L02- PROTEIN STRUCTURE AND FUNCTION Flashcards
Describe the primary structure of a protein
- Linear structure/ order of amino acids
- bonds = covalent peptide bonds between AA
- From the N terminus to the C terminus
- Can have projecting AA side chains
Describe the types of projecting AA side chains
- Non polar, aliphatic side chain e.g glycine
- Polar, uncharged e.g Serine
- Positively charged
- Negatively charged
- Aromatic
Which AA groups tend to be found on the inside of a protein?
- Non polar, aliphatic amino acids
Which AA groups tend to be found on the outside of a protein?
- Polar, uncharged amino acids
Which terminal does the primary structure start at?
Amino terminal (n terminus)
Describe the secondary structure of a protein
- folds in the amino acid chain –> beta sheet, alpha helices
- hydrogen bonds between atoms in peptide bond
- bonds not covalent
- R groups influence shape of secondary structure as they influence where bonds are formed
Which way do R groups face in the alpha helices?
Outwards
Describe the tertiary structure
- Final 3D structure
- Further folding - more H bonds, ionic bonds, disulphide bridges
- most stable/ lowest amount of energy - there are not two negatively charged molecules near each other or a hydrophilic and hydrophobic near each other
Describe H bonding in tertiary proteins
Can have H bonding between different R groups, between R groups and peptide bonds, and between different peptide atoms
Quaternary?
multiple polypeptide chains
Name 4 different types of tertiary structures
- Fibrous - long, elongated , collagen
- Globular - round balls, enzymes
- Helix - interacting with other proteins
- Beta pleated sheet - involved in protein folding
How to determine protein shape?
- X- ray crystallography
- NMR
What are heteromers and homomers?
Hereromers = protein with two or more different polypeptide chains
Homomers = protein with two or more identical polypeptide chains
Charcteristics of proteins (2)
- flexible, can change their conformity e.g enzymes
- Ability to be phosphorylated
Functions of proteins (4)
- Binding, (receptors, ligands, antibodies)
- Catalysis, (enzymes)
- Switching things on and off, (cell signalling pathways)
- Structural support, (cytoskeleton)
What is the name of proteins that help other proteins to fold?
Chaperone proteins
Which factors regulate the function of proteins? (4)
- Synthesis - has the protein been made or not
- Localisation - Is the protein in the correct location to carry out its function or not
- Modification - is the protein active or inactive
- Degradation - is the protein needed anymore
How are proteins localised ? (3 steps)
- produced in the RER
- have a sorting signal which tells them where to go
- are transported from cytosol into organelles via transporter vesicles
Explain what type of reaction is needed to regulate protein function
Phosphorylation - A phosphate group is covalently attached to amino acid side chains which have a hydroxy group.
They can inhibit or activate a protein and they induce a conformational change
What enzyme catalyses a phosphorylation reaction?
Kinase enzyme which uses ATP
Which protein is responsible for dephospho rylation?
Phosphatase
What is unfolded protein response (UPR)?
This is a homeostatic mechanism and it tries to keep folding in the cell in balance with the cell’s needs.
What can happen if there is an imbalance in the UPR process?
It results in the ER becoming stressed. It causes an increase in unfolded proteins. It can inhibit translation and cause potential cell death
Give 3 consequences as a result of a lack of protein folding
- Sickle cell anaemia
- Type II diabetes
- Cataract
