Lecture 3 - Protiens Flashcards
Structure of proteins
- non-branching polymers that form macromolecules about 50-100 A in size
- composed of a specific sequence of amino acids joined together by chemical bonds called peptide bonds
- each protein has a distinct unique sequence
- there are 20 different amino acids used to make proteins - they are arranged in a different order and a different length in each different protein.
To understand function, you need to know ___
Structure (3D arrangement of the atoms of a protein)
Different techniques for the routine determination of protein structure
- protein crystallography
- cryo-electron microscopy
- NMR spectroscopy
Almost all completed protein structures are publicly available at locations like the____
Protein data bank
3 different ways of depicting chemical structure
Hydrogens are sometimes omitted from these structures for clarity
‘Ase’ suffix means
Enzyme
Protein responsible for oxygen transport
Hemoglobin
What does hemoglobin do
- binds oxygen in the lungs and carries it in the blood to tissues for use in metabolism
Hormone used in cell signalling
Insulin
What is insulin?
- a peptide hormone secreted after a meal, which b Indy’s to the insulin receptor, signalling cells to take up glucose
Protein involved in metabolism
Hexokinase
Alcohol dehydrogenase
What does hexokinase do?
- hexokinase is an enzyme that adds a phosphate tot glucose, after glucose is taken up by the cell
- kinases are enzymes that usually add phosphate to molecules
Protein involved in digestion
Trypsin
Amylase
What does trypsin do?
- an enzyme that breaks down proteins during digestion
- enzymes that break down proteins are called proteases
____ and ____ make proteins too
Viruses and bacteria make proteins too
HIV makes a protease that is essential for…
…HIV replication
HIV PROTESASE (talking)
- HIV gets inside cells and replicate
- it does this by having its genome read and turned into an RNA - then turned into proteins
- HIV makes one long RNA which needs to be chopped up to make lots of smaller RNAs
- HIV protease is made up of two chains with an active site in the middle
- HIV protease binds to poly peptide and breaks the chain at specific points along the polypeptide to make smaller poly peptides that fold up into HIVs proteins - allowing new virus to form
- green structure below shows the inhibitor - allows HIV to be manageable
What is amylase ?
An enzyme that breaks down starch into sugars
- it is found in saliva as well and pancreatic juices
What is alcohol dehydrogenase
- an enzyme that helps metabolise ethanol
Membrane protein involved in metabolism and energetics
ATP SYNTHASE
What is ATP synthase
- ATP synthase is a remarkable membrane protein that generates ATP for use in cellular functions
Proteins involved in Immune protection
- antibodies bind to cellular invaders like bacteria and viruses to help protect the body from infection
Proteins involved in replication and maintenance
- DNA polymerase
- RNA polymerase
What does DNA polymerase do?
DNA polymerase binds to one strand of DNA and adds the complementary stand to it
What does RNA polymerase do?
Creases a single strand of RNA that is complementary to one of the strand of duplex DNA
Are cells crowded inside?
Yes
Cells as a bag of proteins, lipids and nuclei acids
Cells are very crowded inside.. ribosomes, enzymes, RNA
Cells as a ___ of _____,____ and ___ ___
Cells as a bag of proteins, lipids and nuclei acids
Alpha helix fun facts
• 3.6 residues (AA) per turn
• Pitch of 5.4 angstrom, 1.5 angstrom per residue
• C=O hydrogen Bonds to NH 4 Residues along
– About 2.9 angstroms apart
• Φ=~-57°,ψ=~-47°
• Stabilised by Hydrogen Bonds
• Side Chains point out from the centre
• Disrupted by Glycine and Proline
• One side often polar residues, the other non polar
• Dipole
