Protein biochemistry Flashcards
what is a hormone?
Small proteins that travel around the bloodstream and binds to specific receptors elsewhere in the body
what is an antibody
Recognition of foreign material, allowing the immune system to respond
What is a DNA binding protein?
Bind to specific DNA sequences and affect gene expression
Name the roles of a protein
recognition of specific molecules (hormones, antibody’s, DNA binding)
Movement of other molecules (porin, ferritin)
Structural functions (microtubules)
Enyzmes
What are the roles of ferritin and porin?
Porin sits in the outer membrane of bacteria, and allows diffusion of certain molecules into the cell
Ferritin stores, transports, and releases iron
What are microtubules made up from? what is its role?
many alpha and beta tubulin subunits
-structure of cell
-separate chromosomes (mitosis)
-cilia and flagella
-strong yet dynamic
What are enzymes?
proteins that accelerate (often very dramatically) the rate of chemical reactions
- dont change equilibrium
-reduces activation energy
What are proteins made from and what bond holds these together?
amino acids, peptide bonds( loss of water)
amino acid structure
Conserved structure
Side chains vary
Join to make polypeptide chains
what is the primary structure?
= order of amino acids (“residues”) in the polypeptide.
Rotation is not possible around the peptide bonds but more flexibility for other bonds
What is another word for a folded protein? and what may some require to become folded?
Native
a chaperone
What is the secondary structure?
Regular, repeating structures
Between amino acids close together in the primary sequence
Stabilised by hydrogen bonds
Why is water polar?
rel neg at O
rel pos at H
Describe and alpha helix
Helical (spiral) structure with side chains on the outside
How does an alpha helix form?
H-bonds between amino (relatively positive) and carboxyl (relatively negative) groups of amino acids 4 residues apart
What is a beta sheet?
H-bonds between amino and carboxyl groups of amino acids further away from each other in the primary sequence – on different strands
may be parallel or anti parallel
What is tertiary structure?
Tightly-packed thermodynamically stable 3D structure of the protein
Determined by noncovalent interactions between the side chains (interactions of differing strengths)
Electric charges: similar charges repel / opposite charges attract
Size and shape of side chains also constrains
Amino acids interact differently w water.
Hydrophillic: form H-bonds/ ionic interaction. Hydrophobic: no Hbonds/ionic 9non-polar)
Why do hydrophobic amino acids tend to be on the inside of the tertiary structure?
Polar residues tend to end up on the outside of the protein, where they can interact with polar water molecules
Nonpolar residues tend to fold into the centre of the protein, away from the aqueous environment of the cell
What are disulfide bridges?
Interactions between sulphur atoms in Cysteine amino acids
Oxidation -> CROSSLINKS between different parts of the primary sequence
Strengthen the tertiary structure
What is a protein domain?
regions that fold tightly
Separated by flexible regions that are less tightly folded
Domains often carry out a specific part of the protein’s function
The same domain can appear in several evolutionarily linked proteins
What is quaternary structure?
When polypeptides have a more complex structure with 2 or more sub-units
Dimer, trimer, tetramer = quaternary structures made of two, three, four subunits
What are post-translational modifications?
removal of specific parts of the sequence or Addition of molecules, modulating protein function
What are 3 named types of addition?
Methylation: addition of -CH3 group(s).
(used in controlling which parts of the genome are expressed)
Glycosylation: addition of various sugars. Especially on cell surface and secreted proteins
Ubiquitination: addition of a 76-aa polypeptide. Ubiquitin polymers mark out a protein for degradation
What is phosphorylation?
Reversible addition of phosphate (PO3) groups
By a class of enzymes called kinases
An important way of regulating enzyme function
Phosphorylation of amino acids in or around the active site can change the properties of the region and alter substrate binding, for instance
Why is Protein targeting important?
proteins contain short signal to show where needed, may be synthesised in cytoplasm and delivered to target
What process allows for proteins to target the cell membrane?
SECRETORY PATHWAY
Ribosomes associate with the endoplasmic reticulum
proteins on membrane, Hydrophobic regions go through the membrane, Soluble regions on the inside and outside
Others associate with a trans-membrane protein
Or directly with the polar heads of the membrane lipids
What is another role of post-translational modification?
to anchor membrane proteins, by additional hydrophobic groups added to protein sequence.
An example…
addition of fatty acid groups to small G proteins (such as Ras, which you will meet again later in the module) – insert into membranes
When at the membrane: involved in signalling pathways
Modification allows them to be removed from the membrane: inactive in the cytosol
Cycle on and off the membrane
