Protein biochemistry

Question 1

what is a hormone?

Answer 1

Small proteins that travel around the bloodstream and binds to specific receptors elsewhere in the body

Question 2

what is an antibody

Answer 2

Recognition of foreign material, allowing the immune system to respond

Question 3

What is a DNA binding protein?

Answer 3

Bind to specific DNA sequences and affect gene expression

Question 4

Name the roles of a protein

Answer 4

recognition of specific molecules (hormones, antibody’s, DNA binding)
Movement of other molecules (porin, ferritin)
Structural functions (microtubules)
Enyzmes

Question 5

What are the roles of ferritin and porin?

Answer 5

Porin sits in the outer membrane of bacteria, and allows diffusion of certain molecules into the cell
Ferritin stores, transports, and releases iron

Question 6

What are microtubules made up from? what is its role?

Answer 6

many alpha and beta tubulin subunits
-structure of cell
-separate chromosomes (mitosis)
-cilia and flagella
-strong yet dynamic

Question 7

What are enzymes?

Answer 7

proteins that accelerate (often very dramatically) the rate of chemical reactions
- dont change equilibrium
-reduces activation energy

Question 8

What are proteins made from and what bond holds these together?

Answer 8

amino acids, peptide bonds( loss of water)

Question 9

amino acid structure

Answer 9

Conserved structure
Side chains vary
Join to make polypeptide chains

Question 10

what is the primary structure?

Answer 10

= order of amino acids (“residues”) in the polypeptide.

Rotation is not possible around the peptide bonds but more flexibility for other bonds

Question 11

What is another word for a folded protein? and what may some require to become folded?

Answer 11

Native
a chaperone

Question 12

What is the secondary structure?

Answer 12

Regular, repeating structures

Between amino acids close together in the primary sequence

Stabilised by hydrogen bonds

Question 13

Why is water polar?

Answer 13

rel neg at O
rel pos at H

Question 14

Describe and alpha helix

Answer 14

Helical (spiral) structure with side chains on the outside

Question 15

How does an alpha helix form?

Answer 15

H-bonds between amino (relatively positive) and carboxyl (relatively negative) groups of amino acids 4 residues apart

Question 16

What is a beta sheet?

Answer 16

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

Question 17

What is tertiary structure?

Answer 17

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)

Question 18

Why do hydrophobic amino acids tend to be on the inside of the tertiary structure?

Answer 18

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

Question 19

What are disulfide bridges?

Answer 19

Interactions between sulphur atoms in Cysteine amino acids
Oxidation -> CROSSLINKS between different parts of the primary sequence
Strengthen the tertiary structure

Question 20

What is a protein domain?

Answer 20

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

Question 21

What is quaternary structure?

Answer 21

When polypeptides have a more complex structure with 2 or more sub-units
Dimer, trimer, tetramer = quaternary structures made of two, three, four subunits

Question 22

What are post-translational modifications?

Answer 22

removal of specific parts of the sequence or Addition of molecules, modulating protein function

Question 23

What are 3 named types of addition?

Answer 23

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

Question 24

What is phosphorylation?

Answer 24

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

Question 25

Why is Protein targeting important?

Answer 25

proteins contain short signal to show where needed, may be synthesised in cytoplasm and delivered to target

Question 26

What process allows for proteins to target the cell membrane?

Answer 26

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

Question 27

What is another role of post-translational modification?

Answer 27

to anchor membrane proteins, by additional hydrophobic groups added to protein sequence.

Question 28

An example…

Answer 28

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