Introduction to protein biochemistry

Question 1

Proteins are diverse and important

Answer 1

Very versatile biomolecules
Large variety structural properties lead to wide variety of jobs e.g:
- Hormones - small, travel in bloodstream, bind specific receptor in different place to start
- Antibodies - recognise foreign material, communicate to immune system
- DNA binding proteins - binding specific DNA sequences, affect gene expression

Question 2

Movement of other molecules

Answer 2

Porin - On outside bacteria membrane, allows diffusion certain molecules, makes hole in membrane
Ferritin - Stores, transport and releases iron

Question 3

Structural Functions

Answer 3

Lots of protein components of cytoskeleton e.g. microtubules

Question 4

Enzymes

Answer 4

Are proteins accelerate rate chemical reactions
Don’t change final equilibrium, just make reaction faster
Reduces energy required for reaction
Enzymes have active site, bind to substrate, yields product

Question 5

Protein structure and folding

Answer 5

Protein made of amino acids with varied side chains
Have many different shapes, size, electric charge, polarity

Question 6

Primary structure

Answer 6

Order of amino acids (called residues) in polypeptide/protein
protein sequence defined by gene sequence
DNA transcribed to RNA translated to protein
3 bases = 1 amino acid

Question 7

Amino acids joined by peptide bonds

Answer 7

Peptide bond - loss of water
N-terminus and C-terminus - shows chains beginning (N) and ending (C)
Proteins generally between 50-2000 amino acids
Can be tens of thousands
Shorted than 50 called peptides not proteins
Rotation can’t occur around peptide bond as rigid but other bonds more flexible

Question 8

Proteins fold into 3D structure

Answer 8

Folding based on properties of component amino acids
Unfolded = denatured
Folded = native
Denatured proteins are simply an amino acid chain and is thermodynamically unstable
Bond form between amino acids - native protein

Question 9

Secondary structure

Answer 9

Regular repeating structure
Between amino acids close together in first sequence
Stabilised by hydrogen bonds (relatively negative electric charge O, relatively positive H)
H bond not relatively strong on own but strong when there’s lots of them

Question 10

Alpha helix

Answer 10

H-bond between NH (relatively positive) and CO (relatively negative) groups of amino acids that are 4 residues apart
Gives spiral structure with side chains sticking out

Question 11

Beta sheet

Answer 11

H-bonds between NH and CO groups of amino acid are further away from each other on 1st sequence and on different strands
Parallel - adjacent strands, run in same direction
Anti-parallel - run opposite to each other

Question 12

Tertiary structure

Answer 12

Tightly packed, thermodynamically stable, 3D structure
Determined by noncovalent interactions of side chains, interactions have different strengths
Electrical charges - similar repel, opposite attract
Size, shape side chains also important can limit structures that can be made

Question 13

Interaction of amino acids with polar water molecules

Answer 13

Hydrophobic - dislike water, nonpolar, no H bonds/ionic interactions
Hydrophilic - like water, can form H bonds/ionic interactions

Question 14

Hydrophobic amino acids

Answer 14

Usually on inside tertiary structure
Polar residues tend to be on outside of protein so can interact with polar water
Non-polar residues tend to fold into centre of protein, away from aqueous environment of cell

Question 15

Disulphide bridges between cysteine residues

Answer 15

Interactions between sulphur atoms in cysteine amino acids
Oxidation to Crosslinks between different parts of primary sequence
Rigid strengthening of tertiary structure e.g. insulin

Question 16

Protein domains

Answer 16

Some proteins (e.g. Myoglobin) fold into single compact structures
Many proteins fold into several domains - regions fold tightly
Separated flexible regions that less tightly folded
Domains often carry out specific part of proteins function
Same domain can appear in several evolutionary linked proteins

Question 17

Quaternary structure

Answer 17

Some polypeptides form part of a more complex structure with 2 or more subunits
Subunits can be identical or different
Dimer, trimer, tetramer - quaternary structure made of 2, 3 ,4 subunits
E.g. haemoglobin made 2 alpha and 2 beta subunits

Question 18

Post-translational modification

Answer 18

Removal specific part sequence e.g. of signal peptides
Addition molecules, modulating protein function e.g:
- Methylation - add CH3 groups - methylation histones used to control which parts genome expressed
- Glycosylation - addition of sugars - especially on cell surface and secreted proteins
- Ubiquitination - add of a 76 amino acid polypeptide - Ubiquitin polymers marl out protein for degradation

Question 19

Phosphorylation

Answer 19

Reversible addition of PO3 groups
Added by enzymes cladded as kinases
Important way to regulating enzymes function
Phosphorylation amino acids in/around active site can change properties of region e.g. alter substrate binding

Question 20

Protein tareting

Answer 20

Different organelles require different types of proteins
Some proteins need to be moved to the membrane or secreted from cell
Many proteins contain short ce

Question 21

Protein target to cell membrane

Answer 21

Can occur via secretory pathways
Ribosomes associated with endoplasmic reticulum

Question 22

Posttranslational modifications anchor membrane proteins

Answer 22

Other proteins anchored in membrane by additional hydrophobic groups added to protein sequence e.g:
- Addition of fatty acid groups to small G proteins (e.g. RAS) - inserted into membrane