Unit 1 - Proteomics

Question 1

Genome

Answer 1

An organism’s complete set of DNA including both protein-coding genes and non-coding RNA genes (that produce tRNA, rRNA and RNA molecules that control other genes).

Question 2

Proteome

Answer 2

The entire set of proteins that can be expressed from a genome.

Question 3

Alternative RNA splicing

Answer 3

Different mature mRNA transcripts are produced, depending on which RNA segments are treated as exons and introns in a primary RNA transcript.

Question 4

Factors affecting gene expression

Answer 4

Cell type - proteins characteristic for that type of cell are produced, along with essential proteins (eg. proteins involved in respiration).

Also, metabolic activity of the cell, cellular stress and response to signalling molecules.

Proteins produced by a cell can be changed by disease and can act as early indicators.

Question 5

Prokaryotic cells

Answer 5

Bacteria and archaea.

Much smaller than eukaryotic cells (1-5 micrometres in size, compared to 10-100 micrometres for eukaryotes) due to the absence of intracellular (internal) membrane structures (including the absence of a true membrane-bound nucleus).

Question 6

Eukaryotic cells

Answer 6

Contain a system of internal membranes to increase the total area of membrane available for vital metabolic processes.

They have a true membrane bound nucleus and organelles.

Question 7

Endoplasmic reticulum (ER)

Answer 7

A network of membrane tubules continuous with the nuclear membrane.

Used for lipid (smooth ER) and protein (rough ER) synthesis.

Question 8

Vesicles

Answer 8

Sacs made of membrane that transport materials between compartments or to the plasma membrane.

Question 9

Lysosomes

Answer 9

Membrane bound organelles containing hydrolase enzymes that digest proteins, lipids, nucleic acids and carbohydrates.

They digest damaged organelles to allow component molecules to be recycled by the cell.

They are involved in phagocytosis by white blood cells in the immune system.

Question 10

Golgi apparatus

Answer 10

A series of flattened membrane discs where proteins undergo post-translational modification.

Question 11

Cytosol

Answer 11

The liquid component of the cytoplasm.

The ribosomes and organelles are suspended in the cytosol, forming the cytoplasm.

Question 12

Cytosolic ribosomes

Answer 12

Synthesise proteins and release them directly into the cytosol.

Signal sequences may direct the proteins to chloroplasts, mitochondria or the interior of the nucleus.

Question 13

Smooth endoplasmic reticulum (SER)

Answer 13

Used for synthesis of lipids (oils, phospholipids and steroid hormones).

These are made by enzymes embedded in the SER. Phospholipids are inserted directly into the SER membrane.

The SER has no ribosomes attached to it.

Question 14

Glycoprotein

Answer 14

Made by enzymes in the Golgi apparatus that attach sugars to polypeptides in multiple steps as they move through the flattened discs.

Most secreted proteins are glycoproteins, and they are important for ‘self’ recognition by the immune system.

Question 15

Rough Endoplasmic reticulum (RER)

Answer 15

Used for the synthesis of transmembrane proteins.

Cytosolic particles attached to partially completed polypeptides (at the signal sequence) cause cytosolic ribosomes to dock with protein pores in the ER, forming RER.

Translation is completed, the cytosolic particle is removed and the polypeptide chain is inserted directly into the ER membrane.

Question 16

Inactive precursor

Answer 16

Many secreted proteins are synthesised in an inactive form as precursors, which require proteolytic cleavage to produce active proteins. eg. insulin, pepsin.

Question 17

Secretory vesicles

Answer 17

Bud off the Golgi apparatus. Used to package proteins which are to be secreted out of the cell.

The vesicles move along microtubule pathways before fusing with the plasma membrane, releasing the proteins out of the cell.

Question 18

Polypeptide (Higher version)

Answer 18

An amino acid polymer. The sequence of amino acids determines the structure of a protein.

Question 19

Amino acid

Answer 19

Join together to create a polypeptide.

Have a central carbon atom with 4 groups bonded to it : NH2 (amine group); COOH (carboxylic acid group); hydrogen and a variable ‘R’ group.

Question 20

R group

Answer 20

The variable part of an amino acid, containing different types of functional group.

They vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity, and this leads to a wide range of protein functions.

They are vital in determining the structure and location of proteins.

Question 21

Acidic amino acids

Answer 21

These become negatively charged due to the extra carboxylic acid in the R group.

When the R group interacts with the aqueous solutions inside the cell, the carboxylic acid group (COOH) becomes negatively charged (COO-)

eg. aspartic acid

Question 22

Basic amino acids

Answer 22

These become positively charged due to the extra amine group in the R group.

When the R group interacts with the aqueous solutions inside the cell, the amine group (NH2) becomes positively charged (NH3+)

eg. lysine

Question 23

Polar amino acids

Answer 23

Polar R groups (eg. those containing OH) have groups which are slightly charged and can form hydrogen bonds with other molecules such as water.

eg. serine

Question 24

Hydrophobic amino acids

Answer 24

These amino acids carry no charge so do not form hydrogen bonds with water. They do not mix readily with water.

They contain hydrocarbons in the R group eg. CH3 or benzene rings.

eg. alanine

Question 25

Polypeptide (AH version)

Answer 25

Formed when amino acid monomers are linked together using an enzyme which causes a condensation reaction.

A water molecule is removed when the OH of the COOH of one amino acid joins to a hydrogen from the NH2 of another, forming a peptide bond.

Question 26

Primary structure

Answer 26

The sequence in which amino acids are synthesised into a polypeptide chain during translation.

It runs from the N-terminus (NH2 end) to C- terminus (COOH end) of the polypeptide chain, as all amino acids are lined up facing the same way before being joined together.

Primary structure determines the structure of the protein, as R-groups of the individual amino acid residues (amino acids with water removed) interact with the environment.

The structure of the protein determines its function

Question 27

Secondary structure

Answer 27

A polypeptide strand is folded and stabilised by hydrogen bonds between different peptide bonds in the chain.

N-H in one bond (weak positive) is attracted to C=O (weak negative) in another.

There are 3 types - alpha helix, beta pleated sheet and turns (where the chain folds back on itself)

Question 28

Alpha helix

Answer 28

A type of secondary protein structure.

It is a spiral with R-groups sticking outwards.

Question 29

Beta-pleated sheet

Answer 29

Parts of the polypeptide chain run alongside one another, to form a corrugated (ridged) sheet with the R-groups sitting above and below.

They are usually anti-parallel with chains running in the opposite direction, but can be parallel with chains running in the same direction (with respect to N-C polarity).

Question 30

Tertiary structure

Answer 30

The final folded 3-D conformation of a protein.

It contains regions of secondary structure, stabilised in position by interactions between R-groups of the amino acids, which come close together as the chain folds.

These bonds are affected by changes in temperature and pH, causing the protein to denature as its conformation changes.

Question 31

R-group interactions

Answer 31

Include hydrophobic interactions, ionic bonds, London dispersion forces, hydrogen bonds and disulfide bridges.

Question 32

Quaternary structure

Answer 32

The spatial arrangement of polypeptide subunits in a protein containing more than one subunit, such as haemoglobin.

Subunits are connected by bonding between their R-groups.

Question 33

Prosthetic group

Answer 33

A non- protein group which is tightly bound to a polypeptide, and is essential for its function.

Myoglobin and haemoglobin contain the prosthetic group haem.

Question 34

Ligand

Answer 34

The general term for any substance that binds to a protein.

Protein folding produces ligand binding sites on the surface of the globular protein, which have a complementary shape and chemistry to their ligand.

Ligand binding results in conformational change, which is crucial for protein function.

Question 35

Allosteric site

Answer 35

A spatially distinct site on the same protein. eg. an enzyme may have an active site and an allosteric site.

Question 36

Modulators

Answer 36

Regulate the activity of an enzyme when they bind to the allosteric site.

Binding of a modulator leads to conformational change which alters the affinity of the active site for its substrate, thus affecting the enzyme’s activity.

Question 37

Positive modulator

Answer 37

Increase the affinity of an enzyme for it’s substrate by altering its conformation.

Question 38

Negative modulator

Answer 38

Decrease affinity, and therefore the enzyme’s activity. (eg. non-competitive inhibitors).

Question 39

Cooperativity (general)

Answer 39

Allosteric proteins made of multiple subunits show cooperativity, where binding at one subunit affects the affinity of the other subunits.

Question 40

Cooperativity in haemoglobin

Answer 40

Oxygen binds to the 1st subunit causing conformational change, and triggering conformational change in the remaining subunits, thus increasing their affinity for oxygen.

Leads to rapid oxygen uptake when there is a small increase in oxygen concentration, and produces an S-shaped curve when plotting % saturation of haemoglobin against oxygen concentration of the tissues.

Question 41

Protein kinases

Answer 41

Enzymes that catalyse phosphorylation - the transfer of a phosphate group from ATP tp other proteins.

Adding a phosphate adds negative charges, which disrupts ionic interactions.

Protein kinases are mostly dephosphorylated and inactive. They need to be activated by other kinases, which phosphorylate them. This is important in signal transduction cascades and control of the cell cycle. (See later sections)

Question 42

Protein phosphatases

Answer 42

Enzymes that catalyse de-phosphorylation (the removal of phosphate from a molecule).

De-phosphorylation is the reverse of phosphorylation by kinases.

Question 43

ATPases

Answer 43

A group of transmembrane enzymes that hydrolyse ATP and use the phosphate to phosphorylate themselves, rather than their substrate.

The binding of phosphate changes their conformation, and alters their function.

eg. the sodium-potassium pump (Na+/K+ATPase).

Question 44

Reversible conformational change

Answer 44

A change in shape caused by the addition or removal of a phosphate.

Important method for regulating the activity of many cellular proteins, eg. enzymes.