AH Bio 1.2

what is the proteome?

the entire set of proteins expressed by a genome

is the proteome larger in eukaryotes or prokaryotes?

eukaryotes

why is the proteome larger in eukaryotes?

more than one protein can be produced from a single gene due to RNA splicing

what are 4 factors that affect the set of proteins expressed by a given cell type

- metabolic activity of the cell
- its state of cellular stress
- its response to signalling molecules
- its state of health or disease

what are genes that do not code for proteins transcribed to produce?

tRNA, rRNA and RNA molecules that control the expression of other genes

why do eukaryotic cells have a relatively small surface area to volume ratio?

their relatively large size

what is the internal system of specialised membranes called that increases the total membrane that eukaryotic cells have?

endoplasmic reticulum

what is the difference between the RER and the SER?

the RER has docked ribosomes on its cytosolic face

what is the Golgi apparatus?

a series of flattened membrane discs

what transports materials between membrane compartments in the golgi apparatus?

associated vesticles

what are lysosomes?

membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates

is the interior of a lysosome acidic or basic?

acidic

where are lipids synthesised?

SER and inserted into its membrane

where does the synthesis of proteins begin?

cytosolic ribosomes

What happens in the Golgi apparatus?

post-translational modification

what is post-translational modification?

covalent modifications which are made to proteins after translation

what is one example of a major post-translational modification?

the addition of carbohydrate groups

when vesticles leave the golgi apparatus, where do they take the proteins?

plasma membrane and lysosomes

what do vesticles move along?

microtubules

what happens to proteins for secretion or those that will become lysosome hydrolases?

they are translated in the ribosome and enter its lumen

what are proteins for secretion packaged inside as they move through the golgi apparatus?

secretory vesticles

what is proteolytic cleavage?

a type of post-translational modification

what are many secretory proteins produced as?

inactive precursors

what are proteins?

polymers of amino acid monomers

what do amino acids form when liked together by peptide bonds?

polypeptides

what is the only thing that differs between all amino acids?

the R group

what 4 things can an R group be?

- hydrophobic
- hydrophilic
- alkaline
- acidic

what 5 things can R croups differ in?

- size
- shape
- charge
- hydrogen bonding capacity
- chemical reactivity

what is the primary structure of a protein?

the sequence in which amino acids are synthesised into a polypeptide chain

how are hydrogen bonds formed?

weak positive charges on hydrogen atoms are attracted to weak negative charges on oxygen or nitrogen atoms

where does hydrogen bonding occur?

along the backbone of the protein

what does hydrogen bonding result in?

regions of secondary structure

what are 3 examples of secondary structure?

- alpha helices
- parallel or anti-parallel beta-peated sheets
- turns

what do turns do?

join different structures together and allow a change in direction in the polypeptide

what does a tertiary structure do?

gives the molecule an overall shape in space

what are the 5 interactions that affect a polypeptides conformation?

- hydrophobic interactions
- ionic bonds
- disulphate bridges
- london dispersion forces
- hydrogen bonds

what can interactions of R groups be influenced by?

temperature and pH

how does temperature affect a polypeptide?

high temperatures denature it

in what proteins does quaternary structure exist?

proteins with two or more connected polypeptide subunits

what does quaternary structure describe?

the spatial arrangement of the subunits

what is a prosthetic group?

a non-proteins unit tightly bound to a protein and necessary for its specific function

what is a ligand?

a substance that can bind to a protein

what allows ligand binding?

R groups that are not involved in protein folding

what do binding sites have that are complementary to the ligand?

shapes and chemistry

what happens to the protein when a ligand binds to the binding site?

the conformation changes

what does a conformational change in a protein do to the protein?

changes the function

where do allosteric interactions occur?

between spatially distinct sites on a proteins surface

what does the binding of a substrate molecule to an enzymes active site do?

increases the affinity of the other active sites for other substrate molecules

what can the activity of allosteric enzymes vary as a consequence of?

small changes in substrate concentration

what do allosteric proteins with multiple subunits show?

co-operativity in binding

what two sites do allosteric enzymes have?

active and allosteric

what regulates the activity of the enzyme as they bind to the substrate?

modulators

what happens to an enzyme following the binding of a modulator?

conformational change

what is another word for negative modulators?

inhibitors

what do positive modulators do?

Increase the enzyme's affinity for the substrate

what do negative modulators do?

Reduce the enzymes affinity for the substrate

what can the addition or removal of phosphate from particular R groups be used to cause?

reversible conformational changes to proteins

what catalyses the transfer of phosphate groups to other proteins?

protein kinases

what does phosphorylation bring about in a protein?

conformational changes

does adding a phosphate group add a positive or negative charge?

negative