proteins and protein structure

also includes amino acids!!

what can/do proteins serve as

• structural components

• enzymes

• molecular motors

a cell’s function is dependent on what

it’s proteins

amino acids are the what? (monomers or polymers)

monomers

polypeptides/proteins are the what? (monomers or polymers)

polymers

each amino acid has 4 chemical groups covalently bound to a what

a central alpha carbon

what 4 chemical groups are bound to the central alpha carbon of an amino acid?

• amino group

• hydrogen

• carboxyl group

• R group (functional group)

the R-group determines what about the amino acid

the chemistry (how it interacts/bonds with other molecules)

protein native shape/confirmation

• the one stable folded conformation that protein likes to take

• can vary slightly

denatured protein

protein that’s “unfolded” and not all nice and wound up?

what are the 2 2nd degree protein structures

alpha helices and beta sheets

alpha helix

• stabilized bc of hydrogen bonding between peptides/amino acids

• the R-groups stick out from the backbone

• polar R-groups face inward to create a hydrophobic core (idk if i have to know)

beta sheet

• stabilized using hydrogen bonds between peptides on chains next to each other

• the R-groups stick out from the peptide backbone

• parallel and non-parallel beta sheets

parallel beta sheets

beta sheets go in the same direction

anti-parallel beta sheets

different directions

what is 3rd degree protein structure

• alpha helices and beta sheets being put together

• a single “domain” that performs one function

• the “final” polypeptide

domain

• 3rd degree protein structure

• a compact stable structure

• performs a specific function

• contain multiple polypeptides

• beta sheets and alpha helices together

what is 4th degree protein structure

• multiple domains bound together

• has multiple functions

• not every single protein can achieve this structure

orthologs

• genes in seperate species that came from the same ancestral gene

• ex: human myoglobin and chick myglobin

paralogs

• related genes within a single genome that resulted from a gene duplication event

• related genes within the same species

• ex: paralogs btwn chicks: chick Hb beta and chick Hb epsilon

• ex: paralogs btwn humans: human Hb beta and human Hb sigma(? idk the letter)

homolog

• describes genes that are related by descent

• includes orthologs and paralogs

homologous gene family

• the entire set of related genes

• includes orthologs and paralogs

a protein’s function is determined by its what

• interactions apparantly

• need a real good surface to bind to

ligand (proteins)

what a protein binds to

binding site (proteins)

where the ligand binds to in proteins

affinity

the strength of the interaction btwn the binding site and the ligand