class 10-11

what type of bonds can nonpolar groups form with their sidchains?

induced dipole-dipole

isoelctric point

point when there is an equal balance of charges and net charge is neutral

in an amino acid, the carboxyl group has a ___ pKa while the amino group has a ___ pKa

carboxyl group: acidic (pK1)

amino group: basic (pK2)

what are glycine’s two buffer regions?

1. centered around pKa of carboxyl group (pK1=2.34)

2. centered around pKa of amino group (pK2=9.6)

how to calculate the isoelectric point?

average of pK1 and pK2

when pH=pI

net charge is 0

• AA doen’t move in the electric field

• AA least soluble in water

pH>pI

net negative charge because protein wants to donate it’s proton to the solution because it needs it more

pH<pI

net positive charge

• accepting proton from environment to make the solution less acidic

ionizable side chain (4)

• have pKa value

• act as buffers

• influence pI of AA

• can be titrated

how to tell when looking at a graph where the pI, or net charge of 0 would be

typically between pKr and pH2

peptides

chains of AAs

peptide bonds

• covalent

• formed through condensation

• broken through hydrolysis

dipeptide vs. tripeptide vs. oligopeptide vs. polypeptide vs. protein

• dipeptide- 2 AAs 1 peptide bond

• tripeptide- 3 AAs 2 peptide bonds

• oligopeptide- a few AAs (5-25)

• polypeptide- single chain more than 20is

• protein- hundreds of to thousands of AAs, molecular weight >10 kDa (1 or more polypeptides that work together)

where does number and naming of AAs start?

amino-terminal residue (N-terminus)

net charge of what parts of a protein are important?

• not the whole protein’s net charge

• net charge of active sites, bindings sites → tell us what can interact

how to estimate the number of amino acids

molecular weight/110

• 128 Da (avg. weight of AA)- 18 Da (weight of H2O removed)= 110

average molecular weight of AA

128 Da

molecule of water removed removed to form a peptide bond weigh?

18 Da

why is amount of a specific AA in dif proteins variable?

• role

• location

• organism preference

multisubunit

protein with 2+ polypeptide chains

• di, tri, tetra, etc… mer

hetero(di, tri, tetra, etc)mer

more than one polypeptide chain, but different subunits (ex. \alpha \beta )

homo(di, tri, tetra)mer

multiple polypeptide chain, but same subunit

• ex actin

oligomeric protein

long chain of the same protein repeating over again

protomers

identical subunits in an oligomeric protein

conjugated proteins

any protein that has smth permanently attached to it (covalently or strong ionic)

• ex. prosthetic group (non-amino)

lipoproteins

conjugated proteins that contain lipids

glycoproteins

conjugated proteins that contain sugar

metalloproteins

conjugated proteins that contain specific metals

• ionically bonded

primary protein structure

all proteins have it

• order of AAs that make up the chain

• critical to function

proproteins

made in an inactive form→ have to get a part removed to become active

secondary structure

• how adjacent AAs interact with each other

• shape with neighbors is determined by angles of bonds of the polypeptide backbone

Phi (\Phi ) bond

between a-carbon and the its amino group

• can rotate

Psi (\Psi) bond

bond between a-carbon and the carbonyl carbon

• can rotate

how to determine were you can fit around your neighbors

how the Phi and Psi bond can rotate

peptide bond

bond between amino acids

• acts like a 2 bond because of resonance → can’t rotate

only places to have rotations

Phi, Psi, and R group bond

regular structure

if all the same type of bonds have the same angles along a backbone

\alpha - helix

• 2nd structure

• right handed spiral (as you turn counterclockwise → you turn up)

• 3.6 AA per complete rotation

• R groups on the outside

• allow polar and nonpolar side of the spiral

\beta -sheet

• a zigzag of polypeptide → then loop that loops around → 2nd zigzag that’s next to first zigzag→ 2 zigzags held together by hydrogen bonds

where are sig chains on a \beta sheet?

sticking up and down above and below the sheet

what determines the secondary confirmation of the polypeptide?

which AAs there are

what happens if there are unequal bond angles in a 2nd structure?

random/disorder structure

what does proline do to a structure?

forces things to change their phi and psi angles → disordered structure

effect of position on order of a structure?

closer to 1= more all of the atoms are in the same chemical environment

• more ordered

• if on ends → usually denatured/flops around

tertiary structure

how do all the 2ndary structures fit together

• can be fibrous, globular

• usually has disorder regions

what type of interactions stabilize 3° structure

noncovalent interactions

• some disulfide bonds to provide extra strength

• hydrogen, dipole dipole, ionic

globular proteins

enzymatic

• weird glob with parts that can interact with thing differently

  • ex. bend and crevices can interact with dif things

fibrous tertiary structure

often structural long braided proteins

x-ray crystallography

get a lot of protein → mix in dif solvents → solvents slowly evaporate→ protein forms organized crystal→ x-ray shines on crystal and bounces off atoms→ then look at picture and figure out where electron dense spaces→ figure out how that shape can be made

when do we use NMR to determine protein structure?

when proteins are smaller than 100 AAs

circular dichroism (CD)

bends light to see how much the light is absorbed by the protein (we can tell a-heleciesvs b-sheets)

• a-helices- absorbs light rly well

• b- sheets- diff wavelengths

motifs

groupings of 2ndary structures commonly found near each other

• ex. helix-turn-helix

homeodomain protein motif

3 helicies that bind to a specific AA secience of another protein

domain

a large chunk of 2+ structural regions

• each have a specific function

• we can tell what a big protein w/ dif domains will do based on the domains

bioinformatics

identifying the function of a protein by identifying the dif domain’s functions