Structural Biochemistry

how many common amino acids

20

how are amino acids joined together

peptide bonds

what are the main agents of biological funtion

proteins

what do proteins do

catalysis, transpot, structure, motion

what are the building blocks of proteins

amino acids

protiens are what?

linear heteropolymers of alpha amino acids

why are they called alpha maion acids

the carbon is attached to the R group is a alpha carbon

when is it called an amino acids or a residue

amino acids is a free staning molecule and a residue is the same molecule after its been incorporated into a protein chain, it lost water because of the peptide bond

amino acids have how r common functional groups, what are they

carboxyl group, amino group, alpha hydrogen connected to alpha carbon

all amino acids are ___ and proteins only contain __ amino acids

chiral ; L conformation

how many nonpolar aliphatic amino acids are there

7

how many aromatic amino acids are there

3

how mahny polar, uncharged amino acids are there

5

how many positive charge amino acids

3

how many negative amino acids

2

aromatic R group side chains obsorb UV light at

270-280 nm

why is cystein polar?

it can form disulfide bonds

why is cysteine R group polar

The electronegativity of sulfur is 2.58, and hydrogen is 2.2; the difference is .28, which makes the S-H bond polar covalent with a small dipole moment at the hydrogen end

uncommon amino acids in protien are

not incorporated by ribosomes except selenocysteine

uncommon amino acids arise by

post translational modifications

the side chain of the amino acid cysteine is polar T/F

True

The lysine side chain is negativelty charged at pH 7 T/F

False

glutamate and glutamine side chains are both negatively charged T/F

False

selenocysteine is created post translationally T/F

false

the side chain of the amino acid cystein allows cystein to be chiral

True

the phospho-serine side chain is created post translationally

True

tyrosine does not absorb UV in a significant way

False

how does the formation of peptide bonds occur

condensation

what group acuds as a nucleophile during the formation of peptides

alpha amino group acts as a nucleophile to displace the hydroxyl group from another amino acid

amino groups are good ___ and hydroxy group is a ____

good nucleophile ; poor leaving group

peptides are ___ compared with proteins

smaller

oligopeptide

a few amion acids joine together , <5kDa

polypeptide

molecular weight less than 10,000 , about 91 amino acids

protein

molecular weight greater than 10,000 , more than 91 amino acids

naming peptides starts where

the N-terminus

what are some functions of peptides

horomons and pheromones, neuropeptides, antibiotics, protection

why are artificial sweeteners not a good idea

they trick tho body to intaking sugar/glucose and raise insulin levels

proteins are

polypeptides ( covalently linked alpha amino acids ) plus cofactors, coenzymes, prosthetic groups, other modifications

titin is also known as what

connectin

what is connectin (titin)

a protein in humans that is encoded by a TTN gene

how big is titin

1 micormemter in lenght and is composed of 244 individually folded protein domains connected by unsaturated peptide sequences

when do the titin domains unfold

when the protein is stretched and will refold when the tension is removed

why do we substract 18 from the average molecular weight of a amino acid composition

because of the water bonds

proteins can form multisubunits such as

oligomeric (hemoglobin) , protomers (one subunit or builfing block of an oligomeric complex)

what is a conjugated protein

Prosthetic group is the non-amino acid part (lipoproteins, glycoproteins, metalloproteins)

why use prosthetic groups and not amino acid side chains

because some amino acids cant perfrom some of the functions needed to operate

The alpha amino group of one amino acid can act as a nucleophile and displace the hydroxyl group of another amino acid to form a peptide bond (and release water). This reaction is catalyzed by ribosomes

true

how many peptide bonds in a penta-peptide

4

glutaminylleucyglycine can also be written as

QLG

when nature cany find an amino acid with characteristics required for a particular function it will make use of a cofactor or prosthetic gfroup to obtain the requied function

True

how many amino termini does this peptide have

lecture 3 slide 16

at physiological pH peptide bond formation occurs spontaneously

False

beta-galactosidase (116 kDa) can be considered a

protein

what is protein purification

crude extraction of cells

what is the stationary phase of column chromatography

solid porour material supported inside a columnwh

what is the mobile phase of column chromotography

a solution that flows through the matrix

what is the remocval of a protien from the column called

elution

what is fractionation

collection of the protein as it elutes from the column

what are cation exchangers in ion exchange chromotography

exchange positivelty charged ions (cations ) and have negative charged resin beads

what is antion exchanfers in ion exchance chromotography

exchanve negaticely charged ion (anions) and has positivelty charged resin beads

how do you elute the protein from the column

change the conditions of the buffer to mess up the interaction between the protin and the columns stationary phase

proteins that are to be separated based on charge (ion exchanged chromotography) are eluded using a salt gradient from high salt to low salt

false

in ion exchange chromotography the resin that you choose must have a charge ion its surface that is opposite to the net charge on the protin of interest

true

in ion exchange chromotography it is also possible to elute proteins using a different saly such as magnesium sulfase

true

what is separation by size also known as

gel filtration or size exclusion chromotography

what do small proteins interact with in gel filtration

beads

large proteins interaction with the beads in size exlusion chromotography T/F

True

how to elute in separation by size

with only a buffered water with a bit of saly so the protein of interaste is stable, no gradient is needed

what does affinity chromotography do

separates proteins by their binding specificites

what will the beads have in in affinity chromotography

they will have ligand that the protein likes to bind to

how is protein eluted from the column in affinity chromotographty

using histidine of emidizole

removal of protein from the column is called extraction

False

in ion exchange chromatography, proteins are separated based on size, where small proteins interact with small pits on the surface of the matrix beads, and large proteins are too large and simply fall through without interacting

False

some phi and psi combinations are more favorable because of a chance to

form favorable h-bonding interactions

The Ramachandran plot shows the distribution

of phi and psi dihedral angles that are found in protein

ramachandran plot shows the common

secondary structure elements

ramachandran plot reveals

the regions with unusual backbone structure

the overall conformation of the protein backbone is exclusively determined by the phi and omega angles

false

The Ramachandran plot describes

allowed and disallowed phi and psi angles in proteins and likely secondary structural elements based on phi and psi angles

A peptide bond is

planar and rotation about the omega angle is not permitted

how are alpha helix stabalized

hydrogen bonds between nearby residues

how are beta sheets stabalized

A hydrogen bond between adjacent segments that may not be nearby

what is a irregular arrangement of a polypeptide chain called

random coil

how many residues does a right hand helix have

3.6 residues per turn (5.4 A)

peptide bonds are aligned

roughly parallel with the helical axis

in a alpha helix side chains point

outward from the center axis and are roughly perpendicular with the helical axis

the inner diameter of the helix

4-5 A and to small for anything to fit inside

the outer diameter of the helix

10-12 A and happens to fit well into the major groove of dsDNA

What residues align nicely on an alpha helix

1 and 8

What kind of sequence gives an alpha helix with one hydrophobic face

Every 3 or 4 residues, there will be a hydrophobic residue, which will fold off into a helix

What are strong hydrophobic residues

Alanine and leucine

proline acts as a what in helix stability

helix breaker because the rotation around the N-C_a bond is impossible

glycine is a helix

breaker because of the small r group supports other conformations (too flexible)

charges near each other

repel or attract and destabilize the helix

C-O dipole

negative

N-H dipole

positive

alpha helix has a

large macroscopic dipole moment that is enhances by unpaired amides and cabonyls near the ends of the helix

in a helix negatively charged residues often occur

near the positive end of the helix dipole

alpha helix uses up all the hydrogen bonding potential of the backbone

true

the r gorups or amino acid side chains will normally point toward the interor of an alpha helix

false