Mcb 102 Biochemistry Flash Cards- Terms And Concepts

Front 1

the pKa

Back 1

pH at which half of the acid or base is dissociated

Front 2

Henderson-Hasselbach equation

Back 2

pH = pKa + log ([A-]/[HA])

Front 3

Amino Acid Residue convention for polypetides

Back 3

amino acid end is shown to the left and carboxyl end is drawn to the right

Front 4

primary

Back 4

level of protein structure consisting of the amino acid sequence and location of S-S bonds

Front 5

secondary

Back 5

consists of special repeating structures such as alpha helices and beta-pleated sheets

Front 6

Tertiary

Back 6

Total fold of a protein including repeating and unusual structures

Front 7

Quaternary

Back 7

the arrangement of different polypeptide chains in a protein complex

Front 8

prosthetic groups

Back 8

accessory components of proteins

Front 9

Differential centrifugation

Back 9

if a cell contains organelles, the first step of a purification might be this. Cell membranes will be centrifuged into a pellet at 1000 x gravity for 10 min and 20,000 x gravity at 20 minutes will yields a pellet with organelles

Front 10

solubility

Back 10

a cell extract containing soluble proteins is often fractionated by adding increasing concentrations of ammonium sulfate. Some proteins precipitate at rather low ammonium sulfate concentration while others require more.

Front 11

anion exchange chromatography

Back 11

chromatographic materials that contain cations such as DEAE as the stationary phase

Front 12

cation exchange chromatography

Back 12

chromatographic materials that contain anions such as phosphate and carboxymethyl as the stationary phases

Front 13

enzyme assay

Back 13

determines whether the proteins of interest is in the pellet or supernatant. Can use either a color assay or a radioactive tracer assay

Front 14

protein assay

Back 14

- Measures total protein by staining with the Bradford Reagent. The Bradford uses Coomassie brilliant blue dye which is brown at acid pH (max. absorption at 465 nm) and is blue when it binds to proteins (595 max. absorption)

Front 15

specific activity

Back 15

the number of enzyme activity units divided by the milligrams of protein

Front 16

SDS-PAGE

Back 16

sodium dodecyl sulfate polyacrylamide gel electrophoresis. SDS causes unfolding of the protein and makes proteins very negatively charged in rough proportion oto their mass.

Front 17

isoelectric focusing

Back 17

- the first step in a two dimensional gel electrophoresis which is a separation on the basis of isoelectric point. Each protein has positive and negative charges with different pKa’s and therefore has no charge at a specific pH, called the isoelectric point. Proteins are then separated on the basis of charge.

Front 18

Sanger reagent

Back 18

2,4-dinitrofluorobenzene reacts with amino groups

Front 19

Edman Degradation

Back 19

Amino terminal end of the protein reacts with phenyl isothiocyanate, releasing a phenylthiohydantoin derivative of N-terminal amino acid. The amino acid in this derivative can be identified and the procedure can be repeated for about 50 cycles. Cleavage is only 99% complete so the date become unclear after many embryos

Front 20

overlapping peptides

Back 20

used to help determine the entire sequence of protein when using edman degradation

Front 21

trypsin

Back 21

cleaves on the carboxyl side of positively charged amino acids

Front 22

chymotrypsin

Back 22

cleaves on the carboxyl side of aromatic amino acids

Front 23

cyanogen bromide

Back 23

cleaves on the carboxyl side of methionine

Front 24

locating s-s bonds

Back 24

one often finds S-S bridges between cysteine residues; make peptides by cleaving with trypsin for example on the native protein containing those bridges. The peptides can be seperated and then the separated peptides can be reduced by dithiothreitol to break the S-S ridges giving one cysteine in each peptide. Reaction of the reduced peptides with iodoacetate gives hydrogen iodide and carboxymethylated cysteines which are now stable and cannot reform S-S bonds. chomatography and electrophoresis on paper will separate two peptides that were linked, and their sequence analysis will indicate the location of the S-S bridges

Front 25

mass spectrometry

Back 25

used to determine an animo acid sequence by analyzing the fragments produced for molecular weight.

Front 26

Peptide synthesis

Back 26

carboxyl terminal amino acid is protected at its amino terminus with something called FMoc. The protected amino acid is reacted with resin to give linkage btw the resin and protected A.A. The protected A.A is deprotected by treatment with a mild organic base. The next amino acid is supplied in a form that is protected at its amino end by FMoc and activated at its carboxyl group by dicyclocarbodiimide. The second amino acid is added to the first and then deprotected with mild organic base. This addition can go on for many cycles. When the desired peptide has been made, it is released from the resin by treatment with hydrofluoric acid.

Front 27

x-ray diffraction analysis

Back 27

x-rays are passed through a crystal which are diffracted in specific ways that can be recorded on film. The nearer the atoms are to one another, the larger the angle of diffraction. This information can be used to work out the distribution of electrons, and eventually the structure of the molecule in the crystal

Front 28

Planar peptide bond

Back 28

The C-N bond of a peptide has double bonded character which means its rigid and planar

Front 29

trans configuration

Back 29

O and H have trans configuration in a peptide

Front 30

alpha helix

Back 30

a secondary structure of proteins; each amino acid takes up 1.5 A and there are 3/6 amino acids per turn. Can be a clockwise or counterclockwise helix.

Front 31

right-handed alpha helix

Back 31

an alpha helix that goes in a clockwise direction

Front 32

alpha keratin

Back 32

found in hair, wool, feathers, nails, and porcupine quills; keratin has a coiled coil which means it has two alpha helices coiled around one another

Front 33

structure of alpha-keratin

Back 33

two alpha helices wound around one another in a left handed coiled-coil and joined by S-S bonds

Front 34

Curling

Back 34

to curl hair, S-S bonds are reduced by a smelly S-H containing shampoo. Then, the hair is re-oxidized to stabilize the curly hair conformation.

Front 35

Helix breakers

Back 35

proline because it has no H on its amide N; amino acids 3 or 4 apart that are on the same side of the helix and are neighbors that are either ++ or --

Front 36

Helix makers

Back 36

amino acids 3 or 4 apart that are on the same side of the helix and are neighbors. Attraction (+) and (-) is a helix maker.

Front 37

B-pleated sheets

Back 37

common secondary structure; can be antiparallel or parallel in confirmation

Front 38

Anti-parallel B-pleated sheets

Back 38

C -> N and N -> C on reverse side; 3.5 A/amino acid in B-sheets. Spacing between is as follows: 3.5 for the glycine rows and 5.7 for alanine.

Front 39

Beta-turn

Back 39

3 or 4 amino acids per turn

Front 40

Beta-Alpha-Beta

Back 40

When a parallel B-sheet is joined by an alpha helix and forms a beta-alpha-beta moftif

Front 41

Beta-Barrel

Back 41

Beta-pleated sheet forms a barrel like structure; found in viral capsid proteins and in a bacterial enzyme that lyses red blood cells

Front 42

Collagen Helix

Back 42

Three left-handed helices joined in a right handed superhelix.
Structure of G X Y
G: glycine
X: often proline
Y: Often 4-hydroxyproline
Hydroxyprolines form H-bonds and make collagen stronger

Front 43

Forces holding tertiary structure in place

Back 43

ionic bonds, H-bonds, van der waals interactions, the hydrophobic effect

Front 44

hydrophobic effect

Back 44

considerable clustering of aliphatic residues (valine, leucine, isoleucine, and phenylalanine) in the interior of the protein. It is like the separation of organic solvents and water. It is driven by an increase in molecular entropy

Front 45

S-S bonds

Back 45

disulfide bridges

Front 46

Ramachandran Plot

Back 46

plot of the allowed bond angles for amino acids in polypeptides. Only a minority of psi and phi angles are allowed.

Front 47

Denaturation

Back 47

when a protein becomes misfolded

Front 48

Renaturation

Back 48

When a protein folds back into its native conformation

Front 49

chaperonin

Back 49

a protein that helps some proteins fold. example of this is groE

Front 50

groE structure

Back 50

GroE consists of a small subunit and a large subunit. An unfolded protein has hydrophobic residues on its outside and these can associate with hydrophobic residues at the mouth of the GroEL cylinder.

Front 51

prion

Back 51

proteinaceous infectious only

Front 52

NMR

Back 52

nuclear magnetic resonance solves structures in solutions. utilizes the spins of 1H 13C and 15N to generate a magnetic dipole which align either parallel or antiparallel in a electric filed. A pulse cause some nuclei to reverse orientation. The absorption spectrum gives information about the nuclei and their environment

Front 53

Myoglobin

Back 53

protein that picks up oxygen in tissues

Front 54

Hemoglobin

Back 54

Blood protein that picks up oxygen in the lungs and deposits it in the tissues. Also picks up carbon dioxide in tissues and releases it into the lungs

Front 55

Heme

Back 55

porphyrin ring consisting of four linked pyrrole rings

Front 56

Porphyrin

Back 56

structure of heme

Front 57

Pyrrole

Back 57

coordinate a ferrous iron

Front 58

CO poisoning

Back 58

CO binds free heme irreversibly but at right angles to the heme group. To prevent this, the distal histidine of these protein changes the bonding angle between heme and CO so that CO's binding affinity is 100-fold reduced.

Front 59

hyperbolic binding curve

Back 59

myoglobin's binding curve is a hyperbola and is half-saturated at only .26 kPa

Front 60

sigmoidal binding curve

Back 60

hemoglobin's binding curve is sigmoidal (s-shaped) and is half saturated at 4 kPa

Front 61

hill coefficient

Back 61

measure of cooperativity; hemoglobin's hill coefficient is 2.8

Front 62

cooperativity

Back 62

in terms of hemoglobin allows subsequent oxygens to be able to bind better (ex. 1st doesn't bind that well but allows second to bind better and so on)

Front 63

2,3-bis-phosphoglycerate (BPG)

Back 63

BPG is needed for hemoglobin to dump oxygen to the tissues; at higher altitudes, BPG increases twofold over 36 hours.

Front 64

Bohr Effect

Back 64

Reducing the pH shifts the oxygen binding curve to the right sot hat oxygen is more easily lost in the tissues; same effect is seen when CO2 concentration is raised

Front 65

Allosteric transition

Back 65

change from one structure to the other

Front 66

tense state of hemoglobin

Back 66

deoxygenated form of hemoglobin

Front 67

relaxed state of hemoglobin

Back 67

oxygenated form of hemoglobin

Front 68

The effect of oxygen on the shape of hemoglobin

Back 68

binding of the first oxygen to one subunit bring the iron in hemoglobin into the plane of the of the porphyrin ring which draws the proximal hisdine toward the porphyrin ring shifting the position of the F-helix

Front 69

the effect of the shape of heme on the F-helix

Back 69

causes the contacts between the B2FG region and alpha1c helix to change dramatically