Water And Proteins

Front 1

How many moles of H+ and -OH are there in 1 liter of water? (55.5moles)?

Back 1

1x10^-7 moles of each

Front 2

How do you calculate pH?

Back 2

pH=-log[H+]

Front 3

BL Acid

Back 3

substance that can donate a proton

Front 4

BL base

Back 4

Substance that can accept a proton

Front 5

Henderson-Hasselbalch Equation

Back 5

pH=pKa + log([base]/[acid])

Front 6

What are the two surface proteins on the influenza virus?

Back 6

haemagglutinin(H)(Senses pH change in virus that allows virus to enter cell) and neuraminidase (N)

Front 7

What is the proton concentration presence in water?

Back 7

10^-7 M

Front 8

Amino acid side chain modifications and functions

Back 8

Gamma-carboxylglutamate (blood clotting)

Hydroxyproline (collagen component)

methylhistidine and acetyllysine (on histone proteins)

Front 9

pKa of the n-terminus?

Back 9

~7

Front 10

pKa of the c-terminus?

Back 10

~4

Front 11

What are the targets of antibiotics on the ribosome?

Back 11

mRNA binding channel, factory binding site, peptidyl-transferase center, tRNA binding site

Front 12

Amino acid derivatives

Back 12

amino-butyric acid (GABA) - glutamine

Histamine - histidine

dopamine and thyroxine - tyrosine

Front 13

What are two disulfide-bonded cysteines called?

Back 13

Cystine

Front 14

Types of protein purification procedures

Back 14

Salting out, selective dialysis, gel filtration chromatography, ion exchange, affinity chromatography

Front 15

Solubitility purification (salting out, fractionation)

Back 15

1. have a mixture of proteins

2. salt is added, centrifuged. Proteins are precipitated and removed; analyzed

Front 16

Selective dialysis

Back 16

Sorting out by size

1. semipermeable membrane (bag around it); ions and solution can diffuse out, proteins can't because of size

Front 17

Gel filtration chromatography

Back 17

filter solution through beads that are permeable for smaller molecules but not large proteins. Larger ones flow through first

Front 18

Ion exchange

Back 18

Separate molecules based on surface charge. pH determines what gets attracted.

Front 19

What is the isoelectric point? (pI)

Back 19

The pH at which the net charge of the molecule is 0.

If the pH is above the pI, the protein is negative

If the pH is below the pI, the protein is positive

Front 20

Affinity chromatography

Back 20

Separating proteins by filtering through beads that express affinity tag of designed choice

Front 21

UV Spectroscopy

Back 21

Aromatic amino acids absorb UV light; can determine determines protein concentration because proteins contain a lot of aromatic side chains

Front 22

Coomassie Blue

Back 22

Used to determine if general protein is present, not for specific proteins.

Front 23

ELISA

Back 23

Enzyme-linked immunosorbent assay

finds specific proteins

Use an antibody that specifically binds protein of interest.

Add second antibody that binds to same protein, except linked to an enzyme.

Then you wash and detect for target protein

Front 24

What is mass spec used for?

Back 24

Amino acid sequence

Front 25

SDS-Page

Back 25

Add sodium dodecyl sulfate; denatures and binds to protein (makes it negative because of anion of sulfate)

run through a gel, migrates toward cathode; large proteins move slower

Front 26

Amino acid sequence determination

Back 26

Amino acid chains are blown apart in different places with proteases (break peptide based on adjacent amino acids), then lined up next to each other and compared to see the actual sequence

Front 27

Trypsin

Back 27

(n-1) = Arg/Lys (positives)

n can't be proline

Front 28

Chymotrypsin

Back 28

(n-1)=aromatic

n can't be proline

Front 29

Elastase

Back 29

(n-1)=Ala, Gly, Ser, Val (small)

n can't be proline

Front 30

Thermolysin

Back 30

(n-1) can't be Pro

n= Ile, Met, Valine, aromatic

Front 31

Pepsin

Back 31

(n-1) can't be proline

n = leucine, aromatic

Front 32

Endopeptidase V8

Back 32

(n-1) = Glu

Front 33

How much of an ampere change is there per residue?

Back 33

1.5 A per residue

Front 34

how many residues per turn on an alpha helix?

Back 34

3.6 residues per turn

Front 35

Structure of myoglobin

Back 35

structure containing 8 alpha helices with a heme group in the middle (Fe2+)

Front 36

Wheel diagram

Back 36

2 amino acids are supposed to be non polar residues

Front 37

Protein class of Triose Phosphate Isomerase

Back 37

alpha/Beta class. 8 beta barrels in between alpha helices

Front 38

Protein class of calmodulin

Back 38

all alpha helices

Front 39

What type of symmetry does GroEL have, and what is its function?

Back 39

D7 (14 subunits), folds improperly folded proteins

Front 40

GroES symmetry

Back 40

C7

Front 41

Structure of actin

Back 41

rotation of subunits around a helical axis (spiral staircase)

Front 42

Cholera toxin symmetry

Back 42

1 alpha subunit and 5 beta subunits. 5 betas surround the alpha to make C5

Front 43

Hemoglobin structure

Back 43

2 alpha and 2 beta subunits (sinusoidal curve)

Front 44

Hemocyanin structure

Back 44

D3 dihedral

Front 45

Myoglobin structure

Back 45

8 alpha helices, hyperbolic oxygen curve

Front 46

Ribonuclease A

Back 46

cleaves single stranded RNA, all beta protein with four disulfide bridges with two histidine,

Front 47

What is the catalytic triad?

Back 47

Histidine, serine, and asparagine

Front 48

What is DANA?

Back 48

Transition state analog