Biochemistry 1 Exam 1

Front 1

Glycine

Back 1

Nonpolar, Gly, G

Hint 1

Only achiral amino acid

Front 2

Alanine

Back 2

Nonpolar, Ala, A

Hint 2

Methyl

Front 3

Valine

Back 3

Nonpolar, Val, V

Hint 3

Looks like a v

Front 4

Leucine

Back 4

Nonpolar, Leu, L

Hint 4

Similar to valine

Front 5

Isoleucine

Back 5

Nonpolar, Ile, I

Hint 5

Leucine rearranged

Front 6

Methionine

Back 6

Nonpolar, Met, M

Hint 6

Has sulfur

Front 7

Phenylalanine

Back 7

Nonpolar, Phe, F

Hint 7

Phenyl group

Front 8

Tryptophan

Back 8

Nonpolar, Trp, W

Hint 8

Trippy, 2 rings

Front 9

Proline

Back 9

Nonpolar, Pro, P

Hint 9

Amine group part of ring

Front 10

Serine

Back 10

Polar, Ser, S

Hint 10

Alcohol

Front 11

Threonine

Back 11

Polar, Thr, T

Hint 11

Serine plus methyl

Front 12

Cysteine

Back 12

Polar, Cys, C

Hint 12

Disulfide bridges

Front 13

Tyrosine

Back 13

Polar, Tyr, Y

Hint 13

Like F plus a little extra

Front 14

Asparagine

Back 14

Polar, Asn, N

Hint 14

Amine and ketone

Front 15

Glutamine

Back 15

Polar, Gln, Q

Hint 15

Like asn but longer

Front 16

Aspartate

Back 16

Acidic, Asp, D

Hint 16

Carboxylate

Front 17

Lysine

Back 17

Basic, Lys, K

Hint 17

4C

Front 18

Glutamte

Back 18

Acidic, Glu, E

Hint 18

Glutamine but -ate instead of amine

Front 19

Arginine

Back 19

Basic, Arg, R

Hint 19

3 Ns on side chain

Front 20

Histidine

Back 20

Basic, His, H

Hint 20

5 membered ring with 2 Ns

Front 21

Ionization of water

Back 21

Hint 21

It's a formula you seek

Front 22

pH =

Back 22

- log [H+]

Hint 22

No hint here

Front 23

Ka =

Back 23

[H+][A-]/[HA]

Hint 23

Think about ionization of water

Front 24

Higher Ka = ? acid

Back 24

Stronger acid = ? Ka

Hint 24

Relationship

Front 25

Lower pka (-log Ka) = ? acid

Back 25

Stronger acid = ? pka

Hint 25

Relatioship

Front 26

Henderson-Hasslebach equation

Back 26

pH = pka + log [A-]/[HA]

Hint 26

David Hasslehoff

Front 27

Best buffer range

Back 27

+/- 1 pH unit from pka

Hint 27

Hahahaha. You thought you were gonna get a hint. :)

Front 28

Which amino acids can be phosphorylated?

Back 28

S, T, Y

Hint 28

There are 3

Front 29

Which amino acids can be hydroxylated?

Back 29

P and K

Hint 29

Only 2

Front 30

Which amino acids can be glycolsylated?

Back 30

S, T, N, Q

Hint 30

4 4 4 4 4 4 4 4 4

Front 31

Hierarchy of protein structure

Back 31

Primary<Secondary<Tertiary <Quaternary

Hint 31

Primary first

Front 32

Water's amazing properties

Back 32

Polarity, solid structure allows ice to float, ionization-can act as acid or base

Hint 32

3 things

Front 33

Dilution formula

Back 33

M1V1 = M1V2

Hint 33

Seriously? You want a hint?

Front 34

Titration curves show ____________

Back 34

__________ shows the progressive dissociation of a weak acid.

Hint 34

Graph

Front 35

Buffer

Back 35

Solution that resists changes in pH as acids or bases are added

Hint 35

Boondoggle is a funny word

Front 36

Buffers are typically made of what 2 ingredients?

Back 36

Weak acid and conjugate base

Hint 36

Nah

Front 37

What is unique about Gly?

Back 37

Only achiral amino acid

Hint 37

Glycine

Front 38

Zwitterion

Back 38

Has acidic and basic properties (like amino and carboxylic acid)

Hint 38

Amino acid is an example

Front 39

Peptide bond has __% double bond character.

Back 39

40%

Hint 39

Less than 50

Front 40

Oligopeptide

Back 40

12 - 20 peptides

Hint 40

Large writing

Front 41

pI

Back 41

Protein has a neutral charge

Hint 41

Allison rocks

Front 42

Micelle

Back 42

Lipid sphere with hydrophobic center

Hint 42

Yada yada yada

Front 43

D and L refer to ______________.

Back 43

____________ refer to the configuration of a chiral molecule as compared to a standard (glyceraldehyde)

Hint 43

Sbubisbinoma o nebi as non

Front 44

Approximate pka of carboxyl group

Back 44

pka ~ 2

Hint 44

=-O

Front 45

Approximate pka of amino group

Back 45

pka ~ 9

Hint 45

(:V)

Front 46

Which amino acids can be seen under UV light?

Back 46

Phe, Trp, & Tyr

Hint 46

3 3 3 3 3 3 3 3 3 3

Front 47

Ways to separate proteins (6)

Back 47

Solubility, size, shape, charge, amino acid sequencing, ligand binding

Hint 47

s,s,s,c,a,l

Front 48

Dialysis

Back 48

Separates proteins by size while maintaining native state

Hint 48

Not the kidney kind

Front 49

Gel filtration chromatography

Back 49

Smaller proteins go inside gel beads and move through column slower than larger proteins

Hint 49

Size separation

Front 50

SDS-PAGE

Back 50

Gel electrophoresis. Detergent denatures proteins

Hint 50

I'm done with hints. Sorry

Front 51

Ion exchange

Back 51

Separates proteins by charge (anion and cation)

Hint 51

@@@@@@@@@

Front 52

Ways to detect protein with color change

Back 52

Coommassie brilliant blue and BCA - copper reduction causes punk color

Hint 52

Blue & pink

Front 53

Common protein tags

Back 53

His6, FLAG, HA, myc

Hint 53

I like chocolate

Front 54

Crude extract

Back 54

Complex mixture of proteins and other molecules after cell lysis and centerfuging

Hint 54

Blow up some cells. Woo hoo

Front 55

Specific activity

Back 55

Total activity/total protein

Hint 55

Units/mL

Front 56

Yield

Back 56

Activity @ that step/activity of crude extract

Hint 56

Sooooooo tired

Front 57

Purification level

Back 57

Specific activity@ that step/specific activity of crude extract

Hint 57

BOLD

Front 58

Step 1 of sequencing a.a.:separate chains

Back 58

extreme pH, urea, guanidine, high salt

Hint 58

4 ways

Front 59

Step 2 of sequencing a.a.: cleave disulfide bridges

Back 59

BME or DTT then iodacetate to keep from reforming

Hint 59

Reducing agent + alkylating agent

Front 60

Step 3 of sequencing a.a.: N- and C- terminals

Back 60

N: Edman degredation C: carboxypeptidase (a-all except pro, arg, lys; b-arg and lys)

Hint 60

Different for n and c

Front 61

Step 4 of sequencing a.a.: fragment the chains

Back 61

Done multiple time. (Trypsin, chymotrypsin, clostripain, staphylococcal protease, cyanogen bromide)

Hint 61

5 kinds

Front 62

Step 6 of sequencing a.a.: reconstruct the sequence

Back 62

Overlap sets of fragments

Hint 62

Mass spec can make fragments too

Front 63

Trypsin

Back 63

Arg or Lys

Hint 63

C side

Front 64

Chymotrypsin

Back 64

Phe, Trp, Tyr, Leu

Hint 64

C side again

Front 65

Clostripain

Back 65

Arg

Hint 65

C side still

Front 66

Staphylococcal protease

Back 66

Asp or Glu

Hint 66

Sea side

Front 67

Cyanogen bromide

Back 67

Met

Hint 67

Always c side

Front 68

Mass spec advantages/disadvantages sequencing proteins

Back 68

Good: can ID mix of prpteins; fast and little material needed

Bad: need some knowledge of genome; doesn't always work

Hint 68

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