Biochemistry - Test 1

Front 1

Two properties of water

Back 1

hydrogen bonding, polar

Front 2

Four non-covalent interactions

Back 2

1. hydrogen bonding
2. electrostatic interaction
3. Van der Waals
4. Hydrophobic interaction

Front 3

What is a Strong Acid?

Back 3

fully dissociates into H+ and A- ; large Ka value

Hint 3

ex. H2SO4, HCl

Front 4

What is a Weak Acid?

Back 4

does not dissociate completely; Ka measures how strong or weak the weak acid is

Hint 4

ex. Acetic Acid, Citric acid, Amino acids

Front 5

Henderson Hasselbalch Equation

Back 5

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

Front 6

What is a good buffer range?

Back 6

within +/- 1 of the pKa

Front 7

The only amino acid without 2 stereoisomers

Back 7

Glycine

Front 8

Amino Acids with aliphatic R group

Back 8

Gly, Ala, Val, Leu, Ile

Front 9

Amino acids with aromatic R group

Back 9

Phe, Tyr, Trp

Front 10

Amino acids with sulfur in R group

Back 10

Cys, Met

Front 11

"imino acid"

Back 11

Proline

Front 12

Amino acid with alcohol R group

Back 12

Ser, Thr

Front 13

Amino acid with basic R group

Back 13

Lys, Arg, His

Front 14

Amino acid with acid R group

Back 14

Asp, Glu

Front 15

Amino acid with amide R group

Back 15

Asn, Gln

Front 16

pI

Back 16

"Isoelectric point"; pH where net charge is 0

Hint 16

(pKa(1-0) +pKa(0-1))/2

Front 17

Trypsin

Back 17

molecular scissor; cleaves after amino acid that is positively charged at pH 7

ex. Arg, Lys

Front 18

Chymotrypsin

Back 18

molecular scissor; cleaves after amino acid that contains aromatic R group

ex. Phe, Tyr, Trp

Front 19

S. aureus V8

Back 19

molecular scissor; cleaves after Glu & Asp

Front 20

Cyanogen bromide, BrCN

Back 20

chemical molecular scissor, cleaves after Met

Front 21

Two common methods to deduce AA sequence of polypeptide

Back 21

1. Edmon degradation
2. deduce AA sequence from DNA sequence

Front 22

non-covalent forces that stabilize tertiary and quartenary structures

Back 22

1. hydrophobic effect
2. hydrogen bonding
3. electrostatic interactions
4. Van der Waals interactions
5. metal coordination

Front 23

3 things that denature proteins

Back 23

1. addition of denaturing agent
2. heat
3. pH

Front 24

advantage of xray crystallography for proteins

Back 24

no size limitation of protein molecular weight

Front 25

Function of myoglobin

Back 25

store oxygen / bind oxygen in tissues

Front 26

Function of hemoglobin

Back 26

deliver oxygen from lungs to tissues via blood stream

Front 27

Which amino acids absorb UV around 280nm?

Back 27

Phe, Tyr, Trp

Front 28

ideal pitch and rise of alpha helix

Back 28

pitch = 0.54nm, rise = 0.15nm

Front 29

psy and phi angles of an alpha helix

Back 29

phi = -57 ; psy = -47

Front 30

hydrogen bonds in antiparallel beta strands

Back 30

hydrogen bonds are perpendicular

Front 31

hydrogen bonds in parallel beta strands

Back 31

hydrogen bonds are not perpendicular; less stable therefore, hydrogen bonds are distorted

Front 32

Secondary structure is stabilized by...

Back 32

hydrogen bonds of alpha C and N on backbone

Front 33

Tertiary structure is stabilized by...

Back 33

noncovalent interactions (hydrophobic effect) between side chains

Front 34

3 things explained in Alfinson's experiment

Back 34

1. proteins can refold to native conformation
2. primary structure determines tertiary structure
3. AA sequence is stored in polypeptide

Front 35

Proteins can be denatured by two things

Back 35

1. Chaotropic agents
2. Detergents

Front 36

How does Urea and Guanidinium salt denature proteins?

Back 36

Allows water to get in the interior of proteins (disrupting hydrophobic interactions)

Front 37

How do detergents denature proteins?

Back 37

hydrophobic tails penetrate protein interior (disrupting

Front 38

Denaturation of a protein

Back 38

disruption of native conformation of protein; some proteins may unfold completely, others may keep internal structure

Front 39

One letter code for Tryptophan

Back 39

W

Front 40

One letter code for Asparagine

Back 40

N

Front 41

Three letter code for glycine

Back 41

Gly

Front 42

One letter code for Valine

Back 42

V

Front 43

One letter code for Cysteine

Back 43

C

Front 44

Three letter code for Asparagine

Back 44

Asn

Front 45

One letter code for Histidine

Back 45

H

Front 46

One letter code for Aspartate

Back 46

D

Front 47

Three letter code for Tyrosine

Back 47

Tyr

Front 48

Three letter code for Isoleucine

Back 48

Ile

Front 49

One letter code for Lysine

Back 49

K

Front 50

One letter code for Arginine

Back 50

R

Front 51

What are two similarities in the structures between hemoglobin and myoglobin?

Back 51

1) Both contain heme which binds oxygen
2) Secondary structure is primarily alpha helix

Front 52

What are two differences in the structures between hemoglobin and myoglobin?

Back 52

1) Hb is a tetramer; Mb is a monomer
2) Hb has 4 hemes; Mb has 1 heme

Front 53

What is the difference between hair and silk at the molecular level?

Back 53

Hair is made of keratin which is primarily alpha helices; silk is made of a beta sheet structure

Front 54

Why is proline frequently found at the places where the polypeptide chains turn over?

Back 54

The geometry of proline restricts it from fitting well into an alpha helix, however, it does fit well in a beta turn

Front 55

What leads to the loss of protein function?

Back 55

a radical change in size, charge, or polarity

Front 56

How does the oxygen binding curve of fetal hemoglobin differ from the oxygen binding curve of adult hemoglobin?

Back 56

Fetal Hb binds more strongly to oxygen than adult Hb

Front 57

How are the differences in the oxygen binding curves related to differences in structure of fetal Hb and adult Hb?

Back 57

Fetal Hb has a alpha-2-gamma-2 structure with less lysine residues to bind BPG. Adult Hb has the structure alpha-2-beta-2