Biochm Final Review

Front 1

Quick expl. of AA charge?

Back 1

ph<pka for NH3 = +1
ph>pka for NH3 = 0

ph<pka for COOH = 0
ph>pka for COOH = -1

(requires understanding of AA structures for side groups maybe)(if no side groups you don't include em)(left AA = NH3 and side groups Right = COOH and any side groups)

Front 2

What are enantiomers?

Back 2

mirror image stereoisomers

Front 3

What are diasteromers?

Back 3

not mirror images

Front 4

What are stereoisomers?

Back 4

molecules with same bonds but different stereochemistry

Front 5

What is the ^G eqn?

Back 5

^G = ^H - T^S

Front 6

What is ^G?

Back 6

-gibbs free energy change

Front 7

When is a rxn exergonic?

Back 7

when ^G<O...spontaneous towards products

Front 8

When is a rxn endergonic?

Back 8

when ^G>O...nonspontaneous towards rxnts

Front 9

What is ^H?

Back 9

enthalpy change

Front 10

When is a rxn exothermic?

Back 10

when ^H<O (heat is generated, released, ie, explosion)

Front 11

When is a rxn endothermic?

Back 11

when ^H>O (heat energy is transformed)

Front 12

List the 4 weak intxns?

Back 12

1. hydrogen bds

2. ionic intxns

3. hydrophobic intxns

4. van der waals

Front 13

Give 4 ex. of H-bds?

Back 13

1. alcohol and H2O

2. ketone

3. between polypeptides

4. dna bases

Front 14

Name the 4 colligative properties?

Back 14

1. VP

2. BP

3. Mp and FP

4. Osm. P

Front 15

What is osmotic pressure?

Back 15

forcing H2O thru a membrane in an attempt to equalize conc.s (isotonic,etc)

-the higher the conc. of solute the higher the pressure
(if conc. dbls osm. p. dbls)

Front 16

What is isotonic?

Back 16

conc in sol. same as insid cell (same osm. pressure)

Front 17

What is hypertonic solution?

Back 17

conc greater outside cell, cause water to rush out of cell

Front 18

What is hypotonic soln?

Back 18

conc. greater inside cell so water rushes in

Front 19

What is ionization related to?

Back 19

acids and bases

Front 20

What is a buffer?

Back 20

bio systems are very sens to pH

-buffers help maintain pH and all cells have them

-best buffering is at pH near Pka (+or-1)

-weak acid and weak base(conj., salt)

-enzyme activity is pH sensitive

Front 21

2 important buffers?

Back 21

1. H2CO3

2. H3PO4

Front 22

What does primary struc. of proteins involve?

Back 22

sequencing and edmond degradation

1. hydrolysis (doesn't help)

2. edmond deg = good for about 50AAs...label NH3 end and remove AA, ID...can det. seq
3. mass spectrometry

Front 23

Most common way of obtaining proteins?

Back 23

lab synthesis

Front 24

3 ways to obtain peptides?

Back 24

1. isolate/purify from tissue or cell culture

2. direct chm. synthesis (merrifield, primary way)
(but expensive)

3. Genetic engineering (DNA>RNA>protein)

-ideally can make an protein about 100 AA long

Front 25

What is in the plane of a protein?

Back 25

6 carbons atoms in plane...(can rotate relative to eachother)
-always 6 atoms
-always planar
-2 carbon ends can twist

Front 26

The general char.s of 2ndary structure?

Back 26

-local 3-D strucs
-kink
-communication due to spatial arrangement

Front 27

The 2 types of 2ndary structures?

Back 27

1. alpha helix (kink, 5.4 or 3.6 turn)

2. beta sheet (parallel, 6.5)antiparallel

Front 28

Describe tertiary structures?

Back 28

1. 3-D overall

2. involves long range intxns

Front 29

The 2 major tertiary structures?

Back 29

1. fibrous (long, struc.)

2. globerular (enzymes, most proteins, most compact)

Front 30

What level of structure do only some proteins have?

Back 30

quaternary

Front 31

What is quaternary struc?

Back 31

3-D rel. of subunits

Front 32

Domains vs. subunits of quaternary struc.?

Back 32

domain = covalent bond, same polypep. with different regions

subunits - no cov. bds, different polypeps with each subunit

Front 33

What are fibrous proteins?

Back 33

a tertiary structure

Front 34

Name 3 fibrous proteins?

Back 34

1. alpha keratin (strong RH helix)(LH superhelix)(disulfide links)

2. silk fibroin (beta sheets, no cross links)

3. collagen (LH helix, not an alpha helix,RH super helix)(novel cross links)

Front 35

What is a motif?

Back 35

collection of 2ndary struc. in globerular protein

Front 36

What is a domain?

Back 36

inv. with glob. protein...two distinct polypeptides that are attached by thin region and can move rel. to eachother

Front 37

Describe Oxygen binding?

Back 37

1. it is important but poorly soluble because it is nonpolar
2. Transition metals (like Fe) can transport it but they can damage cells
3. so we need to sequester (hide) Fe but still have it the oxygen accessible.
4. this is accomplished by the heme group

Front 38

Describe the heme binding Oxygen?

Back 38

1. central Fe
2. bound to Oxygen
3. bount to two heme groups
4. prevents oxidation of Fe2 to Fe3+
5. also bound to N in histidine
6. oxygen can be bound and released
7. this heme group is hidden inside of either myoglobulin or hemoglobulin

Front 39

Describe myoglobulin?

Back 39

1. It is primarily a storage form for Oxygen.
2. It is alpha-helical.
3. It is relatively insensitive to [Oxygen] when binding, always the same affinity

Front 40

Describe Hemoglobulin?

Back 40

1. a free heme (not in Hb) binds CO 20,000X better than it binds Oxygen (so Kd for CO is 1/20,000 that of Kd for oxygen)
2. When heme is in hemoglobulin it binds CO only 200X better than oxygen
3. change is due to steric hindrance
4. Hb is very sensitive to [oxygen]

Front 41

Hemoglobulin vs. Myoglobulin structure?

Back 41

very similar 3-D structures but there is a lot of difference between AAs
-myoglobulin is mostly alpha-helical

Front 42

What does theta represent?

Back 42

fraction of sites occupied

theta = [L]/([L] + Kd)

theta = 50% when [L] = Kd = 1/Ka (this is when 1/2 the binding sites are occupied

Front 43

What is cooperative binding as it relates to Hb?

Back 43

As it binds oxygen at each site the binding subunits conformation changes and the affinity for oxygen increases
-the rich get richer

Front 44

What is the Bohr effect?

Back 44

The inversely proportional relationship between [CO2] and [H] with [O2] binding in Hb

Front 45

In bohr effect if hydrogen conc increase what happens to oxygen affinity?

Back 45

decreases

Front 46

In high altitudes what occurs?

Back 46

[BPG] goes up and affinity decreases for hemoglobin and affects affinity for O2

Front 47

Keq and ^G indicate what? What do they not indicate?

Back 47

they indicate equilibrium
-nothing about rate

Front 48

^Gb = what mathematically?

Back 48

the difference between the uncatalyzed and catalyzed ^G

Front 49

Michaelis-Menten eqn?

Back 49

Vo = (Vmax[S])/(Km+[S])

Front 50

Where does Km = [S]

Back 50

where Vo = 1/2 Vmax


rate constant for rate determining step

something to do with inhibitors

Front 51

What are epimers?

Back 51

sugars that differ only in their configuration at one chiral center (when compared to glucose, not when compared to eachother) They are epimers at the #C of wherever the difference may occur.

Front 52

Maltose monomers and activity?

Back 52

Glc-Glc (reducing)

Front 53

Lactose monomers and activity?

Back 53

Gal-Glc (reducing)

Front 54

Sucrose monomers and activity?

Back 54

Fru-Glc (non-reducing)

Front 55

Trehalose monomers and acivity?

Back 55

Glc-Glc (non-reducing)

Front 56

Polysaccharides are also known as what?

Back 56

glycans

Front 57

4 types of polysaccharides?

Back 57

1. storage homopolysaccharides

2. structural homopolysacch-

3. Structural heteropolysacc-

4. Glyconjugates (information carriers) (Carbohydrate and other molecule..like protein, lipid, etc)

Front 58

What are storage homopolysacch.s?

Back 58

food molecules stored in cell

Front 59

What are structural polysacch.s?

Back 59

stay in cell as framework

Front 60

What is the composition of nucleosides?

Back 60

base + pentose

Front 61

What is the composition of nucleotides?

Back 61

base + pentose + phosphate

Front 62

Name the purines

Back 62

Adenine and guanine

Front 63

Name the pyrimidines?

Back 63

cytosine, thymine, uracil

Front 64

Which nucleotide base is in DNA but not RNA?

Back 64

thymine

Front 65

Which nucleotide is in RNA but not DNA?

Back 65

uracil

Front 66

Each sugar in DNA has one less what then RNA?

Back 66

one less -OH group (see slides, very clear)...you will see H group in RNA where you see an OH group in DNA

Front 67

How many bonds between G and C pairs?

Back 67

3

Front 68

How many bonds between A and T or A and U?

Back 68

2

Front 69

What kind of linkage do you see in RNA and DNA polymers?

Back 69

phosphodiester linkage with 5' to 3' directionality...alternating sugar and phosphate groups form the backbone...in a chain there is usually a phosphate at the 5' end but not the 3'

Front 70

A, B, Z in DNA?

Back 70

A = RH, not seen, short and fat

B = common, RH

Z = LH, seen sometimes

Front 71

A, B, Z, in RNA?

Back 71

A = common

B = not seen

Z = lab only

Front 72

DNA cloning steps?

Back 72

1. cut DNA with restriction enzymes

2. select app. cloning vector

3. join frag.s with ligase

4. insert into host cell

5. grow and ID those with the desired recombinant DNA

Front 73

What is a restriction endonuclease?

Back 73

enzyme...recognizes specific palindromic DNA sequences, binds to DNA at those sites, and cuts the DNA...leaving either sticky or blunt ends

Front 74

What is pbr322?

Back 74

a plasma cloning vector...closed circular DNA...several restriction enzyme sites (confers resistance to ampicillin and tetracycline)