Biochemistry Exam 1

Front 1

What is the molecular hierarchy of the cell

Back 1

cells
organelles
supramolecular complexes
macromolecules= biopolymers
monomers
metabolites
inorganic precursors

Front 2

What is compartmentalization?
What does it do?

Back 2

Protects from adverse conditions. Prevents diffusion (loss of cell compounds). Can maintain or change to a specific pH.

Front 3

Standard features of a prokaryote.

Back 3

Nucleoid (contains DNA), plasma membrane (inhibits diffusion), peptidoglycan cell wall (strong mechanical strenth).

Front 4

Optional features of a prokaryote.

Back 4

Outer membrane/periplasmic space (gram negative, large pores), flagellum (simple filament, spins around like a motor), mesosome (invagination of pm which an serve as a site for DNA replication, metabolic pathways).

Front 5

Standard features of eukaryote.

Back 5

Nucleaus (DNA storage):
*double membrane
*nuclear pores: decisions for passage in and out
*nucleolus: ribosomal RNA synthesis/processing
Plasma Membrane
Endoplasmic reticulum
*RER: ribosomes, protein synthesis
*SER: phospholipid synthesis
Golgi Apparatus: packaging center
Mitochondria: *power plant of cell (ATP production)
*Oxidation center: breakdown CHO, Lipids, proteins
Peroxisomes: uses O2 to oxidize problem molecules
Cytoskeleton: give structure, provide roadways

Front 6

Optional features of eukaryote.

Back 6

Chloroplasts: production of Oxygen, fixing CO2 to sugars
Cilia/Flagella: bending machine, sensory organ

Front 7

K eq (equilibrium constant)

Back 7

[H+][OH-]/[H2O]
[H+][OH-]= 1.O X 10 -14

Front 8

what is pH

Back 8

convenient way to designate [H+]. pH= log 1/[H+] or
-log [H+].
Logarithmic measure of [H+].

Front 9

What do strong acids and bases do? Weak acids and bases?

Back 9

Strong completely dissociates in water.
Weak only partially dissociates in water.

Front 10

What is a buffer and what does it do.

Back 10

It is a weak acid and its conjugate base. It permits solution to resist change in pH when H+ ions or OH- ions are added to the system.

Front 11

Dissociation constant Ka

pKa

Back 11

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

-log Ka

Front 12

What is the Henderson-Hasselbalch equation?

Back 12

pH=pKa-log [HA]/[A-]

Front 13

What is the H-H equation used for?

Back 13

It is used to understand and prepare buffers.

Front 14

What are the restrictions on buffers?

Back 14

Buffers stabilize the pH of a solution when and only when the pH of the solution is fairly close to pKa of that buffer (+/- 1 unit from pH)

Front 15

Why does the cell care about pH?

Back 15

Cellular machinery requires a specific range of pH to carry out funtions.

Front 16

Typical bonding behavior of
Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus, and Sulfur.

Back 16

H: loses only electron to form a proton (H+), shares 1 e- for covalent bonds, participates in hydrogen bonding
C: Tends to share 4 e-'s with combinations of elements listed here
N: Tends to share 3 e-'s with combos of H and C, sometimes bonds an additional C or H+ (carries positive charge)
O: electron loving, strong electronegativity, tends to share 2 e-'s, often forms poar or charged funct. groups
P: bonds primarily with O2
S: Bonds primarily w/ C, H, O

Front 17

Covalent bonds are

Back 17

formed by the sharing of e- between 2 atoms
very strong

Front 18

Electrostatic bonds occur

Back 18

between oppositely charged atoms

Front 19

Hydrogen bonds:

Back 19

two electronegative atoms share a hydrogen
Most common, N and O, Carbon never H-bonds

Front 20

hydrogen donor

Hydrogen acceptor

Back 20

atom to which H is most closely associated
Atom to which H is less closely associate

Front 21

Van der Waals attractions occur

Back 21

when two atoms are w/in 3-4 A there will be a weak bonding which dissipates quickly if the two atoms move apart
also produce very high repulsive forces if two atoms get too close

Front 22

Though H-bonds and Van der Waals attractions are weak they

Back 22

help and play critical roles in stabilizing and defining 3-d structures of protiens, nucleic acids, lipids

Front 23

Bond strenth

Back 23

covalent > ionic, hydrogen > Van der Waals

Front 24

Energy conversions

Back 24

1 J (KJ)= .239 cal (Kcal)
1 cal (Kcal)= 4.184 J (KJ)

Front 25

What does it mean that water is polar

Back 25

The hydrogen carries a partial positive charge and the Oxygen carries a partial negative charge (wants the e-'s more)

Front 26

Why is the H2O molecule linear. The geometry is tetrahedral like.

Back 26

Oxygen has 2 pairs of unshared e-'s that approximate a tetrahedron

Front 27

Why is H2O highly cohesive?

Back 27

Each molecule is polar
Bond geometry is tetrahedral
Extensive H-bonding in solid or liquid

Front 28

Each hydrogen atom in ice is h-bonded to

each hydrogen atom in water is h-bonded to

Back 28

4.0 H2O molecules


3.4 H2O molecules

Front 29

Why isn't H20 a thick viscous syrup?

Back 29

The half life of h-bonds change rapidly (10 -9 seconds)

Front 30

Why are the melting points of other molecules so much lower that H2O?

Back 30

They do not have h-bonding.

Front 31

How does water drive hydrophobic interactions?

These interactions are the driving force behind:

Back 31

H2O tends to exclude nonpolar, noncharged molecules.
* the folding of proteins, DNA, RNA, lipid bilayers
*the formation of membranes
*the solubilization of grease/oil/lipids by soaps.

Front 32

Describe hydrophobic interaction

Back 32

H2O forms a stable cage around the hydrophobic tail which decreases entropy (more order). The caged water stays in place longer than 10 -9 seconds. Lipid molecules become clustered so only lipid portions at the edge of the cluster force the ordering of water. Entropy is increased. Micelles, all hydrophobic groups are sequestered from water, ordered shell of h2o molecules is minimized, entropy increases.

Front 33

How does a soap bubble work?

Back 33

The liquid is a two phase system where a layer of H2O solvates the polar head of the soap
molecules while the hydrophobic tails of the soap molecules stick out into the air layer.

Front 34

Who discovered that urea could be synthesized from heating ammonium cyanate?

Back 34

Freidreick Wolher in 1828.
Marked the end of the vital force theory (organic compounds could only be synthesized within a living organism or w/ organism extract.

Front 35

Tetrahedral geometry

Back 35

four single bonds
free rotation

Front 36

trigonlal planar

Back 36

two single bonds and one double bond
no rotation

Front 37

linear

Back 37

onle triple bond and one single bond
no rotation

Front 38

Hydrocarbons

Back 38

only carbon and hydrogen
-saturated: all C atoms are single bonded
-unsaturated: at least one double (or triple) bond
-polyunsaturated: two or more double (triple) bonds

Front 39

Describe nucleophilic acyl substition

Back 39

the carbon atome of the carbonyl group has a net partial positive charge while the oxygen has a net partial negative charg. the partially positive carbonyl carbon is very susceptible to nucleophilic attack by bases (unshared electron pairs)

Front 40

What are proteins?

Back 40

Biological macromolecules; linear arrays of amino acids

Front 41

Amino acids contain

Back 41

at least one of the following
-amine/amino group
-acid

Front 42

What is a zwitterion?

Back 42

When groups each carry a charge but balance each out to make a neutral molecule
(ex. glycine)

Front 43

How do the amino acids behave?

Back 43

The amino group is charged/protonated at neutral and acidic pH, the carboxylate group is deprtonated at neutral and basic pH.

Front 44

What are the pKa's of the carboxylate and amino groups?

Back 44

Carboxylate: 2-3
Amino: 9-10

Front 45

pH < 2

3 < pH < 9

pH > 10

Back 45

NH3+, COOH

NH3+, COO-

NH2, COO-

Front 46

For every chiral carbon (4 different groups bound to a single carbon) what can there be?

Back 46

Two different mirror image isoforms, L&D isomers. Only the L form of amino acids occur in proteins.

Front 47

What are peptide bonds and how are they formed?
What is it an example of?

Back 47

a specific class of amide bonds which are formed when the alpha carboxyl group of one aa condenses with the alpha amine of a second aa. It is and example of nucleophilic acyl substitution and results in the loss of H2O.

Front 48

The forward direction of peptide bond formation is...

Back 48

thermodynamically unfavorable and requires energy input.

Front 49

What is the reverse reaction of peptide bond formation?

Back 49

Hydrolysis, occurs when H2O is consumed while breaking a single bond; it is energy releasing.

Front 50

What did Linus Pauling and Robert Corey discover in the late 1930's?

Back 50

The peptide unit is rigid and planar, it did no freely roate as one would expect from single bond.

Front 51

Why does the C-N bond have partial double bond character?

Back 51

Resonance, the bond is 1.32 A away which is halfway between typical C-N bonds (1.49) and C=N double bonds (1.27).

Front 52

What is amino acid analysis?

Back 52

Complete hydrolysisof polypeptides/proteins. The individual aa are derivatized with phenylisothiocyanate so each aa can be identified.
Reveals what aa and in what ratio. Does not reveal size or primary aa sequence.

Front 53

mass spectrometry

Back 53

measures mass precisely and accurately to < 1.0 da
fast and sensitive, but can require fairly pure protein and equipment and technical expertise.

Front 54

Electrophoresis

Back 54

separates proteins and measures apporximate size.
fast, cheap, easy, show purity, but not precise for Molecular weight

Front 55

Edman degradation:

Back 55

uses phenylisothiocyanate to remove one aa from NH2 terminus and form a PTH-aa. sequences entire aa, once amino terminal identified, the next one can be and so on.

Front 56

CNBr:

Back 56

cleaves specifically on the C-terminal side of Methionine (Met M).

Front 57

Trypsin:

Back 57

cleaves specifically on the C-terminal side of most basic amino acids, Lysine (Lys K)and arginine (Arg R)

Front 58

Chymotrypsin:

Back 58

cleaves specifically on the C-terminal side of aromatic amino acids; phenylalanine (Phe, F), Tyrosin (Tyr T), Tryptophan (Trp W)

Front 59

Elastase:

Back 59

cleaves specifically on the C-terminal side of smallest amino acids.
Brief: Alanine (Ala A), Glycine (Gly G)
Long term: Serine (Ser S), Cysteine (Cys C)

Front 60

What does electrophoresis do?

Back 60

Separate molecules based on size and charge. charge particles feel a force when placed in electric field.

Front 61

What is PAGE and why is it most commonly used?

Back 61

polyacrylamide gel elctrophoresis. the gel impedes the movement of larger molecules, producing better separation between polypeptids of varying size.

Front 62

Native PAGE

Back 62

no reductants or denaturants, not common or trivial, proteins retain 3-d structure, multimeric protein complexes stay together

Front 63

Non-reducing gels

Back 63

protein is denatured (unfolded) with either 8-10 M urea or 6 M guanidine HCl. protein is not reduced

Front 64

what happens to protein with SDS PAGE

Back 64

protein is reduced and denatured. most common for routine and analytical analysis of polypeptide composition.

Front 65

What is the full name of SDS?

Back 65

sodium dodecyl sulfate

Front 66

Why do we use SDS

Back 66

It is an anionic (-) detergent and binds to the polypeptide 1 SDS/2 aminon acid. it unfolds the protein and generates consistant charge to mass ratio for all proteisn so separation is based on size.

Front 67

What does beta-mercaptoethanol do?

Back 67

Reduces (cleaves) disulfide bonds.

Front 68

What are the two most common stains to visualize the separated amino acids.

Back 68

Coomassie blue
silver stain

Front 69

Isoelectric focusing:

Back 69

occurs when a protein is electrophoresed in a gel that contains a pH gradient (generated by a fairly complex mixture of buffer molecules call ampholytes). It moves through the field until it reaches its isolectric point. at that point the net charge on the portein is 0.00.

Front 70

Isoelectric point (pI)

Back 70

the pH at which the net charge of the protein is zero.

Front 71

2 dimensional gel electrophoreses comebines...

Back 71

isoelectric focusing and SDS PAGE. separates by pH gradient and size.