chem 430 exam 3

Importance of Glucose; when to degrade; when to synthesize; when to store it

glycolysis, gluconeogenesis, glycogen

how many enzymes in glycogen synthesis

6

how many enzymes in glycogen degradation

4

gluconeogenesis and glycolysis are…

reciprocally regulated

pathways that create biomolecules

anabolism

pathways that degrade biomolecules

catabolism

When cell needs NADH + H+ + ATP: Gly D; Gly S; Glycolysis; Gluconeo.

on, off, on, off

When cell HAS NADH + H+ + ATP: Gly D; Gly S; Glycolysis; Gluconeo.

off, on, off, off

circumstances for gluconeogenesis

no influx of glucose, glycogen stores are depleted in the muscle and liver, glucose is badly needed in brain (only source of energy is glucose)

under what specific condition in what vertebrates does gluconeogenesis occur

starvation conditions in higher vertebrates

another name for gluconeogenesis reactions that replace glycolysis steps 10, 3, and 1

bypass reactions

Fill in blanks: [x] term synthesis of glucose from [x] in [x]

Short, 2 pyruvate, liver

Where does glucose go after liver

blood —> brain and muscles

what kind of energy does gluconeogenesis provide

limited

tissues that synthesize glucose

liver, kidney cortex

tissues that use glucose as primary energy source

brain, muscle, kidney medulla, erythrocytes, testes

what else breaks down along with gluconeogenesis

triacyl glycerols (beta oxidation of fatty acids) and proteins

Glucose is transported from liver via

bloodstream

downside of gluconeogenesis

energy expensive

glucagon protein

29AA hormone

insulin protein

21AA + 30AA polypeptide hormone

insulin is linked by

3 disulfides

glucagon is secreted from [x] when glucose is [x], stimulating glycogen [x]

pancreas, scarce, degradation

insulin is secreted from [x] when glucose is [x], stimulating glycogen [x]

pancreas, abundant, synthesis

what are main enzymes associated with glycogen synthesis

hexokinase, phosphoglucomutase, UDP-glucose phyrophosphorylase, glycogen synthase, branching enzyme, nucleoside diphosphate kinase

the G delta under standard conditions of the UDP pyrophosphorylase rxn is close to 0, but

the rapid hydrolysis of pyrophosphate by the ubiquitous enzyme pyrophosphatase shifts the equilibrium in favor of UDP glucose formation

glycogen synthase catalyzes a reaction using [x] to add glucose residues one at a time to the [x] ends of glycogen

UDP glucose, nonreducing

UTP is regenerated from UDP by the enzyme [x], which uses [x] as a [x] donor

nucleoside diphosphate kinase, ATP, phosphoryl

what is the energy cost of adding 1 glucose to nonreducing end of glycogen

1 atp

glycogen branching enzyme creates a new [x] branch point and a new [x] end by transferring [x] glucose residues from the end of a growing chain to an internal point no closer than [x] glucose residues from another branch point

alpha(1 → 6), nonreducing, 7, 4

main enzymes associated with glycogen degradation

glycogen phosphorylase, phosphoglucomutase, glucose 6 phosphatase, glycogen debranching enzyme

how to identify glycogen deposits in liver cell?

PAS method

glycogen granules are [x] and represent approximately [x] hours worth of energy in higher vertebrates

large, 24

glycogen deposits are [x] stained

darkly

activity of glycogen phosphorylase:

(Glcn) → Glcn-1 + G1P

glycogen phosphorylase uses the [x] [x] to generate product glucose-1-P

coenzyme PLP

glycogen phosphorylase will cleave from nonreducing ends of glycogen until it is too close to an [x]

alpha(1 → 6) branch point

glycogen phosphorylase stops within [x] glucoses of branch point

8

glycogen debranching enzyme encodes both a [x] activity and an [x] activity

glycosyltransferase, alpha-1,6-glucosidase

glycogen phosphorylase cannot cleave fewer than [x] residues from a branch point

4

debranching enzyme releases

free glucose

Pompe disease

type 2 glycogen storage disease

which component of nucleic acids is most acidic

phosphate backbone

nucleotide contains

nitrogenous base, 5 carbon sugar, phosphate

adenine name

6 amino purine

guanine name

2 amino 6 oxy purine

[x] and [x] tautomers are lower energy and more stable at pH 7 than [x] and [x] forms

amino, keto, imino, enol

cytosine name

2 oxy 4 amino pyrimidine

uracil name

2,4 dioxy pyrimidine

thymine

2,4 dioxy 5 methyl pyrimidine

[x] drives base pairing in nucleic acid secondary structures in both DNA and RNA

h-bond donors and acceptors

how many h-bonds form between C and G

3

how many h-bonds form between A and T/U

2

Base names (ACGUT)

Adenine, Cytosine, Guanine, Uracil, Thymine

Nucleoside names (ACGUT)

Adenosine, Cytidine, Guanosine, Uridine, Deoxythymidine

What do you add to nucleoside names to get nucleotide full name?

5’-monophosphate

generic name of nucleotides (ACGUT)

adenylate, cytidylate, guanylate, uridylate, deoxythymidylate

generic name of nucleotides abbreviation (ACGUT)

AMP, CMP, GMP, UMP, dTMP

what do N-bases share in common

heterocyclic, aromatic, delocalized pi electrons, absorbs light at 260 nm, planar, weakly basic, contains h-bond donors and acceptors

[x] of the bases leads to [x] in the rings, leading to [x] and [x]

aromaticity, electron delocalization, partial double bond character, planarity

rank molecules from most soluble in aqueous buffer to least soluble: ATP, AMP, adenylate, adenosine, adenine

ATP > AMP > adenylate > adenosine > adenine

what carbons of furanose ring are puckered

C-2’ and C-3’

what position is a puckered carbon

endo

what factors contribute to flexibility of nucleic acids

rotation around phosphodiester linkages, rotation around glycosidic linkages, conformations of ribose

what does the anti conformation do

reduces steric and electrostatic clashes

what type of base is glycosidic linkage rotation more evident for

purine

phosphodiester linkage: successive nucleotides are linked [x] through [x] of one nucleotide and [x] of the next

covalently, 5’ phosphate, 3’ OH

which phosphodiester bonds in DNA and RNA have the same orientation along the chain

all

how does flexibility of DNA compare to polypeptides

more free rotation allowed

histone proteins bind to DNA in a [x] manner

sequence-independent

each nucleosome particle consists of

147 bp of ds DNA, 2 of H2A, H2B, H3, and H4, H1

RNA is less stable than DNA due to

alkaline hydrolysis of 2’ OH

Single stranded DNA and ds DNA are much more stable than RNA [x]

in vitro

alkaline hydrolysis rxn name

alkaline-mediated autocleavage

in alkaline hydrolysis, what type of attack occurs on phosphate that breaks the bond

base-catalyzed nucleophilic attack

DNA handedness (ABZ)

right, right, left

DNA diameter (ABZ) in A

26, 20, 18

DNA length per bp (ABZ) in A

2.6, 3.4, 3.7

DNA bps per turn (ABZ)

11, 10.5, 12

DNA base tilt (AZ) in degrees

20, 7

DNA sugar pucker conformation (ABZ)

C3’, C2’, C2’ for pyr and C3’ for pur

DNA glycosyl bond conformation (ABZ)

anti, anti, anti for pyr and syn for pur

DNA form condition (AZ)

dehydrated, in vivo

what is Z-form DNA used for

regulatory signal for transcription

which DNA forms are antiparallel

all

stacked bases provide [x]

stability

sugar phosphate backbone confers great [x] in aqueous sln

solubility

[x] is used to determine stability in DNA

thermal denaturation

increase in A260 as dsDNA → ssDNA is called

hyperchromic shift

X and Y axis of absorbance spectra

wavelength, molar extinction coefficient

point at which strands are halfway from unzipping each other

Tm

what other factors contrite to stability of nucleic acids (besides bonds)

G-C content, temperature, salt

why does high salt concentration make nucleic acids more stable

salt screens P-P negative charge repulsion

on a thermal denaturation plot, lines to the [x] represent higher ionic strength

right

on a thermal denaturation plot, lines to the [x] represent longer dsDNA due to base stacking and hydrogen interactions

right

Chargaff rule states that in typical DNA:

A+G = T + C

what question where Hershey and Chase asking in their 1952 experiment?

whether DNA or protein was responsible for transmitting genetic info

In Hershey Chase experiment, DNA was labeled [x] and protein was labeled [x]

P32, S35

P32 was in [x] and S35 was in [x]

pellet, supernatant