BIOL541 Fu Exam 2

aldose

aldose

contains aldehyde functionality, carbonyl is at the end of the chain

ketose

has ketone functionality, carbonyl is located in any other position aside from the ends of the chain

enantiomers

mirror images of one another, often labelled as D and L

Fischer projection formulas

used to show 3D sugars on paper, dash is down and wedge is up

epimers

two sugars that differ only in the configuration around ONE carbon atom

glucose epimers

1. D-mannose (epimer at C2)

2. D-galactose (epimer at C4)

ribose

standard five carbon sugar

glucose

standard six carbon sugar

fructose

ketose form of glucose (six carbons)

dihydroxyacetone

three carbon ketose

D-erythulose

four carbon ketose

D-ribulose and D-xylulose

five carbon ketoses

Which molecules readily undergo intermolecular cyclization?

pentoses and hexoses

What is the anomeric carbon?

The old carbonyl carbon that becomes a new chiral center after cyclization

What happens to the former carbonyl oxygen after cyclization?

it becomes a hydroxyl group, determining alpha or beta position

--if the hydroxyl group is trans of the ring it is alpha, cis is beta

What is the product of cyclization?

hemiacetals and hemiketals (and sugar rings)

How does cyclization occur?

alcohol attacks ketone or aldehyde, forming ring with oxygen, former carbonyl oxygen becomes hydroxyl group

pyranoses

six membered oxygen-containing rings

furanoses

five membered oxygen-containing rings

What side is the anomeric carbon usually drawn on?

the right side

reducing sugars via aldehyde

-glucose for example

-Tollens (Ag+ to Ag) and Fehlings (Cu2+ to Cu+) test for these sugar

use of calorimetric glucose analysis

enzymatic method to quantify reducing sugars (like glucose)

What enzyme is used in calorimetric glucose analysis and what does it do?

-glucose oxidase

-catalyzes the conversion of glucose to glucono-lactone and hydrogen peroxide

What is the purpose of hydrogen peroxide in calorimetric glucose analysis?

oxidizes organic molecules into highly colored compounds

What is glycogen?

(Animals)

-branched homopolysaccharide of glucose

-main storage polysaccharide of animal cells

-glucose monomers (alpha 1->4) linked chains

-branch-points with (alpha 1->6) linkers every 8-12 residues

-MW: several million

What is starch?

(Plants)

-mixture of two homopolysaccharides of glucose

-amylose: unbranched polymer of (alpha 1-->6) linked residues

-amylopectin: branched (like glycogen) but branch points are every 24-30

-main storage polysaccharide in plants

-MW: 200 million

What is cellulose?

-branched homopolysaccharide of glucose

-glucose monomers form (beta 1-->4) linked chains

-H bonds form between adjacent monomers, additional H bonds between chains

-structure tough and water insoluble

-most abundant polysaccharide in nature

-think cotton

agar

-complex mixture of hetereopolysaccharides containing modified galactose units

-component in cell wall of some seaweeds

agarose

-one component of agar

agar solutions

-form gels used for growing bacteria

agarose solutions

-DNA separation (electrophoresis)

What do all bacteria have in common?

-lipid A region

-endotoxin (core oligosaccharide)

-O specific chain (determinant of serotype or immunological reactivity)

What is significant about the membranes of S. typhimurium and E. coli?

They have so many lipopolysaccharide molecules that the cell surface is virtually covered with O-specific chains

What changes across bacteria?

they have subtly different lipopolysaccharide structures

oligosaccharide linkages in glycoproteins

-O-linked: Ser and Thr

-N-linked: Asn

What are the three stages of respiration?

1. Acetyl-CoA production

2. Acetyl-CoA oxidation

3. Oxidative Phosphorylation

What occurs in stage one of respiration?

-acetyl-CoA production

-oxidation of fatty acids, glucose and some amino acids yield acetyl-CoA

-generates some ATP, NADH, and FADH2

-think GLYCOLYSIS

What occurs in stage two of respiration?

-acetyl-CoA oxidation

-acetyl groups are oxidized in CAC

-generates more NADH, FADH2 and one GTP per acetyl-CoA

What occurs in stage three of respiration?

-oxidative phosphorylation

-ETC in mitochondria

-reduces O2 to H2O and generates lots of ATP

What is the last electron acceptor in respiration?

O2

What enzyme catalyzes oxidation of pyruvate formed in glycolysis to acetyl-CoA and CO2?

pyruvate dehydrogenase (PDH) complex

Is the conversion of pyruvate into acetyl-CoA a reversible process?

NO

-oxidative decarboxylation is irreversible

How many coenzymes are required in the PDH complex?

five

What are the prosthetic groups of the PDH complex?

TPP, lypolysine and FAD

What are the cosubstrates for the PDH complex?

NAD+ and CoA-SH

What happens to the first carbons of glucose in its conversion to pyruvate and acetyl-CoA?

fully oxidized

List the sequence of events of the CAC.

1. C-C bond formation to make citrate

2. isomerization via dehydration/rehydration

3-4. oxidative decarboxylations to give TWO NADH

5. substrate level phosphorylation to give GTP

6. dehydrogenation to give reduced FADH2

7. hydration

8. dehydrogenation to give NADH

How is citrate formed?

the methyl carbon of acetyl-CoA attacks the electrophilic carbonyl of oxaloacetate in a Claisen condensation reaction

What is significant about step 1 of the CAC?

it is the only step with C-C bond formation

What is the role of citrate synthase in step one of the CAC?

essentially deprotonates the methyl group of acetyl-CoA to make it a good nucleophile

What is the rate limiting step of the CAC?

Step One

What does Step one of the CAC depend on?

oxaloacetate concentration

Is step one of the CAC reversible?

NO, it is highly thermodynamically favorable and virtually irreversible

What is the enzyme in step two of the CAC?

aconitase

What occurs in Step Two of the CAC?

-OH group of citrate is repositioned in isocitrate to set up the decarboxylation in the next step

What is the intermediate formed in step two of the CAC?

cis-Aconitate

What is the enzyme in step three of the CAC?

isocitrate dehydrogenase

What occurs in step three of the CAC?

isocitrate is converted to alpha-ketoglutarate

-OH group is oxidized into a carbonyl

-facilitates decarboxylation on adjacent carbon

What is the enzyme in step four of the CAC?

alpha-ketoglutarate dehydrogenase

What is significant about step four of the CAC?

it is the last oxidative decarboxylation of the CAC,

basically all of the carbons of glucose are now fully oxidized

What occurs in step four of the CAC?

-alpha-ketoglutarate runs through another oxidative decarboxylation and is converted to succinyl-CoA

What steps form NADH?

3,4,8

3- isocitrate dehydrogenase

4- succinyl-CoA

8- L-malate dehydrogenase

Which two molecules have high energy thioester bonds?

acetyl-CoA and succinyl-CoA

What is the enzyme in step five of the CAC?

succinyl-CoA synthetase

What occurs in step five of the CAC?

-substrate level phosphorylation

-the high energy thioester bond is broken in succinyl-CoA

-that energy is used to drive phosphorylation and form GTP

What bond is formed in the synthesis of GTP?

phosphoanhydride bond

What is the enzyme in step six of the CAC?

succinate dehydrogenase

What occurs in step six of the CAC?

oxidation of succinate (alkane) to fumarate (alkene)

Why is FADH2 used to accept electrons in step six?

the reduction potential of NAD is too low

Where is succinate dehydrogenase found?

mitochondrial inner membrane

What is the enzyme in step seven of the CAC?

fumarase

What is significant about fumarase?

-step seven of CAC

-stereospecific

----water addition is always trans

----catalyzes trans double bond NOT cis double bond

What is formed in step seven of the CAC?

-L-malate

What is the enzyme in step eight of the CAC?

L-malate dehydrogenase

What occurs in step eight of the CAC?

-NAD-linked enzyme catalyzes the oxidation of L-malate (alcohol) to oxaloacetate (ketone)

What are the products from one turn of the CAC?

-three NADH (steps 3,4,8)

-one FADH2 (step 6)

-one GTP (step 5)

-two CO2 (steps 3 and 4)

When is the PDH complex inhibited?

When ATP/ADP, acetyl-CoA. NADH and fatty acid ratios are high.

What does each complex of the ETC consist of?

-multiple redox centers:

-FMN and FAD

- Cytochrome a,b,c

- iron-sulfur cluster protein

What is significant about FMN and FAD in the ETC?

-initial electron acceptors for complex 1 and 2

-can carry two electrons by transferring one at a time

What is ubiquinone?

a lipid-soluble conjugated dicarbonyl compound that readily accepts electrons

What happens when ubiquinone after it accepts two electrons?

-picks up two protons

-turns into alcohol called ubiquinol

What is the significance of ubiquinol?

-can freely diffuse into membrane

-carries ELECTRONS from one side of the membrane to the other

-mobile electron carrier that transports electrons from complexes one and two to complex three of ETC

Describe what occurs at Complex 1 of the ETC.

-2e- pass through a series of Fe-S centers to the N-2 center in the matrix arm

-electrons are transferred from N-2 to Q on the membrane arm (QH2 formed)

-QH2 diffuses into the lipid bilayer

-drives the expulsion of 4 protons per electron pair

How is ubiquinone a proton pump at complex one?

transfer of two electrons from NADH to Q is always accompanied by the expulsion of four protons from the matrix to the intermembrane space

How are the four protons pumped out of the matrix accompanying ubiquinone electron transfer transported?

by proton wires

--basically a series of amino acids that undergo protonation and deprotonation to generate a net effect of one proton transferred from the matrix to the intermembrane space

What is complex two?

succinate dehydrogenase

What happens at complex two of the ETC?

-FAD accepts two electrons

-electrons are passed one at a time through Fe-S centers to ubiquinone

-doesn't transport protons, just forms QH2

Subunit A of Complex 2

succinate binding site (just behind FAD)

Subunit B of Complex 2

-three Fe-S centers

-where ubiquinone is bound

-heme b sandwiched between C and D subunits, prevents formation of ROS

Subunits C and D of Complex 2

-transmembrane subunits

How is complex 3 structured?

11 different subunits

What is Complex 4?

cytochrome oxidase

How is complex 4 structured?

13 different subunits, two heme groups (a and a3), contains copper ions

What are the two copper ion functions in complex 4?

CuA: two ions that accept e- from Cyt C

CuB: bonded to heme a3, forms binuclear center that transfers four e- to oxygen

How does cytochrome oxidase pass e- to oxygen?

uses 4 e- to turn one O2 molecule into 2 H2O molecules (CuB)

-requires picking up 4 protons from the matrix

-4 addition protons are pumped from the matrix to the intermembrane space

What is the proton-motive force?

electrochemical proton gradient

What are the four major pathways of glucose utilization?

structure, storage, oxidation and PPP

What are the two steps of glycolysis?

1. preparatory phase

2. payoff phase

Step one of glycolysis

hexokinase catalyzes phosphorylation of glucose into glucose-6-phosphate

step two of glycolysis

glucose-6-phosphate is converted into fructose-6-phophate (making it available to attach a phosphate group to carbon 1)

--catalyzed by phosphohexose isomerase