BIOL541 Fu Exam 2

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aldose

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

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ketose

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

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enantiomers

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

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Fischer projection formulas

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

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epimers

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

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glucose epimers

1. D-mannose (epimer at C2)

2. D-galactose (epimer at C4)

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ribose

standard five carbon sugar

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glucose

standard six carbon sugar

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fructose

ketose form of glucose (six carbons)

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dihydroxyacetone

three carbon ketose

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D-erythulose

four carbon ketose

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D-ribulose and D-xylulose

five carbon ketoses

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Which molecules readily undergo intermolecular cyclization?

pentoses and hexoses

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What is the anomeric carbon?

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

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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

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What is the product of cyclization?

hemiacetals and hemiketals (and sugar rings)

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How does cyclization occur?

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

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pyranoses

six membered oxygen-containing rings

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furanoses

five membered oxygen-containing rings

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What side is the anomeric carbon usually drawn on?

the right side

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reducing sugars via aldehyde

-glucose for example

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

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use of calorimetric glucose analysis

enzymatic method to quantify reducing sugars (like glucose)

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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

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

oxidizes organic molecules into highly colored compounds

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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

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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

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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

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agar

-complex mixture of hetereopolysaccharides containing modified galactose units

-component in cell wall of some seaweeds

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agarose

-one component of agar

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agar solutions

-form gels used for growing bacteria

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agarose solutions

-DNA separation (electrophoresis)

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What do all bacteria have in common?

-lipid A region

-endotoxin (core oligosaccharide)

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

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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

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What changes across bacteria?

they have subtly different lipopolysaccharide structures

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oligosaccharide linkages in glycoproteins

-O-linked: Ser and Thr

-N-linked: Asn

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What are the three stages of respiration?

1. Acetyl-CoA production

2. Acetyl-CoA oxidation

3. Oxidative Phosphorylation

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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

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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

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What occurs in stage three of respiration?

-oxidative phosphorylation

-ETC in mitochondria

-reduces O2 to H2O and generates lots of ATP

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What is the last electron acceptor in respiration?

O2

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

pyruvate dehydrogenase (PDH) complex

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

NO

-oxidative decarboxylation is irreversible

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How many coenzymes are required in the PDH complex?

five

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What are the prosthetic groups of the PDH complex?

TPP, lypolysine and FAD

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What are the cosubstrates for the PDH complex?

NAD+ and CoA-SH

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

fully oxidized

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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

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How is citrate formed?

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

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What is significant about step 1 of the CAC?

it is the only step with C-C bond formation

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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

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What is the rate limiting step of the CAC?

Step One

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What does Step one of the CAC depend on?

oxaloacetate concentration

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Is step one of the CAC reversible?

NO, it is highly thermodynamically favorable and virtually irreversible

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What is the enzyme in step two of the CAC?

aconitase

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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

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

cis-Aconitate

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What is the enzyme in step three of the CAC?

isocitrate dehydrogenase

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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

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What is the enzyme in step four of the CAC?

alpha-ketoglutarate dehydrogenase

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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

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What occurs in step four of the CAC?

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

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What steps form NADH?

3,4,8

3- isocitrate dehydrogenase

4- succinyl-CoA

8- L-malate dehydrogenase

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Which two molecules have high energy thioester bonds?

acetyl-CoA and succinyl-CoA

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What is the enzyme in step five of the CAC?

succinyl-CoA synthetase

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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

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What bond is formed in the synthesis of GTP?

phosphoanhydride bond

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What is the enzyme in step six of the CAC?

succinate dehydrogenase

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What occurs in step six of the CAC?

oxidation of succinate (alkane) to fumarate (alkene)

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Why is FADH2 used to accept electrons in step six?

the reduction potential of NAD is too low

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Where is succinate dehydrogenase found?

mitochondrial inner membrane

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What is the enzyme in step seven of the CAC?

fumarase

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What is significant about fumarase?

-step seven of CAC

-stereospecific

----water addition is always trans

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

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What is formed in step seven of the CAC?

-L-malate

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What is the enzyme in step eight of the CAC?

L-malate dehydrogenase

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What occurs in step eight of the CAC?

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

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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)

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When is the PDH complex inhibited?

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

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What does each complex of the ETC consist of?

-multiple redox centers:

-FMN and FAD

- Cytochrome a,b,c

- iron-sulfur cluster protein

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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

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What is ubiquinone?

a lipid-soluble conjugated dicarbonyl compound that readily accepts electrons

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What happens when ubiquinone after it accepts two electrons?

-picks up two protons

-turns into alcohol called ubiquinol

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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

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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

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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

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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

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What is complex two?

succinate dehydrogenase

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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

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Subunit A of Complex 2

succinate binding site (just behind FAD)

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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

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Subunits C and D of Complex 2

-transmembrane subunits

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How is complex 3 structured?

11 different subunits

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What is Complex 4?

cytochrome oxidase

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How is complex 4 structured?

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

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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

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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

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What is the proton-motive force?

electrochemical proton gradient

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What are the four major pathways of glucose utilization?

structure, storage, oxidation and PPP

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What are the two steps of glycolysis?

1. preparatory phase

2. payoff phase

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Step one of glycolysis

hexokinase catalyzes phosphorylation of glucose into glucose-6-phosphate

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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

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