Biochemistry II Midterm #2

Monosaccharide

one sugar containing either an aldehyde or a ketone and an alcohol attached to each of the other carbons

What are the two isomers of monosaccharides?

D or L

L isomer

if the OH points to the left

D isomer

if the OH points to the right

natural sugars are generally what type of monosaccharide isomer?

D isomer

Epimers

two monosaccharides that differ in the -OH position around one chiral carbon

How are epimers different than enantiomers?

Epimers are a type of diastereomer that differ at only one chiral center, while enantiomers are non-superimposable mirror images of each other, differing at all chiral centers

Monosaccharides can exist in which forms?

Linear (fischer projection) and cyclic (Hayworth perspective) forms

Monosaccharides with how many carbons are more stable in cyclized form in an aqueous environment? and why?

5-6; minimizes angle strain, so it is more energetically favorable

Monosaccharides exist in an equilibrium between

cyclic and linear forms

anomeric carbons

carbonyl/ketone carbon that was attacked to form a cyclic sugar

Equatorial position is more

favorable

aldoses that cyclize

pyranoses (6C ring)

Ketoses that cyclize

furanoses (5C ring)

Which is more stable in solution, pyranoses or furanoses?

Pyranoses because of less angle strain

How are O-glycosidic bonds formed?

disaccharide formation (formed through condensation reaction between 2 monosaccarides)

Two common disaccharides

Lactose and sucrose

How to name disaccharides?

monosaccharide on left, the glycosidic linkage between the two monosaccharides (in parentheses), and then the monosaccharide on the right

glycolysis

“splitting” of 1 molecule of glucose into 2 molecules of pyruvate

3 fates of pyruvate:

acetyl-CoA, lactate, and ethanol

What is the primary pathway for ATP generation under anaerobic conditions?

Glycolysis

Metabolites are precursors for

a large number of independent pathways, including mitochondrial ATP synthesis

Under aerobic conditions (via the ETS), 1 glucose can produce

32 ATP

Where does glycolysis happen?

in the cytosol

Glycolysis consists of two stages:

Stage 1: ATP investment (reactions 1-5), stage 2: ATP production (reactions 6-10)

How does phosphorylation trap glucose in the cell?

Glucose transporter is site specific and only recognizes the dephosphorylated glucose

What are the two purposes of glycolysis reaction 1?

to activate glucose and trap glucose in the cell

Why does it make sense that glycolysis reaction 1 has an induced fit mechanism?

conformational changes block water from the active site to promote phosphorylation otherwise phosphorylation can’t happen

hexokinase

found in all cells, high affinity for substrates, phosphorylates a variety of hexose sugars, controlled via negative feedback inhibition

glucokinase

found in all liver/pancreas cells, low affinity for substrate, substrate specific (glucose), not affected by product concentrations

glycokinase is highly specific for

glucose

hexokinase has

broad substrate specificity: can phosphorylate glucose, mannose, and fructose

Which glycolysis reaction is the rate-limiting step of the entire pathway?

reaction 3

What’s the difference between bisphosphate and disphosphate?

bisphosphate means that there are 2 phosphates anywhere in the molecule and diphosphate means that there are 2 phosphates together

Which reaction is the first committed step in the glycolytic pathway?

reaction 3

Why is reaction 6 a critical glycolysis step?

It generates a molecule with high phosphoryl transfer potential (allows for ATP synthesis and the product makes hydrolysis more favorable than for other molecules)

Why does it make sense that a glycolytic metabolite would be a negative effector of hemoglobin?

2,3-bisphosphoglycerate acts as a negative effector of hemoglobin because it binds to deoxyhemoglobin and facilitates oxygen delivery to tissues that need it (since this causes hemoglobin to have a low affinity for oxygen)

Mutase

transfers functional group between the same molecule

transferase

transfers functional group between molecules

What is the role of glucokinase? And how does it fulfill its role?

to trap dietary glucose in the cell for glycogen synthesis, which helps glucokinase fulfill its role because we don’t want negative feedback

glucose transport cannot transport

phosphorylated glucose

In the fed state (when blood glucose levels are very high), glucokinase is gonna be

active

Why is the liver called the “mother” of the body?

because it is responsible for most aspects of glucose regulation

What does glucokinase also function as?

a high blood glucose sensor, stimulating insulin release from beta-pancreatic cells when blood glucose is high (fed state)

Which enzyme catalyzes the first commitment step to glycolysis?

phosphofructokinase-1

AMP and ADP are indicators of

low energy change in the cell

what are the inhibitors of phosphofructokinase-1 and why?

citrate and ATP because high concentration of citrate means there is high energy production from the citrate cycle, so more citrate does not need to be produced

which conformations does PFK-1 exist in?

inactive T state (ATP bound to allosteric site) and active R state (ADP bound to allosteric site)

Why does it make sense that the active form (R state) of pyruvate kinase is stabilized by F-1,6-BisP binding through a positive allosteric effector?

It prevents a bottle-neck situation (big to small) by revving up the last enzyme in glycolysis to use substrates from earlier in the pathway

What happens to pyruvate in aerobic conditions?

ATP production (citrate cycle and ETC)

What happens to pyruvate in anaerobic conditions?

ethanol production (yeast/other microorganisms), production of lactate

What is the point of the alternative routes for the metabolic fates of pyruvate?

to regenerate NAD+

Why does it make sense that tumor cells carry out glycolysis at a much higher rate than normal tissue, even when oxygen is available?

most tumor cells grow under hypoxic conditions and develop a tolerance due to the low pH from the amount of lactic acid that is produced

How do tumor cells achieve increased rates of glycolysis?

glycolytic enzymes and non-insulin dependent glucose transporters are upregulated through production of HIF-1

Why would it be beneficial for later stage cancer cells to produce VEGF, which stimulates outgrowth of blood vessels (angiogenesis) toward the tumor?

Gives you direct access to oxygen and a way to get rid of waste

Gleevec (Imatinib)

inhibits a specific TKR, preventing the increased synthesis of hexokinase normally triggered by that kinase; blocks binding site on hexokinase where ATP normally binds

in skeletal muscle, heart, and adipose tissue, glucose uptake and metabolism depend on

the normal release of insulin by pancreatic beta cells in response to elevated blood glucose

Type I diabetes

patients have too few beta cells and cannot release sufficient insulin to trigger glucose uptake; causes hyperglycemia in the fed state

in the liver, acetyl-CoA is converted to _______ in the fasting state? And exported to ________________________?

ketone bodies (acetoacetate and beta-hydroxybutyrate), and exported to other tissues as a fuel source

ketoacidosis

buildup of ketone bodies

In the fed state, adipose cells break down what as a fuel source?

FAs

Reducing sugars

open-chained aldose sugars that can be oxidized to carboxylic acids

Gluconeogenesis

cells synthesize glucose from noncarbohydrate compounds when dietary sources of glucose are insufficient and glucose stores have been depleted

where does gluconeogenesis happen?

cytosol mostly and takes place mainly in the liver

What type of process is gluconeogenesis?

anabolic

What controls the direction of reversible enzymes?

concentration of the substrate

What are the main points of difference between glycolysis and gluconeogenesis?

Hexokinase, PFK-1, pyruvate kinase (“valve enzymes”)

Why does it make sense that 4 separate enzymes have evolved in gluconeogenesis to bypass the valve enzymes in glycolysis?

because these glycolytic enzymes catalyze irreversible reactions, and gluconeogenesis needs to reverse these steps to synthesize glucose from non-carbohydrate sources

carbons for gluconeogenesis in the liver come from

lactate and amino acids

Biotin

cofactor in all carbon dioxide additions, covalently linked the epsilon amino group on Lys in the active site

Pyruvate carboxylase (gluconeogenesis enzyme)

mitochondrial enzyme, requires biotin cofactor to act as a CO2 carrier

Since the mitochondrial membrane has no transporter for oxaloacetate, pyruvate must be

reduced to malate by the enzyme malate dehydrogenase which makes sense because cytosolic NADH/NAD+ is 100k times lower than that of the mitochondria and gluconeogenesis requires NADH

What happens when pyruvate is reduced to malate in gluconeogenesis?

malate is reoxidized to oxaloacetate in the cytosol and oxaloacetate is then converted to phosphoenolpyruvate by PEP carboxykinase

Which ion is required by PEP carboxykinase?

Mg2+

What is the predominant path in aerobic conditions for gluconeogenesis?

the conversion of pyruvate to PEP when pyruvate or alanine is the gluconeogenic precursor

What is the predominant path in anaerobic conditions for gluconeogenesis? And where does it happen?

when the second pyruvate is converted to PEP bypass predominates when lactate is the gluconeogenic precursor (happens in the liver and yields NADH so the export of reducing equivalents from mitochondria is unnecessary)

Why might alanine impede pyruvate kinase?

Pyruvate can be converted to alanine through transamination and in the fasting state, alanine is a key gluconeogenic precursor

Alanine and glutamate are easily

transaminated

when alanine concentration is high, that means

there is enough pyruvate so glycolysis can slow or be revved down

Insulin promotes

fructose-2,6-bisphosphate synthesis through dephosphorylation of PFK-2/FBPase-2 enzyme

glucagon decreases

fructose-2,6-bisphosphate

How do you name polysaccharides?

Start by naming the non-reducing end (glycosidic bonds impede linearization so the sugar can no longer be reduced). If both are non reducing sugars, you start from the left. Give the configuration (alpha or beta) at the anomeric C joining the 1st monosaccharide unit to the 2nd, indicate in parentheses the 2C atoms joined by the glycosidic bond, with an arrow connecting the #’s

glucose is stored in mammals as

glycogen

glycogen is a (structurally)

a highly branched polymer of (alpha1-4)-linked subunits of glucose, with (alpha1-6)-linked branches every 8-12 residues

where is glycogen mainly stored in?

skeletal muscle and liver (especially abundant in the liver because it is important for maintaining blood glucose homeostasis)

in glycogen degradation, the substrate is the

free (non-reducing) end

Large number of branch points in glycogen generates

multiple nonreducing ends

the generation of multiple nonreducing ends provides a highly efficient mechanism to either?

release glucose from glycogen to meet energy needs or to rebuild glycogen particles when excess dietary glucose is available

glycogen synthesis occurs in the

cytosol of liver and muscle cells

what is glycogen stored as?

glycogen granules consisting of beta-particles and about 20-40 beta-particles form alpha-rosettes (aka glycogen deposits)

glycogen granules

complex aggregates of glycogen and the enzymes that synthesize it and degrade it as well as the machinery that regulates these enzymes

why store glucose in glycogen? why not store glucose monomers?

more compact, efficient, helps with solubility because of more branching, more polar, can be stored in smaller concentrations

what is the purpose of glycogen in the liver cells?

stores glucose that can be accessed and administered to other cells during the fasting state (10% liver weight), depleted within 12-24 hours

what is the purpose of glycogen in skeletal muscle cells?

to generate G6P for use as a chemical energy source in anaerobic and aerobic glycolysis (1-2% muscle weight), used for glycolysis in fasting state or when exercising, can be depleted in less than 1 hour during exercise

degradation and synthesis of glycogen is regulated by three key enzymes?

glycogen phosphorylase, glycogen synthase, and glycogen branching and debranching enzymes

glycogen phosphorylase

catalyzes the first step in glycogen degradation (glycogenolysis)

how does glycogen phosphorylase catalyze glycogenolysis?

releases G1P from non-reducing end in a phosphorolysis reaction that cleaves alpha(1,4) glycosidic bond until four glucose residues remain before an alpha(1,6) branch point

debranching enzyme in glycogenolysis

after glycogen phosphorylase catalyzes the first step, oligo (alpha1,6) to (alpha1,4) glucantransferase (the debranching enzyme) catalyzes two reactions after that to transfer 3 glucose branches to the nearby non-reducing end, then the (alpha1,6) branch is hydrolyzed

what happens after the debranching enzyme catalyzes reactions in glycogen degradation?

G1P, the end product of the glycogen phosphorylase reaction, is converted to G6P by phosphoglucomutase, which catalyzes the reversible reaction

In the muscle, G6P enters

glycolysis