Carbs You have to memorize + hints + biochem general test #2

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Last updated 3:49 AM on 3/18/26
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68 Terms

1
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D-Dihydroxyacetone (ketose or aldose) (draw the fisher projection and turn it to a hawthorn projection) - no hawthorn

knowt flashcard image
2
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D- Fructos (ketose or aldose)(draw the fisher projection and turn it to a hawthorn projection)

didi

<p>didi</p>
3
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D- Aldoese (draw the fisher projection and turn it to a hawthorn projection)- okay what are teh differnt types of alsdos and how do you c harachterise them triose to hexose-

<p></p>
4
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D- Glucose (draw the fisher projection and turn it to a hawthorn projection)

The Haworth Projection – Master Organic Chemistry

5
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D- ribose (draw the fisher projection and turn it to a hawthorn projection)

whwhw

<p>whwhw</p>
6
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D- galactose(draw the fisher projection and turn it to a hawthorn projection)

pray for me

<p>pray for me</p><p></p>
7
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How to tell teh difference between a ketose and an aldose

Aldoses and Ketoses - Chemistry Steps

8
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How do you tell th diference betwen a d/l projection for fisher and hawthorn projection

fisher

  • D the trminal oh is to the right

  • L the terminal oh is to the left

Hawtorn

  • D- the terminal Ch2oh is facing Upwards

  • L- the terminal Ch2oh is facing Downwards

    Converting a Fischer Projection To A Haworth (And Vice Versa)
    • note this is the opposite for regular stuff

9
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What is the difference between alphas and beta in the hawthron form

alphas, the oh on the anomer carbon is facing opposite direction ofr the end group

beta - anomer oh is facing same directino f the end group

10
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What is the difference between aldoses and ketone anomeric carbons

aldoses

  • the anomeric carbbon s bound to two oxigens (C1)

ketoses

  • the anomeric carbon is bound to an oxygen and a cooh (C2)

Ketoses vs Aldoses : r/Mcat

11
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What directino do non trminal and non anomeric carbons face (the oh grops when convirting to hawthorn frm fisher)

d = down

Converting a Fischer Projection To A Haworth (And Vice Versa)

L = up

12
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What is glucose metabolis, what is formed, what are the parts, and what conditions do they take place (where does it take place)

glucose = metabolized insied the cytoplasm

into what = 2 pyruvate later broken down inthe krebs cycle), NADH, ATP

there are arobic and anarobic parts = pyruvate becomes lactate or ethanol (

13
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What parts of glucose metabolism are aerobiv and anarobic

anarobic glycolisis in the cytoplasm

anarobic - lactic acid fermentation

earobic = in the mitochondria for the citric acid cdyle and oxidative pohsophrilation

14
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What are the 3 stages of glucose metabolis and how many stepas are in there

  1. Stage oen - traps glucose in the cell ( destabalization + investment stage)

    1. steps 1-3

  2. stage 2 - breakdown of lguocse (into 2 components)

    1. steps 4-5

  3. step 3 - atp and pyruvate production (oxidation (nadh) = pay off stage

    1. Step 6-10

<ol><li><p>Stage oen  - traps glucose in the cell ( destabalization + investment stage)</p><ol><li><p>steps 1-3</p></li></ol></li><li><p>stage 2 - breakdown of lguocse (into 2 components)</p><ol><li><p>steps 4-5</p></li></ol></li><li><p>step 3 - atp and pyruvate production (oxidation (nadh) = pay off stage</p><ol><li><p>Step 6-10</p></li></ol></li><li><p></p></li></ol><p></p>
15
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<p>What are the steps to glycolosis  by stage, steps, what is produced, what enzymes are there, what are the kinetic regulatory stages. what are the relative energies of each)</p>

What are the steps to glycolosis by stage, steps, what is produced, what enzymes are there, what are the kinetic regulatory stages. what are the relative energies of each)

Stage 1: - trapping glucose in teh cell for (consumption)

Step 1. phosphate addition to glucose - destabilization and clevage (allosteric inhibition)

  • glucose + atp; —-(hexokinase/glucokinase) (in the liver)—→ Glucose 6 phosephate + atp + h+

  • energy = (delta)G -33.5 kg/mol - spontaneous and irreversible) -kinetic regulatory stage

Step 2- glucose to furctose (creation of symmetry)

  • Glucose 6-phosephate —(phosphoglucose isomoerase)—> fructose 6-phosphate

  • energy= (Delta) G =-2.5kj/mol

Step 3- addition of the second phosphate group (further desttabaliation)

  • fructose 6-phosephate + ATP —-(Phosphofructokinase)—> Fructoose 1, 6 biphosphate + adp + h+

  • energy = (delta)G -33.5 kg/mol - spontaneous and irreversible + committed step) -kinetic regulatory stage

Stage 2: Gap production (cleavage)

Step 4- Split of fructose into DHAP + GAP

  • Fructose 1-6 biphosphoros —-(aldolase)—> DHAP( not convertible) + GAP

  • Energy- (Delta G) = -1.3 kj/mol

Step 5 - Conversion of DHAP to GAP

DHAP —- (Triose phosphate Isomerase) —→ GAP

Energy- Delta G = +2.5 kj.mol (unfavorable to favorable)

Stage #3 - ATP production (note happens twice) (allosteric activation)

Step #6 - NADH prodution + phosphorilation of GAP

  • GAP + NAD+ —-(Gap Dehydrogenase)—> 1,3 BPG (has 2 phosphate groups) + NADH +h+

  • Energy = -1.7kj/mol)

Step #7- Phosphate group transfer to ATP (2 atp produced total)

  • 1,3 BPG + ADP + H+ —-(Phosphoglycerate Kinase)—> 3 phosphoglycerate (3-PG)

  • Energy- (delta) G = +1.3kj/mol

Step #8 - intermolecular phosphaete transefer (Destabalization)

  • 3-PG —-(phosphoglycerate mutase)—> 2 phosphate glycerate (2pg)

  • Energy: +0.8kj/mol

Step #9 - Enol formation

  • 2-PG —(Enolase)—> phosphenolpyruvate (pep) (very high energy intermediate)

  • Energy: Delta G = -3.3 kj/mom

Step #10 - pyruvate formation + ATP formation (allosteric inhibition)

  • Pep + adp + H+ —-(pyruvate kinase)-→ pyruvate + ATP

  • energy = -61.8 kj per mol ( irrevrsible, spontaneous, kinetic regulatory step)

Net atp producced =4 atp

total energy = -96.32

<p><strong>Stage 1:</strong> - trapping glucose in teh cell for (consumption)</p><p>Step 1. phosphate addition to glucose - destabilization  and clevage (allosteric inhibition)</p><ul><li><p>glucose + atp; —-(hexokinase/glucokinase) (in the liver)—→ Glucose 6 phosephate + atp + h+</p></li><li><p>energy = (delta)G -33.5 kg/mol - spontaneous and irreversible) -<strong>kinetic regulatory stage</strong></p></li></ul><p>Step 2- glucose to furctose (creation of symmetry)</p><ul><li><p>Glucose 6-phosephate  —(phosphoglucose isomoerase)—&gt; fructose 6-phosphate</p></li><li><p>energy= (Delta) G =-2.5kj/mol</p></li></ul><p></p><p>Step 3- addition of the second phosphate group (further desttabaliation)</p><ul><li><p>fructose 6-phosephate + ATP —-(Phosphofructokinase)—&gt; Fructoose 1, 6 biphosphate + adp + h+</p></li><li><p>energy = (delta)G -33.5 kg/mol - spontaneous and irreversible + committed step) -<strong>kinetic regulatory stage</strong></p></li></ul><p></p><p><strong>Stage 2:</strong> Gap production (cleavage)</p><p>Step 4- Split of fructose into DHAP + GAP</p><ul><li><p>Fructose 1-6 biphosphoros —-(aldolase)—&gt; DHAP( not convertible) + GAP</p></li><li><p>Energy- (Delta G) = -1.3 kj/mol</p></li></ul><p>Step 5 - Conversion of DHAP to GAP</p><p>DHAP —- (Triose phosphate Isomerase) —→ GAP</p><p>Energy- Delta G = +2.5 kj.mol (unfavorable to favorable)</p><p></p><p><strong>Stage #3 </strong>- ATP production (note happens twice) (allosteric activation)</p><p>Step #6 - NADH prodution + phosphorilation of GAP</p><ul><li><p>GAP + NAD+ —-(Gap Dehydrogenase)—&gt; 1,3 BPG (has 2 phosphate groups) + NADH +h+</p></li><li><p>Energy = -1.7kj/mol)</p></li></ul><p></p><p>Step #7- Phosphate group transfer to ATP (2 atp produced total)</p><ul><li><p>1,3 BPG + ADP + H+ —-(Phosphoglycerate Kinase)—&gt; 3 phosphoglycerate (3-PG)</p></li><li><p>Energy- (delta) G = +1.3kj/mol</p></li></ul><p></p><p>Step #8 - intermolecular phosphaete transefer (Destabalization)</p><ul><li><p>3-PG —-(phosphoglycerate mutase)—&gt; 2 phosphate glycerate (2pg)</p></li><li><p>Energy: +0.8kj/mol</p></li></ul><p></p><p>Step #9 - Enol formation</p><ul><li><p>2-PG —(Enolase)—&gt; phosphenolpyruvate (pep) (very high energy intermediate)</p></li><li><p>Energy: Delta G = -3.3 kj/mom</p></li></ul><p></p><p>Step #10 - pyruvate formation + ATP formation (allosteric inhibition)</p><ul><li><p>Pep + adp + H+ —-(pyruvate kinase)-→ pyruvate + ATP</p></li><li><p>energy = -61.8 kj per mol ( irrevrsible, spontaneous, kinetic regulatory step)</p></li></ul><p></p><p>Net atp producced =4 atp</p><p>total energy = -96.32</p><p></p><p></p><p></p><p></p>
16
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What are the different types of isomers (constitutional sterioisomers, Diasterimers, Epimers, Anomers, Conformers)

  1. constituttional isomers - same formula but different structures

  2. sterioisomrs = different in spacial arrangemnt

    1. Enantomers

      1. non souperimposible mirror images (D or l form for carbs)

    2. Diasterioisomers

      1. Isomers that are not mirror images

    3. epimers

      1. they differ at one of several asymettric carbon atoms

    4. Anomers

      1. differe at a new asymetctruc carbon + fixed ring of carbon

<ol><li><p>constituttional isomers - same formula but different structures</p></li><li><p>sterioisomrs = different in spacial arrangemnt </p><ol><li><p>Enantomers </p><ol><li><p>non souperimposible mirror images (D or l form for carbs)</p></li></ol></li><li><p>Diasterioisomers</p><ol><li><p>Isomers that are not mirror images </p></li></ol></li><li><p>epimers </p><ol><li><p>they differ at one of several asymettric carbon atoms</p></li></ol></li><li><p>Anomers</p><ol><li><p>differe at a new asymetctruc carbon + fixed ring of carbon</p></li></ol></li></ol></li></ol><p></p>
17
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How is ring formation formed bteween carbohydrates and what is the difference in fformation for ketones and aldoses

6 membered rings = pyranose

5 membered rings - furanose

<p>6 membered rings = pyranose</p><p>5 membered rings - furanose</p>
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What are the different monosaccharide derrivatives and how are they formed - sugar acids

Sugar Acids: Formed from sugars with free anomeric carbons (reducing sugars) via the reduction of oxidizing agents

  • will reduce a benedicts reagent or fehling solution (must have a free aldehyde or kettone

<p>Sugar Acids: Formed from sugars with free anomeric carbons (reducing sugars) via the reduction of oxidizing agents</p><ul><li><p>will reduce a benedicts reagent or fehling solution (must have a free aldehyde or kettone</p></li></ul><p></p>
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<p>What molecule is this and what is its function</p>

What molecule is this and what is its function

Glycerol

  • versitiles sugar alcohol that is used as a swetener

<p>Glycerol</p><ul><li><p>versitiles sugar alcohol that is used as a swetener</p></li></ul><p></p>
20
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<p>What molecule is this and what is its function</p>

What molecule is this and what is its function

Glyceraldehyde

  • serving as a key intermediate in glycolysis and fructose metabolism, converting into energy-producing compounds

<p>Glyceraldehyde</p><ul><li><p><span>serving as a key intermediate in glycolysis and fructose metabolism, converting into energy-producing compounds</span></p></li></ul><p></p>
21
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<p>What momecule si this and what is its function</p>

What momecule si this and what is its function

Dihydroxyacetone

  • acts as a carbon source for microorganisms, a metabolite in human cells, and a non-enzymatic skin-tanning agent through the Maillard reaction with amino acids

<p>Dihydroxyacetone </p><ul><li><p><span>acts as a carbon source for microorganisms, a metabolite in human cells, and a non-enzymatic skin-tanning agent through the Maillard reaction with amino acids</span></p></li></ul><p></p>
22
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

Pyruvate

  • a central hub in metabolism, serving as the final product of glycolysis and a crucial branch point for energy production or biosynthesis

<p>Pyruvate</p><ul><li><p><span>a central hub in metabolism, serving as the final product of glycolysis and a crucial branch point for energy production or biosynthesis</span></p></li></ul><p></p>
23
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

ATP

  • providing readily releasable energy to drive vital biochemical reactions through the hydrolysis of its high-energy phosphate bonds into ADP and inorganic phosphate

<p>ATP</p><ul><li><p><span>providing readily releasable energy to drive vital biochemical reactions through the hydrolysis of its high-energy phosphate bonds into ADP and inorganic phosphate</span></p></li></ul><p></p>
24
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

ADP

  • acts as the primary precursor for ATP regeneration and a product of energy-releasing reactions

<p>ADP</p><ul><li><p><span>acts as the primary precursor for ATP regeneration and a product of energy-releasing reactions</span></p></li></ul><p></p>
25
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

NAD+

  • acting as a crucial electron carrier in redox reactions to drive energy metabolism, specifically ATP production via glycolysis, the TCA cycle, and oxidative phosphorylation

<p>NAD+</p><ul><li><p><span>acting as a crucial electron carrier in redox reactions to drive energy metabolism, specifically ATP production via glycolysis, the TCA cycle, and oxidative phosphorylation</span></p></li></ul><p></p>
26
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<p>What molecule is this and what iis its function- really know the difference betwn the two pairings </p>

What molecule is this and what iis its function- really know the difference betwn the two pairings

NADH

  • a vital coenzyme acting as a primary electron carrier in cellular respiration, shuttling electrons from catabolic pathways like glycolysis and the TCA cycle to the electron transport chain (ETC

<p>NADH</p><ul><li><p><strong><mark data-color="rgba(0, 0, 0, 0)" style="background-color: rgba(0, 0, 0, 0); color: inherit;">a vital coenzyme acting as a primary electron carrier in cellular respiration, shuttling electrons from catabolic pathways like glycolysis and the TCA cycle to the electron transport chain (ETC</mark></strong></p></li></ul><p></p>
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

FAD

  • primarily as an electron acceptor in oxidation-reduction reactions, such as the Citric Acid Cycl

<p>FAD</p><ul><li><p><span>primarily as an electron acceptor in oxidation-reduction reactions, such as the Citric Acid Cycl</span></p></li></ul><p></p>
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<p>What molecule is this and what iis its function</p>

What molecule is this and what iis its function

FADH2

  • (flavin adenine dinucleotide, reduced form) acts as a critical electron carrier in cellular respiration and metabolism, generating approximately ATP via the electron transport chain (ETC)

<p>FADH2</p><ul><li><p><span>(flavin adenine dinucleotide, reduced form) acts as a critical electron carrier in cellular respiration and metabolism, generating approximately ATP via the electron transport chain (ETC)</span></p></li></ul><p></p>
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The reactants and products, the number and kind of cofactors, and the cellular locations for Glycolysis

Location

  • cytosol of the cell

Reactants

  1. 1 mole glucose, 2nad+, 2adp, 2pi

Products

  1. 2 pyruvate

  2. 2nadh

  3. 2atp net

  4. 2 h2o

  5. 2H+

ATP accounting

  1. Investment phase = -2 atp

  2. energy payoff phase +4atp

  3. net atp 2atp

Cofactors Used

  • NAD⁺ → reduced to NADH

  • Mg²⁺ (required for ATP binding in several enzymes)

Overall reaction

  • Glucose + 2 NAD⁺ + 2 ADP + 2 Pi
    → 2 Pyruvate + 2 NADH + 2 ATP + 2 H₂O

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What are the 3 irreversible steps of glycolisis and how do they work - what is the reaction, waht is the type of reaction, what is the purpose, and vaguely how is it regulated

  1. Step 1 (hexokinase -muscle, Glucokinase - liver

    1. Reaction

      1. Glucose + ATP → Glucose-6-phosphate + ADP

    2. Type of reaction
      Phosphorylation

      Purpose

      • Traps glucose in the cell

      • Commits glucose to metabolism

      Regulation

      • Inhibited by Glucose-6-phosphate

      • In liver: glucokinase regulated by insulin

  2. STep 3 - phosphofructokinase-1 PFK-1

    1. Reaction

      1. Fructose-6-phosphate + ATP → Fructose-1,6-bisphosphate + ADP

    2. Type of reaction

      1. Phosphorylation

        1. it is a rate limiting step of glycolisis

    3. REgulation

    4. activators

      1. AMP, ADP, Fructose-2.6 bisphospate

    5. inhibitors

      1. ATP, citrate, lowph

    6. concept

      1. high atp levels = cell has eneryg = inhibition of glycolisis

  3. Step 10- pyruvate kinas

    1. reaction

      1. Phosphoenolpyruvate (PEP) + ADP → Pyruvate + ATP

    2. Type of reaction

      1. substrate level phosphorilation

    3. activated by

      1. fructose 1,6 biphosephate (feed forward activation)

    4. inhibitied by

      1. atp alanine (3 memberd ring carbon), acytel co a

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What are the different types of reactions inmetabolic pathwasy: what type is used for hexokinase, wwhat happens, what is the enzyme class invovled

reaction type

  • phosphorilation

    • addition of phosphate groups

  • enzyme class (transferases - kinases)

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What are the different types of reactions in metabolic pathwasy: what type is used for glucose-6 phosphate to frucotes 6 phosephate change, what is the enzyme class invovled, what happens,

reaction type

  • isomerization

    • rearrangement of atoms

  • enzyme class - isomerases

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Different types of reactions in metabolic pathways: reaction type, enzyme class, effect: aldolase (enzyme)

reaction type

  • nonhydrolitic cleavagge

    • splittin gof a molecule by non h ydroxyl process

enzyme type

  • lysases

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Different types of reactions in metabolic pathways: reaction type, enzyme class, effect: G3p dehydrogenase

reaction type

  • oxidation reduction

    • electron transfer

    • enzyme type

      • oxidoreductases (dehydrogenases)

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Different types of reactions in metabolic pathways: reaction type, enzyme class, effect: pyruvase kinase

reaection type

  • substrate level phosphorilation

    • atp produced directly

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Different types of reactions in metabolic pathways: reaction type, enzyme class, effect: Enolase

reaction type

  • dehydration reactio (hydrolotic cleavage/hydrolisi_

    • clevage of bonds by water to remove fuctional groups to water

enzyme type

  • hydrolases

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Different types of reactions in metabolic pathways: reaction type, enzyme class, effect: Ligases/ synthases

  • reaction type

    • bond formation using. energy

  • formtation of carbon-carbon and other bond s with energy from atp

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What are the different. types of catalyitic stratagies used for glycolisis and how does it do it: acid baes, covalent, metal ion, what amino acids are in voled

  1. acid base

    1. enzyme donates or accepts protions (h+)

      1. often involves histinde, aspartate, glutamate

    2. covalent catalissts

      1. temporary covalent bodn between enzyme and substrate

        1. invovles

          1. serein, cystine, lysine

      2. metal ion

        1. metal ions stablize chargs

        2. mg2+ stabilszes many glyclisizs enzymes

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What are the different monosaccharide derrivatives and how are they formed - sugar alcohols (altidolss)

formation

  • formed form mild reduction (gaining of electrion) of carbyonyl groups of aldoses

<p>formation</p><ul><li><p>formed form mild reduction (gaining of electrion) of carbyonyl groups of aldoses</p></li></ul><p></p>
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What are the different monosaccharide derrivatives and how are they formed - Sugar esther

formation

  • phospate esters of onosaccharides are importatt metabolic intermediates

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What are the different monosaccharide derrivatives and how are they formed- deoxy sugars

formation

  • monosaccharides with one or more hyudroxyl groups replased by hydrogens

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What are the different monosaccharide derrivatives and how are they formed- amino sugars

formation

  • contain an amio group in place of a hydroxyl grop at the c-2 position

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How are glycosidic bonds formed- what is the difference between an n and an o glucosidic vond, what catalises the reaction. what is the distinctive difference

o-glycosidic vond (glycosides)

  • formed between the anomeric carbon atom and hydroxyl group of another molecule

n - glycosidic vond

  • formed between teh anomeric carbon and an amine

  • catalized by - glycotransferase

Diffferences

  • o linked

    • proteins contain convalently attached saccharides via the hydroxyl (OH) groups of ser, thr

      • used for cell surface

  • n l inked

    • proteins contain covalently attached saccharides via the amide nitoriges of asparigine residues

    • usd o be folded er

<p>o-glycosidic vond (glycosides)</p><ul><li><p>formed between the anomeric carbon atom and hydroxyl group of another molecule</p></li></ul><p>n - glycosidic vond</p><ul><li><p>formed between teh anomeric carbon and an amine</p></li></ul><p></p><ul><li><p>catalized by - <strong>glycotransferase</strong></p></li></ul><p></p><p>Diffferences</p><ul><li><p>o linked</p><ul><li><p>proteins contain convalently attached saccharides via the hydroxyl (OH) groups of<strong> ser, thr</strong></p><ul><li><p>used for cell surface</p></li></ul></li></ul></li><li><p>n l inked</p><ul><li><p>proteins contain covalently attached saccharides via the amide nitoriges of <strong>asparigine </strong>residues</p></li><li><p>usd o be folded er</p></li></ul></li></ul><p></p>
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Describe the different types of glycosidic bonds for the following disaccharides: sucrose, lactose, and moltose

Lactose

  • bond between beta galactose (same side) and glucose

    • zigzag pattern (galactose beta 1,4 glucose)

Maltose

  • bond between alpha glucose and regular glucose (u shaped pattern)

  • glucose alpah 1,4 gluocose)

Sucrose

  • bond between glucos alpha (opposite sides) and fructose (beta 5 memberd ringO

  • forms u shaped structure

    • nnon reducing because t here is no free oh group at either end

<p>Lactose</p><ul><li><p>bond between beta galactose (same side) and glucose</p><ul><li><p>zigzag pattern (galactose beta 1,4 glucose)</p></li></ul></li></ul><p>Maltose</p><ul><li><p>bond between alpha glucose and regular glucose (u shaped pattern) </p></li><li><p>glucose alpah 1,4 gluocose)</p></li></ul><p>Sucrose</p><ul><li><p>bond between glucos alpha (opposite sides) and fructose (beta 5 memberd ringO</p></li><li><p>forms u shaped structure </p><ul><li><p>nnon reducing because t here is no free oh group at either end</p></li></ul></li></ul><p></p>
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Starch: what are teh bonding patterns for amulose an d amylopectin, and cellulose

amulose

  • alpha 1,.4 linkages of gluocse with one reducing end

  • forms helical structure

amylopectin

  • alpha 1.6 structures with glucose = branches in every 12-30 resuidues. more linear structure

    • note glycogen is similar to amylopectin iwth alpha 1,6 bonding and branches every 8 -12 residues

cellulose

  • lienar homopolymer of D-gluocse with beta 1-4 glycosidic bonds (fors zig zag pattern

  • straight chain

    • note its a hmopolymer of glucose

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Blood types and glycosylation patternsh. what are the bonding patterns for each blood type, a, b and o

A

  • n-acetylgalatosamine is added to the O by a spcific glycotransferase

B

  • galactose is added by another transferase

O

  • produces no active glycotransferase

<p>A</p><ul><li><p>n-acetylgalatosamine is added to the O by a spcific glycotransferase</p></li></ul><p>B</p><ul><li><p>galactose is added by another transferase </p></li></ul><p>O</p><ul><li><p>produces no active glycotransferase</p></li></ul><p></p>
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What are the different typs of cromatography and how do they work? what are the ways that you can purify proteins ( Separation by solubiliy, size, net charge, specific binding affinnity, higher performance liquid chromotryphy

Methods

  • solubility size charge, and specific binding affinity

Method 1. sparation by solubility

  1. happens at high salt concentrations = proteins precipitate out of a solution

    1. how does it happen

      1. charges from the proteins - prefferibly negative come to react with water. Filtration methods are used to sparate the small molecules

      2. large stuff is trapped inside while smaller moleules diffus outide

Separation by size

  1. Gell flltration chromotrophy = molecular exculsion chromotrophy

    1. what happens

      1. small molecules can enter the beads but large molecules cannot = filration

      2. larger molecuels leave the filtraiton column first followed by the bound small molecules

Separation by net charge

  1. ion exchange chromotrhohy

    1. neaural charged protens bind with negativley charged carboxylae groups

    2. negatviely charged particals are unable to bind/have a difficult time binding

    3. positively charged = couple with the positlvey charged groups on the binding plate

      1. can work both ways

        1. cation exchagne = pisitive proein bind to negative beads

        2. anion exchange = negatively charged bead bind to pisitive

        3. leftover proteins pass to the bottom and out of the solution to be filterd

Separation by specific binding affinity

  1. affinity chromotrophy = motst powerful mehtod of protein purification

    1. uses glucose binding

    2. glucose binds to proteins that are able to favoribley bind to glucose

    3. nonbinding proteins are reoved

    4. glucose is whashed out and the required proteins are left behind

Higher performance liquid chromotrophy

  1. its like a more enhanced version of cholumn techinechs

    1. beads are finley dividd = more interactions = more pressure =. more rapid separation

<p>Methods</p><ul><li><p>solubility size charge, and specific binding affinity</p></li></ul><p></p><p>Method 1. sparation by solubility</p><ol><li><p>happens at high salt concentrations = proteins precipitate out of a solution</p><ol><li><p>how does it happen</p><ol><li><p>charges from the proteins - prefferibly negative come to react with water. Filtration methods are used to sparate the small molecules </p></li><li><p>large stuff is trapped inside while smaller moleules diffus outide</p></li></ol></li></ol></li></ol><p></p><p>Separation by size</p><ol><li><p>Gell flltration chromotrophy = molecular exculsion chromotrophy</p><ol><li><p>what happens</p><ol><li><p>small molecules can enter the beads but large molecules cannot = filration</p></li><li><p>larger molecuels leave the filtraiton column first followed by the bound small molecules</p></li></ol></li></ol></li></ol><p>Separation by net charge</p><ol><li><p>ion exchange chromotrhohy</p><ol><li><p>neaural charged protens bind with negativley charged carboxylae groups</p></li><li><p>negatviely charged particals are unable to bind/have a difficult time binding</p></li><li><p>positively charged = couple with the positlvey charged groups on the binding plate</p><ol><li><p>can work both ways</p><ol><li><p>cation exchagne = pisitive proein bind to negative beads</p></li><li><p>anion exchange = negatively charged bead bind to pisitive </p></li><li><p>leftover proteins pass to the bottom and out of the solution to be filterd</p></li></ol></li></ol></li></ol></li></ol><p></p><p></p><p>Separation by specific binding affinity</p><ol><li><p>affinity chromotrophy = motst powerful mehtod of protein purification</p><ol><li><p>uses glucose binding</p></li><li><p>glucose binds to proteins that are able to favoribley bind to glucose</p></li><li><p>nonbinding proteins are reoved</p></li><li><p>glucose is whashed out and the required proteins are left behind</p></li></ol></li></ol><p></p><p></p><p>Higher performance liquid chromotrophy</p><ol><li><p>its like a more enhanced version of cholumn techinechs</p><ol><li><p>beads are finley dividd = more interactions = more pressure =. more rapid separation</p></li></ol></li></ol><p></p>
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Whta is gel electrophorisis and how does it relates to chromotrophy. How does SDS used

  1. gel electrophorisis = used to tell if purification methods are effective

    1. what steps does it use

      1. molecules with electric charges move towerd the feild (negatice cathode to psitive anode)

        1. smaller moleucles move faster and furhte rwhile larger moleucels are pracitcally immoble in teh fluid

SDS is needed to separate by mase

  1. method

    1. the negatively charged SDS = denatures proteins = binds at a 1:2 ration sds to aino acid protein

    2. Betamericapoethanol is added to reduce the disfulfide bond sof the amino acids = li nearization of proteins

    3. allows for smaller molecules to move it down

  • Salting out: A separation technique that takes advantage of the fact that the solubility of proteins varies with the salt concentration. As the salt concentration is increased, different proteins will precipitate at different salt concentrations, a process called salting out.

  • Polyacrylamide Gel Electrophoresis (PAGE): allows the separation of proteins on the basis of their mass to charge ratios (m/e). Remember gel electrophoresis for DNA? This method sorts proteins using the same properties: charge (which is more variable in proteins than DNA) and mass. SDS-PAGE can be used to separate proteins based on ONLY their masses, because it disrupts proteins charges.

  • Size exclusion chromatography (SEC) (Gel filtration chromatography): allows the separation of proteins on the basis of size– which is only slightly different from mass. In this case, there is a porous material that slows down smaller proteins. This might be counterintuitive: larger proteins are separated first, because smaller proteins move more slowly

  • Ion exchange chromatography (IEC): allows separation of proteins on the basis of charge. This may seem redundant with PAGE, but it uses an entirely different technique of a column that acts as a sort of filter. There are two types, named after which type of protein will stick to the stationary phase.

    1. Anion exchange chromatography: the resin is positively charged, so anions will stick.

    2. Cation exchange chromatography: resin is negatively charged, so cations will stick.

  • Affinity chromatography (AC): takes advantage of the fact that some proteins have a high affinity for specific chemicals or chemical groups. Perhaps it is easiest to understand with an example. Maybe you want to find a protein that binds to sugar. So, you coat beads with that sugar, and filter a bunch of proteins through. The proteins that come out of the column do not bind to the sugar. So separate the bound proteins, you do a “wash”

<ol><li><p>gel electrophorisis = used to tell if purification methods are effective</p><ol><li><p>what steps does it use</p><ol><li><p>molecules with electric charges move towerd the feild (negatice cathode to psitive anode)</p><ol><li><p>smaller moleucles move faster and furhte rwhile larger moleucels are pracitcally immoble in teh fluid</p></li></ol></li></ol></li></ol></li></ol><p></p><p>SDS is needed to separate by mase</p><ol><li><p>method</p><ol><li><p>the negatively charged SDS = denatures proteins = binds at a 1:2 ration sds to aino acid protein</p></li><li><p>Betamericapoethanol is added to reduce the disfulfide bond sof the amino acids = li nearization of proteins</p></li><li><p>allows for smaller molecules to move it down</p></li></ol></li></ol><p></p><ul><li><p><strong>Salting out: </strong>A separation technique that takes advantage of the fact that the solubility of proteins varies with the salt concentration. As the salt concentration is increased, different proteins will precipitate at different salt concentrations, a process called salting out.</p></li><li><p><strong>Polyacrylamide Gel Electrophoresis (PAGE):</strong> allows the separation of proteins on the basis of their mass to charge ratios (m/e). Remember gel electrophoresis for DNA? This method sorts proteins using the same properties: charge (which is more variable in proteins than DNA) and mass. SDS-PAGE can be used to separate proteins based on ONLY their masses, because it disrupts proteins charges.</p></li><li><p><strong>Size exclusion chromatography (SEC) (Gel filtration chromatography)</strong>: allows the separation of proteins on the basis of size– which is only slightly different from mass. In this case, there is a porous material that slows down smaller proteins. This might be counterintuitive: <em>larger proteins</em> are separated first, because <em>smaller proteins </em>move more slowly</p></li><li><p><strong>Ion exchange chromatography (IEC):</strong> allows separation of proteins on the basis of charge. This may seem redundant with PAGE, but it uses an entirely different technique of a column that acts as a sort of filter. There are two types, named after which type of protein will stick to the stationary phase.</p><ol><li><p>Anion exchange chromatography: the resin is positively charged, so anions will stick.</p></li><li><p>Cation exchange chromatography: resin is negatively charged, so cations will stick.</p></li></ol></li><li><p><strong>Affinity chromatography (AC):</strong> takes advantage of the fact that some proteins have a high affinity for specific chemicals or chemical groups. Perhaps it is easiest to understand with an example. Maybe you want to find a protein that binds to sugar. So, you coat beads with that sugar, and filter a bunch of proteins through. The proteins that come out of the column do not bind to the sugar. So separate the bound proteins, you do a “wash”</p></li></ul><p></p>
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look at your notes about allosteric enzymes, differences in charting. What is the differnece between a muchalis meten graph and an alllosteric enzyme. know how to draw the charts - know abou the te 3 horsemen of enzyme inhiibtion = competative uncompetative and noncompetative inhibiton

  1. how does the state of an allosteric enzyme play into its form

look at notes bae

  1. allosteric enzymes have multiple activaiton sytes

  2. the enzyme can exist in 2 states = t state and r state

  3. concentrated modle show s that all subunits or activesites must be in teh same states (T state or R state)

    1. note the R state is more favorable to binding while the t state is more stable - you can inhibit enzymes by forcing binding into the t state to make it more stable

      A chart I memorized for the different types of inhibitors : r/Mcat

<p>look at notes bae</p><ol><li><p>allosteric enzymes have multiple activaiton sytes</p></li><li><p>the enzyme can exist in 2 states = t state and r state</p></li><li><p>concentrated modle show s that all subunits or activesites must be in teh same states (T state or R state)</p><ol><li><p>note the R state is more favorable to binding while the t state is more stable - you can inhibit enzymes by forcing binding into the t state to make it more stable</p><img src="https://preview.redd.it/a-chart-i-memorized-for-the-different-types-of-inhibitors-v0-msvpxi22ymc51.jpg?auto=webp&amp;s=2b54d3a1854ee8cc6e8d7eaa3837c60f4718c2a4" data-width="100%" data-align="center" alt="A chart I memorized for the different types of inhibitors : r/Mcat"></li></ol></li></ol><p></p>
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What are the 4 differnet ypses of catalists used by enzymes

  1. covalent catalists

    1. active site contaiing a reacive groups that reacts whith incoming groups

  2. General Acid base catalists

    1. any thing other than water that acts like a protein donor or accptor

  3. metal ion catalists

    1. Serves as a neutrophile catalist = stabalizes the negative charge on the (reaction intermediate)

    2. can also bind to the substrate by increses the interactsion with the enzyme

  4. Catalists by approxiation

    1. reactions with 2 distinct substrates

    2. reaction rats must be consiterabley close by eachter to allow for conformational change

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What are teh steps to chromotripsion function as a n enzyme. How does it work, how does it utilize reaction intermediates. Know the genral steps and what interactions take place. Waht is the resulting binding energies of each

  1. Histidine attacks the serine and removes the hydrogen to. make it a good nucleophyle

  2. substrate binds to the enzyme

    1. the substrate binds to the sibtrate via noncolvaent forces- attaches to the serine (nuclophile)

  3. neturophile attack (tetrahedral intermediate formation

    1. oxygen hole binds the new found negative moleucle on the substrate as it attaches to the histidine (via its lone hydrogen)

    2. the carbonyl part attaches to teh oxygen hole

  4. collapse of the tetrahedral intrmeidate

    1. the oxygen hole is released and teh amine and carbonlyl secont are cleved leaving 2 new residues

  5. release of the amine component

    1. amine component lost - acyl-enzyme is used to release this

  6. water binds to open site on carbonyl

    1. using the acyl enzyme h2o comes in and binds tothe carbonyl group

  7. nuclophile attack of watr to the acytl enzyme (tetrahedral intermediate formation)

    1. new oxynation hole comes to stabilize the carbonyl group = hdyrgen bond with the nigrogen on histidine

  8. collapse of the tetrahedral intermedate

    1. stabalization of histidine

      1. release of the new substrate

Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The  Reaction Free Energy Profiles of the Acylation Process | Journal of the  American Chemical Society
  • note chromotripsin cleves petide bons selelcively on the carbonyl terminal syde of large hydrophobic amino acids

    • tryptophan, tyrosine, phenyl, methonine, isoleucine

<ol><li><p>Histidine attacks the serine and removes the hydrogen to. make it a good nucleophyle </p></li><li><p>substrate binds to the enzyme</p><ol><li><p>the substrate binds to the sibtrate via noncolvaent forces- attaches to the serine (nuclophile)</p></li></ol></li><li><p>neturophile attack (tetrahedral intermediate formation</p><ol><li><p>oxygen hole binds the new found negative moleucle on the substrate as it attaches to the histidine (via its lone hydrogen)</p></li><li><p>the carbonyl part attaches to teh oxygen hole</p></li></ol></li><li><p>collapse of the tetrahedral intrmeidate</p><ol><li><p>the oxygen hole is released and teh amine and carbonlyl secont are cleved leaving 2 new residues</p></li></ol></li><li><p>release of the amine component</p><ol><li><p>amine component lost - acyl-enzyme is used to release this</p></li></ol></li><li><p>water binds to open site on carbonyl</p><ol><li><p>using the acyl enzyme h2o comes in and binds tothe carbonyl group</p></li></ol></li><li><p>nuclophile attack of watr to the acytl enzyme (tetrahedral intermediate formation)</p><ol><li><p>new oxynation hole comes to stabilize the carbonyl group = hdyrgen bond with the nigrogen on histidine</p></li></ol></li><li><p>collapse of the tetrahedral intermedate</p><ol><li><p>stabalization of histidine</p><ol><li><p>release of the new substrate</p></li></ol></li></ol></li></ol><img src="https://pubs.acs.org/cms/10.1021/ja021369m/asset/images/medium/ja021369mf00010.gif" data-width="100%" data-align="center" alt="Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The  Reaction Free Energy Profiles of the Acylation Process | Journal of the  American Chemical Society"><ul><li><p>note chromotripsin cleves petide bons selelcively on the carbonyl terminal syde of large hydrophobic amino acids</p><ul><li><p>tryptophan, tyrosine, phenyl, methonine, isoleucine</p></li></ul></li></ul><p></p>
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What is the function of alpha-amulase and where does it cleve and not gleve

  • alpha amilas e= pancreatic enzyme usd for glucose digesiton

  • celves at the 1,4 linkages not 1,6 linkages

<ul><li><p>alpha amilas e= pancreatic enzyme usd for glucose digesiton</p></li><li><p>celves at the 1,4 linkages not 1,6 linkages</p></li></ul><p></p><p></p>
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What are the differnt ypes of glucose transportors uses

  1. Sgluts = sodiu, glucose linked transport

    1. gluoces + galactose uptake into intestanal cells

    2. fructose is small enough to diffuse across the cell membrane using GLUt 5

    3. Glut 2 releases monosachharides into the blood streme

<ol><li><p>Sgluts = sodiu, glucose linked transport</p><ol><li><p>gluoces + galactose uptake into intestanal cells</p></li><li><p>fructose is small enough to diffuse across the cell membrane using GLUt 5</p></li><li><p>Glut 2 releases monosachharides into the blood streme</p></li></ol></li></ol><p></p>
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 Explain what is meant by metabolism in terms of both catabolic and anabolic processes.

Catabolism = breakdown of coplex molecuels

  • allows for enrgy release

  • building block for biosyntehis ( NADH and FADH2)

Anabolyzm

= upatake of eneryg to make prdocut

usesATP + NADPH to form

Reaction coupling can help make an unfoavorable reaction fravorable

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Identify factors that make ATP and other phosphoesters useful molecules for capturing and transforming chemical energy. (4 methods)

  1. electrostatic repulsiotn

    1. 4 negative chargers present when atp is present = higer energy due to strong erpulsive forces

  2. resonance stablaization

    1. After ATP hydrolysis:

      ATP → ADP + Pi

      The inorganic phosphate (Pi) has many resonance forms, making the products more stable.

      Greater stability → energy release.

  3. increase in entropy’

    1. more disorder = higher energy for relase

  4. stabalization due to water

    1. water helps stabilizes

    2. The products of hydrolysis (ADP + Pi) interact with water more favorably than ATP.

      This stabilization also contributes to a negative ΔG.

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Explain how ATP can power reactions that would otherwise not occur.

  • the high energy output from when phospahte gorps are removed from atp = makes unfavoral reactions more favorable = reaction coupling

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Describe the relationship between the oxidation state of a carbon molecule and its usefulness as a fuel.

Reduced molecules

Contain many:

  • C–H bonds

  • Few oxygen atoms

These molecules store large amounts of chemical energy.

Examples:

  • Fatty acids

  • Hydrocarbons

They release energy when oxidized to CO₂.


Oxidized molecules

Contain many:

  • C–O bonds

Examples:

  • CO₂

  • Carboxylic acids

These molecules already lost most of their energy and therefore cannot serve as effective fuels.

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 Summarize the recurring motifs and regulation principles in metabolic pathways.

Metabolic pathways are organized into stepwise enzyme-catalyzed reactions with a committed (rate-limiting) step that is often irreversible. They are regulated by allosteric control (activators/inhibitors like ATP), feedback inhibition (end product inhibits an early step), and covalent modification (e.g., phosphorylation). Pathways are also compartmentalized and use common energy carriers (ATP, NADH, NADPH) to coordinate energy flow.

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Describe the following shoot: NAD+/NADH, FAD/FADH2, Coenzyme A

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Differentiate among the structures and functions of glycoproteins and lectins.: What are the general function of glycoproteins (3 major classes): Glycoprotins, proteoglycnans, mucans

  • what are their general strcuture

Back (Answer):

General Function:

  • Many are membrane proteins (largest component by weight)

  • Often carbohydrate-rich

  • Roles include:

    • Structural support

    • Cell recognition (receptors)

    • Lubrication


Glycoproteins:

  • Proteins with covalently attached carbohydrates

  • Found especially in cell surface receptors

Types:

  • O-linked glycoproteins

    • Sugar attached to –OH group of serine (Ser) or threonine (Thr)

  • N-linked glycoproteins

    • Sugar attached to amide nitrogen of asparagine (Asn)

    • Formed in the endoplasmic reticulum (ER)


Proteoglycans:

  • Proteins attached to glycosaminoglycans (GAGs)

  • GAGs = long chains of repeating disaccharide units:

    • One amino sugar derivative

    • One negatively charged sugar

  • Function:

    • Provide structural support

    • Act as hydrated gels/lubricants


Mucins:

  • Heavily glycosylated proteins (mostly carbohydrate)

  • Carbohydrates attached via N-acetylgalactosamine (O-linked)

  • Function:

    • Form mucus

    • Provide lubrication and protection (e.g., in respiratory & digestive tracts)

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What are lectins, their structure, funciton and whatnot

Structure:

  • Proteins that bind carbohydrates (NOT covalently attached)

  • Have specific carbohydrate-binding sites

Function:

  • Recognize and bind specific sugars on glycoproteins/glycolipids

  • Mediate:

    • Cell-cell interactions

    • Immune responses

    • Cell targeting

Lectins — What You Should Definitely Know

  • Act like “carbohydrate recognition molecules”

  • Highly specific (can distinguish small sugar differences)

  • Important in:

    • Immune system (pathogen recognition)

    • Cell communication

  • Can cause cell agglutination (clumping) by cross-linking glycoproteins

  • Used in labs to:

    • Identify cell types

    • Study glycosylation patterns


Easy Way to Remember

  • Glycoprotein = HAS sugar

  • Lectin = GRABS sugar

<p><strong>Structure:</strong></p><ul><li><p><strong>Proteins that bind carbohydrates (NOT covalently attached)</strong></p></li><li><p>Have <strong>specific carbohydrate-binding sites</strong></p></li></ul><p><strong>Function:</strong></p><ul><li><p><strong>Recognize and bind specific sugars</strong> on glycoproteins/glycolipids</p></li><li><p>Mediate:</p><ul><li><p>Cell-cell interactions</p></li><li><p>Immune responses</p></li><li><p>Cell targeting</p></li></ul></li></ul><p></p><p></p><p><strong>Lectins — What You Should Definitely Know</strong> </p><ul><li><p>Act like <strong>“carbohydrate recognition molecules”</strong></p></li><li><p>Highly <strong>specific</strong> (can distinguish small sugar differences)</p></li><li><p>Important in:</p><ul><li><p><strong>Immune system</strong> (pathogen recognition)</p></li><li><p><strong>Cell communication</strong></p></li></ul></li><li><p>Can cause <strong>cell agglutination</strong> (clumping) by cross-linking glycoproteins</p></li><li><p>Used in labs to:</p><ul><li><p>Identify cell types</p></li><li><p>Study glycosylation patterns</p></li></ul></li></ul><p> </p><div data-type="horizontalRule"><hr></div><p> <strong>Easy Way to Remember</strong> </p><ul><li><p><strong>Glycoprotein = HAS sugar</strong></p></li><li><p><strong>Lectin = GRABS sugar</strong></p></li></ul><p></p>
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Describe the irreversible and commited steps of glycolisis. what makes them what them what they are

use chat to fill this out- look at your notes.

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Describe how and why the aldolase mechanysm works generally

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What are schiff bases and what is their role in aldolase

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Describe the role of the thioesterintermediate in G3p dehydrogenates

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What are the equations for glycolisis and lactate/ ethanol fermentation glycolisis

<img src="https://assets.knowt.com/user-attachments/81a22863-441c-4ec4-a86a-261ba0151a9c.png" data-width="100%" data-align="center"><p></p>
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