Biochemistry MCAT

Intermembrane space mitochondria

- where protons pump into from e- transport chain - bw outer & inner membranes

What is the most common protein, found in microfilaments, found in most human cells?

Actin

Active transport moves substances _________ a concentration gradient.

Active transport moves substances AGAINST a concentration gradient.

What is the name for a five carbon sugar with an aldehyde group? Six carbon sugar with a ketone group?

Aldopentose, ketohexose

Negatively Charged (acidic) side chains

Aspartic acid (deprotonated form is aspartate)(pka=4), Glutamic Acid (Glutamate) Related to asparagine and glutamine but with carboxylate groups in side chains, rather than amides Negative charged side chains at pH 7.4

A deficiency in thiamine (vitamin B1) can result in:

Beriberi: Congestive heart failure/nerve damage Wernicke-Korsakoff syndrome: Difficulty walking, uncoordinated eye movements, confusion, memory problems (alcoholics) Giving glucose to someone with thiamine deficiency = severe lactic acidosis and other problems because pyruvate cant be converted in acetyl CoA without vitamin B1

Glucose

C6H12O6

Holoenzymes

Complex formed when enzymes bind their cofactors The enzyme that results when the cofactors are absent is an apoenzyme An enzyme devoid of its necessary cofactor is called an apoenzyme and is catalytically inactive.

Pyruvate dehydrogenase

Converts pyruvate to acetyl CoA Located in the mitochondrial matrix Therefore, every enzyme that comes after it in aerobic respiration is also located in mitochondrion Pyruvate Kinase is the last enzyme of glycolysis (cytosolic process)

Induced fit model

Currently accepted model for enzyme activity Replaced the lock and key model

Bradford (Coomassie Brilliant Blue) protein assay

Determines protein concentration

Sickle Cell Disease

Mutation in hemoglobin (protein in RBCs that transport oxygen) Change in single amino acid on hemoglobin surface -> glutamic acid to valine -> Allows deoxygenated form of HbS to aggregate E6V indicates that the 6th amino acid (Glutamic acid, E) has been changed to valine (V)

semiconservative replication

Parental strands serve as templates for daughter strands: Semiconservative replication (one parental strain retained in each of the 2 resulting identical double stranded DNA molecules New double helix made from one old parent strand and one new daughter strand

Bohr Effect

Right shift of the oxyhemoglobin dissociation curve due to a decrease of blood pH (High H+), high pCO2, or High 2,3-BPG. Results in a decreased affinity for oxygen All occur during exercise (Exercise is the RIGHT thing to do)

Half Reactions

Spontaneous oxidation-reduction reactions have - delta G and + E (electromotive force)

Isozyme

The different structural forms of enzymes that have the same function

Three stop codons that end protein synthesis:

UAA UAG UGA U are annoying U go away U are gone

Edman Degredation

Useful in determining primary structure of protein

Western Blot

a test that detects HIV antibodies and confirms the results of earlier EIA tests Specific antibody of interest binds to proteins that were spectated on gel. Band appears when antibody successfully binds to protein

Nonpolar, nonaromatic amino acids

glycine (H side chain), alanine (CH3 side chain), valine (CH2CH3 side chain), leucine (3 carbon side chain), isoleucine (4 carbon side chain), methionine (1 of only 2 amino acids to have sulfur in side chain), proline (5 carbon ring)

Isoforms

slightly different versions of the same protein

Binding Proteins

- Transport or sequester molecules by binding to them - Hemoglobin, calcium-binding proteins, DNA-binding proteins (transcription factors) -Affinity curve for each: When we want molecule, binding proteins high affinity -Transport protein likely needed

Mixed Inhibition

A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; mixed inhibitors bind to the free enzyme and to the substrate-bound enzyme with different affinities. They cannot be overcome by addition of substrate and impact both Km and vmax Noncompetitive is a type of mixed inhibitor with allosteric site, binds equally well to free enzyme and substrate-bound enzyme

Micelle

A single-layered structure with hydrophilic groups pointing outward Forms when lipids reach a critical concentration in water Micelle's surface is exposed to water = hydrophilic *A vesicle is a double-layered structure with hydrophilic groups on the exterior surfaces

Glycerol

A three-carbon alcohol to which fatty acids are covalently bonded to make fats and oils.

Urea cycle in the mitochondria

Ammonia (weak base) converted to urea becuase ammonia cant be excreted easily Begins inside mitochondrial matrix : Ammonia and HCO-3 + 2 ATP Combines with aspartate in cytoplasm, becomes arginine and fumarate. Arginine acted on by arginase, becomes urea (soluble, dissolves into blood) and ornithine Basic amino acid side chains feed into urea cycle, while other side chains act like carbon skeleton and produce energy through gluconeogenesis or ketone production

Given the following pKa values, what is the value of the pI for each of the amino acids listed below? Aspartic acid: (pKa1 = 1.88, pka2 = 3.65, pka 3 = 9.60) Arginine: (pka1 = 2.17, pka2 = 9.04, pka = 12.48)

Aspartic acid: (pKa1 = 1.88, pka2 = 3.65, pka 3 = 9.60) 1.88 + 3.65 /2 = about 2.7 Arginine: (pka1 = 2.17, pka2 = 9.04, pka = 12.48) 9.04 + 12.48 / 2 About 10.75

Which of the following describes the bond that is broken and the products that are formed during a retro-aldol reaction?

Bond between alpha and beta carbon of carbonyl; aldehydes and/or ketonesCorrect Answer ImageCorrect answer In this reaction, a bond is broken between the α-and β-carbons of a carbonyl, forming two aldehydes, two ketones, or one aldehyde and one ketone. A retro aldol reaction is the reverse of an aldol condensation reaction where two carbonyl molecules are joined with the loss of a molecule of water. To push the reaction in a retro-aldol direction, aqueous base is added and heat is applied. The retro-aldol reaction breaks bonds between the α- and β- carbons of a carbonyl when there is a hydroxyl group on the β- carbon. The products are two aldehydes, two ketones, or one aldehyde and one ketone.

Oxidoreductases

Catalyze redox reactions

Hydrolase

Catalyzes cleavage by adding water

Glyceraldehyde-3-Phosphate Dehydrogenase

Catalyzes oxidation and addition of inorganic phosphate (Pi) to its substrate, glyceraldehyde 3-phosphate, which results in the intermediate 1,3-bisphosphoglycerate and reduction on NAD+ to NADH NADH can be oxidized in aerobic glycolysis by electron transport chain, providing ATP synthesis by oxidative phosphorylation

After an overnight fast, which of the following enzymes would be expected to have little, if any, physiological activity? A. Malate dehydrogenase B. Glucokinase C. α-Ketoglutarate dehydrogenase D. Phosphofructokinase-1

Correct Answer: B Explanation: After an overnight fast, the liver is producing glucose and glucokinase activity would be insignificant. Glucokinase is used to trap extra glucose in liver cells as part of a storage mechanism; with low blood glucose, liver cells would be generating new glucose, not storing it. It is also in the pancreas, where it serves as a glucose sensor; if glucose levels are low, it has little activity in this tissue as well. Malate dehydrogenase, choice (A), and α-ketoglutarate dehydrogenase, choice (C), are citric acid cycle enzymes. Phosphofructokinase-1, choice (B), is a glycolytic enzyme. Other enzymes used in glycolysis, the citric acid cycle, or gluconeogenesis, such as phosphofructokinase-1, would be expected to maintain normal activity after an overnight fast, using glucose derived from glycogen or gluconeogenesis, rather than orally ingested glucose.

Fatty acids are synthesized in the _________ and modified in the ________

Fatty acids are synthesized in the cytoplasm and modified in the smooth endoplasmic reticulum

Nucleolus

Found inside the nucleus and produces ribosomes

What is the ratio of free fatty acids to glycerol produced through lipid mobilization?

Free fatty acids to glycerol = 3:1 Triacylglycerol = glycerol and 3 fatty acids

Gel Electrophoresis and Southern Blotting

Gel Electrophoresis: Separates Macromolecules (DNA, proteins, etc) by size and charge DNA (negatively charged) migrates towards anode (positive) Agarose gel preferred for DNA< polyacrylamide gel for protein Longer strand = slower migration Gel Electrophoresis often used with Southern blot: Detects presence and quantity of DNA strands (cut and separated by Gel Electrophoresis) -DNA fragments transfered to membrane, probed with copies of single stranded DNA, and probe will bind to its complementary sequence and form double stranded DNA Probes labeled with radioisotopes or indicators

high energy bonds in ATP

Highest energy bond around the second and third O in phosphate groups

Strand Separation and Origins of Replication

Human genome has 3 billion base pairs in multiple chromosomes Replisome/replication complex is a set of specialized proteins that assist the DNA polymerases Process of replication begins when DNA unwinds at origin of replication New DNA proceeds in both direction, creating replication forks on both sides

A diabetic patient begins insulin injections for management of blood glucose levels. What is expected impact on patients weight?

Increase in insulin will increase lipid storage and decrease lipid mobilization from adipocytes, leading to weight gain

Formation of recombinant plasmid vector

Need ori (origin of replication), ampR (gene for resistance to ampicillin/antibiotic) and gene (w/ restriction enzyme site) DNA vectors have at least 1 sequence recognized by restriction enzymes Vector also requires origin of replication and at least one gene for antibiotic resistance to allow for selection of colonies

DNA Sequencing

Need template DNA, primers, appropriate DNA polymerase, and all four deoxyribonucleotide triphosphates Also need modified base called dideoxyribonucleotide in lower concentration : dideoxyribonucleotides (ddATP, ddCTP, ddGTP, ddTTP) contain H at C'3 rather than OH group, so once these have been added the polymerase cant add to chain anymore

Negative Control and Positive Control Inducible and Repressible System

Negative Control: binding protein to DNA stops transcription Positive control: Binding of protein to DNA increases transcription Inducible System: The system is normally off, but turned on with certain signal Repressible: Transcribed under normal conditions, normally on but can be turned off bycorepressor coupling with repressor and binding of this complex to operator site Lac operon is a negative inducible system, Trp operon is negative repressible system Trp: only represses when Trp present Lac: only represses when Lac not present

Fructose Metabolism

Part of disaccharide sucrose (table sugar) Sucrose hydrolyzed by duodenal brush border enzyme sucrase -> yields glucose and fructose (absorbed into hepatic portal vein) Liver phosphorylates fructose with fructokinase to trap it in cell => fructose-1-phosphate -> cleaved into glyceraldehyde and DHAP by aldolase B Small amount metabolized in renal proximal tube Dihydroxyacetone phosphate (DHAP) and glyceraldehyde (products of fructose metabolism) are below regulatory and rate limiting enzyme of glycolysis (PFK-1), so high fructose are quick source of energy in aerobic and anerobic cells

Cori Cycle

RBC lack mitochondria so they cant do aerobic metabolism So, pyruvate converted to lactic acid to regenerate NAD+ But lactate is acidic and must be removed from blood RBCs delver lactate to liver where its converted back into pyruvate and through gluconeogenesis becomes glucose for RBC to use Glucose to lactate in RBC, and lactate to glucose in liver

In an enhancer, what are the differences between signal molecules, transcription factors, and response elements?

Signal molecules include steroid hormones and second messengers, which bind to their receptors in nucleus Receptors are transcription factors that use their DNA binding domain to attach to particular sequence in DNA called a response element. Once bonded to response element, transcription factor promote increased expression of gene Specific transcription factors bind to a specific DNA sequence, such as an enhancer, and to RNA polymerase at a single promoter sequence. They enable the RNA polymerase to transcribe the specific gene for that enhancer more efficiently. Enhancers are transcriptional regulatory sequences that function by enhancing the activity of: A. RNA polymerase at a single promoter site.

Synthesis of DNA from: Reaction: 3' OH acts as a ______________, attacking ______________ of the next ______, causing ______ to hop off

Synthesis of DNA from: 5' to 3' Reaction: 3' OH acts as a nucleophile, attacking 5' phosphate of the next dNTP, causing pyrophosphate (PPi) to hop off The covalent bond that is formed is a 3'-5' phosphodiester bond

Glycogenesis

Synthesis of glycogen granules Begins with core protein: glycogenin Glucose to glucose 6-phosphate to glucose - 1 phosphate activated by coping to molecule of uridine diphosphate (UDP) This permits integration into glycogen chain by glycogen synthase Activation occurs when glucose 1 phosphate interacts with uridine triphosphate (UTP), forming UDP-glucose and pyrophosphate (PPi)

Stop Codons

UAA, UAG, UGA No charged tRNA molecules that recognize there, leads to release of protein from ribosome

Southern Blotting

Useful when searching for particular DNA sequence because it separates DNA fragments by length and then probes for sequence of interest Sample transferred to membrane that can be probed with single stranded DNA molecules to look for sequence of interest

G6PD deficiency

X-linked recessive. Most common inherited enzyme defect in the world PPP maintains glutathione, which helps break down peroxides , so no G6PD = oxidative stress, especially in RBC Maybe evolved from resistance to malaria G6PD: G6P + NADP+ -> 6PG + NADPH; NADPH needed to reduce GSSG to 2GSH (glutathione reductase) for H2O2 to 2H2O conversion. Only pathway for making reduced GSH in RBC, so can't detoxify free radicals / peroxides (dont ingest, will cause hemolysis: fava beans, sulfa drugs, primaquine, anti-TB drugs); leads to hemolytic anemia. More common in blacks (inc malaria resistance), #1 human enzyme deficiency. Heinz bodies (Hb precipitates in RBC) & WB cells (macrophage phagocytosis of heinz bodies - bite out of cell)

4 types of reversible inhibition of enzymes Reversible Inhibition: Characterized by ability to replace the inhibitor with compound of greater affinity or to remove it using lab

competitive: occupation of the Active site -Substrates can't access enzymatic binding sites if inhibitor in the way -BUT: if you add way more substrate than inhibitor, you wills till have some proper binding Does not alter the value of V max, because if enough substrate is added, it will out compete the inhibitor and run at max velocity Increases Km because the substrate concentration has to be way higher to reach have the maximum velocity in presence of inhibitor -Methanol poisoning treated by ethanol because it competes with methanol for active sites of the enzymes involved noncompetitive: binding to an allosteric site (instead of active site), changing enzyme conformation -Inhibitor binds with equal affinity to the enzyme and enzyme-substrate complex -Allosteric sites are non-catalytic regions of the enzyme that bind regulators -Molecules don't compete for the same site (non competitive) -Doesn't matter how much substrate you add -Bind equally well to enzyme and enzyme - substrate complex -Once the confirmation is altered, no amount of extra substrate will be conductive to forming an enzyme-substrate complex -Decreases V max because there is less enzyme to react, but it does not alter Km because any copies of the enzyme that are active maintain the same affinity for substrate mixed: can bind to the enzyme or the complex with different affinity for each -Inhibitor binds with unequal affinity to the enzyme and the enzyme-substrate complex. V maxis decreased, Km is increased or decreased depending on if the inhibit has higher affinity for enzyme or enzyme-substrate complex uncompetitive: can only bind to the enzyme-substrate complex, lock substrate in enzyme, preventing the release of the substrate -Increase affinity between enzyme and substrate -Complex has already been formed, so binding must be at allosteric site (in fact, formation of complex creates conformational change that allows uncompetittive inhibitor to bind -Lowers Km and Vmax (parallel line) -Does not prevent substrate from binding to enzyme, but when inhibitor binds, it prevents complex from making products SO: *Competitive: Binding site: Active site Impact on Km: Increases Impact on V max: None Noncompetitive: Binding site: Allosteric site Impact on Km: None Impact on V max: Decreases Uncompetitive: Binding site: Allosteric site Impact on Km: decreases Impact on V max: decreases Mixed: Binding site: Allosteric site Impact on Km: Increases or decreases Impact on V max: decreases

malate-aspartate shuttle

cytosolic oxaloacetate cannot pass through the inner membrane so oxaloacetate is transferred into malate through *malate dehydrogenase* and the oxidation of NADH to NAD+ malate crosses the inner membrane and then reverse the reaction to form NADH NADH can now go into the ETC making 2.5 ATP More efficient, good for highly aerobic organs, like heart

Aspartic acid, Asp, D

pka 3.9

Catecholamines

secreted by the adrenal medulla ->> basically just increase glucose in blood levels ex. epinephrine (adrenaline) (image shown) norepinephrine (noradrenaline) increase the activity of liver and muscle glycogen phosphorylase - promotes glucogenolysis (breakdown of glycogen)- increasing the rate at which the liver can release glucose into the blood glycogenolysis also increases in the muscle but muscle lacks glucose 6 phosphatase which means that glucose cannot be released by skeletal muscle into the blood stream - glucose here is metabolized by the muscle itself act on adipose tissue to increase lipolysis by increasing the activity of hormone sensitive lipase the glycerol and triglyceride breakdown are substrates for the gluconeogenesis Epi can also act directly on organs

+ ΔS and +ΔH + ΔS and -ΔH - ΔS and +ΔH - ΔS and -ΔH

ΔG = ΔH - T ΔS + ΔS and +ΔH Nonsponatneous at low temp Spontaneous at high temp + ΔS and -ΔH Spontaneous - ΔS and +ΔH Non spontaneous at all temps - ΔS and -ΔH Non spontaneous at high temps Spontaneous at low temps

Cholesterol

Ubiquitous (found everywhere) component of all cells in human Major role in synthesis of cell membranes, steroid hormones, bile acids, and vitamin D Many cells derive it from LDL or HDL May be synthesized de novo (new) --> occurs in liver, driven by acetyl coa and ATP Citrate shuttle carries mitochondrial acetyl coa into cytoplasm, where synthesis occurs NADPH from pentose phosphate pathway supplies reducing equivalents Synthesis of Mevalonic acid in smith ER is rate limiting step (catalyzed by 3-hydroxy-3-methylglutaryl (HMG) CoA reductase Regulating cholesterol: -Cholesterol can inhibit further synthesis -Insulin can promote synthesis -De novo cholesterol synthesis dependent on regulation of HMG CoA reductase gene expression *HMG-CoA reductase (located in smooth endoplasmic reticulum) is most active in the absence of cholesterol and when stimulated by insulin (cholesterol reduces activity) Transport of cholesterol: LCAT (activated by HPL apoproteins) makes it soluble by adding fatty acid = soluble cholesteryl esters (LCAT catalyzes esterification of cholesterol to form cholesteryl esters LCAT catalyzes the production of cholesteryl esters. CETP facilitates transfer process: Promotes transfer of cholesteryl esters from HDL to IDL, forming LDL LCAT adds a fatty acid to cholesterol, producing cholesteryl esters, which dissolve in the core of HDL, allowing HDL to transport cholesterol from the periphery to the liver.

Fat-Soluble Vitamins (A, D, E, K)

Vitamin: Cant be synthesized by body and must be consumed in diet Lipid soluble vitamins can accumulate in stored fat, but excess water soluble vitamins are peed out The fat-soluble vitamins (A, D, E, K) are all: Isoprene-based lipids Vitamin A (carotene): Unsaturated, important in VISION, growth, development, and immune function -Metabolite of vitamin A is aldehyde form, retinal -Retinol is storage form of V A, oxidized to retinoid acid (hormone that regulates gene expression during epithelial development) Vitamin D (Cholecalciferol): Converted to calcitriol in liver and kidneys (biologically active form) -Increases calcium and phosphate uptake in intestines, promotes bone production-Calcium and phosphate regulation -Lack of vitamin D = rickets (curved long bones, impeded growth) Vitamin E: Group of closely related lipids called tocopherols and tocotrienols Vitamin E is made up of tocopherols, which are biological antioxidants -Substituted aromatic ring with long isoprenoid side chain -HYDROPHOBIC -Antioxidants -> aromatic rings reacts with and destroys free radicals (prevents oxidative damage) -Free radicals linked to aging and cancer Vitamin K: Group of compounds, including phylloquinone (K1) and menaquinone (K2) -Posttranslational modifications required to form prothrombin (clotting factor) -Aromatic ring undergoes oxidation and reduction -Introduces calcium-binding sites -Warfarin (anticoagulant) blocks recycling of vitamin K

Hormonal Regulation of Metabolism

Water soluble peptide hormones like insulin adjust metabolic processes of cells via second messenger cascades, while certain fat soluble amino acid derivative hormones (Like thyroid hormones and steroid hormones (like cortisol)) enact longer range effects by exerting regularity actions at transcriptional level *Steroid hormones are fat/ lipid soluble and can pass through membrane, hydrophobic *Insulin causes decrease in blood glucose, which removes trigger for continued insulin release

Watson-Crick Model What is the complementary and antiparallel sequence for 5'-ATCG-3'?

What is the complementary and antiparallel sequence for 5'-ATCG-3'? 5'-CGAT-3' Double helical model with specific base pairing 2 linear polynucleotide chains of DNA wound together is spiral 2 strands are antiparallel (oriented in opposite directions, when one strand has polarity 5' to 3' down the page, the other strand has 5' to 3' up the page) Sugar phosphate backbone is on the outside of the helix with nitrogenous base on inside Complementary base pairingL A always paired to T (in DNA) via 2 H bonds G always paired to C with 3 H bonds (stronger interactions) *So, the amount of A = amount of T, and the amount of G always = the amount of C, so the total purines = total pyrimidines (Chargaff's Rule) H bonds + strong hydrophobic interactions = stability Right handed helix: Forms B-DNA Makes a turn every 3.4 nm and contains 10 bases within that span Major and minor grooves: provide binding sites for regulatory proteins Z-DNA: left handed helix that has a turn every 4.6 nm and contains 12 bases within each turn High GC content or high salt concentration may contribute to formation of this form of DNA (unstable and difficult to research)

Question on next slide

What is the product of the following reaction? Correct Answer: B Explanation: When glucose reacts with ethanol under acid catalysis, the hemiacetal is converted to an acetal via replacement of the anomeric hydroxyl group with an alkoxy group. The result is a type of acetal known as a glycoside. This corresponds with choice (B). Choice (A) is incorrect because the -OH on the C-6 carbon would not be converted to -OCH3.

Uncharged aromatic side chain amino acids

tryptophan (largest), phenylalanine (smallest), tyrosine (phenylalanine + OH)

Debranching Enzyme

two enzyme complex deconstructs branches in glycogen that have been exposed by glycogen phosphorylase breaks alpha 1,4 bond adjacent to branch point and moves small oligoglucose chain (about 3 glucose) released to the exposed end of the other chain and forms new alpha 1, 4 bond (alpha 1,4:alpha 1,4 transferase) hydrolyzes alpha 1,6 bond and releases single residue at branch point as free glucose (only free glucose produced directly in glycogenolysis) (alpha 1,6 glucosidase)

VLDL

very low density lipoprotein Lots of lipids, not lots of proteins lipid transporter phospholipids are used for membrane synthesis and can produce hydrophilic surface layer on lipoproteins like VLDL

Prostaglandins

*Produced by almost all cells * 20 carbon molecules *unsaturated carboxylic acids derived from arachidonic acid *contain 1 five carbon ring * act as paracrine or autocrine signaling molecules *regulate synthesis of cAMP (intracellular messenger that regulates action of other hormones) -> cAMP involved in many pathways, including those that drive pain and inflammation *influence sleep-wake cycles, have effects on smooth muscle, involved in elevation of body temp due to fever Aspirin inhibits the enzyme cyclooxyrgenase (COX), which aids in production of prostaglandins

Aromatic Rules

- Huckel's Rule: 4n+2 (where n is any integer) pi electrons - Conjugated pi electrons (alternating single and multiple bonds or lone pairs, creating at least 1 unhybridized p-orbital for each atom in the ring )(for every pi bond you have 2 pi electrons, + charge has no pi electrons, lone pair is also 2 pi electrons) - planar molecule (sp2 = trigonal planar, no tetrahedral (sp3) allowed) - cyclic molecule Aromatic compounds are extra stable because of delocalized pi electrons Fairly unreactive Benzene: All 6 carbo atoms are sp2, and each of the 6 orbitals overlaps equally with 2 neighbors -Delocalized electrons form 2 pi electron clouds (one above and one below)

Repressible Systems

- allow constant production of a protein product unless corepressor binds to repressor to stop transcription - the repressor maintains inactivity until bound with a corepressor, this complex then binds to the operator to prevent transcription - Usually negative feedback: Final product can serve as corepresor (as levels increase, it binds to repressor and complex attaches to operator) Trp operon: Negative repressible (System normally on) -When trp is high, it acts as corepressor, binding of 2 molecules of tryptophan to repressor causes repressor to bind to operator, turns cell machinery off

Respirometry Respiratory Quotient (RQ)

- allows accurate measurement of the respiratory quotient, which differs depending on the fuels being used by the organism RQ = CO2 produced / O2 consumed RQ for carbs is about 1, for lipids is around 0.7, in resting people = 0.8, with exercise it increases (approaches 1) Calorimeters can measure basal metabolic rate (BMR) based on heat exchange with environment -BMR can be estimated based on age, weight, height, gender

Goldman-Hodgkin-Katz voltage equation

- derived from Nernst equation - calculates the resting potential of a membrane at physiological temperature -P represents permeability for relevant ion -Chloride inverted because it has negative charge

glycerol 3-phosphate shuttle

- electrons are transferred from NADH to dihydroxyacetone phosphate (DHAP), forming glycerol 3-phosphate - these electrons can then be transferred to mitochondrial FAD, forming FADH2 -Complex 2 : generates 1.5 ATP for every molecule of cytosolic NADH *glycerol 3-phosphate is link between lipid metabolism and glycolysis -> can be converted to DHAP (intermediate of glycolysis)

postprandial (absorptive) state

-"well-fed" state, occurs shortly after eating (lasts 3-5 hours) -greater anabolism (synthesis of biomolecules) and fuel storage (Less catabolism (breakdown of biomolecules for energy)) -Nutrients from gut through hepatic portal vein to liver where they are stored/distributed to other tissues -blood glucose levels rise, which stimulates release of insulin -> 3 major targets for insulin are liver, muscle, and adipose tissue -Insulin promotes glycogen synthesis in liver and muscle -After glycogen stores are filled, liver converts excess glucose to fatty acids and triacylglycerols (triacylglycerol synthesis in adipose tissue and protein synthesis in muscle, glucose entry into both) -After meal, most energy needs met in liver by oxidation of excess amino acids 2 Types of cells: nervous tissue and RBC, are insensitive to insulin-> NT gets energy from oxidizing glucose to CO2 and water (Only changes in prolonged fasting), RBC use glucose anaerobically only

Cell adhesion molecules (CAMs) (Membrane Proteins)

-Membrane proteins found on surface of most cells -aid in binding the cell to the extracellular matrix or to other cells 3 Major families: Cadherins: Holds two cells of the same or similar type using calcium -Glycoprotiens that mediate calcium dependent cell adhesion -Hold similar cells types together -Type specific Integrins: One cell to proteins in the extracellular matrix -Two membrane spanning chains (alpha and beta) -Bind and communicate with extracellular matrix -Cellular signaling -Tells cell to migrate, divide, die..... Selectins: -Bind to carb molecules that project from other cell surfaces -Binds one cell to carbohydrates, usually on the surface of other cells -Weakest CAM -On WBC and endothelial cells that line blood vessels -Like interns, play role in host defense (inflamtion and cell migration)

Citric Acid Cycle (Krebs Cycle)(TCA Cycle)

-Occurs in the mitochondrial matrix -Main function is to oxidize acetyl-coa to CO2 and H2O -Produces high energy e- carrying molecules NADH and FADH2 -Indirectly requires oxygen because without O2, NADH and FADH2 will buildup becuase nothing excepts their electrons at the end of ETC Starts with acetyl-coa coupling to oxaloacetate Mnemonic: Please Answer Officer: Can I keep selling seashells for money officer? Pyruvate, Acetyl coa + oxaloacetate, citrate, isocitrate, a-Ketoglutarate, succinyl-coa, succinate, fumarate malate, oxaloacetate

Pentose Phosphate Pathway (PPP)

-aka hexose monophosphate (HMP) shunt -occurs in the cytoplasm of all cells -two major functions/ 2 major metabolic products : producing NADPH and serving as a source of ribose-5-phosphate for nucleotide synthesis First part beings with glucose 6 phosphate, ends with ribose-5-phosphate (irreversible) *This enzyme is an important factor in the pentose phosphate pathway because it provides a source of raw materials for nucleotide synthesis. If this pathways is disrupted, nucleotide synthesis would suffer. -Produces NADPH, involves rate limiting enzyme: Glucose-6-phosphate dehydrogenase (G6PD) G6PD Induced by insulin because abundance of sugar entering cell under insulin stimulation shunted into fuel utilization (glycolysis and aerobic respiration) and fuel storage pathways (fatty acid synthesis, glycogenesis, and PPP) Shunt inhibited by product: NADPH Activated by NADP+ Second part of pathway: Begins with ribulose 5 phosphate: reversible, produce equilibrium of sugars, including ribose 5 phosphate Fructose 6 phosphate and glyceraldehdye 3 phosphate are among sugars produced, so intermediates can feed back into glycolysis, and pentoses can be made from glycolytic intermediates without going through G6PD reaction (interconversion accomplished by transketolase and transaldolase) The ribulose 5 phosphate created in PPP is isomerize to ribose 5 phosphate, backbone of nucleic acids. When coupled to N base, it forms nucleotide that can be integrated into RNA

Proton Motive Force

-as [H+] increases, pH drops in intermembrane space and voltage difference increases due to proton pumping: Electrochemical gradient (both chemical and electrostatic properties)(AKA PMF) -energy harnessed by ATP synthase to form ATP from ADP+Pi NADH Shuttles: Remember, we get 30-32 ATP per glucose -Variablility comes because cytosolic NADH formed through glycolysis can't directly cross into mitochondrial matrix (can't contribute to ETC directly) -So, NADH uses shuttle mechanisms (transfers high energy electrons of NADH to carier that can cross inner mitochondrial membrane) Two shuttles: Glycerol 3-phsophate shuttle and malate-aspartate pathway

Telomeres and Centromeres

-bc DNA replication cannot extend to the end, you would lose some sequence with each round of replication, but telomeres are repetitive units (TTAGGG) that act as caps at the ends of chromosomes (replaced by telomerase when some is lost after each round of replication) -More highly expressed in rapidly dividing cells -Progressive shortening of telomeres = aging -high GC content (strong bonds) prevents unraveling (knotting off the end of a chromosome) -centromeres: Region fo DNA found in center of chromosomes -Sites of constriction -> noticeable indentations - composed of heterochromatin (high GC content) which hold sister chromatids connected at centromere until microtubules separate them during anaphase *not to be confused with centrioles, which help in the formation of the spindle fibers that separate the chromosomes during cell division (mitosis), and are located at the poles

3 fates of pyruvate

-conversion to acetyl-CoA by PDH -conversion to lactate by lactate dehydrogenase -conversion to oxaloacetate by pyruvate carboxylase for gluconeogenesis

Conjugated proteins

-derive funciton form covalently attached molecules called protheitic gropus -Can be organic molecules (vitamins) or metal ions (iron) Proteins with lipid, carb, or nucleic acid prosthetic groups are referred to as lipoproteins, glycoproteins, and nucleoproteins Major role in determining function Each of hemoglobin (and myoglobin) subunits contains heme prosthetic group (has iron in core, binds to and carries oxygen, hemoglobin inactive without it) can direct protein to be delivered to certain location

Waxes

-esters of long-chain fatty acids w/ long chain alcohols -VERY hydrophobic, rarely found in cell membranes of animals - form pliable solids at room temp. -High melting temp - function as protection for plants and animals -Structural building (form stability and rigidity in non polar tail region only)

Other pathways capable of producing acetyl-CoA (other than glycolysis)

-fatty acid oxidation (beta-oxidation): In cytosol, thioester bond formed between carboxyl group of activated fatty acids and CoA-SH cant cross inner mitochondrial membrane, so fatty acyl group transferred to carnitine (crosses inner membrane with fatty acyl groups), then transfers it to mitochondrial CoA-SH. Then, 2 carbon fragment removed from carboxyl end -amino acid catabolism: Amino group lost via transamination, carbon skeleton forms ketone body (ketogenic amino acids) -ketones: Used when PDH complex is inhibited, reverse can occur too -alcohol: Alcohol dehydrogenase and acetaldehyde dehydrogenase can convert some alcohol to acetly-coa, but it causes buildup of NADH, which inhibits Krebs cycle, so this is mainly used to synthesize fatty acids

Rate Limiting Enzymes

-glycolysis: phosphofructokinase-1 (Controlled by F26BisP, which is activated by insulin)(more F26BisP and AMP = more PFK-1, ATP and citrate inhibit PFk-1 becuase we dont want to run glycolysis in these conditions) *high fructose 2,6 bisphosphate = increases amount of FPK 1,6 BP = yes glycolysis, no gluconeogenesis *Low fructose 2,6 bisphosphate = no glycolysis, yes gluconeogenesis -fermentation: lactate dehydrogenase -glycogenesis: glycogen synthase -glycogenolysis: glycogen phosphorylase -gluconeogenesis: fructose-1,6-biphosphatase -pentose phosphate pathway: glucose-6-phosphate dehydrogenase

pyruvate kinase

-last enzyme in glycolysis -catalyzes substrate level phosphorylation of ADP using PEP (phosphoenolpyruvate)(high energy substrate) -activated by Fructose 1,6-bisphosphate from PFK-1 reaction (F 1,6 BP) (feed fwd) so a previous product influences a later rxn in glycolysis

Polysaccharides

-long chains of monosaccharides linked together by glycosidic bonds -A polysaccharide composed entirely of one type of monosaccharide (like glucose) is called a homopolysaccharide -Polymer made up of more than one type of monosaccharide = heteropolysaccharide 3 Most common: Cellulose, starch, and glycogen (all composed of D-glucose, but differ in anomeric carbon configuration and position of glycosidic bonds) -Can be linear or branched (when internal monosaccharide in polymer chain forms at least 2 glycosidic bonds)

Types of Sphingolipids

1) Ceramide - H as head group 2) Sphingomyelins - major component of plasma membrane of oligodendrocytes and Schwann cells. 3) Cerebrosides - single sugar 4) Globosides - two or more sugars 5) Gangliosides - "gangly" sphingolipids, the most complex structure. Contain NANA negatively charged head group. *Sphingolipids don't contain glycerol but they are similar to glycerophospholipids because they contain hydrophilic region and 2 fatty acid derived hydrophobic tails *difffer in identity of hydrophilic region

Titration of amino acids

-looks like a combo of two or three monoprotic acids (three is acidic or basic R group) -when add base, carboxyl group deprotonates first, than amino group When you add 0.5 equivalents of base to the solution, the concentrations of the fully protonated amino acid and zwitterion are = (pH = pKa1)(+NH3 COOH = +NH3 COO-) When the pH of a solution is approximately = to pKa of solute, the solution acts as a buffer (Titration curve relatively flat -> blue area of graph shown) When we add one equivalent, we have 100% zwitterion (NH3+ and COO-) (Imagine we started with 1 equivalent of glycine) -> Every molecule is electrically neutral: pH = isolecletric point (pI) of glycine *isoelectric Point = pH at which the molecule is neutral For neutral amino acids, this is found by averaging the two pKa values for the amino and carboxyl group pI = about 5.97 *when molecule is neutral, it is especially sensitive to pH changes (titration curve nearly vertical) When 1.5 equivalents have been added, zwitterion concentration = concentration of fully deprotonated form (pH = pka2) -two equivalents of base to fully deprotonate one equivalent of most amino acids Amino Acids with charged side chains: Glutamic acid: 2 carboxyl groups, so still +1 at fully protonated state (Side chain pKa of about 4.2, when it loses second proton from second carboxyl group), so it has a much lower pI than glycine pI acidic = pKa R group (instead of pKa of NH2 group) + pKa COOH group / 2 -> 4+2 /2 = about 3 Lysine, on the other has has two amino groups: Fully protonated has +2 charge, losing Carboxyl group at pH 2 brings it to +1, becomes neutral at pH 9, gets negatively charged at pH 10.5 pI basic = pKa of NH2 group + pKa of R group (instead of pKa of carboxyl group) /2 -> 9+10.5 /2 = about 9.75 Amino acids with acidic side chains have pI values well below 6, amino acids with basic side chains have pI values well above 6

Isoelectric Focusing

-proteins separated based on isoelectric point (pI) -Acidic gel at positive anode, basic gel and negative cathode -electric charge is applied to the sample - protein migrates and stops when it reaches its isoelectric point (pH= pI)(stops b/c equal number of positive and negative charges) -Neutral called Zwitterion *Isoelectric focusing uses a gel with a pH gradient that encourages a variable charge. Acids at the Anode (Acids have more protons, more protons at anode, positive charge) , Bases at the cathode:

Important intermediates of glycolysis

1. Dihydroxyacetone phosphate (DHAP) - used in hepatic and adipose tissue for triacylglycerol synthesis; formed from F1,6-BP and can be isomerized to G-3-P which can be converted to glycerol (backbone of triacylglycerols) 2. 1,3-Bisphosphoglycerate (1,3-BPG) and PEP - high energy intermediates used to generate ATP by substrate level phosphorylation; only ATP gained in anerobic respiration

Three types of Stereoisomers

1. Same sugar, in different optical families (D and L) = enantiomers 2. Same sugar, same family (aldoses or ketoses), same number of carbon, but not identical and not mirror images = diastereomers 3. Special kind of diatereomer: differs at 1 chiral center = epimers (D-ribose and D-arabinose) Image: 2 optical forms of erythrose and 2 optical forms of threose L-erythrose and D-Erythrose are enantiomers, and L-threose and D-threose are enantiomers Enantiomerization and racemization mean the same thing as each other: the formation of a mirror-image or optically inverted form of a compound L-erythrose and D threose are enantiomers, and they are epimers

Palmitate

16:0 Only fatty acid synthesized de novo Humans can only synthesize one fatty acid, palmitic acid. Palmitic acid is fully saturated and therefore does not contain any double bonds. Palmitic acid has 16 carbons, and is synthesized from eight molecules of acetyl-CoA. In shorthand notation, palmitic acid is written as 16:0 (16 carbons, no double bonds).

DNA Structure

2 chemically distinct forms of nucleic acids in eukaryotes: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Most DNA found in chromosomes in nucleus, some found in mitochondria and chloroplasts There are 6 billion bases of DNA in each human cell DNA divided up among 46 chromosomes

Purines and pyrimidines

2 families of nitrogen containing bases on nucleotides: both are biological aromatic heterocycles 2 types of Purines, have 2 rings (found in DNA and RNA): Adenine (A) and guanine (G) 3 types of pyrimidines, 1 ring each (CUT): Cytosine (C), thymine (T), and uracil (U) (Cytosine is found in DNA and RNA, but T is only found in DNA and U is only found in RNA *PUR As Gold (Purines: A and G) *U R only found in RNA *Instead of DNA, think TNA

The minimum energy a biochemical reaction must release in order for it to be coupled to ATP synthesis from ADP and inorganic phosphate is approximately:

30 kJ/mol

Steps and proteins involved in DNA replication

5 DNA polymerases in eukaryotes: a, B, y, g, and E (alpha, beta, gamma, delta, epsilon) a, g, and E work together to synthesize both leading and lagging strandsDNA poly g fills in gaps left when RNA primers are removed DNA poly y replicates mitochondria DNA B and E important for DNA repair g and E are assisted by PCNA protein, which assembles trimer to form sliding clamp ( helps strengthen interaction between polymerases and template strand)

Given the following data, calculate the resting membrane potential of this cell: (image shown)

61.5 * log (0.05X140 + 1X4 + 0X12 / 0.05X14 _ 1X120 + 0X120) = 60 log (7+4 / 0.7 + 120) => 60 log (1/10) = -60 mV

The pressure for net movement of fluid across capillary membranes can be estimated using a modified form of the Starling equation: flow pressure = (Pc-Pi) - (πc-πi), where Pc and Pi represent the hydrostatic pressures in the capillary and interstitial fluids, respectively, and πc and πi represent the oncotic pressures in the capillary and interstitial fluids, respectively; positive numbers represent the tendency to push fluid out of a given compartment. A particular capillary has the pressure characteristics shown in the table below. Pressure type mmHg Capillary hydrostatic pressure 17 Capillary oncotic pressure 26 Interstitial fluid hydrostatic pressure 0 Interstitial fluid oncotic pressure 1 Based on this table and the modified Starling equation, what is the magnitude and direction of the flow pressure? 8 mmHg, directed out of the capillary 8 mmHg, directed into the capillary 10 mmHg, directed out of the capillary 10 mmHg, directed into the capillary

8 mmHg, directed into the capillary This question simply requires translating the descriptive names of various quantities into the variables which represent them, and then plugging the values gleaned from the table into the equation from the question stem, to calculate the flow pressure. Note also, that the values in the table are not presented in the order in which they appear in the equation, so we must be be careful: flow pressure = (17 mmHg - 0 mmHg) - (26 mmHg - 1 mmHg) = -8 mmHg The question stem also states that positive pressures indicate that fluid tends to be pushed out of a compartment, so the negative value indicates that the force is directed into the capillary. Thus, (B) is correct.

Normal Blood Glucose Concentration

80-120 mg/dL Around 100 (5.6 mM, ranging from 4-6 mM) High blood sugar: Long term damage to retina, kindey, blood vessels, nerves Low BS: Autonomic disturbances, seizures, coma

Ribose

A five-carbon sugar present in RNA RNA more reactive than DNA

Glucagon

A hormone secreted by the pancreatic alpha cells that increases blood glucose concentration (Think: Glucose is gone) It stimulates the conversion of stored glycogen (stored in the liver) to glucose, which can be released into the bloodstream. Glucagon is a hormone that is involved in controlling blood sugar (glucose) levels. It is produced by the alpha cells, found in the islets of Langerhans, in the pancreas, from where it is released into the bloodstream. The glucagon-secreting alpha cells surround the insulin-secreting beta cells, which reflects the close relationship between the two hormones. Glucagon's role in the body is to prevent blood glucose levels dropping too low. To do this, it acts on the liver in several ways: It stimulates the conversion of stored glycogen (stored in the liver) to glucose, which can be released into the bloodstream. This process is called glycogenolysis. It promotes the production of glucose from amino acid molecules. This process is called gluconeogenesis. It reduces glucose consumption by the liver so that as much glucose as possible can be secreted into the bloodstream to maintain blood glucose levels. Glucagon also acts on adipose tissue to stimulate the breakdown of fat stores into the bloodstream. How is glucagon controlled? Glucagon works along with the hormone insulin to control blood sugar levels and keep them within set levels. Glucagon is released to stop blood sugar levels dropping too low (hypoglycaemia), while insulin is released to stop blood sugar levels rising too high (hyperglycaemia). The release of glucagon is stimulated by low blood glucose, protein-rich meals and adrenaline(another important hormone for combating low glucose). The release of glucagon is prevented by raised blood glucose and carbohydrate in meals, detected by cells in the pancreas. In the longer-term, glucagon is crucial to the body's response to lack of food. For example, it encourages the use of stored fat for energy in order to preserve the limited supply of glucose.

Angiotensin

A normal blood protein produced by the liver, angiotensin is converted to angiotensim I by renin (secreted by kidney when blood pressur falls). Angiotensin I is further converted to angiotensim II by ACE (angiotensin converting enzyme). Angiotensin II is a powerful systemic vasocontrictor and stimulator of aldosterone relase, both of which result in an increase in blood pressure.

noncompetitive inhibitor

A second type of inhibition employs inhibitors that do not resemble the substrate and bind not to the active site, but rather to a separate site on the enzyme (rectangular site below). The effect of binding a non-competitive inhibitor is significantly different from binding a competitive inhibitor because there is no competition. In the case of competitive inhibition, the effect of the inhibitor could be reduced and eventually overwhelmed with increasing amounts of substrate. This was because increasing substrate made increasing percentages of the enzyme active. With non-competitive inhibition, increasing the amount of substrate has no effect on the percentage of enzyme that is active. Indeed, in non-competitive inhibition, the percentage of enzyme inhibited remains the same through all ranges of [S]. *The inhibitor binds to the allosteric site and changes the shape of the enzyme so it can't bind the substrate anymore Non-competitive inhibition effectively reduces the amount of enzyme by the same fixed amount in a typical experiment at every substrate concentration used Vmax is reduced in non-competitive inhibition compared to uninhibited reactions. This makes sense if we remember that Vmax is dependent on the amount of enzyme present. Reducing the amount of enzyme present reduces Vmax. In competitive inhibition, this doesn't occur detectably, because at high substrate concentrations, there is essentially 100% of the enzyme active and the Vmax appears not to change. Additionally, KM for non-competitively inhibited reactions does not change from that of uninhibited reactions. This is because, as noted previously, one can only measure the KM of active enzymes and KM is a constant for a given enzyme.

Heterochromatin and Euchromatin

A small percentage of chromatin reminds compacted during S phase of interphase, when DNA replication occurs = heterochromatin -Appears dark and is transcriptionally silent (dark, dense, and silent) -Often highly repetitive Dispersed chromatin is called euchromatin -Appears light -Contains genetically active DNA Both seen in nucleus Note: Chromatin is the material that makes up a chromosome that consists of DNA and protein. The major proteins in chromatin are proteins called histones. They act as packaging elements for the DNA. A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin

Codons

A three-nucleotide (3 base) sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. 64 codons (61 of the codons code for 1 of the 20 amino acids, 3 codons encode termination of translation) 5' -> 3' Each codon is specific for one amino acid, but most amino acids are represented by multiple codons Universal Across species During translation, codon of mRNA recognized by complementary anticodon on tRNA: For example tRNA has anticodon sequence 5' - GAU-3' pairs with isoleucine codon 5'-AUC-3' on mRNA Every preprocessed eukaryotic protein starts with sam amino acidL Methionine : AUG (start codon for translation of mRNA into protein)

Anticodon

A three-nucleotide sequence on a tRNA molecule that pairs with a corresponding mRNA codon during translation (image shown) A codon is a 3 nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation

Which of the following molecular formulas corresponds to the fatty acid with the HIGHEST melting point? A. C18H36O2 B. C18H34O2 C. C16H34O2 D. C18H32O2

A. C18H36O2 B. C18H34O2 (1 double bond = 15 degC) C. C16H34O2 (63 degC) D. C18H32O2 (Two double bonds = MP of -5 degC) More Carbons = higher melting point With fatty acids, highest melting point = most saturated (most hydrogens)

How does acetyl-CoA shift the metabolism of pyruvate?

Acetyl Coa inhibits pyruvate dehydrogenase complex and activates pyruvate carboxylase Shift from burning pyruvate in CAC to creating new glucose for body acetyl coa for this regulation comes mostly from b oxidation, not glycolysis

Thyroid Hormones

Activity is largely permissive (levels kept pretty constant) Increase basal metabolic rate (increased O2 consumption and heat production ), and potentiate activity of other hormones Increase in metabolic rate from thyroxine (T4) occurs after latency of several hours, but may last several days Triidothyronine (T3)= more ra[id increase in metabolic rate and has shorter duration Subscript numbers = number of iodine atoms T4 is precursor for T3 Deiodonases (enzymes that remove iodine) convert T4 to T3 Primary effects on lipids and carbs Accelerate cholesterol clearance form plasma and increase rate of glucose absorption from small intestine Epi needs thyroid hormones to work well Thyroid hormones not responsible for day to day adjustments Insufficient thyroid hormone levels (hypothyroidism) can cause cold intolerance, fatigue, weight gain, depression Hyperthyroidism: rapid weight loss, anxiety, jitteryness, fever *Thyroid storm = super high levels: High BP, high respiratory rate, tachycardia

Functions of NADPH

Acts as the bodies primary reducing agent. Important for: 1) Biosynthesis of fatty acids and cholesterol 2) Assisting in bactericidal activity: Assisting in cellular bleach production in certain white blood cells 3) Maintain supply of glutathione for protection against free radicals caused by peroxides/ reactive oxygen specieis (natural antioxidant) *Free radicals can attack lipids, including phospholipids (especially in RBC because they have more oxygen) *Glutathione is reducing agent that can help reverse radical formation before damage is done NADPH and NADH are not the same. NAD+ is an energy carrier (high energy electron acceptor)(Potent oxidizing agent, is itself reduced in the process), NADPH is used in biosynthesis and immune system and to help prevent oxidative damage . Acts primarily as electron donor. Potent reducing agent -> is oxidized in the process

Insulin-dependent GLUT4 transporters are key regulators of glucose uptake in cells of which of the following tissues? Hepatic Adipose Skeletal muscle Brain

Adipose and skeletal muscle Insulin acts on skeletal muscle and adipose tissue to stimulate glucose uptake through the insertion of GLUT4 transporters into the cellular membrane. Glucose uptake in brain and hepatic tissue is NOT insulin dependent, as these tissues uptake glucose via different GLUT transporter isoforms.

Complex Carbohydrates: Disaccharides

All carbs with at least 2 sugar molecules linked together (disaccharides, oligosaccharides, and polysaccharides) Disaccharides : Glycosidic bonds formed between hydroxyl groups of two monosaccharides result in formation of disaccharide The hydroxyl group on the anomeric carbon reacts with the hydroxyl of another sugar to form an acetal or ketal with 1,2; 1,4; or 1,6 glycosidic linkages Non-specific Only have to specify alpha or beta for anomeric carbon. Maltose: 2 glucose molecules linked by alpha 1,4 glycosidic bond Cellobiose: 2 glucose molecules linked by beta 1,4 glycosidic bond

Glycolysis in red blood cells

All cells carry out glycolysis In red blood cells, glycolysis is the only energy yielding pathway available because RBCs dont have mitochondria (which are required for citric acid cycle, ETC, oxidative phosphorylation, fatty acid metabolism / beta oxidation) *not having mitochondria help RBC do their job by maximizing volume available for hemoglobin (primary oxygen carrying protein) *Stops RBC from utilizing O2 its supposed to be carrying to tissue that need it

quaternary structure of a protein

All proteins have primary, secondary, and tertiary, (like letters, to words, to sentences) but only some have quaternary (like paragraphs) Protein must contain more than 1 polypeptide chain Aggregate of smaller globular peptides (subunits) Represent functional form of protein Hemoglobin (4 distinct units that bind to 1 molecule of Oxygen each) and immunoglobulin G (IgG) antibodies (also 4 subunits) Can be more stable by further reducing surface area of protein complex Can reduce amount of DNA needed to encode protein complex Can bring catalytic sites close together, allowing intermediates from one reaction to be shuttled to second reaction Can induce cooperatively (allosteric effects) -> one subunit can undergo conformation or structural changes which either enhance or reduce the activity of other subuntis Reduction of genetic material is crucial for viruses. The genome for most viruses is tiny so their viral coats typically consist of one small protein repeated a bunch of times Stabilizing bonds: Van der Waals, H bonds, ionic bonds, covalent bonds

Regulated Enzymes

Allosteric Enzymes: Multiple binding sites: active site and site that can regulated availability of active site (allosteric sites) Allosteric enzymes alternate between active and inactive (no reaction) Molecules that bind allosteric site may be allosteric activators or allosteric inhibitors. Both cause conformational shift Activator makes active site more available for binding , inhibitor makes it less available Covalently modified Enzymes: Enzymes subject to covalent modification -Can be activated or deactivated by phosphorylation or dephsophorylation (don't know which does the activating until you perform experiment) -Glycosylation (covalent attachment of sugar moieties) is another covalent enzyme modification -> can tag enzyme for transport within cell, or modify protein activity and selectivity What property of protein-digesting enzymes allows for a sequence to be determined without fully degrading the protein? Selectivity Zymogens: Precursors of active enzymes (we need some things to remain inactive until they are at target site) Digestive enzymes, tryspin, released from pancreas, would be pretty dangerous if not regulated -To avoid danger, enzymes and others are secreted as inactive zymogens like trypsinogen -Look for suffix -ogen -Contain catalytic (active) domain and regulatory domain (must be altered or removed to expose active site) -Apoptotic enzymes (caspases) exhibit similar regulation

Resonance in the Peptide Bond

Amide groups have delocalizble pi electrons in carbonyl and in the lone pair on the amino nitrogen , they can have resonance (C-N bond in amide has partial double bond character) Rotation around the protein backbone around C-N amide bonds is restricted (more rigid) Everything else is a single bond (not restricted) Free amino end = N terminis Free carboxyl end = C terminus

Protonation and Deprotonation

Amino Acids are amphoteric species: can accept a proton or donate a proton -> depends on pH of environment Ionizable groups tend to gain protons under acidic conditions (low pH) and lose protons under basic conditions The pKa of a group is the pH at which on average, half of the molecules of that species are deprotonated HA = A- (acid = conjugate base) pH < pKa = protonated (H) pH > pKa = deprotonated (No H) All amino acids have at least 2 pKas: 2 for carboxylic acid and 9 for amino group Amino acids with ionizable side chain have three pKa values At pH there are plenty of protons in solution, so everything has a proton on it! (instead of NH2 we have. NH3+, instead of COO- we have COOH), so at acidic values, amino as will be positively charged overall Zwitterions at intermediate pH (Carboxylic group is not protonated, but amino group is -> NH3+ and COO-) so overall we are neutral -> exist in water as internal salts Negatively charged under basic conditions: Both groups deprotanted (NH2 and COO-) above pH 9 *At very alkaline pH values, amino acids tend to be negatively charged

Hydrophobic and Hydrophilic amino acids

Amino acids with long alkyl side chains (Alanine, isoleucine, leucine, valine, phenylalanine) = strongly hydrophobic and more likely to be found INSIDE protein Surface of protein tends to be rich in amino acids with charged side chains Strongly hydrophobic amino acids tend to be found in the interior of proteins (away from water at surface) All amino acids with charged side chains (histidine arginine and lysine with + charge and glutamate and aspartate with - charge) are hydrophilic, as are the amides asparagine and glutamine

peptidyl transferase Peptidyl transferase connects the carboxylate group of the one amino acid to the amino group of an incoming amino acid. What type of linkage is created in this peptide bond? A. Ester B. Amide C. Anhydride D. Ether What role does peptidyl transferase play in protein synthesis? A. It transports the initiator aminoacyl-tRNA complex. B. It helps the ribosome to advance three nucleotides along the mRNA in the 5′ to 3′ direction. C. It holds the protein in its tertiary structure. D. It catalyzes the formation of a peptide bond.

An enzyme in the ribosome responsible for peptide bond formation during translation. *Peptidyl Transferase: enzyme that catalyzes the formation of peptide bond between incoming amino acid in A site and growing polypeptide chain in P site Correct Answer: B Explanation: Peptidyl transferase connects the incoming amino terminal to the previous carboxyl terminal; the only functional group listed here with a carboxyl and amine group is the amide. Peptide bonds are thus amide linkages, and the correct answer is choice (B). Correct Answer: D Explanation: Peptidyl transferase is an enzyme that catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the growing polypeptide chain in the P site. Initiation and elongation factors help transport charged tRNA molecules into the ribosome and advance the ribosome down the mRNA transcript, as in choices (A) and (B). Chaperones maintain a protein's three-dimensional shape as it is formed, as in choice (C).

Effects of Local Conditions on Enzyme Activity /Velocity / Rate (all mean the same thing)

An enzyme's activity can be affected by General environmental factors, such as temperature and acidity or alkalinity (pH)(in vivo), and high salinity (in vitro, high salt can disrupt H and ionic bonds, causing partial conformation change) Temperature: Enzyme catalyzed reactions tend to double in velocity for every 10 deg C increase in temp until the optimum temp is reached. (37 deg C or 310 K) After this point, activity falls off sharply, as the enzyme will denature -Some enzymes regain function when cooled pH Most enzymes depend on pH to function -Effect ionization of active site -Can lead to denaturation Acidemia: Human blood pH below 7.35 BUT: Pepsin, in stomach, works best at pH2 and pancreatic enzymes in small intestine work best around 8.5

glycolysis in erythrocytes

Anaerobic glycolysis represents only pathway for ATP production, yielding net 2 ATP per glucose Red blood cells lack the mitochondria required for aerobic metabolism and are thus dependent on anaerobic metabolism of glucose for their energy source. -red blood cells have biphosphoglycerate mutase, which produces 2,3-biphosphoglycerate (2,3-BPG) from 1,3-BPG in glycolysis *Mutases: Enzymes that move functional group (moves phosphate from 1 to 2) -2,3-BPG binds allosterically to the β-chains of hemoglobin A (HbA) and decreases its affinity for oxygen (higher Km) -2,3-BPG does not bind well to fetal hemoglobin (HbF), thus HbF has a higher affinity for oxygen than maternal HbA, allowing transplacental passage of oxygen from mother to fetus

Ribosome

Anticodon of tRNA binds codon on mature mRNA in ribosome (composed of proteins and rRNA) In prokaryotes and eukaryotes, there are large and small subunits that only bind together during protein synthesis Ribosome brings mRNA message together with the charged aminoacyl-tRNA complex to make protein 3 binding sites for tRNA: A (aminoacyl) site, P site (peptide) and E (exit) site Eukaryotic ribosomes contain 4 strands of rRNA : 28S, 18S, 5.8S, and 5 S (S indicates size) 28S, 18S, 5.8S are found in nucleolus . RNA poly 1 transcribes here 3 in single unit, resulting in 45S ribosomal precursor RNA 45S pre rRNA processed to become 18S rRNA of the 40S (small) ribosomal subunit and the 28S and 5.8 S rRNA of the 60 S (large) ribosomal subunit RNA poly 3 transcribes 5S rRNA (also founding 60S) outside nucleolus 60S and 40S subunits joined during protein synthesis to form 80S ribosome Prokaryotes have 50S (large) and 30S (Small) subunits that come together to create 70S "S" not additive exactly because it is based on size and shape

Consider a reaction catalyzed by enzyme A with a Km value of 5 × 10-6M and vmax of 20 mmol/min At a concentration of 5 × 10^-6 M substrate, the rate of the reaction will be: At a concentration of 5 × 10-4 M substrate, the rate of the reaction will be:

At a concentration of 5 × 10-6 M, enzyme A is working at one-half of its vmax because the concentration is equal to the Km of the enzyme. Therefore, one-half of 20 mmol/min is 10 mmol/min At a concentration of 5 × 10-4 M, there is 100 times more substrate than present at half maximal velocity. At high values (significantly larger than the value of Km) the enzyme is at or near its vmax, which is 20) Use equation v = v max * [S] / km + [S]

polymerase chain reaction

Automated process the produces millions of DNA sequence copies without amplifying the DNA in bacteria Knowing sequence that flanks desired DNA region allows for amplification of sequence in between Requires primers (with high GC content) that are complementary to DNA that flanks region of interest, nucleotides (dATP, dTTP, dCTP, dGTP) and DNA polymerase , and HEAT so double helix denatures Human DNA denatures at high temp, but DNA polymerase from thymus aquatics (lives in hot springs) is used instead During PCR, DNA of interest is denatured, replicated, and cooled and reannealed several times, doubling DNA each cycle

B Vitamins

B1: thiamine B2: riboflavin B3: niacin B5: pantothenic acid B6: pyridoxal phosphate B7: biotin B9: folic acid B12: cyanocobalamin

Sugar-Phosphate Backbone

Backbone of DNA composed of alternating sugar and phosphate groups -> determines directionality ALWAYS READ (and written) 5' to 3' 5'-ATG-3' can be written as 3'-GTA-5' *position of phosphates whiten as pApTpG *d may be shorthand for deoxyribose: dAdTdG Formed as nucleotides are joined by 3'-5' phosphodiester bonds (phosphate group links 3' carbon of one sugar to the 5' phosphate group of the next sugar Phsophates carry negative charge (DNA and RNA have overall negative charge ) DNA strands run antiparallel: Enzymes that replicate and transcribe only in 5 to 3 prime direction The 5' end of DNA has -OH or phosphate bonded to C5' of the sugar, while the 3' end has a free -OH *DNA is double stranded, RNA is single stranded (except when you get to viruses)

DNA replication in prokaryotes and eukaryotes

Bacterial chromosome is closed, DOUBLE stranded circular DNA molecule with single origin of replication -> 2 replication forks move away in opposite direction around circle, eventually meet back up and produce 2 identical circular molecules (Single origin of replication) (DNA replication occurs in cytoplasm of prokaryotes, and in the nucleus of eukaryotes) Eukaryotes have to copy more bases so it is a slower process Each eukaryotic chromosome has 1 linear molecule of double stranded DNA with multiple origins of replication (multiple origins of replication) -Replication fork moves towards each other: sister chromatids created and connected at centromere

Gene Amplification

Basal (low level) transcription usually maintained at moderate levels, but can be amplified in eukaryotic cells through enhancer and gene duplication The DNA regulatory base sequences (promoters, enhancers, response elements) are known as cis regulators because they are in same vicinity as genes that they control Transcription factors have to be produced and translocated back to nucleus, so they are trans regulators (travel to site of action) Several response elements can be grouped together to form enhancer: allows for control of one genes expression by multiple signals Signal molecules like cAMP, cortisol, estrogen bind to specific receptors -> CREB (cyclic AMP response element binding protein), the glucocorticoid (cortisol) receptor, and the estrogen receptor (all are transcription factors that bind to their respective response elements within enhancer) *Large distance between enhancer and promoter regions means DNA must bend into hairpin loop to bring elements together (image shown) -Enhancers can even be inside intron / non coding region -Differ from upstream promoter elements because upstream promoter elements must be within 25 bases of start of gene *Promoter are within 25 base pairs of transcription start site, enhancers are more than 25 base pairs away Gene Duplication: can be in series on same chromosome (yielding many copies in a row of same genetic info) or in parallel by opening gene with helices and letting DNA replication of just that gene

Carbohydrates Empirical Formula: Cn(H2O)n for simple sugars and Cn(h2O)m for complex sugars

Basic Structural Units: Monosaccharides -Contain both hydroxyl group (can serve as nucleophile) and carbonyl group (super common electrophile) -> can form hemiacetals and hemiketals -Contain alcohols and either aldehydes or ketones (so they can undergo oxidation and reduction, esterification, and nucleophilic attack creating glycosides ) -Simplest monosaccaride: 3 carbon atoms (triodes) -Followed by tetroses (4 carbon atoms). pentoses, and hexoses -Carbs with aldehyde = aldose, carbs with ketone = ketose The simplest aldose is glyceraldehyde (aldotriose) -Aldehyde carbon can participate in glycosidic linkages It makes more sense for carbs (primary energy source) to be oxidized while reducing other groups because aerobic metabolism requires reduced forms to carry electrons Simplest ketone sugar (ketose) is dihydroxyacetone (ketotriose) -Carbonyl carbon most oxidized again Generally attached to protein molecules on extracellular surface of cells -Genenrally hydrophilic -Can act as signaling and recognition molecules (Blood group ABO antigens on RBCs are sphingolipids that only differ in carb sequence) *Staphylococcus Aureus bacteria embedded in bands of extracellular polysaccharides and glycolipids form biofilm *Membrane receptors are generally proteins, but some are carbs and lipids, especially in viruses

Posttranscriptional processing

Before hnRNA can leave nucleus, it undergoes 3 things to allow interaction with ribosome 1. Slicing Introns and Exons -Remove Introns: Non-coding sequences, and ligate coding sequences (exons) -Accomplished by spliceosome: Small nuclear RNA (snRNA) molecules couple with proteins known as small nuclear ribonucleoproteins (snRNPs) -snRNP/snRNA complex recognizes 5'a nd 3' splice sites of introns (Excised out in lariat (lasso shaped structure and then degraded)) -Introns play role in regulation of gene expression? Rapid protein evolution? 2. 5' Cap At the 5' end of the hnRNA molecule, a 7-methylguanylate triphosphate cap is added -> protects mRNA from degradation in the cytoplasm 3. 3' Poly A tail (Polyadenosyl) -Added to 3' end of mRNA transcript -Protects message from rapid degradation (longer tail = longer life) -Composed of adenine bases -Also assists with export of mature mRNA from nucleus When only exons remain, and cap and tail have been added, cell has created mature mRNA now transported into cytoplasm for protein translation Untranslated regions of mRNA (UTRs) exist at edges of transcript because ribosome initiates translation at start codon (AUG) and ends at one of the 3 stop codons (UAA, UGA, UAG) The untranslated regions of the mRNA will not be turned into amino acids. Translation will begin with codon 1 (which would be AUG).

Cyanide effect on ETC

Binds to complex IV of cytochrome oxidase and prevents cells from using oxygen, causing rapid death. Cyanide is a deadly poison because it cripples the electron transport chain. Cyanide binds to the last complex in the chain and, in so doing, blocks oxygen from binding. Recall that during the operation of the electron transport chain, NADH donates electrons to the beginning of the chain. The process of electron transport fuels the pumping of protons across the membrane. However, with cyanide already bound, oxygen cannot grab the electrons at the end of the chain. Therefore, no new electrons from NADH can be added at the beginning. Under these conditions, electron transport and proton pumping grind to a halt. Without the active pumping of protons to one side of the membrane, the proton concentrations on both sides soon equalize. No longer do protons rush through the ATP-producing complex, and no more ATP is produced. Cells can't live long on the small quantity of ATP made by glycolysis, so without the ATP that comes from the electron transport chain, cells die.

Acetyl-CoA Pyruvate + CoA-SH + NAD+ -> acetyl-CoA + CO2 + NADH + H+

Can be obtained from metabolism of carbs, fatty acids, amino acids After glucose goes through glycolysis, the product (pyruvate) enters mitochondrion and is oxidized and decarboxylated (catalyzed by pyruvate dehydrogenase complex) -Pyruvate cleaved from 3 carbon molecule to 2 carbon molecule and CO2 (irreversible, so glucose can't be formed from acetyl coa directly) -Pyruvate to Acetyl CoA is exergonic (-33.4 kJ.mol) Inhibited by buildup of acetyl coa and NADH caused by ETC not working CoA is a thiol: contains SH group, forms covalent bond to acetyl group -> forms thioester

Oncogenes and Tumor Suppressor Genes

Cancer cells proliferate excessively because they can divide without stimulation and they are no longer under normal control Able to migrate by local invasion or metastasis (migration to distant tissue by bloodstream or lymphatic system) Cancer cells tend to accumulate mutations Mutated genes that cause cancer = oncogenes : primarily encode cell cycle related proteins (proton-oncogenes) Abnormal alleles encode proteins that are more active than normal Tumor suppressor genes like p53 or Rb encode proteins that inhibit cell cycle or DNA repair -Normally, they stop tumor suppression (so they are called antioncogenes), but there is a mutation that results in loss of tumor suppression activity While the outcome of oncogenes and mutated tumor suppressor genes is the same (cancer), the actual cause is different. Oncogenes promote the cell cycle (think speed it up, step on the gas), mutated tumor suppressors can no longer slow cell cycle (cutting the breaks)

Glycogen

Carbohydrate storage unit in animals (branched polymer/ storage form of glucose) Stored in cytoplasm as granules, each with central protein core with poly glucose chains forming sphere -Branched chains have highest glucose density at periphery(more rapid release) Glycogen in liver and muscle very different roles: Liver glycogen broken down to maintain constant level of glucose in blood Muscle glycogen broken down for muscle food during exercise (energy reserve) Similar to starch but it has more alpha 1,6 glycosidic bonds (1 for every 10 glucose, while amylopectin has one for every 25) *Plants store excess glucose in long alpha linked chains of glucose called starch Energy efficient due to lots of branching Allows enzymes that cleave glucose from glycogen (glycogen phosphorylase) to work on many sites at the same time -> cleaves glucose from non-reducing end and phosphorylates it to glucose - 1 phosphate The body has two primary energy stores: glycogen and triacylglycerols Glycogen more rapidly mobilized but requires water of hydration, w which increases its weight. Triacylglycerols serve as long term energy, but hard to utilize

Cell undergoes DNA replication during _ phase

Cell undergoes DNA replication during S phase of interphase and having the DNA uncondensed and accessible makes the process more efficient

Cell-Cell Junctions Gap Junctions

Cells in tissues form a cohesive layer via intercellular junctions -provide direct pathways for communication between neighboring cells or between cells and the extracellular matrix -generally composed of cell adhesion molecules (CAM): Proteins that allow cells to recognize each other and contribute to differentiation / development Gap Junctions (AKA Connexons): Image shown Direct cell-cell communication Often found in small bunches Connexons are formed by alignment and interaction of pores composed of 6 connexin molecules Permit movement of water and some solutes directly between cells Generally do not transfer proteins Gap junctions allow intracellular transport and do not prevent paracellular transport, tight junctions are not used for intracellular transport and do prevent paracellular transport Gap junctions are discontinuous, tight junctions form bands

Cerebrosides and gangliosides are best characterized as: A. triacylglycerides B. steroids C. Waxes D. sphingolipids

Cerebrosides and gangliosides are subclasses of sphingolipids, which are derivatives of the fatty acid derivative spingospine, which contains TWO fatty acid groups, one of which is bound to the amino group in spingospine. Sphingolipids are not triacylglyerides, since, by definition, the latter have THREE fatty acid groups. Sphingolipids also do not contain glycerol.Sphingolipids are not steroids, as they do not have the ring structure normally observed in steroids.Sphingolipids are not waxes, as these are highly insoluble esters of fatty acids and alcohol. Sphingolipids can either have a phosphodiester bond, and therefore be phospholipids, or have a glycosidic linkage and therefore be glycolipids. Not all sphingolipids have a sphingosine backbone, as in statement II; some have related (sphingoid) compounds as backbones instead.

Modified Standard State At 25°C the ΔG° for a certain reaction A → B + 2 C is 0. If the concentration of A, B, and C in the cell at 25°C are all 10 mM, how does the ΔG compare to the measurement taken with 1 M concentrations? A. ΔG is greater than ΔG°, thus the reaction is spontaneous. B. ΔG is less than ΔG°, thus the reaction is spontaneous. C. ΔG is greater than ΔG°, thus the reaction is nonspontaneous. D. ΔG is less than ΔG°, thus the reaction is nonspontaneous.

Change in free energy (ΔG = ΔH - TΔS) occurs at any concentration at any temp In contrast, ΔG˚ (standard free energy) is energy change at standard concentrations of 1 M, 1 atm, and 25 deg C Therefore, ΔG° values are dependent on the concentrations of the reactants and products. ΔG = ΔG˚ + RT ln (Q) R is universal gas constant (8.314 J / mol·K) Q is reaction quotient BUT this doesn't work for pH, so the modified standard state Instead of 1 M, we use [H+] = 10^-7 M and pH is 7 Usually, more products than reactants have more negative delta G (spontnaeous forward) More reactants than products have more positive delta G (non spontaneous) Correct Answer: B Explanation: To solve this question, we can use the equation ΔG = ΔG° + RT ln Q. Q, the reaction quotient, is B*C^2 / A for this reaction. Plugging in the variables, we get ΔG = 0 + RT ln 10^-4 -> RT*-4 Because both R and T are positive, we know that ΔG must be negative and therefore lower than the original value. A negative ΔG corresponds to a spontaneous reaction.

Which of the following side effects would be anticipated in someone taking leptin to promote weight loss? A. Drowsiness B. Increased appetite C. Irritability D. Fever

Correct Answer: A Explanation: Leptin acts to decrease appetite by inhibiting the production of orexin. Orexin is also associated with alertness, so decreasing the level of orexin in the body is expected to cause drowsiness. Even without this information, the answer should be apparent because the body tends to maintain an energy balance. If consumption decreases, energy expenditures are expected to decrease as well.

Chylomicrons VLDL IDL/VLDL Remnants LDL HDL

Chylomicrons are least dense, with highest fat to protein ratio: Transport dietary triacylglycerols, cholesterol, and cholesteryl esters from intestine to tissues VLDL (very low density lipoprotein) is slightly more dense: Transport triacylglycerols and fatty acids from liver to tissues Next, it goes IDL (intermediate density: transition between VLDL and LDL, occurs as primary lipid changes from triacylglycerol to cholesterol)/ VLDL remnants (pick up cholesteryl esters from HDL to become LDL, VLDL remnants packed up by liver), LDL (low density, less protein)(Delivers cholesterol into cells), and HDL (high density)(picks up cholesterol accumulating in blood vessels, delivers cholesterol to liver and steroidogenic tissues, transfers apolipoproteins to other lipoproteins) Chylomicrons (highly soluble, assembly in intestinal lining) and VLDL (assembled in liver) primarily carry triacylglycerols, but also contain small quantities of cholesteryl esters Once triacylglycerol is removed from VLDL, resulting particle = VLDL remnant or IDL (some is reabsorbed and some is further processed) LDL and HDL transport cholesterol Blood tests for cholesterol measure LDL and HDL in blood LDL: majority, makes bile acids and salts HDL (High density lipoprotein) thought of as "good" cholesterol because it picks up excess cholesterol from blood vessels for excretion -> Synthesized in liver and intestines, released as dense, protein rich particles VLDL and chylomicrons are primary triacylglycerol transporters Lipoproteins synthesized mostly by LIVER and INTESTINE

Oxaloacetate, the precursor of citrate in the citric acid cycle, has: A. 3 carbons B. 4 carbons C. 5 carbons D. 6 carbons

Citrate (citric acid) has 6 carbons. It is generated in the first step of the Krebs cycle from oxaloacetate and acetyl CoA, which has 2 carbons. Therefore, oxaloacetate has 4 carbons (6-2).

Triacylglycerols (triglycerides)

Class of lipids used for energy storage Carbon atoms of fatty acids are more reduced than sugars, which have a bunch of alcohol groups, so the oxidation of triacylglycerols yields 2X as much energy per gram as carbs (Lipids far more energy dense system compared to polysaccharides like glycogen) Also, triacylglycerols are hydrophobic (do not draw in water, do not require water for stability) -> decreases their weight compared to hydrophilic polysaccharides Layer of lipids serves dual purpose: energy storage + insulation (less energy required to maintain homeostasis) Triacylglycerols (triglycerides) are composed of 3 fatty acids bonded by ester linkages to glycerol -Nonpolar and hydrophobic (insoluble) -Triacylglycerol deposits = oily droplets in cytosol (depots of metabolic fuel that can be recruited when needed) (In plants this is oil in seeds) -Adipocytes store large amounts of fat (found primarily under skin around mammalary glands and in abdominal cavity -Bidirectionality in bloodstream between liver and adipose tissue -Characteristics determined by saturation Methods of energy storage: Glycogen offers access to metabolic energy faster in water-soluble form, low energy density so it can't provide energy for as long. Triacylglycerols take more time to mobilize but can provide energy for longer

Nucleic Acids

Classified by the pentose they contain: If pentose is ribose, nucleic acid is RNA If pentose is deoxyribose (ribose with 2' -OH group replaced by -H) then it is DNA

Operon Structure

Cluster of genes transcribed as single mRNA *E.Coli trp operon *common in prokaryotic cells *Order: RPOS -> Regulator, promoter, operator, structural Jacob-monod model says operons composed of structural genes (codes for protein, gene of interests, repressor needs to be absent from operator), operator site (upstream of structural site, non transcribable region of DNA capable of binding repressor), promoter site (Further upstream, similar function to eukaryotic promoters, provides place for RNA poly to bind), and regulator gene (furthest upstream, codes for repressor protein) Essentially an "on-off" switch that regulates gene expression. 2 Types of operons: Inducible and repressible systems

Osmotic Pressure

Colligative property: Physical property of solutions that is dependent on concentration of dissolved particles but not on chemical identity of dissolved particles (like vapor pressure depression (Raoults Law), boiling point elevation, freezing point depression) As osmotic pressure increases (sucking pressure), more water will tend to flow into compartment to decrease solute concentration 2 compartments separated by semipermeable membrane: one with pure water, one with water and dissolved solutes. Membrane allows water but not solutes to pass. Water goes from area of high concentration (pure water) to low concentration (side with water and solute) Net flow causes water level in compartment with solution to rise Concentration of solutes can never be equal, but the hydrostatic pressure from water level will eventually oppose influx of water. Thus, water level will only rise to the point at which it exerts sufficient pressure to balance tendency of water to flow: this is osmotic pressure (II= iMRT) II (osmotic pressure) = iMRT where M is molarity of solution, R is ideal gas constant, T is absolute temperate in kelvins, I is van't Hoff factor (number of particles obtained from molecule in solution) *Glucose remains intact, so I = 1 *NaCl becomes Na+ and Cl-, so I = 2 Osmotic pressure depends only on presence and number of particles in solution, but not actual identity Think of sucking pressure: drawing water into cell in proportion to concentration of solution

The electron transport chain

Complex I: (NADH-CoQ oxidoreductase) -Transfer of NADH to coenzyme Q (CoQ) -Includes protein with iron-sulfur cluster and flavoprotein (with coenzyme flavomononucleotide -> FMN) that oxidized NADH -NADH transfers electrons to FMN (Oxidizing NADH to NAD+ and reducing FMN to FMNH2) then to CoQ (AKA ubiquinone) (becomes CoQH2) -4 protons are moved to inter membrane space Complex II: (Succinate-CoQ oxidoreductase) -Trasfers electrons to coenzyme Q -Succinate is CAC intermediate that is oxidized to fumarate (gives E- to FAD reducing it to FADH2) -FADH2 reoxidized and reduces iron-sulfur protein, then iron-sulfur reoxidized and electrons given to CoQ -NO HYDROGENS PUMPED Complex III (CoQH2-cytochrome C oxidoreductase) : -Facilitates E- transfer from CoQ to -Oxidation and reduction of cytochromes: Proteins with heme group in which iron is reduced to Fe2+ and reoxidized to Fe3+ -Complex 1 and 2 drop e- off at complex 3 -Only 1 e- transferred per reaction, but CoQ has 2 electrons to transfer, so 2 cytochrome C molecules are needed -Q cycle: 2 electrons shuttled from molecule ubiquinol (CoQH2) to ubiquinone (CoQ) (Ubiquinol is reduced form of ubiquinone) -2 more electrons attached to heme, reducing two molecules to Cytochrome C -4 protons displaced -Both coenzyme Q and cytochrome C aren't technically part of complexes, but they can move freely in inner mitochondrial membrane and can carry electrons Complex IV: (Cytochrome C oxidase) -Transfer of electrons from Cyt C to final e- acceptor -Includes cytochrome a and a3 (together make up cytochrome oxidase), and Cu2+ ions -Cytochrome oxidase oxidized as oxygen, becomes reduced to form water -2 protons pumped -Cyanide inhibits cytochrome a and a3 (attaches to iron and prevents e- transport)

Peptides

Composed of amino acid subunits (residues) Dipeptides = 2 amino acid residues Tripeptides = 3 amino acid residues Oligopeptide -> relatively small peptides, up to 20 residues (but has to be more than 1) Polypeptide: Longer chains of peptidesResidues of peptides are joined together through peptide bonds (specialized form of amide bonds Peptide bonds are formed in the context of ribosomes Peptide bond formation is an example of condensation or dehydration reaction because it results in the removal of a water molecule (H2O) -Also viewed as acyl substitution reaction -Electrophilic carbonyl carbon on the first amino acid attacked by nucleophilic amino group on second amino acid -> hydroxyl group of COOH is kicked off = formation of peptide (amide ) bond Peptide drawn in the same order that it is synthesized by ribosomes -> from N terminus to C terminus In living organisms, hydrolysis is catalyzed by hydrolytic enzymes like trypsin and chymotrypsin -> trypsin cleaves at the carboxyl end of arginine and lysine, chymotrypsin cleanse at the carboxyl nd of phenylalanine, tryptophan, and tyrosine Just know that both break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon

Nonenzymatic protein Analysis

Concentration determination: Spectroscopy -aromatic side chains analyzed with UV spectroscopy without treatment Very sensitive to contaminants Colorimetric changes: Bicinchonic acid (BCA) assay, Lowry reagent assay, Bradford protein assay Bradford protein assay; Brown dye is protonated, gives up proton upon binding to amino acid groups, and turns blue Ionic attractions stabilize Limited by presence of detergent in sample or by excessive buffer Acidic form (left) has brown hue, basic form (right), created by interactions with proteins in solution, bright blue

Amino Acids

Contain 2 functional groups: amino group (NH2) and carboxyl group (COOH) Focus on alpha amino acids: amino group bound to alpha carbon of carboxylic acid Alpha carbon also has hydrogen and side chain (R) attached --> side chain determines properties and functions *Note: Amino acids dont technically need both amino and carboxyl group bonded to the same carbon (GABA has amino group three carbons away (on gamma carbon)) *Also, not every amino acid in body has codon in genetic code (ornithine is intermediate in urea cycle, the metabolic process by which body excretes excess nitrogen) But, need to know 20 alpha amino acids: Proteinogenic amino acids All amino acids except for glycine are chiral (stereogenic center) so they are optically active Glycine is achiral because R group is hydrogen All chiral amino acids used in eukaryotes are L-amino acids, so the amino group is one the left in Fischer projection -> all have S absolute configuration, except for cysteine has R configuration excuse -CH2SH has priority over COOH group (because sulfur weight more) only two of the 20 amino acids—threonine and isoleucine— also have a chiral carbon in their side chains as well.

tRNA (transfer RNA)

Converts language of nucleic acids to language of amino acids and peptides: Translates codon into correct amino acid Each tRNA contains folded RNA that includes three nucleotide anticodon -> recognizes and pairs with appropriate codon on mRNA while in ribosome 20 amino acids represented by at least 1 codon Amino acids connected to a specific tRNA molecule are charged / activated with amino acid Mature tRNA in cytoplasm Each type of amino acid activated by different aminoacyl-tRNA synthetase that requires 2 high-energy bonds from ATP (energy rich bond) aminoacyl-tRNA synthetase transfers activated amino acid to 3' end of correct tRNA (each has CCA nucleotide sequence t bind)

Each of the following catalyzes a rate-limiting step of a carbohydrate metabolism pathway EXCEPT: A. hexokinase. B. glycogen synthase. C. glucose-6-phosphate dehydrogenase. D. fructose-1,6-bisphosphatase.

Correct Answer: A Explanation: Hexokinase catalyzes an important irreversible step of glycolysis, but it is not the rate-limiting step. Phosphofructokinase-1 catalyzes the rate-limiting step of glycolysis. Glycogen synthase (choice (B)) catalyzes the rate-limiting step of glycogenesis, glucose-6-phosphate dehydrogenase (choice (C)) catalyzes the rate-limiting step of the pentose phosphate pathway, and fructose-1,6-bisphosphatase (choice (D)) catalyzes the rate-limiting step of gluconeogenesis.

Which of these amino acids has a side chain that can become ionized in cells? A. Histidine B. Leucine C. Proline D. Threonine

Correct Answer: A Explanation: Histidine has an ionizable side chain: its imidazole ring has a nitrogen atom that can be protonated. None of the remaining answers have ionizable atoms in their side chains.

How do hormonal controls of glycogen metabolism differ from allosteric controls? A. Hormonal control is systemic and covalent. B. Hormonal control is local and covalent. C. Hormonal control is systemic and noncovalent. D. Hormonal control is local and noncovalent.

Correct Answer: A Explanation: Hormonal controls are coordinated to regulate the metabolic activity of the entire organism, while allosteric controls can be local or systemic. The modification of the enzymes of glycogen metabolism by insulin and glucagon is either through phosphorylation or dephosphorylation, both of which modify covalent bonds.

A 4-year old toddler with cystic fibrosis (CF) is seen by his physician for an upper respiratory infection. Prior genetic testing has shown that there has been a deletion of three base pairs in exon 10 of the CFTRgene that affects codons 507 and 508. The nucleotide sequence in this region for normal and mutant alleles is shown below (X denotes the missing nucleotide): Codon number506507508509510511 Normal gene (coding strand)ATCATCTTTGGTGTTTCC Mutant gene (coding strand)ATCATXXXTGGTGTTTCC -> ATCATTGGTGTTTCC What effect will this mutation have on the amino acid sequence of the protein encoded by the CFTR gene? A. Deletion of a phenylalanine residue with no change in the C-terminus sequence. B. Deletion of a leucine residue with no change in the C-terminus sequence. C. Deletion of a phenylalanine residue with a change in the C-terminus sequence. D. Deletion of a leucine residue with a change in the C-terminus sequence.

Correct Answer: A Explanation: In this table, we are given the sequence of the sense (coding) DNA strand. This will be identical to the mRNA transcript, except all thymine nucleotides will be replaced with uracil. With the deletion of these three bases, codon 507 changes from AUC to AUU in the transcript; these both code for isoleucine due to wobble. However, codon 508 (UUU in the transcript) has been lost. UUU codes for phenylalanine. The C-terminus sequence will remain unchanged because the deletion of three bases (exactly one codon) will not throw off the reading frame. For reference, the mutant reading frames would be: AUCAUUGGUGUUUCC

The dynamic properties of molecules in the cell membrane are most rapid in: A. phospholipids moving within the plane of the membrane. B. phospholipids moving between the planes of the membrane. C. proteins moving within the plane of the membrane. D. proteins exiting the cell through exocytosis.

Correct Answer: A Explanation: Movement of individual molecules in the cell membrane will be affected by size and polarity, just as with diffusion. Lipids are much smaller than proteins in the plasma membrane and will move more quickly. Lipids will move fastest within the plane of the cell membrane because the polar head group does not need to pass through the hydrophobic tail region in the same way that it would if it were moving between the membrane planes.

Statin drugs inhibit HMG-CoA reductase. As such, they are likely prescribed for: A. hypercholesterolemia (high cholesterol). B. hypertriglyceridemia (high triacylglycerol). C. hypocholesterolemia (low cholesterol). D. visceral adiposity (obesity).

Correct Answer: A Explanation: Statins are drugs that are prescribed to treat high cholesterol and act as competitive inhibitors of HMG-CoA reductase. HMG-CoA reductase is the rate-limiting enzyme of de novo cholesterol synthesis; inhibition of this enzyme lowers production of cholesterol, thus lowering overall levels of cholesterol.

Which of the following is LEAST likely to result from protein degradation and processing by the liver? A. Fatty acids B. Glucose C. Acetoacetate D. 3-Hydroxybutyrate

Correct Answer: A Explanation: The degradation of protein and processing by the liver implies a prolonged starvation state; protein will not be used for energy unless absolutely necessary. Thus, gluconeogenesis is the most likely process. When gluconeogenesis is not possible, easily metabolized molecules, such as ketone bodies, are synthesized. Fatty acid production occurs when energy is being stored; proteins would not be broken down to store energy in fatty acids.

The unique enzymes of gluconeogenesis are used to circumvent specific irreversible steps of glycolysis. Which of the following correctly pairs an enzyme from glycolysis with its corresponding enzyme(s) used in gluconeogenesis? A. Phosphofructokinase-1 / fructose-1,6-bisphosphatase B. Pyruvate dehydrogenase / pyruvate carboxylase and phosphoenolpyruvate carboxykinase C. Hexokinase / glucokinase D. Pyruvate kinase / glucose-6-phosphatase

Correct Answer: A Explanation: The irreversible enzymes in glycolysis are hexokinase (or glucokinase in liver and pancreatic β-cells), phosphofructokinase-1, and pyruvate kinase. Pyruvate dehydrogenase is not considered a glycolytic enzyme because it requires the mitochondria to function. The list below shows the correct pairing of glycolytic enzymes with gluconeogenic enzymes: Hexokinase or glucokinase/glucose-6-phosphatase Phosphofructokinase-1/fructose-1,6-bisphosphatase Pyruvate kinase/pyruvate carboxylase and phosphoenolpyruvate carboxykinase (PEPCK)

Which of the following is true of diffusion and osmosis? A. Diffusion and osmosis rely on the electrochemical gradient of only the compound of interest. B. Diffusion and osmosis rely on the electrochemical gradient of all compounds in a cell. C. Diffusion and osmosis will proceed in the same direction if there is only one solute. D. Diffusion and osmosis cannot occur simultaneously.

Correct Answer: A Explanation: The movement of any solute or water by diffusion or osmosis is dependent only on the concentration gradient of that molecule and on membrane permeability.

The diagram below shows the effects of arsenic on the metabolism of glyceraldehyde 3-phosphate. As a result, in the presence of arsenic, how many molecules of ATP would be created directly from the conversion of two glucose molecules to four pyruvate molecules? A. 0 B. 1 C. 2 D. 4

Correct Answer: A Explanation: The net ATP yield from glycolysis is 2 ATP per glucose. According to the question, arsenic bypasses glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase, directly forming 3-phosphoglycerate. 3-phosphoglycerate kinase is one of the two substrate-level phosphorylation steps and normally produces 2 ATP (one for each of the two molecules of glyceraldehyde 3-phosphate formed from glucose). If these two ATP molecules are lost, the net yield of glycolysis is now 0 ATP.

Which of the following is LEAST likely to be required for a series of metabolic reactions? A. Triglyceride acting as a coenzyme B. Oxidoreductase enzymes C. Magnesium acting as a cofactor D. Transferase enzymes

Correct Answer: A Explanation: Triglycerides are unlikely to act as coenzymes for a few reasons, including their large size, neutral charge, and ubiquity in cells. Cofactors and coenzymes tend to be small in size, such as metal ions like choice (C) or small organic molecules. They can usually carry a charge by ionization, protonation, or deprotonation. Finally, they are usually in low, tightly regulated concentrations within cells. Metabolic pathways would be expected to include both oxidation-reduction reactions and movement of functional groups, thus eliminating choices (B) and (D

In high doses, aspirin functions as a mitochondrial uncoupler. How would this affect glycogen stores? A. It causes depletion of glycogen stores. B. It has no effect on glycogen stores. C. It promotes additional storage of glucose as glycogen. D. Its effect on glycogen stores varies from cell to cell.

Correct Answer: A Explanation: Uncouplers inhibit ATP synthesis without affecting the electron transport chain. Because the body must burn more fuel to maintain the proton-motive force, glycogen stores will be mobilized to feed into glycolysis, then the TCA, and finally oxidative phosphorylation.

Which of the following tissues is most dependent on insulin? A. Active skeletal muscle B. Resting skeletal muscle C. Cardiac muscle D. Smooth muscle

Correct Answer: B Explanation: Adipose tissue and resting skeletal muscle require insulin for glucose uptake. Active skeletal muscle, choice (A), uses creatine phosphate and glycogen (regulated by epinephrine and AMP) to maintain its energy requirements.

Adding concentrated strong base to a solution containing an enzyme often reduces enzyme activity to zero. In addition to causing protein denaturation, which of the following is another plausible reason for the loss of enzyme activity? A. Enzyme activity, once lost, cannot be recovered. B. The base can cleave peptide residues. C. Adding a base catalyzes protein polymerization. D. Adding a base tends to deprotonate amino acids on the surface of proteins.

Correct Answer: B Explanation: Bases can catalyze peptide bond hydrolysis. Choice (A) is incorrect: enzyme activity can be recovered in at least some cases. Choice (D) is a true statement, but fails to explain the loss of enzyme activity.

How do chylomicrons and VLDLs differ? A. Chylomicrons contain apoproteins, VLDLs do not. B. Chylomicrons are synthesized in the intestine, VLDLs are synthesized in the liver. C. Chylomicrons transport triacylglycerol, VLDLs transport cholesterol. D. VLDLs are another term for chylomicron remnants; they differ in age.

Correct Answer: B Explanation: Chylomicrons and VLDLs are very similar. Both contain apolipoproteins and primarily transport triacylglycerol, eliminating choices (A) and (C). The only major difference between them is the tissue of origin. Chylomicrons transport dietary triacylglycerol and originate in the small intestine, while VLDLs transport newly synthesized triacylglycerol and originate in the liver.

During a myocardial infarction, the oxygen supply to an area of the heart is dramatically reduced, forcing the cardiac myocytes to switch to anaerobic metabolism. Under these conditions, which of the following enzymes would be activated by increased levels of intracellular AMP? A. Succinate dehydrogenase B. Phosphofructokinase-1 C. Isocitrate dehydrogenase D. Pyruvate dehydrogenase

Correct Answer: B Explanation: Phosphofructokinase-1 (PFK-1), which catalyzes the rate-limiting step of glycolysis, is the only enzyme listed here that functions under anaerobic conditions. The other enzymes are all involved in the oxygen-requiring processes discussed in this chapter. Succinate dehydrogenase, choice (A), appears in both the citric acid cycle and as part of Complex II of the electron transport chain. Isocitrate dehydrogenase, choice (C), catalyzes the rate-limiting step of the citric acid cycle. Pyruvate dehydrogenase, choice (D), is one of the five enzymes that make up the pyruvate dehydrogenase complex

In the absence of oxygen, which tissue will experience damage most rapidly? A. Skin B. Brain C. Red blood cells D. Liver

Correct Answer: B Explanation: The brain uses aerobic metabolism of glucose exclusively and therefore is very sensitive to oxygen levels. The extremely high oxygen requirement of the brain (20% of the body's oxygen content) relative to its size (2% of total body weight) implies that brain is the most sensitive organ to oxygen deprivation.

Which of the following INCORRECTLY pairs a metabolic process with its site of occurrence? A. Glycolysis—cytosol B. Citric acid cycle—outer mitochondrial membrane C. ATP phosphorylation—cytosol and mitochondria D. Electron transport chain—inner mitochondrial membrane

Correct Answer: B Explanation: The citric acid cycle takes place in the mitochondrial matrix, not the outer mitochondrial membrane. While most citric acid cycle enzymes are located within the matrix, succinate dehydrogenase is located on the inner mitochondrial membrane.

Which enzyme converts GDP to GTP? A. Nucleosidediphosphate phosphatase B. Nucleosidediphosphate kinase C. Isocitrate dehydrogenase D. Pyruvate dehydrogenase

Correct Answer: B Explanation: The conversion of GDP to GTP is a phosphorylation reaction, in which a phosphate group is added to a molecule. Such reactions are catalyzed by kinases. Nomenclature is helpful here, as nucleosidediphosphate kinase is the only enzyme that contains kinase in its name.

When trypsin converts chymotrypsinogen to chymotrypsin, some molecules of chymotrypsin bind to a repressor, which in turn binds to the operator and prevents further transcription of trypsin. This is most similar to which of the following operons? A. trp operon during lack of tryptophan B. trp operon during abundance of tryptophan C. lac operon during lack of lactose D. lac operon during abundance of lactose

Correct Answer: B Explanation: The example given is a sample of repression due to the abundance of a corepressor. In other words, this is a repressible system that is currently blocking transcription. For the trp operon, an abundance of tryptophan in the environment allows for the repressor to bind tryptophan and then to the operator site. This blocks transcription of the genes required to synthesize tryptophan within the cell. The system described is a repressible system; the lac operon is an inducible system, in which an inducer binds to the repressor, thus permitting transcription -> repression due to absence

Why is the α-anomer of d-glucose less likely to form than the β-anomer? A. The β-anomer is preferred for metabolism. B. The β-anomer undergoes less electron repulsion. C. The α-anomer is the more stable anomer. D. The α-anomer forms more in l-glucose.

Correct Answer: B Explanation: The hydroxyl group on the anomeric carbon of the β-anomer is equatorial, thereby creating less steric hindrance than the α-anomer, which has the hydroxyl group of the anomeric carbon in axial position.

A patient has been exposed to a toxic compound that increases the permeability of mitochondrial membranes to protons. Which of the following metabolic changes would be expected in this patient? A. Increased ATP levels B. Increased oxygen utilization C. Increased ATP synthase activity D. Decreased pyruvate dehydrogenase activity

Correct Answer: B Explanation: The increased permeability of the inner mitochondrial membrane allows the proton-motive force to be dissipated through locations besides the F0portion of ATP synthase. Therefore, ATP synthase is less active and is forming less ATP, invalidating choices (A) and (C). The body will attempt to regenerate the proton-motive force by increasing fuel catabolism, eliminating choice (D). This increase in fuel use requires more oxygen utilization in the electron transport chain.

How does the ideal temperature for a reaction change with and without an enzyme catalyst? A. The ideal temperature is generally higher with a catalyst than without. B. The ideal temperature is generally lower with a catalyst than without. C. The ideal temperature is characteristic of the reaction, not the enzyme. D. No conclusion can be made without knowing the enzyme type.

Correct Answer: B Explanation: The rate of reaction increases with temperature because of the increased kinetic energy of the reactants, but reaches a peak temperature because the enzyme denatures with the disruption of hydrogen bonds at excessively high temperatures. In the absence of enzyme, this peak temperature is generally much hotter. Heating a reaction provides molecules with an increased chance of achieving the activation energy, but the enzyme catalyst would typically reduce activation energy. Keep in mind that thermodynamics and kinetics are not interchangeable, so we are not considering the impact of heat on the equilibrium position.

You have just sequenced a piece of DNA that reads as follows: 5′—TCTTTGAGACATCC—3′ What would the base sequence of the mRNA transcribed from this DNA be? A. 5′—AGAAACUCUGUAGG—3′ B. 5′—GGAUGUCUCAAAGA—3′ C. 5′—AGAAACTCTGTAGG—3′ D. 5′—GGATCTCTCAAAGA—3′

Correct Answer: B Explanation: To answer this question correctly, we must remember that mRNA will be antiparallel to DNA. Our answer should be 5′ to 3′ mRNA, with the 5′ end complementary to the 3′ end of the DNA that is being transcribed. Thus, the mRNA transcribed from this strand will be 5′—GGAUGUCUCAAAGA—3′. mRNA contains uracil, rather than thymine.

Which of the following directly provides the energy needed to form ATP in the mitochondrion? A. Electron transfer in the electron transport chain B. An electrochemical proton gradient C. Oxidation of acetyl-CoA D. β-Oxidation of fatty acids

Correct Answer: B Explanation: While all of the other answers contribute to energy production, it is the electrochemical gradient (proton-motive force) that directly drives the phosphorylation of ATP by the F1 portion of ATP synthase.

Which of the following enzymes cleaves polysaccharide chains and yields maltose exclusively? A. α-Amylase B. β-Amylase C. Debranching enzyme D. Glycogen phosphorylase

Correct Answer: B Explanation: β-Amylase cleaves amylose at the nonreducing end of the polymer to yield maltose exclusively, while α-amylase, choice (A), cleaves amylose anywhere along the chain to yield short polysaccharides, maltose, and glucose. Debranching enzyme, choice (C), removes oligosaccharides from a branch in glycogen or starches, while glycogen phosphorylase, choice (D), yields glucose 1-phosphate. Maltose is a disaccharide composed of 2 glucose molecules

Which of the following statements is FALSE? A. Growth hormone participates in glucose counter-regulation. B. T4 acts more slowly than T3. C. ATP stores are turned over more than 10,000 times daily. D. Catecholamines stimulate the sympathetic nervous system.

Correct Answer: C Explanation: ATP stores are turned over about 1,000 times per day, not 10,000.

A particular α-helix is known to cross the cell membrane. Which of these amino acids is most likely to be found in the transmembrane portion of the helix? A. Glutamate B. Lysine C. Phenylalanine D. Aspartate

Correct Answer: C Explanation: An amino acid likely to be found in a transmembrane portion of an α-helix will be exposed to a hydrophobic environment, so we need an amino acid with a hydrophobic side chain. The only choice that has a hydrophobic side chain is choice (C), phenylalanine. The other choices are all polar or charged.

An investigator is measuring the activity of various enzymes involved in reactions of intermediary metabolism. One of the enzymes has greatly decreased activity compared to reference values. The buffer of the assay contains citrate. Which of the following enzymes will most likely be directly affected by the use of citrate? A. Fructose-2,6-bisphosphatase B. Isocitrate dehydrogenase C. Phosphofructokinase-1 D. Pyruvate carboxylase

Correct Answer: C Explanation: Citrate is produced by citrate synthase from acetyl-CoA and oxaloacetate. This reaction takes place in the mitochondria. When the citric acid cycle slows down, citrate accumulates. In the cytosol, it acts as a negative allosteric regulator of phosphofructokinase-1, the enzyme that catalyzes the rate-limiting step of glycolysis.

In which part of the cell is cytochrome c located? A. Mitochondrial matrix B. Outer mitochondrial membrane C. Inner mitochondrial membrane D. Cytosol

Correct Answer: C Explanation: Cytochrome c carries electrons from CoQH2-cytochrome coxidoreductase (Complex III) to cytochrome c oxidase (Complex IV) as part of the electron transport chain. The ETC takes place on the inner mitochondrial membrane. The citric acid cycle takes place in the mitochondrial matrix, except for succinate dehydrogenase is located on the inner mitochondrial membrane.

During fatty acid mobilization, which of the following occur(s)? I. HSL is activated. II. Free fatty acids are released. III. Gluconeogenesis proceeds in adipocytes. A. I only B. III only C. I and II only D. II and III only

Correct Answer: C Explanation: During fatty acid mobilization, there is a breakdown of triacylglycerols in adipocytes by hormone-sensitive lipase (HSL). This breakdown results in the release of three fatty acids and a glycerol molecule. The glycerol may be used by the liver for gluconeogenesis, but adipocytes do not have the ability to carry out gluconeogenesis.

Fatty acids enter the catabolic pathway in the form of: A. glycerol. B. adipose tissue. C. acetyl-CoA. D. ketone bodies.

Correct Answer: C Explanation: Fat molecules stored in adipose tissue can be hydrolyzed by lipases to fatty acids and glycerol. While glycerol can be converted into glyceraldehyde 3-phosphate, a glycolytic intermediate, a fatty acid must first be activated in the cytoplasm by coupling the fatty acid to CoA-SH, forming fatty acyl-CoA. The fatty acid is then transferred to a molecule of carnitine, which can carry it across the inner mitochondrial membrane. Once inside, the fatty acid is transferred to a mitochondrial CoA-SH, reforming fatty acyl-CoA. Through fatty acid oxidation, this fatty acyl-CoA can become acetyl-CoA, which enters the citric acid cycle.

Hormones are found in the body in very low concentrations, but tend to have a strong effect. What type of receptor are hormones most likely to act on? I. Ligand-gated ion channels II. Enzyme-linked receptors III. G protein-coupled receptors A. I only B. III only C. II and III only D. I, II, and III

Correct Answer: C Explanation: For a ligand present in low quantities to have a strong action, we expect it to initiate a second messenger cascade system. Second messenger systems amplify signals because enzymes can catalyze a reaction more than once while they are active, and often activate other enzymes. Both enzyme-linked receptors and G protein-coupled receptors use second messenger systems, while ion channels do not.

The conversion of ATP to cyclic AMP and inorganic phosphate is most likely catalyzed by which class of enzyme? A. Ligase B. Hydrolase C. Lyase D. Transferase

Correct Answer: C Explanation: Lyases are responsible for the breakdown of a single molecule into two molecules without the addition of water or the transfer of electrons. Lyases often form cyclic compounds or double bonds in the products to accommodate this. Water was not a reactant, and no cofactor was mentioned; thus lyase, choice (C), remains the best answer choice.

Why might uracil be excluded from DNA but NOT RNA? A. Uracil is much more difficult to synthesize than thymine. B. Uracil binds adenine too strongly for replication. C. Cytosine degradation results in uracil. D. Uracil is used as a DNA synthesis activator.

Correct Answer: C Explanation: One common DNA mutation is the transition from cytosine to uracil in the presence of heat. DNA repair enzymes recognize uracil and correct this error by excising the base and inserting cytosine. RNA exists only transiently in the cell, such that cytosine degradation is insignificant. Were uracil to be used in DNA under normal circumstances, it would be impossible to tell if a base should be uracil or if it is a damaged cytosine nucleotide.

When fatty acid β-oxidation predominates in the liver, mitochondrial pyruvate is most likely to be: A. carboxylated to phosphoenolpyruvate for entry into gluconeogenesis. B. oxidatively decarboxylated to acetyl-CoA for oxidation in the citric acid cycle. C. carboxylated to oxaloacetate for entry into gluconeogenesis. D. reduced to lactate in the process of fermentation.

Correct Answer: C Explanation: Pyruvate is converted primarily into three main intermediates: acetyl-CoA (choice (B)) for the citric acid cycle (via pyruvate dehydrogenase), lactate (choice (D)) during fermentation (via lactate dehydrogenase), or oxaloacetate (choice (C)) for gluconeogenesis (via pyruvate carboxylase). High levels of acetyl-CoA, which is produced during β-oxidation, will inhibit pyruvate dehydrogenase and shift the citric acid cycle to run in the reverse direction, producing oxaloacetate for gluconeogenesis. Acetyl-CoA also stimulates pyruvate carboxylase directly

Glucocorticoids have been implicated in stress-related weight gain because: A. they increase appetite and decrease satiety signals. B. they increase the activity of catabolic hormones. C. they increase glucose levels, which causes insulin secretion. D. they interfere with activity of the leptin receptor.

Correct Answer: C Explanation: Short-term glucocorticoid exposure causes a release of glucose and the hydrolysis of fats from adipocytes. However, if this glucose is not used for metabolism, it causes an increase in glucose level which promotes fat storage. The net result is the release of glucose from the liver to be converted into lipids in the adipose tissue under insulin stimulation

When the following straight-chain Fischer projection is converted to a chair or ring conformation, its structure will be:

Correct Answer: C Explanation: Start by drawing out the Haworth projection. Recall that all the groups on the right in the Fischer projection will go on the bottom of the Haworth projection, and all the groups on the left will go on the top. Next, draw the chair structure, with the oxygen in the back right corner. Label the carbons in the ring 1 through 5, starting from the oxygen and moving clockwise around the ring. Now, draw in the lines for all the axial substituents, alternating above and below the ring. Remember to start on the anomeric C-1 carbon, where the axial substituent points down. Now start filling in the substituents. The substituent can be in either position on the anomeric carbon, so skip that one for now. The -OH groups on C-2 and C-4 should point downwards while the -OH group on C-3 should point upwards; choice (C), the β-anomer of d-glucose, is the only one that matches.

Steroid hormones are steroids that: I. have specific high-affinity receptors. II. travel in the bloodstream from endocrine glands to distant sites. III. effect gene transcription by binding directly to DNA. A. I only B. III only C. I and II only D. I and III only

Correct Answer: C Explanation: Steroid hormones are produced in endocrine glands and travel in the bloodstream to bind high-affinity receptors in the nucleus. The hormone's receptor binds to DNA, but the hormone itself does not. Steroid hormones are fat/ lipid soluble and can pass through membrane, hydrophobic

Why are triacylglycerols used in the human body for energy storage? A. They are highly hydrated, and therefore can store lots of energy. B. They always have short fatty acid chains, for easy access by metabolic enzymes. C. The carbon atoms of the fatty acid chains are highly reduced, and therefore yield more energy upon oxidation. D. Polysaccharides, which would actually be a better energy storage form, would dissolve in the body.

Correct Answer: C Explanation: Triacylglycerols are highly hydrophobic and therefore not highly hydrated (which would add extra weight from the water of hydration, taking away from the energy density of these molecules), eliminating choice (A). The fatty acid chains produce twice as much energy as polysaccharides during oxidation because they are highly reduced. The fatty acid chains vary in length and saturation.

A student is trying to determine the type of membrane transport occurring in a cell. She finds that the molecule to be transported is very large and polar, and when transported across the membrane, no energy is required. Which of the following is the most likely mechanism of transport? A. Active transport B. Simple diffusion C. Facilitated diffusion D. Exocytosis

Correct Answer: C Explanation: We are asked to identify the type of transport that would allow a large, polar molecule to cross the membrane without any energy expenditure. This scenario describes facilitated diffusion, which uses a transport protein (or channel) to facilitate the movement of large, polar molecules across the nonpolar, hydrophobic membrane. Facilitated diffusion, like simple diffusion, does not require energy, which explains why no ATP was consumed during this transport process.

Val-tRNAVal is the tRNA that carries valine to the ribosome during translation. Which of the following sequences gives an appropriate anticodon for this tRNA? (Note: Refer back to Figure 7.5 for a genetic code table.) A. CAU B. AUC C. UAC D. GUG

Correct Answer: C Explanation: So valine is from the codon, we are looking for the anticodon There are four different codons for valine: GUU, GUC, GUA, and GUG. Through base-pairing, we can determine that the proper anticodon must end with "AC." Remember that the codon and anticodon are antiparallel to each other, and that nucleic acids are always written 5′ → 3′ on the MCAT. Therefore, we are looking for an answer that ends with "AC" (rather than starting with "CA").

Which of the following is a reason for conjugating proteins? I. To direct their delivery to a particular organelle II. To direct their delivery to the cell membrane III. To add a cofactor needed for their activity A. I only B. II only C. II and III only D. I, II, and III

Correct Answer: D Explanation: Conjugated proteins can have lipid or carbohydrate "tags" added to them. These tags can indicate that these proteins should be directed to the cell membrane (especially lipid tags) or to specific organelles (such as the lysosome). They can also provide the activity of the protein; for example, the heme group in hemoglobin is needed for it to bind oxygen. Thus, choice (D) is the correct answer.

Which of the following statements regarding prostaglandins is FALSE? A. Prostaglandins regulate the synthesis of cAMP. B. Prostaglandin synthesis is inhibited by NSAIDs. C. Prostaglandins affect pain, inflammation, and smooth muscle function. D. Prostaglandins are endocrine hormones, like steroid hormones.

Correct Answer: D Explanation: Prostaglandins are paracrine or autocrine hormones, not endocrine—they affect regions close to where they are produced, rather than affecting the entire body. Think of the swelling that happens when you bash your knee into your desk: your knee will swell, turn red, and possibly bruise. Luckily, however, your entire body won't swell as well.

A certain cooperative enzyme has four subunits, two of which are bound to substrate. Which of the following statements can be made? A. The affinity of the enzyme for the substrate has just increased. B. The affinity of the enzyme for the substrate has just decreased. C. The affinity of the enzyme for the substrate is at the average for this enzyme class. D. The affinity of the enzyme for the substrate is greater than with one substrate bound.

Correct Answer: D Explanation: Cooperative enzymes demonstrate a change in affinity for the substrate depending on how many substrate molecules are bound and whether the last change was accomplished because a substrate molecule was bound or left the active site of the enzyme. Because we cannot determine whether the most recent reaction was binding or dissociation, choices (A) and (B) are eliminated. We can make absolute comparisons though. The unbound enzyme has the lowest affinity for substrate, and the enzyme with all but one subunit bound has the highest. The increase in affinity is not linear, and therefore choice (C) is not necessarily true. An enzyme with two subunits occupied must have a higher affinity for the substrate than the same enzyme with only one subunit occupied; thus, choice (D) is correct

Restriction endonucleases are used for which of the following? I. Gene therapy II. Southern blotting III. DNA repair A. I only B. II only C. II and III only D. I, II, and III

Correct Answer: D Explanation: Endonucleases are enzymes that cut DNA. They are used by the cell for DNA repair. They are also used by scientists during DNA analysis, as restriction enzymes are endonucleases. Restriction enzymes are used to cleave DNA before electrophoresis and Southern blotting, and to introduce a gene of interest into a viral vector for gene therapy.

Which of the following is NOT a method by which enzymes decrease the activation energy for biological reactions? A. Modifying the local charge environment B. Forming transient covalent bonds C. Acting as electron donors or receptors D. Breaking bonds in the enzyme to provide energy

Correct Answer: D Explanation: Enzymes are not altered by the process of catalysis. A molecule that breaks intramolecular bonds to provide activation energy would not be able to be reused.

Which two polysaccharides share all of their glycosidic linkage types in common? A. Cellulose and amylopectin B. Amylose and glycogen C. Amylose and cellulose D. Glycogen and amylopectin

Correct Answer: D Explanation: Glycogen and amylopectin are the only polysaccharide forms that demonstrate branching structure, making them most similar in terms of linkage. Both glycogen and amylopectin use α-1,4 and α-1,6 linkages. Cellulose uses β-1,4 linkages and amylose does not contain α-1,6 linkages.

Andersen's disease (glycogen storage disease type IV) is a condition characterized by a deficiency in glycogen branching enzyme. Absence of this enzyme would be likely to cause all of the following effects EXCEPT: A. decreased glycogen solubility in human cells. B. slower action of glycogen phosphorylase. C. less storage of glucose in the body. D. glycogen devoid of α-1,4 linkages.

Correct Answer: D Explanation: In Andersen's disease, glycogen is less branched than normal, thereby inducing lower solubility of glycogen. Branches reduce the interactions between adjacent chains of glycogen and encourage interactions with the aqueous environment. The smaller number of branches means that glycogen phosphorylase has fewer terminal glucose monomers on which to act, making enzyme activity slower than normal overall. Finally, without branches, the density of glucose monomers cannot be as high; therefore, the total glucose stored is lower than normal. Glycogen synthase is still functioning normally, so we would expect normal α-1,4 linkages in the glycogen of an individual with Andersen's disease but few (if any) α-1,6 linkages.

After a brief period of intense exercise, the activity of muscle pyruvate dehydrogenase is greatly increased. This increased activity is most likely due to: A. decreased ADP. B. increased acetyl-CoA. C. increased NADH/NAD+ ratio. D. increased pyruvate concentration.

Correct Answer: D Explanation: In most biochemical pathways, only a few enzymatic reactions are under regulatory control. These often occur either at the beginning of pathways or at pathway branch points. The pyruvate dehydrogenase (PDH) complex controls the link between glycolysis and the citric acid cycle, and decarboxylates pyruvate (the end product of glycolysis) with production of NADH and acetyl-CoA (the substrate for the citric acid cycle). After intense exercise, one would expect PDH to be highly active to generate ATP. ADP levels (choice (A)) should be high because ATP was just burned by the muscle. Acetyl-CoA (choice (B)) is an inhibitor of PDH, causing a shift of pyruvate into the gluconeogenesis pathway. A high NADH/NAD+ ratio (choice (C)) would imply that the cell is already energetically satisfied and not in need of energy, which would not be expected in intensely exercising muscle.

1. At what pH can protein A best be obtained through electrophoresis? (Note: MM = molar mass) Protein pI MM Protein A 4.5 25,000 Protein B 6.0 10,000 Protein C 9.5 12,000 A. 2.5 B. 3.5 C. 4.5 D. 5.5

Correct Answer: D Explanation: In most electrophoresis experiments, we attempt to separate out one component from the others. Because we are attempting to isolate protein A only, a pH that causes protein A to be negative while proteins B and C are neutral or positive will be best. pH 5.5 accomplishes this goal; proteins B and C will be positively charged. A pH of 4.5, choice (C), would make protein A neutral, and it would thus not migrate across the gel. Any neutral impurities would also remain in the well with protein A, making this pH not the best choice.

A membrane receptor is most likely to be a(n): A. embedded protein with catalytic activity. B. transmembrane protein with sequestration activity. C. membrane-associated protein with sequestration activity. D. transmembrane protein with catalytic activity.

Correct Answer: D Explanation: Membrane receptors must have both an extracellular and intracellular domain; therefore, they are considered transmembrane proteins. In order to initiate a second messenger cascade, they typically display enzymatic activity, though some may act strictly as channels.

During which phase of the cell cycle are DNA repair mechanisms least active? A. G1 B. S C. G2 D. M

Correct Answer: D Explanation: Mismatch repair mechanisms are active during S phase (proofreading) and G2 phase (MSH2 and MLH1), eliminating choices (B) and (C). Nucleotide and base excision repair mechanisms are most active during the G1 and G2 phases, also eliminating choice (A). These mechanisms exist during interphase because they are aimed at preventingpropagation of the error into daughter cells during M phase (mitosis).

For most cells, the extracellular calcium concentration is around 10,000 times higher than the intracellular calcium concentration. What is the membrane potential established by this electrochemical gradient? A. -123 mV B. -61.5 mV C. +61.5 mV D. +123 mV

Correct Answer: D Explanation: The Nernst equation relates the intra- and extracellular concentrations of an ion to the potential created by that gradient. At physiological temperature, it can be simplified to E = E0 - (0.06V/n)*logQ or E = 61.5/z (charge) *log (ion outside/ion inside) . For calcium, z = +2 (Ca2+) and the ratio of [ionoutside] to [ioninside] = 10^4. Plugging in, we get. 61.5/2 *4

The majority of triacylglycerol stored in adipocytes originates from: A. synthesis in the adipocyte. B. dietary intake. C. ketone bodies. D. synthesis in the liver.

Correct Answer: D Explanation: The liver is the major metabolic organ in the body and is responsible for much of the synthesis and interconversion of fuel sources. Most of the triacylglycerols that are synthesized in the liver are transported as VLDL to adipose tissue for storage. Both the adipocytes, choice (A) and dietary intake, choice (B), constitute a minor source of triacylglycerol.

Which of the following could result from an absence of apolipoproteins? I. An inability to secrete lipid transport lipoproteins. II. An inability to endocytose lipoproteins. III. A decreased ability to remove excess cholesterol from blood vessels. A. I only B. III only C. I and II only D. I, II, and III

Correct Answer: D Explanation: While the transport and lipid binding functions of most lipoproteins are independent of the apolipoprotein component, the interaction of these lipoproteins with the environment is controlled almost exclusively by apolipoproteins. Lipoproteins cannot exit or enter cells without apolipoproteins, and are unable to transfer lipids without specialized apolipoproteins or cholesterol-specific enzymes.

Glycolysis

Cytoplasmic pathway that converts glucose into 2 pyruvate molecules, releasing small amount of energy captured in 2 substrate level phosphorylations and one oxidation reaction With mitochondria and O2, energy carriers produced (NADH) can feed into aerobic pathway to make energy. If either mitochondria or oxygen is lacking (like in RBCs or exercising muscles) glycolysis may occur anaerobically (some available energy lost) Glycolysis also provides intermediates for other pathways *In the liver, excess glycolysis is part of the process by which excess glucose is converted to fatty acid for storage *No glycolysis = no life. Even partial enzyme defects, like pyruvate kinase deficiency, are super rare

How do cytoskeletal proteins differ from motor proteins?

Cytoskeletal proteins (Collagen, elastin, keratin, actin, tubulin) tend to be fibrous with repeating domains, while motor proteins tend to have ATPase activity and binding heads (Myosin with actin or tubulin, kinesins and dyneins) Both function in cellular motility

Structural Proteins

Cytoskeleton comprised of proteins anchored to cell membrane by embedded protein complexes Collagen, elastin, keratin, actin, and tubulin *Collagen, elastin, keratin = extracellular Highly repetitive secondary structure and "super-secondary structure" which is repetitive organization of secondary structural elements together (motif) Fibrous nature Collagen: Trihelical fiber ( 3 left handed helices (clockwise) woven together to form secondary right (anti clockwise) handed helix ) Makes up most of the extracellular matrix and connective tissue -Strength and flexibility -Has abundance of glycine: if you replace glycine with another amino acid, it can cause improper folding of collagen and lead to bone fragility Elastin: Stretches and recoils like spring to restore original tissue shape Keratins: Intermediate filament proteins found in epithelial cells -Makes up hair and nails -Mechanical integrity of cell -Regulatory protein Actin: -Makes up microfilaments and thin filaments in myofibrils -MOST ABUNDANT PROTEIN IN EUKARYOTIC CELLS -positive and negative side, polarity allows motor proteins to travel one way along actin filament Tubulin: Makes up microtubules -Provide structure, chromosome separation in mitosis/meisosis, intracellular transport with kinesis and dynein -Also has polarity: Negative end located adjacent to nucleus, positive end in periphery

Which of the following would be expected to have the most significant postprandial (after eating) increase? VLDL HDL LDL Chylomicrons

D VLDLs, or very-low-density lipoproteins are formed in the liver and transport triacylglcerols from the liver to other tissues for energy. These levels would be expected to decrease after a meal. HDLs, or high-density lipoproteins, are formed in the liver and are responsible for retrieving excess cholesterol from the blood for excretion. Their levels do not vary significantly with meals. LDLs, or low-denisty lipoproteins, are also formed in the liver and function to deliver cholesterol from the liver to other tissues. Their levels do not vary significantly with meals. Chylomicrons are formed in the liver and function primarily to transport dietary fats to other cells. Following a meal and fat intake, chylomicron production would be expected to increase.

Denaturation and Reannealing

Denature: Disrupt H bonds and base pairing to gain access to DNA -> split into 2 separate strands Covalent links between nucleotides in the backbone break Heat, alkaline pH, and chemicals (formaldehyde and urea) can denature Can be reannealed if denaturing condition slowly removed -Process of annealing important for polymerase chain reactions (PCR) (Probe DNA (known sequence) added to target DNA and binds in process called hybridization)

DNA Libraries and cDNA

DNA Libraries: Large collections of known DNA sequences Can have genomic DNA or cDNA (complementary DNA) cDNA libraries (expression libraries) are constructed by reverse trascribing processed mRNA (lack non-coding regions (introns) and only have expressed genes) Genomic libraries contain large fragments of DNA, both coding (exon) and non-coding (intron) -Genes may be split into multiple vectors by chance, so only cDNA libraries be reliably be used to sequence/produce recombinant proteins/produce transgenic animals

Transcription

DNA contains coding sequence, but machinery is in cytoplasm and DNA can'r leave the nucleus or it will be degraded, so it must use RNA to transmit Creation of mRNA from DNA template is known as transcription Transcription produces a copy of one of the 2 strands of DNA (single strand of mRNA from one of two nucleotide strands of DNA called the template strand (antisense) -> mRNA strand is antiparallel and complementary to DNA template strand) Helices and topoisomerase are involved in unwinding double stranded DNA and preventing formation of supercoils

Recombinant DNA technology

DNA fragment from any source can be multiplied by gene cloning or polymerase chain reaction (PCR) Carrier detection: heterozygote or not Can provide source of specific protein, like recombinant human insulin DNA cloning and restriction enzymes: Goal is to produce a lot of homogeneous DNA Ligate DNA of interest into piece of nucleic acid called vector, forming recombinant vector Vectors are usually bacterial or viral plasmids-> Transferred to host after insertion of DNA of interest Recombinant vector isolated from new colony, ensure that recombinant vector also includes gene for antibiotic resistance (so antibiotics kill off all that do not have gene of interest)

Replicating the ends of the chromosomes

DNA polymerase does a excellent job of synthesizing DNA but it unfortunately cannot complete synthesis of the 5' end of the strand. So, each time synthesis is carried out, chromosome becomes a little shorter To lengthen time that cells can replicate and synthesize DNA, telomeres are located at the tips, and have repetitive GC sequence Prevents loss of function Kinda like the skink sacrificing his tail so the bird doesn't eat the important stuff

Synthesis of Daughter Strands : Leading and Lagging Strands

DNA polymerases read DNA template (parental strand) and synthesize new daughter strand DNA polymerase reads template in 3' to 5 ' and synthesizes complementary strand 5' to 3' Results in new double helix new double helix with antiparallel orientation At each replication fork, one strand is oriented in the correct direction for DNA polymerase, and the other strand is antiparallel *With the exception of DNA polymerase's reading direction , everything is 5' to 3'! (DNA polymerase reads 3' to 5', but DNA synthesis, DNA repair, RNA transcription, and RNA translation (reading of codons) occur 5 to 3) The Leading Strand : in each replication fork, copied in continuous fashion, in same direction as advancing replication fork -Parental strain read 3 - 5 and complement synthesized 5 -> 3 Lagging strand: Copied in direction opposite replication fork -Parental strand has 5 to 3 polarity, so the DNA polymerase can't read it because it can only read 3 to 5 *DNA polymerase can only synthesize in the 5 to 3 direction from reading a 3 to 5 template *So, small strands called Okazaki fragments are produced *As the replication fork moves forward, it clears additional space that DNA polymerase fills in, and each time DNA polymerase completes an Okazaki fragment, it turns and finds another gap to fill Enzymes of DNA replication: Action of DNA helices, gyrase, polymerase, and ligase to create 2 identical molecules of DNA Step 1: Lay down RNA primer (provides 3' OH) (DNA can't be synthesized "de novo" (of nothing), it needs something to hook on to, but RNA can be directly paired with the parent strand. So, primate synthesizes short primer (around 10 nucleotides) in the 5 to 3 direction. These short RNA sequences are aded to lagging strand because each Okazaki fragment starts with new primer. The leading strand only needs one RNA primer ) 2. DNA polymerase 3 (in prokaryotes) or DNA polymerase alpha (a), delta (g), and epsilon (E) (eukaryotes) will begin synthesizing daughter strands of DNA in 5' to 3' 3. Incoming nucleotides are 5' deoxyribonucleotide triphosphates: dATP, dCTP, dGTP, and dTTP. As new bond made, free pyrophosphate (PPi) released 4. RNA must be removed by DNA polymerase 1 (prokaryotes) or RNase H (eukaryotes). Then DNA poly 1 or DNA poly delta (eukaryotes) adds DNA nucleotides where RNA primer was. DNA ligase seals the ends

Histones

DNA that makes up chromosome would around small basic proteins called histones, forming chromatin (The basic repeating structural (and functional) unit of chromatin is the nucleosome, which contains eight histone proteins and about 146 base pairs of DNA) So, 8 histones form nucleosome, and which makes up chromatin? Forms an octamer (Two copies of each protein: four different histones form around the core which winds in a nucleosome) The exterior of histones has a high proportion of positively charged side chains. A nucleosome consists of approximately 200 base pairs wrapped around a histone core: Composed of DNA wrapped around histone proteins Histones are highly conserved across species Five types: H2A, H2B, H3, and H4 ( 2 copies each of these four and about 200 base pairs of DNA are wrapped to form nucleosome) and H1, which seals off the DNA as it enters and leaves nucleosome (Adding to stability) (H1 not found at histone core) Histones are example of nucleoprotein (proteins that associate with DNA): Most are acid soluble and tend to stimulate processes like transcription

Hers disease (Type VI )(glycogen storage disease)(GSD)

Deficiency in liver glycogen phosphorylase Patients can't break down glycogen in liver, so they end up with swollen liver (hepatomegaly) May also have hypoglycemia (low blood sugar) because between meals they can't use glycogen to maintain blood glucose concentrations *body only has 2 primary energy storage molecules: glycogen and triaglycerols

Compared to 37 degC, at 60 degC the activity of most human enzymes is minimal. This is because of protein ___________

Denaturation Inorganic catalysts tend to become more effective at high temp, but enzymes at high temp typically undergo drastic reduction (tend to denature)

Fluid Mosaic Model

Depicts the membrane as a lipid bilayer containing embedded proteins and cholesterol that are capable of moving through bilayer Cell membranes have stretchy/ flexible layer (phospholipids) and stabilizing molecules (proteins and cholesterol) The cell (plasma) membrane is semipermeable phospholipid bilayer -2 layers of phospholipids -Permits fat soluble molecules to cross easily (like steroid hormones), while larger and water-soluble compounds must seek alternative entry Phospholipid bilayer includes proteins and signaling areas within lipid rafts (collections/aggregates of similar lipids with or without associated proteins that serve as attachment points for other biomolecules -> often serve roles in signaling) Carbs associated with membrane bound proteins create glycoprotein coat Cell wall of plants, bacteria, fungi = more carbs Proteins embedded in lipid bilayer act as cellular receptors during signal transduction -> regulate and maintain cellular activity Membrane: Stable semisolid barrier between cytoplasm and environment, constant state of flux -Phospholipids move rapidly in plane of membrane through simple diffusion -Both lipid rafts and proteins travel within plane of membrane, but more slowly -Lipids CAN move between membrane layers, but its unfavorable because polar head region forced through non polar tail region in interior *flippases assist in transition / flip between layers: responsible for movement of phospholipids between layers of plasma membrane because it is otherwise unfavorable Dynamic changes in concentrations of membrane proteins mediated by gene regulation, endocytotic activity, and protein insertion

Lipid Digestion

Dietary fat is mainly triaglycerols (some cholesterol, cholesteryl esters, phospholipids, free fatty acids too) Lipid digestion doesn't really start until small intestine -Lipids enter duodenum (First part of SI), emulsification occurs (fat and water mixed), increases surface area of lipid -Aided by bile (bile salts, pigments, and cholesterol) -> secreted by liver and stored in gallbladder -Pancreas secretes pancreatic lipase, collapse, and cholesterol esterase into small intestine -> hydrolyze lipid components into 2-monoacylglycerol, free fatty acids and cholesterol Micelle Formation: Emulsification followed by absorption of fats by intestinal cells -Free fatty acids + 2-monoacylglycerol + bile salts form micelles (clusters of amphipathic lipids that are soluble in water) Basically, micelles are water soluble spheres with lipid soluble centers At the end of the ileum (Last part of small intestine) bile salts are actively reabsorbed and recycled and fat left goes through colon (poop) Absorption: Micelles diffuse to brush border of intestinal mucosal cells where they are absorbed into mucosa and re-esterfied to form triacylglycerols and cholesteryl esters and packaged with other stuff into chylomicrons Chylomicrons leave intestine through lacteals (vessels in lymph system) and reenter bloodstream through thoracic duct (long lymphatic vessel that empties into left subclavian vein at the base of the neck More water soluble short chain fatty acids can be absorbed by simple diffusion straight into bloodstream

Passive Transport

Does not require intracellular energy stores but rather utilizes the concentration gradient to supply energy for particles to move Simple diffusion: Most basic: Substrates move down concentration gradient directly across membrane -Particles have to be freely permeable to membrane -Potential energy in chemical gradient: Some is dissipated as gradient is used during simple diffusion

Proofreading and Mismatch Repair

During synthesis, 2 double stranded DNA molecules pass through DNA polymerase enzyme for proofreading Incorrect base pairing = instable H bond detected as it passes thorough polymerase Incorrect base excised and replaced Template strand identified because it has been around longer than daughter strand (which is incorrect part), so it is more heavily methylated DNA ligase lacks proofreading ability, so it is more likely to have mutations in lagging strand Mismatch Repair: In G2 phase, mismatch repair takes place by enzymes encoded by genes MSH2 and MLH1, which detect and remove errors missed during S phase *Homologous to MutS and MutL enzymes in prokaryotes Nucleotide and Base Excision Repair : Nucleotide Excision Repair : UV light induces dimers between adjacent thymine residues in DNA -> interferes with DNA replication and expression, distorts shape *Thymine dimers eliminated by Nucleotide Excision Repair (NER) : Cut-and-patch: Proteins scan molecule and recognize bulge in strand, then excision endonuclease nicks phosphodiester backbone on both sides of dimer and cuts it out (remove defective oligonucleotide). DNA poly fills in gaps, synthesizing 5 to 3 Nick sealed with ligase Image: Thymine Dimer formation and nucleotide excision repair Base Excision Repair: Fix non-deforming lesions, like cytosine deamination: Thermal energy absorbed can lead to cytosine deamination (results in conversion of cytosine to uracil) -Uracil should not be in DNA, easily detected -Effected base removed by glycosylase enzyme, leaving apurinic/apyrimidinic (AP) site (also called basic site) -> recognized by AG endonuclease and removed *Nucleotide excision repair corrects lesions large enough to distort double helix, base excision repair corrects lesions small enough to not distort double helix

Endergonic VS exergonic

Endergonic - requires energy (Delta G >0) Exergonic - releases energy (Delta G < 0) The activation energy required for catalyzed reaction is lower than that of uncatalyzed reaction while delta G and delta H remain same

Endocytosis and Exocytosis

Endocytosis: The cell membrane invaginate and engulfs a substance the cell needs to import and then pinches off into a vesicle that is inside the cell. Material encased in vesicle, which is important because cells will sometimes inhest toxic stuff Pinocytosis is endocytosis of fluids and dissolved particles, phagocytosis is ingestion of large solids (like bacteria) -Can be initiated by substrate binding, carried out by vesicle-coating proteins like clathrin Exocytosis: Secretory vesicles fuse with membrane, releasing material from inside cell to extracellular environment Important in nervous system and intercellular signaling

Contrast enzyme-linked receptors with G-protein coupled receptors

Enzyme linked receptors participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades G-protein coupled receptors have membrane-bound protein associated with a trimeric G protein. They also initiate second messenger system

Prokaryotic DNA Gyrase

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix Type of topoisomerase Topoisomerase are involved in DNA replication and mRNA synthesis (transcription)

brush border enzymes

Enzymes secreted by the mucosal cells lining the intestine. disaccharides and dipeptidases digest the smallest peptides and carbohydrates into their respective monomers. present in the brush border or microvilli of the small intestine, which break down disaccharides and starches; examples are sucrase, isomaltase, and lactase.

Propionic Acid Pathway

Even number of carbons yields 2 acetyl coa in last step Odd numbers yield 1 acetyl coa and 1 propionyl coa (requires addition steps to convert it to succinyl-coa for CAC *Odd number fatty acids are exception to rule that fatty acids cant be converted to glucose

Sliding Filament Model

Explains the contraction of muscle cells

The formation of α-d-glucopyranose from β-d-glucopyranose is called: Mutarotation

Exposing hemiacetal rings to water will cause them to spontaneously cycle between open and closed form Single bond between C-1 and C-2 can rotate freely (alpha or beta anomer) = mutarotation (occurs more rapidly when catalyzed with acid or base) Alpha anomeric configuration less favored because hydroxyl group of anomeric carbon is axial = more steric strain

Glucose enters muscle cells from the blood primarily by:

Facilitated diffusion -Utilizes a carrier, but does not require energy Too large and polar to cross membrane via simple diffuse, but the concentration in blood is higher than in tissues

Why does the human body store energy for long-term consumption as lipids rather than as carbohydrates? A. Carbohydrates are more dense than lipids B. Lipids are more hydrophilic than carbohydrates C. The carbon in carbohydrates has a lower oxidation state than lipids D. The carbon in lipids has a lower oxidation state than carbohydrates

Fats are a better source of energy (~9 kilocalories / gram) than carbohydrates (~4 kilocalories / gram). Carbons in lipids are in a lower oxidation state (almost all carbons bonded to hydrogen only in lipids, while most carbons are bonded to at least one oxygen in carbohydrates). Since aerobic respiration is just a highly regulated & drawn out form of combustion, the larger the change in oxidation state, the more high-energy electrons that will be available for generating energy.

Fatty Acid Synthase (Palmitate Synthase) PALMITATE IS THE ONLY FATTY ACID HUMANS CAN SYNTHESIZE DE NOVO *De novo synthesis refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation. For example, nucleotides are not needed in the diet as they can be constructed from small precursor molecules such as formate and aspartate. Methionine, on the other hand, is needed in the diet because while it can be degraded to and then regenerated from homocysteine, it cannot be synthesized de novo.

Fatty Acid Synthase is a large multi enzyme complex in cytosol, rapidly induced in liver following high carb meal (elevated insulin levels) Complex has acyl carrier protein (ACP) that requires vitamin B5 (pantothenic acid) NADPH also required to reduce acetyl groups added by FA 8 acetyl groups = palmitate (16:0) Many reactions reversed in beta oxidation : both involve transport across mitochondrial membrane and series of redox reactions, but opposite direction Activation of growing chain (a), and malonyl-CoA (b) with ACP, bond formation (c), reduction of carbonyl to hydroxyl (d), dehydration (e), and reduction to saturated fatty acid (f) This keep going until palmitate is created

Lipids: Fatty Acids, Triacylglycerols, and phospholipids

Fatty Acids: Carboxylic acids that have hydrocarbon chain and terminal carboxyl group Triacylglycerols/Triglycerides: Storage lipids in human metabolic processes -> 3 fatty acids chains esterified to glycerol molecule Fatty acid chains can be unsaturated (viewed as healthier) and saturated (main component of animals fats, solids at room temp, decrease membrane fluidity, more processed/unhealthy) Unsaturated fatty acids: Double bonds, liquid at room temp, impart fluidity to membrane, most transported as triacylglycerols from intestine inside CHYLOMICRONS -2 important essential fatty acids are alpha-linolenic acid and linoleic acid *Trans fats = partial hydrogenation of unsaturated fatty acids, lower membrane fluidity, form plaques trans glycerophospholipids tend to increase the melting point of the membrane and therefore decrease membrane fluidity. Phospholipids: Substitute one fatty acid chain of triacylglycerol with phosphate group, polar head group joins non polar tails forming glyceriphospholipid (phospholipid) *Assemble into micelles (small monolayer vesicles) or liposomes (bilayered) due to hydrophobic interactions *structural roles and can serve as second messengers in signal transduction -Phosphate groups provide attachment point for water-soluble groups (choline (phosphatidylcholine, or lecithin) or inositol (Phosphatidylinositol))

Which of the following molecules can be utilized as a source of acetyl CoA in humans? I. Fatty acids II. Amino acids III. Ethanol A. I only B. II only C. I and II only D. I, II, and III

Fatty acids (I) CAN be used to generate acetyl CoA via B-oxidation.Amino acids (II) can also be used, if they are KETOGENIC.Ethanol (III) CAN be use too; if that were not the case, alcoholic beverages could not be used as a substitute for glucose, as some alcoholics tend to do.

Regulation of Enzyme activity

Feedback Regulation: Regulation by products further down pathway Feedforward regulation : regulation by intermediates that precede the enzyme Feedback inhibition (negative feedback) more common than feedback activation Negative feedback helps maintain homeostasis Product may bind to enzyme earlier in pathway , competitively inhibiting enzyme (effects whole pathway) Note: biochemistry likes homeostasis: not the same thing as equilibrium ( if it were equilibrium, we wouldn't be able to store energy)

Hexokinase and glucokinase

First steps in glucose metabolism are transport across membrane and phosphorylation by kinases to prevent glucose from leaving *Kinases attach phosphate groups from ATP to their substrates So, glucose enter the cell through facilitated diffusion or active transport, and then hexokinase and glucokinase convert glucose to glucose -6-phosphate (adding phosphate on 6) GLUT transporters want glucose, not glucose-6-phosphate, so glucose cant leave Hexokinase is widely distributed in tissues: inhibited by its product (Glucose 6 phosphate) , low KM (reaches max velocity at low glucose) Glucokinase in only in liver and pancreatic B islet cells (along with GLUT 2 where is acts as glucose sensor): In the liver, glucokinase induced by insulin in hepatocytes, high Km (acts on glucose proportionally to its concentration )

Which of these changes would be most likely to stimulate hormone-sensitive triacylglycerol lipase? A. Increase in aldosterone levels B. Decrease in insulin levels C. Decrease in cortisol levels D. Decrease in epinephrine levels

Hormone-sensitive triacylglycerol lipase breaks down triglycerides in fat tissue when the body has relatively low levels of glucose. Both increased aldosterone levels & decreased insulin levels are observed in such case. Fat cells, however, do not respond to glucagon levels, so the most likely trigger, among the choices, would be a decrease in insulin levels. An INCREASE in cortisol levels or epinephrine levels activates the lipase, not a decrease

The interconversion of glucose-6- phosphate and fructose-6-phosphate is catalyzed by phosphoglucose isomerase. If the two sugars are placed in a sealed container under standard conditions with excess enzyme, given that Kc for the reaction glucose-6-phosphate ⇌ fructose-6-phosphate is 0.5, what will the concentrations of glucose-6-phosphate and fructose-6-phosphate, respectively, be at equilibrium?

First, write the K expression: Kc = [fructose-6-phosphate]/[glucose-6-phosphate]. Since the reactions are under standard conditions, the initial concentrations of each sugar is 1 M. When permitted to react, some amount x of glucose-6-phosphate will be converted to fructose-6-phosphate. Therefore, at equilibrium, the concentration of fructose-6-phosphate will be 1 + x and the concentration of glucose-6-phosphate will be 1-x. Substitute these into the Kexpression: Kc = [fructose-6-phosphate]/[glucose-6-phosphate] = 1 + x/1 - x = 0.5 (1 + x)/(1 - x) = 0.5 1 + x = 0.5(1 - x) 1 + x = 0.5 - 0.5x 1 - 0.5 = -0.5x - x 0.5 = -1.5x x = 0.5/(-1.5) = -0.33 [glucose-6-phosphate] = 1 - x = 1 - (-0.33) = 1.33 [fructose-6-phosphate] = 1 + x = 1 + (-0.33) = 0.67

Plasma Membrane Proteins

Fluid Mosaic model accounts for presence of 3 types of membrane proteins Transmembrane proteins: Pass completely through lipid bilayer (likely serve as channels or receptors) Embedded proteins: Associated only with interior (cytoplasmic) or exterior (extracellular) -Likely have catalytic activity linked to nearby enzymes Embedded + transmembrane together called integral proteins (associated with interior ) Membrane associated (peripheral ) proteins (inside membrane) bound through electrostatic interactions with lipid bilayer (especially at lipid rafts) or other transmembrane or embedded proteins like G proteins on G protein coupled receptors *Membrane associated (peripheral ) protein most likely to be involved in signaling or are recognition molecules Transporters, channels, and receptors generally transmembrane proteins

cystic fibrosis (CF)

Frameshift mutation: Deletion at codon 508 in the polypeptide chain of the CFTR chloride channel gene Loss of phenylalanine residue results in defective chloride ion channel Altered protein never reaches membrane, blocked passage of salt and water in and out of cells Blockage causes cells hat line lungs and organs to produce mucus that traps bacteria and increases infection risks

Free Fatty Acids and Saponification

Free fatty acids are unesterfied fatty acids with free carboxylate group Circulate in the blood bonded noncovalently to serum albumin Saponification is the ester hydrolysis of triacylglycerols using a strong base (usually lye = sodium or potassium hydroxide (KOH or NaOH)) -Basic cleavage of fatty acid and glycerol -Fatty acid salt = soap Soaps can act as surfactants (lowers the surface tension at the surface of a liquid, serving as detergent or emulsifier -If we try and add water and oil, they dont mix. But, if you add soap, the phases appear to combine (forming colloid: mix of large molecules of one substance suspended within another) -> formation of micelles (tiny aggregates of soap with hydrophobic tails inward and hydrophilic heads out, shielding hyprophobic lipid tails and allowing overall solvation) Nonpolar compounds can dissolve in the hydrophobic interior of the water-soluble micelle, so cleaning agents can dissolve water soluble and water insoluble messes

Lipid Transport: Lipoproteins

Free fatty acids transported through blood in association with albumin Carrier protein, triacylglycerol, and cholesterol are transported as lipoproteins (aggregates of apolipoproteins and lipids)(named by density, which increases as proteins concentration increases) Include: Chylomicrons VLDL IDL/VLDL Remnants LDL HDL

Glucocorticoids (like cortisol)

From adrenal cortex Part of stress response glucose rapidly mobilized from liver to fuel muscle wile fatty acids released from adipocytes Secreted with many forms of stress: exercise, cold, emotional Cortisol (image shown) is steroid hormone, promotes mobilization of energy stores through degradation and increased delivery of amino acids and increased lipolysis (break down of lipids) Cortisol elevates BG levels, increasing glucose available for nervous tissue and increase hepatic output of glucose via gluconeogenesis Cortisol enhance activity of epi, glucagon, and other catecholamines Long term exposure to glucocorticoids: hyperglycemia, insulin stimulation, promotes fat storage in adipose tissue rather than lipolysis (the breakdown of fats and other lipids by hydrolysis to release fatty acids.) Endocrine system regulates homeostasis: like glucocorticoids and catecholamines, mineralocorticoids and sex hormones are also synthesized by adrenal glands and play minor role in metabolism ADRENAL CORTEX produces steroid hormones (glucocorticoids, mineralocorticoids, sex hormones)(think cortex = corticoids), but the ADRENAL MEDULLA produces catecholamines

Degeneracy and Wobble

Genetic code is degenerate because more than one codon can specific single amino acid All amino acids (except methionine (AUG) and tryptophan (UGG)) are encoded by multiple codons First 2 bases usually the same, but last one changes = wobble position -Protects against mutations in coding region -Mutations in wobble positions tend to be silent / degenerate (no effect) Mutation in intron won't change protein sequence either because introns are cleaved out of mRNA before translation *Type of point mutation

Ghrelin, Orexin, and Leptin

Ghrelin: secreted by stomach in response to signals of impending meal (sight, sound taste, and SMELL) -Increases appetite and stimulates secretion of orexin Orexin: increases appetite, involved in alertness and sleep-wake cycle -Hypoglycemia is trigger for orexin release Leptin : hormone secreted by fat cells -> decreases appetite by suppressing orexin production -Leptin knockout = obesity Hypothalamus (responsible for hunger, thirst, libido) produces orexin and responds to leptin and ghrelin

postabsorptive (fasting) state

Glucagon, cortisol, epinephrine, and norepinephrine, and growth hormone (counter regulatory hormones) (CENGGH) (Cant everyone not get gun happy on Islam) oppose insulin (released with high glucose) *Greatest decrease in insulin, CENGGH begin to rise CENGGH released with low glucose (fasting) Hepatic gluconeogenesis stimulated by glucagon (takes about 12 hours to hit Vmax), but response is slower than glycogenolysis (begins right at beginning of postabsorpitive state) Release of amino acids from skeletal muscles and FA from adipose tissues stimulated by decrease in insulin and increase in levels of epi Once carried to liver, amino cids and FA can provide energy for gluconeogenesis

Irreversible steps of glycolysis

Gluconeogenesis is mostly just a reversal of glycolysis, but there are three irreversible step in glycolysis (catalyzed by hexokinase, phosphofructokinase-1, and pyruvate kinase), so there are FOUR enzymes required in gluconeogenesis to circumvent the irreversible steps and revert pyruvate to glucose Pyruvate Carboxylase: replaces Pyruvate Kinase in glycolysis Mitochondrial enzyme that is activated by acetyl-CoA (from beta-oxidation) -> Product = oxaloacetate (OAA), reduced to malate -> leaves cytoplasm via malate-aspartate shuttle and oxidized back to OAA *Fatty acids burned to provide energy during gluconeogeneisis so CAC is stopped Phosphoenolpyruvate Carboxykinase (PEPCK): replaces Pyruvate Kinase In cytoplasm, induced by glucagon and cortisol (which usually raise BS) Converts OAA to PEP in reaction that requires GTP PEP goes to fructose 1,6 bisphosphate Together , Pyruvate Carboxylase and PEPCK convert pyruvate back to PEP Fructose-1,6-Bisphosphatase: Replaces phosphofructokinase-1 In cytoplasm Rate limiting step of gluconeogenesis Reverses actions of phosphofructokinase 1 (Rate limiting step of glycolysis) by removing phosphate from Fructose-1,6-Bisphosphate into Fructose-6-phosphate *Phosphotases oppose kinases* Fructose-1,6-Bisphosphatase si activated by ATP and inhibited by AMP and Fructose-2,6-Bisphosphatase (High ATP = cell energetically satisfied enough to give glucose to body, but high AMP means cells need energy and cant afford to give it to the rest of the body) Glucose-6-Phosphatase: Replaces glucokinase Glucose-6-Phosphate found only in lumen in ER in liver cells, transported to ER, free glucose transported back into cytoplasm and diffuses out through GLUT No more Glucose-6-Phosphate in muscle means muscle glycogen cant make glucose for blood and can only be used in muscle Glucose-6-Phosphatase circumvents glucokinase and hexokinase , which converts glucose to glucose 6 phosphate -Alanine is major glycogenic acid but most amino acids are glycogenic too (most converted to maltase) -GLucose made by hepatic gluconeogenesis is not energy for liver: requires expenditure of ATP provided by Beta oxidation of fatty acids in liver. During low BS, adipose tissue release fattyt acids by breaking down triacylglycerols to glycerol (can be converted to DHAP) and free fatty acids Acetyl coa from fatty acids cant become glucose, but can become ketone bodies (good during period of starvation)

Galactose Metabolism

Glucose is primary monosaccharide, but galactose and fructose can also make ATP Galactose in diet from disaccharide lactose in milk. Lactose hydrolyzed to galactose and glucose by lactase (brush border enzyme in duodenum) Reaches liver through hepatic portal vein Phosphorylated by galactokinase in tissues, trapping it in cell, resulting in galactose-1-phosphate converted to glucose 1 phosphate by galactose 1 phosphate uridyltransferase and an epimerase Epimerases are enzymes that catalyze the conversion of one sugar epimer to another (diastereomers) Important enzymes to remember: Galactokinase and galactose-1-phosphate uridyltransferase Genetic deficiencies of galactokinase or galactose 1 phosphate uridyltransferase lead to galactosemia: Can cause cataracts -> Excess galactose converted to galacitol, a polyol (carbon with lots of alcohol), hydrophilic galactose 1 phosphate uridyltransferase deficiency can also cause galactose 1 phosphate to not diffuse out and get stuck

Glycolysis and Gluconeogenesis and Glycogenesis and Glycogenolysis Glycogenolysis is a quick and easy way to move glucose into the blood when your body has an urgent need, but there's another way to get more glucose into your blood that's effective but requires energy. This process is called gluconeogenesis. Glycogenolysis and Gluconeogenesis are two types of processes occurring in the liver to release glucose into blood. Glycogenolysis, as name specifies is the breakdown of glycogen to release glucose molecules. ... Gluconeogenesis is the process which results in the formation of glucose from non-carbohydrate sources.

Glycolysis: the breakdown of glucose by enzymes, releasing energy and pyruvic acid. Glycogenesis: Creation/formation and storage of glycogen from glucose. If glucose and ATP are present in relatively high amounts, then the excess of insulin promotes the glucose conversion into glycogen for storage in liver and muscle cells. One ATP is required per glucose incorporated into the polymeric branched structure of glycogen. Glucose-6-phosphate is synthesized directly from glucose or as the end product of gluconeogenesis. Anabolic synthesis of glycogen. Glucose molecules are phosphorylated to glucose-6-phosphate, converted to glucose-1-phosphate and UDP-glucose, and added to glycogen chains for storage. Glycogenolysis is the breakdown of glycogen branches through catabolic reactions via the sequential removal of glucose monomers via phosphorolysis, catalyzed by the enzyme glycogen phosphorylase. Glycogenolysis takes place in muscle and liver cells in response to hormonal (i.e., glucagon, insulin, and epinephrine) and neural signals Glycogenolysis: Glycogen broken down glycogen stored in the liver and muscles, is converted first to glucose-1- phosphate and then into glucose-6-phosphate. Two hormones which control glycogenolysis are a peptide, glucagon from the pancreas and epinephrine from the adrenal glands. Glucagon is released from the pancreas in response to low blood glucose and epinephrine is released in response to a threat or stress. Both hormones act upon enzymes to stimulate glycogen phosphorylase to begin glycogenolysis and inhibit glycogen synthetase (to stop glycogenesis). Glycogen is a highly branched polymeric structure containing glucose as the basic monomer. First individual glucose molecules are hydrolyzed from the chain, followed by the addition of a phosphate group at C-1. In the next step the phosphate is moved to the C-6 position to give glucose 6-phosphate, a cross road compound. Glucose-6-phosphate is the first step of the glycolysis pathway if glycogen is the carbohydrate source and further energy is needed. If energy is not immediately needed, the glucose-6-phosphate is converted to glucose for distribution in the blood to various cells such as brain cells. Gluconeogenesis: Synthesizing glucose from non-carbohydrate sources -> Make glucose for the bllod The starting point of gluconeogenesis is pyruvic acid, If the concentration of acetyl CoA is low and concentration of ATP is high then gluconeogenesis proceeds. Gluconeogenesis occurs mainly in the liver with a small amount also occurring in the cortex of the kidney. Gluconeogenesis is constantly occurring in the liver to maintain the glucose level in the blood to meet these demands.

Hydrogenation of unsaturated fatty acids can occur with H2 and nickel (catalyst). What does this suggest about hydrogenation reactions?

HIGH ACTIVATION energy in negative enthalpy

Helicase

Helices: enzyme that unwinds DNA, generating 2 single stranded template strands ahead of the polymerase Free purines and pyrimidines seek out molecules to H bond with Single stranded DNA binding proteins (in both eukaryotes and prokaryotes) bind to the unraveled strands and keep them from coming back together and also prevent them from being degraded by nucleases As the helices unwinds, causes positive supercoiling that strains helix ->Supercoiling is the wrapping of DNA on itself as its helical structure is pushed further toward the telomeres during replication To alleviate this torsional strain and reduced the risk of strain breakage, DNA topoisomerase introduce negative supercoiling (work ahead of helices, nicking strands to they can relax, then resealing strands) Any antibiotic ending in -floxacin is called a fluoroquinolone and targets the prokaryotic topoisomerase DNA gyrase. -> stops bacterial replication and slows infection

prolonged fasting (starvation)

High glucagon and epi => rapid degradation of glycogen in liver -As stores are depleted, gluconeogenic activity maintain BG levels during prolonged fasting: after 24 hours, gluconeogenesis is main source of glucose -Lipolysis is rapid, causes excess acetyl coa used in synthesis of ketone bodies -High levels of fatty acids and ketones = muscle used FA as mayor fuel source, brain uses ketones (After several weeks, can use up to 2/3 ketones) -> reduces amount of amino acids degraded to support gluconeogenesis, so you dont have to eat your muscles,,,,, yet RBC still need glucose

Fishcer Projection

Horizontal lines are wedges (out of the page) Vertical lines are dashes (into page) All D-sugars have the hydroxide of their highest numbered chiral center on the right, L sugars have that hydroxide on left (L = OH on LEFT)(D= Derecha (right in Spanish) D-glucose and L-glucose are enantiomers (every chiral center has opposite configuration)

A fall in insulin levels activates: This can also be activated by epinephrine and cortisol

Human adipose tissue does not respond directly to glucagon (low glucose in blood), but a fall in insulin levels activates a hormone sensitive lipase (HSL) HSL can also be activated by epinephrine and cortisol (trigger breakdown of glycogen) HSL hydrolyzes traicylglycerols, yielding fatty acids and glycerol Hormone-sensitive lipase responds to low insulin levels as well as cortisol and epinephrine to mobilize fatty acids from adipocytes. It is not involved in digestion, but rather mobilization of fatty acids. Released glycerol from fat transported to liver for glycolysis or gluconeogenesis HSL effective within adipose cells, but lipoprotein lipase (LPL) is necessary for metabolism of chylomicrons and very low density lipoproteins (VLDL) LPL = enzyme that can release free fatty acids from triacylglycerols in these lipoproteins

Esterification

Hydroxyl group reacts with either carboxylic acid or derivative to form an ester Esterification of glucose: Acetic anhydride used as carboxylic acid derivative Similar to phosphorylation , in which phosphate ester is formed *Phsophate from ATP to glucose, turns ATP to ADP and phosphorylates glucose

Besides ATP, products of reactions in the glycolytic pathway include: I. ADP II. NAD+ III. NADH A. II only B. III only C. I and II only D. I and III only

I. ADP is a product of glycolysis, specifically, in the "investment" phase:In the 1st step of glycolysis, glucose is phosphorylated via hexokinase action to trap it in the cell. II. NAD+ is a reactant in the "payoff" phase of glycolysis:NAD+ is reduced to NADH III. NADH is the product in the payoff phase. Glycolysis yields 2 net ATP and 2 NADH

internal validity vs external validity

INTERNAL VALIDITY - The degree to which a researcher controls for and reduces the effects of extraneous variables than can affect study outcomes so that they represent true outcomes. Internal validity refers to the degree to which an experiment actually supports causality, and so it best describes the reasoning behind the experimenter's choice to control for certain variables. EXTERNAL VALIDITY - The degree to which results from an experiment can be generalized to other individuals beyond the study.

What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?

If the binding protien is present in really high quantities relative to substrate, nearly all substrate will be bound despite low affinity

B-oxidation of the 16-carbon fatty acid hexadecanoic acid

In B-oxidation, a fatty acid LOSES a two-carbon group. Thus, hexadecanoic acid, which has 16 carbons, should end up with 14 carbons (reduces # of carbon atoms). B-oxidation takes place in the mitochondria, not the cytosol. β-Oxidation occurs within the mitochondria, along with the electron transport chain. In contrast, fatty acid synthesis occurs in the cytosol, choice (A). Fatty acyl carriers like the carnitine shuttle allow entry into the mitochondrion for breakdown.

Regulation of chromatin structure: Histone Acetylation and DNA Methylation

In Eukaryotes: DNA packaged in nucleus as chromatin Remodeling allows transcription factors and machinery access to DNA Heterochromatin = tightly coiled, inactive, inaccessible DNA Euchromatin = looser, light, accessible, active Histone Acetylation (addition of acetyl group): Coactivators/ Proteins -> acetylate lysine residues in amino terminal tail regions of histone proteins = decrease in positive charge on lysine and weaker interaction of histone with DNA -Results in open chromatin conformation that allows for easier access of the transcriptional machinery the DNA -Can lead to increased gene expression or histone deacetylases (proteins the remove acetyl groups, resulting in tighter coils and decreased expression) can increase gene silencing DNA Methylation: DNA methylates add methyl groups to cytosine and adenine nucleotides -Methylation of genes linked to silencing gene expression (especially during development) -Heterochromatin = highly methylated Histone deacetylation and DNA methylation = more heterochromatin

a - anomer b - anomer

In chair strucutre: The hydroxyl group on the anomeric carbon of the β-anomer is equatorial, thereby creating less steric hindrance than the α-anomer, which has the hydroxyl group of the anomeric carbon in axial position.

Chargaff's Rule If a sample of DNA has 10% G, what si the % of T?

In double stranded DNA, purines = pyrimidines %A = %T and %G = %C 10%G means 10% C 100- 20 % (G+C) = 80% 80% = A + T, so T = 40% NOTE: RNA is single stranded and thus the complementarity seen in DNA does not hold true (%C may not = % G)

In eukaryotes, the aerobic components of respiration are executed in ____________, while anaerobic process like glycolysis and fermentation occur in:

In eukaryotes, the aerobic components of respiration are executed in mitochondria, while anaerobic process like glycolysis and fermentation occur in cytosol

ACE (angiotensin converting enzyme) inhibitors

In healthy patients, ACE catalyzes peptide conversion from angiotensin I to angiotensin II -> this constricts blood vessels, to raise BP, releases aldosterone which activates kidneys to reabsorb water back in bloodstream (this increases blood volume and further increase BP To lower BP use ACE inhibitors stop path early

Fermentation

In the absence of oxygen Key enzyme: Lactate dehydrogenase (oxidizes NADH to NAD+, replenishing oxidized coenzyme for glyceraldehyde-3-phosphate dehydrogenase ) Without mitochondria and oxygen, glycolysis would stop when all NAD+ reduced to NADH< but by reducing pyruvate to lactate and oxidizing NADH to NAD+, lactate dehydrogenase keeps it going No net loss of carbon (pyruvate and lactate both 3 carbon molecules) Less oxygenation = more lactate produced In yeast, fermentation converts pyruvate (3 carbons) to ethanol (2 carbons) and carbon dioxide (1 carbon) Does not generate ATP or energy carriers, just regenerates coenzymes for glycolysis

Ketone Bodies: 3- Hydroxybutyrate (B-hydroxybutyrate) and acetoacetate Ketogenesis and ketolysis

In the fasting sated, liver converts excess acetyl-coa from beta oxidation of FA into ketone bodies 3-hydroxybutyrate (B-hydroxybutyrate) and acetoacetate KB are essentially transportable forms of acetyl coa Produced by liver and used by other tissues during starvation After a week of fasting, brain can metabolize ketones (can use up to 2/3 ketone bodies) -PDH inhibited, glycolysis and glucose uptake in brain decreases, spares protein in body that would other wise be catabolized (broken down) into glucose Ketogenesis: In mitochondria of liver cells when excess acetyl-coa accumulates in fasting state: HMG-CoA broken into acetoacetate broken into B hydrozybutarate *Acetone = minor side product *High ketone levels can lead to ketoacidosis -> fatty acid breakdown in type 1 diabetic Ketolysis: Generates Acetyl Coa: Acetoacetate picked up from blood, activated by thiophorase -> oxidized to acetoacetyl coa, but liver lacks thiophorase so it cant catabolize ketone bodies it produces *Like ketogeneisis, it is favored during prolonged fast, but ketolysis is stimulated by low energy state in muscle and brain tissues and does not occur in liver FA degradation = lots of acetyl coa, but it cant enter gluconeogenic pathway (needs pyruvate). Only odd numbered fatty acids can act as C source for gluconeogenesis, and even then only the final malonyl-CoA can be used. Energy packed into ketone bodies for consumption by brain and muscles

What is the effect of Aldosterone on blood pressure, where is it synthesized, and where is its major site of action?

Increase; adrenal glands; distal nephron Aldosterone increases salt reabsorption. Salt is a major osmole, and where salt goes, water tends to follow. The effect is an increased body water volume. Aldosterone is a steroid hormone. Aldosterone acts at the distal tubule and collecting ducts. Through a chemical cascade the distal nephron adds sodium channels to the tubular membrane, and upregulates Na/K ATPase activity on the interstitial (basolateral) membrane. The effect is increased reabsorption of salt and water and an increase in blood volume, thus blood pressure.

a-ketoglutarate and CO2 formation

Isocitrate oxidized to oxalosuccinate by ISOCITRATE DEHYDROGENASE Then, it is decarboxylated to make a-ketoglutarate and CO2 ISOCITRATE DEHYDROGENASE is the rate limiting enzyme of CAC First 2 carbons lost First NADH produced

Protein Catabolism (Proteolysis)

Last resort: Body does not want to break down muscle Begins in stomach with pepsin and continues with pancreatic proteases trypsin, chymotrypsin, and carboxypeptidases A and B (all secreted as zymogens) Protein digestion completed by small intestinal brush border enzymes dipeptidase and aminpeptidase *The bulk of protein digestion occurs in the small intestine Produces amino acids, dipeptides and tripeptides Absorption of AA and small peptides through luminal membrane by secondary active transport linked to sodium At basal membrane, simple and facilitated diffusion transport AA into blood Body protein catabolized in liver and muscle -> AA released usually lose amino group by transamination / deamination (ammonia, can be problem, must be excreted by urea cycle in liver: Body way of removing excess N Remaining C skeleton can be used for energy *So: Carbon skeleton transported to liver for processing into glucose or ketone bodies. Amino group will feed into urea cycle, and basic side chains will too. Other functional groups/side chains will be treated like the carbon skeleton Glycogenic amino acids (all but leucine and lysine) can be converted to glucose through gluconeogenesis Ketogenic amino acids: leucine lysine, and also glycogenic amino acids isoleucine, phenylalanine, threonine, tryptophan, and tyrosine can be converted to acetyl coa and ketone bodies

Hepatitis C Virus (HCV)

Leads to cirrhosis of liver/liver failure/scar tissue = liver can't keep up with metabolic demand To fight the virus, infected hepatocytes release interferon (peptide that interferes with viral replication) -Shuts off processes of transcription and translation in infected cells and induces RNase L (cleaves RNA so it can't replicate at all) Even in normal cells, first step in expressing genetic information is transcription of info in the base sequence of double stranded DNA to form single stranded RNA, then that is translated to protein

Which of these classes of enzymes in DNA synthesis is NOT involved in RNA synthesis? A. Helicases B. Topoisomerases C. Polymerases D. Ligases

Ligases (in both eukaryotes and prokaryotes): However, DNA ligase is required to join Okazaki fragments on lagging strand (RNA synthesis doesn't create a lagging strand) Helicases: (in both eukaryotes and prokaryotes) Separate template and non-template strands Topoisomerases: (in both eukaryotes and prokaryotes) Remove the supercoiling from DNA RNA Polymerase: needed to add the nucleotides to the growing RNA chain

Primary Structure of proteins

Linear arrangement of amino acids (order of the amino acids) Listed from N-terminus (amino end) to C terminus (carboxyl end) Stabilized by formation of covalent peptide bond between adjacent amino acids Encodes all the information needed for folding at all structural levels (all the other structures besides primary are just the most energetically favorable arrangements of the primary structure)

List the following membrane components in order from most to least plentiful: Carbs, lipids, proteins, nucleic acids

Lipids, including phospholipids, cholesterol, and others are most plentiful (cell membrane is mostly lipids: lots of phospholipids and a few free fatty acids) Proteins, including transmembrane proteins (channels and receptors), membrane associated proteins, and embedded proteins are next Carbs, including glycoprotein coat and signaling molecules are next Nucleic acids are pretty much absent

Secondary Structure of Protein

Local structure of neighboring amino acids Primarily the result of Hydrogen bonding between nearby amino acids Alpha helices and beta pleated sheets: both result from H bonding Key to stability is formation of intramolecular hydrogen bonds between different residues Alpha Helices: rodlike structure. Peptide chain coils clockwise around a central axis -> stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and amide hydrogen atom four residues down -> side chains point away from helix core -Important for keratin (fibrous structural protein found in human skin, hair, fingernails) Beta pleated sheets: Parallel or antiparallel Peptide chains lie alongside one another, forming rows or strands held together by intramoeluclar hydrogen bonds between carbonyl oxygen atoms on one chain and amide H atoms in adjacent chain (pleated or rippled shape to get as many Hydrogens as possible) R groups of amino residues point above and below plane of sheets Fibroin (primary proton component of silk fibers) Proline: Rigid cyclic structure: introdues kink in peptide chain when its in the middle of an alpha helix (so its rarely found in the middle of ether secondary structure, but its often found in the turns between the chains of a beta pleated sheet and also found as residue at the start of an alpha helix) Stabilizing bonds for primary structures are peptide (amide ) bonds, stabilizing bonds for secondary structures are hydrogen bonds

Microfilaments

Long, thin fibers that function in the movement and support of the cell one can view the microfilament network as an intracellular matrix, which links to the extracellular matrix (Includes Collagen and Elastin) by adhesion molecules.

Which class of enzymes has its normal function as the breaking of one molecule into two smaller molecules without the use of water? Which class of enzymes has its normal function as the breaking of one molecule into two smaller molecules with the use of water?

Lyases (Lyases that work in reverse are often called synthases) Hydrolases

Cellulose

Main structural component of plants Homopolysaccharide Chain of B-D-glucose molecules linked by Beta - 1,4 glycosidic bonds with H bonds holding polymer chains together We lack cellulase enzyme so we cant digest it Great source of fiber, draws water into gut

Mitochondrial Membranes

Mitochondria have ability to produce ATP by oxidative respiration. Contain 2 membranes: inner and outer mitochondrial membrane Outer: Highly permeable -Large pores that passage of ions and small proteins -Outer membrane completely surrounds inner mitochondrial membrane, with presence of small inter membrane space in between 2 layers *No pH gradient between the cytoplasm and inter membrane space because outer mitochondrial membrane has high permeability to biomolecules (PMF across inner mitochondrial membrane, not outer) Inner: More restricted compared to outer -Lots of foldings, called cristae, that increase available surface area for intergral proteins associated with membrane (involved in ETC and ATP synthesis) -CITRIC ACID CYCLE TAKES PLACE IN MITOCHONDRIAL MATRIX -> essential for generating proton motive force -Inner membrane encloses mitochondrial matrix, where citric acid cycle produces high-energy electron carriers used in ETC -High level of cardiolipin, no cholesterol (unlike most biological membranes)

Tissue Specific Metabolism

Major sites of. metabolic activity: liver, skeletal and cardiac muscle, brain, adipocytes Connective and epithelial tissue dont use lots of energy, but epithelial cells are primary secretory cells, so they are important for metabolism too Image: preferred fuels in well-fed and fasting state Liver: Maintains constant level of blood glucose and synthesizes ketones when excess fatty acids are oxidized -When blood glucose is high, liver extracts it and uses it to replenish glycogen stores (any remaining glucose becomes acetyl-coa for fatty acid synthesis -Fatty acids converted to triacylglycerols and released into blood as VLDL -In well fed state, liver derives energy from oxidation of excess amino acids -Lactate, glycerol, and amino acids provide carbon skeletons for glucose synthesis Adipose Tissue -Elevated insulin = glucose uptake by adipose tissue -Insulin triggers fatty acid release from VLDL and chylomicrons (carry triacylglycerols absorbed from gut) -Insulin induces lipoprotein lipase (enzyme in adipose tissue) -Fatty acids that are released from lipoproteins taken up by adipose tissue and re-esterified to triacylglycerols for storage -Glycerol phosphate required for triacyglycerol synthesis (comes from glucose) -Insulin can suppress release of fatty acids from adipose tissue -During fasting state, decreased insulin and increased epi activate Hormone sensitive lipase in fat cells, allowing Fatty acid to be released in blood

Cofactors and Coenzymes

Many enzymes require non protein, small molecules that can bind to the active site of an enzyme and participate in catalyzing the reaction (use ionization, protonation, deprotonation) -Usually kept at low concentrations so they are only recruited when needed Enzymes without cofactors: Apoenzymes, enzymes with cofactors = holoenzymes Prosthetic group: Tightly bound cofactors or coenzymes that are necessary for enzyme function COFACTORS AND COENZYMES: Both act as activators of enzymes, both regulators induce conformation change in enzyme that promote activity -cofactors: usually inorganic molecules or metal ions (generally ingested as dietary minerals) *Deficiencies in vitamin cofactors: Thiamine deficiency ( from excess alcohol) can lead to Wernicke-Korsakoff syndrome (No new memories, delirium, balance issues) -coenzymes: small organic groups such as vitamins or derivatives like NAD+, FAD, CoA Vitamins come in two classes: Fat and water soluble -The water soluble vitamins include B complex and ascorbic acid (vitamin C) -> both easily excreterd -Fat soluble vitamins: A, D, E and K are better regulated by partition coefficients (quantity ability to dissolve in polar vs non polar) Enzyme reactions not restricted to single cofactor or coenzyme

Fructose-2,6-bisphosphate

Marker for satisfactory energy levels in liver Helps liver cells override inhibition of phosphofructokinase-1 that occurs in high levels of acetyl-CoA formed, signals liver cells to shift function from burning to storing fuel Produced by PFK-2 Controls gluconeogeneisis and glycolysis (in liver) PFK-2 activated by insulin and inhibited by glucagon, so glucagon will lower F2,6-BP and stimulates gluconeogenesis, but insulin will increase F2,6-BP and inhibits it More Glucagon = less Fructose-2,6-bisphosphate = more gluconeogenesis More insulin = activates PFK-2 = more Fructose-2,6-bisphosphate = inhibits gluconeogenesis

Mechanisms of Enzyme Activity

May act to provide favorable environment in terms of charge or pH, stabilize transition state bring reactive groups nearer in active site Enzyme substrate binding: Molecule upon which enzyme acts = substrate Physical interaction = enzyme-substrate complex Active site = location within enzyme where substrate held during chemical reaction Active site assumes defined spatial arrangement in complex which dictates specificity of enzyme H bonding, ionic interactions, and transient covalent bonds within active site all stabilize arrangement 2 theories : -Lock and Key : Active site already in appropriate conformation for substrate (key) (no alterations)(not really true) -Induced fit model: More accepted theory: Substrate induces change in enzyme -> induced form or transition state more comfortable for both *Hypothesized that enzyme and substrate undergo conformational changes to interact fully -Shape of active site becomes truly complementary only after substrate begins binding enzyme

Enzyme-linked receptors

May display catalytic activity in response to ligand binding Enzyme linked receptors have 3 primary protein domains: Membrane spacing domain (Anchors receptor in the cell membrane), ligand binding domain (stimulated and induces conformational change that activates catalytic domain), and a catalytic domain -Often results in second messenger cascade -Receptor tyrosine kinases are classic examples (RTKs): composed of monomer the dimerizes upon ligand binding -> dimer is the active form that phosphorylates additional cellular enzymes, including the receptor itself (autophosphorylation) -Serine/threonine-speicifc protein kinases and receptor tyrosine phsophatases

Steroids

Metabolic derivatives of terpenes 4 cycloalkane rings fused together (3 cyclohexane and 1 cyclopentane) Functionality determined by oxidation status Large number of carbons and hydrogens make them (like other lipids) non-polar (a lot of times hydrophobic) Steroid hormones are steroids that act as hormones (they are secreted by endocrine glands into blood and tercel on protein carriers to distant sites where they bind to specific high-affinity receptors and alter gene expression level (released from adrenal cortex) -Testosterone, estrogens, cortisol, aldosterone -Can be used as signaling molecules Cholesterol (shown in image) is a steroid that is major component of phospholipid bilayer -Mediates membrane fluidity -Has both hydrophilic and hydrophobic regions -At low temps, it keeps cell membrane from solidifying, keeps from becoming too permeable at high temp (prevents formation of crystal structure at low temp, increasing fluidity) -At high temp, it decreases fluidity and keeps membrane in tact -Composes 20% of membrane by mass, and 50% by mole fraction - "de novo" = of nothing -> obtained from dietary sources -Precursor to steroid homeones, bile acids, and vitamin D

Michaelis-Menten Equation

Michaelis-Menten: Describes how rate of reaction (v) depends on the concentration of substrate [S] and enzyme [E], which forms product [P] Complexes form at rate k1. The ES complex can either dissociate at rate K-1 or turn into E+P at rate K cat (image) In either case, enzyme is available again Concentration of enzyme kept constant Relate velocity of enzyme to substrate concentration : v = v max [S] / Km + [S] When the reaction rate is = to 1/2 of v max, Km = [S] v max / 2 = Km = [S] So, Km (Michaelis Constant) is substrate concentration at which half the enzymes active sites are full We can assess enzyme affinity for substrate by noting Km. Low Km = high affinity for substrate (low [S] required / not a lot of substrate required for 50% enzyme saturation) High Km reflects low affinity of enzyme for substrate (it takes a lot enzyme to saturate 50% of the substrate) (requires higher substrate concentration to be half saturated ) Km value is intrinsic Property: Can't be altered by changing concentration of substrate or enzyme

Monosaccaride Oxidation Reduction Aldonic acids are compounds that: A. can be oxidized, and therefore act as reducing agents. B. can be reduced, and therefore act as reducing agents. C. have been oxidized, and have acted as reducing agents. D. have been oxidized, and have acted as oxidizing agents.

Monosaccarides switch between anomeric configurations, hemiacetal rings spend short time in open-chain form -> they can be oxidized to carboxylic acids, called aldonic acids (aldoses oxidized to aldonic acids, reduced to alditols) Aldoses can be oxidized, so they are REDUCING agent / reducing sugar When aldsoe is in ring form, oxidation lead to lactone (cyclic ester with carbonyl on anomeric carbon) Aldonic acids are compounds that: C. have been oxidized, and have acted as reducing agents. Two standard reagents detect presence reducing sugars: Tollen's reagent and Benedict's reagent

Cyclic sugar Molecules The cyclic forms of monosaccharides are: I. hemiacetals. II. hemiketals. III. acetals. A. I only B. III only C. I and II only D. I, II, and III Correct Answer: C Explanation: Monosaccharides can exist as hemiacetals or hemiketals, depending on whether they are aldoses or ketoses. When a monosaccharide is in its cyclic form, the anomeric carbon is attached to the oxygen in the ring and a hydroxyl group. Hence, it is only a hemiacetal or hemiketal because an acetal or ketal would require the -OH group to be converted to another -OR group.

Monosaccharides -Contain both hydroxyl group (can serve as nucleophile) and carbonyl group (super common electrophile) -> can form hemiacetals and hemiketals six-membered pyranose rings or five-membered furganose rings Rings are the only form stable in solution because of ring strain (we form ring becuase its more stable) Carbonyl carbon becomes chiral -> anomeric carbon (Only carbon bonded to 2 Oxygens now, one from the bottom and one from the original carbonyl group) (this makes your ring) Downright, up lefting On the right side of Fischer, the substientients are down, if they are only the left they are pointed up Last Carbon group: if it is a d sugar it points up (this is usually the case) Chair diagram: For the HOH on the anomeric carbon *it could be cis to the last carbon, both facing up) (in this case it would be equatorial) a-anomers have the OH on the anomeric carbon trans to the free -CH2OH group, b-anomers have the OH on the anomerica carbon cis to the free -CH2OH group Alpha -> fish -> fish underwater, so the alpha-D glucose chair confirmation points down (trans) Anomeric carbon is constantly opening and closing, so we get beta and alpha Glucose: 36% alpha because trans has some steric hinderance Hexose Confirmations: Haworth projection is useful for describing 3D conformations of cyclic structures

Which of the following will lead to decreased cholesterol in tissue? Increased levels of HDL (wrong) Increased HDL will lead to increased cholester, since it is responsible for cholesterol recovery from the blood and also delivers some cholesterol to tissue like the liver. Decreased expression of HMG CoA reductase (correct) 3-hydroxy-3-methylglutaryl (HMG) CoA reductase catalyzes the rate-limiting step of de novo cholesterol synthesis. Decreasing this enzyme will lead to a decrease in cholesterol in tissues. Decreased levels of glucagon or statin medications (wrong) Glucagon and statin medications lower cholesterol levels. Decreasing these levels would result in an increase in cholesterol in tissue. Increased levels of ATP and NADPH (wrong) De novo synthesis of cholesterol is driven by ATP and NADPH.

Most cells derive cholesterol from LDL and HDL, but some cholesterol can be synthesized de novo. This occurs in the liver and is driven by acetyl-CoA and ATP, and utilizes NADPH as a reducing agent. 3-hydroxy-3-methylglutaryl (HMG) CoA reductase catalyzes the rate-limiting step of de novo cholesterol synthesis. HMG CoA reductase is inhibited by glucagon and statin medications, which lowers cholesterol. Of our options, (C) will lead to less cholesterol in the tissue due to less de novo synthesis.

Van Gierke's disease

Most common glycogen storage disease (all glycogen storage diseases are characterized by accumulation or lack of glycogen) Defect in glucose-6-phosphatase (last step in gluconeogenesis) Hypoglycemia Buildup of intermediates = ->lactate causing lactic acidosis Periods of super low BS between meals Need continuous carb feedings Buildup in glucose 6 phosphate in liver cells (nothing to break it down) causes enlarged liver/ liver damage Cant perform Gluconeogenesis or glucogenolysis: cant produce glucose when fasting

Kinesins and Dyneins

Motor proteins associated with microtubules; important for cell transport, chromosome alignment during metaphase and depolymerizing microtubules during anaphase of mitosis, cilia/flagella. They have 2 heads, but at least 1 always remains attached to tubulin Dyneins : Sliding movement of cilia and flagella Both are important for vesicle transport, but kinesis bring vesicles toward the positive end or the microtubule (stepping motion, one head attached at all times), and dyneins bring vesicles toward the negative end In neurons: Kinesins bring vesicle of neurotransmitter to + end of axonal microtubules (toward synaptic terminal) Dyneins bring vesicle of waste or recycled neurotransmitter back toward negative end of microtubule (toward soma) through retrograde transport

Missense and Nonsense Mutations

Mutation occurs and affects one of the nucleotides in a codon = point mutation Can be silent (Wobble position) or expressed: Missense and nonsense Missense mutation = one amino acid gets replaced by another -Effects range from no effect to abolishing protein's activity -Translation continues properly after the mutation—downstream sequences get translated Nonsense mutation = creates a STOP codon at the site of the mutation (truncation mutation) -Protein is truncated—usually abolishes protein's activity -Translation stops at that point—downstream sequences do not get translated

High Energy Electron Carriers

NADH (glycolysis, fermenation, CAC, ETC), NADPH (PPP< lipid biosynthesis, bleach formation, oxidative stress, photosynthesis), FADH2, ubiquinone (ETC), cytochromes (ETC), glutathione (Oxidative stress) ALL SOLUBLE As electrons are passed down ETC, they give up free energy to form PMF across inner mitochondrial membrane In addition to soluble e carriers, also membrane bound electron carriers within inner MM (Flavin mono nucleotide (FMN) -> bonded to complex I of ETC, act as soluble e carrier) In general, proteins with prosthetic groups (iron sulfur clusters) good at E- transport

sodium-potassium pump

Na+/K+ ATPase maintains low concentration of sodium ions and high concentration of potassium ions intracellularly by pumping 3 Na+ out for every 2 K+ in Maintains negative resting potential of cell Cell membranes more permeable to K+ than Na+ becuase there are more K+ leak channels

Nucleosides and Nucleotides

Nucleosides contain 5-carbon sugar (pentose) and nitrogenous base. Nucleotides are composed of nucleoside + 1 to 3 phosphate groups Nucleosides: Composed of 5-carbon sugar (pentose) bonded to nitrogenous base and formed covalently linking the base to C-1' of sugar Nucleotides: One or more phosphate groups attached to C-5' of nucleoside (the top point on the pentagon is O, so the fifth carbon is extended from ring and phosphate attached to that) -Adenosine di- and triphosphate (ADP and ATP) are named based on how many phosphates are attached to C5 of nucleoside adenosine -High energy compounds: Repulsion from negatively charged groups *NOTE: Bond breaking is usually endothermic, but this is an exception because of all of the negative charges in close proximity, it wants to break apart -> removing terminal phosphate from ATP releases energy, which powers our cells -Building blocks of DNA

Oxidation and Reduction

OIL(Oxidation is loss of electrons) RIG (Reduction is gain of electrons) Can also think of it as Oxidation increases bonds to oxygen or other heteroatom (not C or H), and reduction is increasing bonds to H When you add protons, you add electrons NAD+ is Reduced to NADH (NADH is the reduced form) NAD+ is an oxidizing agent, it accepts electrons and becomes reduced, so it oxidizes something else

Mechanisms of Translation

Occurs in cytoplasm ALL 3 STAGES OF PROTEIN SYNTHESIS (ELONGATION, TERMINATION , INITIAION) REQUIRE LARGE AMOUNTS OF ENERGY *In prokaryotes, the ribosomes start translating before the mRNA is complete, in eukaryotes transcription and translation occur at separate times and in separate locations! Translation occurs in three stages, with specialized factors at each stage: Initiation (Initiation factors), Elongation (elongation factors (EF)), and termination (release factors (RF)) Initiation: Small ribosomal subunit binds mRNA *In prokaryotes, small subunit binds to Shine-Dalgarno sequence in 5' untranslated region of mRNA *Shine delgarno sequence Site of initiation of translation in prokaryotes *In eukaryotes, small subunit binds 5' cap and charged initiator tRNA binds AUG start codon with anticodon within P site of the ribosome *Initial amino acid in prokaryotes is N-formylmethionine (fMet) and methionine in eukaryotes *Large subunit then binds to small subunit, forming initiation complex, assisted by initiation factors (IF) that are not permanently associated with the ribosome Elongation: 3 Step Cycle: repeated for each amino acid added after methionine. Ribosome moves 5' to 3' direction along mRNA, synthesizing protein from amino to carboxyl terminus A site holds incoming aminoacyl-tRNA complex (next amino acid added, determined by mRNA codon within A site P site holds tRNA that carries growing polypeptide chain, and is where MET first binds (Order goes PAPEAPE.......) A peptide bond is formed as polypeptide passed from tRNA in P site to tRNA in A site, requires peptidyl transferase (enzyme that is part of large subunit) GTP is used during bond formation E site (exit site) : Inactive, uncharged tRNA pauses transiently before exiting. Unbinds from mRNA, ready to be recharged Elongation factors (EF) assist by locating and recruiting aminoacyl tRNA along with GTO while helping remove GDP once energy used Termination: One of the three stop codons moves into A site, and protein called release factor (RF) binds to termination codon, causing water to be added, which allows peptidyl transferase and termination factors to hydrolyze from final tRNA -Chain released from tRNA in P site and 2 ribosomal subunits dissociate

Fatty Acid Biosynthesis

Occurs in liver and the products are transported to adipose tissue for storage Major enzymes: acetyl-CoA carboxylase and fatty acid synthase (both stimulated by insulin) Primary end product: palmitic acid (palmitate) After large meal, Acetyl Coa (product of PDH complex) accumulates in mitohcondrial matrix (needs to be moved to cytosol for synthesis) Acetyl coa and oxaloacetate join to form citrate, but isocitrate dehydrogenase is rate limiting step so citrate backs up and slows CAC Citrate diffuses across mitochondrial membrane, and citrate lysine splits it back into acetyl coa and oxaloacetate ( returns back to mitochondrion ) Acetyl coa carboxylase: Acetyl coa activated in cytoplasm Rate limiting step of FA biosynthesis is acetyl coa carboxylase (needs biotin and ATP to function, and adds CO2 tp acetyl coa to form MALONYL-CoA) -Acetyl coa carboxylase activated by insulin and citrate Acetyl-CoA carboxylase is an enzyme which adds CO2 to acetyl-CoA to form malonyl-CoA and is a required step in fatty acid synthesis which occurs in the cytoplasm FA degradation = lots of acetyl coa, but it cant enter gluconeogenci pathway. Only odd numbered fatty acids can act as C source for gluconeogenesis, and even then only the final malonyl-CoA can be used. Energy packed into ketone bodies for consumption by brain and muscles

Terpenes and Terpenoids (sometimes called isoprenoids)

Odifeous chemicals that are metabolic precursors to steroids and other lipid signaling molecules Terpenes: Built from isoprene (C5H8) -Produced mainly by plants and some insects -Smell strongly (Good or bad)(turpentine) -Grouped according to number of isoprene units -1 terpene contains 2 isoprene units -Monoterpenes (C10H16) contain 2 isoprene units -Sesquiterpenes (sesqui means one and a half) contain 3 isporene units, diterpenes contain 4 (20 carbons)(vitamin A, from which retinal (visual pigment for sight is derived) -Triterpenes (6 isporene units can be converted to cholesterol and various steroids)(C30H48) *A triterpene is made of six isoprene moieties (remember, one terpene unit = two isoprene units), and therefore has a 30-carbon backbone. -Carotenoids (like B-carotene and lutein ) are tetraterpenes (8 isoprene units) Polyterpene: up to like 1000 units, like in rubber Terpenoids are derivates of terpenes that have undergone oxygenation or rearrangement of carbon skeleton. -Similar functions to terpenes, smell strong , feed into pathways that produce steroids and vitamin A

2 Systems for naming fatty acids

Omega system (w) starts with the carbon fattest from the carbonyl and counts backwards to the first carbon on the first double bond The other system uses colon with number of carbons : number of double bonds Palmitic acid (16:0) has 16 carbon chain and no double bonds Linolenic acid (image shown): 18:3 all cis 9, 12, 15 is the same as an omega 3 fatty acid

Translation

Once mRNA transcript is created and processed, it can exit through nuclear pores. In cytoplasm, mRNA finds ribosome to begin translation (converting mRNA transcript into functional protein) Translation requires mRNA, tRNA, ribosome, amino acids, and energy in form of GTP DNA -> DNA = replication: new DNA synthesized in 5' to 3' direction DNA -> RNA = transcription: new RNA synthesized 5' to 3' direction (template read 3 to 5) RNA-> protein = translation: mRNA read in 5' to 3' direction

Insulin

Peptide hormone secreted by B cells of pancreatic islets of langerhans Glucose absorbed by peripheral tissues facilitated by glucose transporters in cell membrane -> Adipose tissue and resting skeletal muscle require insulin for glucose uptake Tissues in which glucose uptake not affected by insulin: Nervous tissue, kidney tubules, intestinal mucosa, RBC, B-cells of pancreas For carbs, insulin increase = increase in uptake of glucose = increase carb metabolism Increased glucose in muscle can be burned during excessive or stored as glycogen -Insulin also increase amino acid uptake by muscle cells, increasing protein synthesis, decreasing protein breakdown Insulin increases glycogen syntheses (storing glucose) in liver by increasing glucokinase and glycogen synthase activity , and decreasing glycogen phosphorylase and glucose -6- phosphate (promote glycogen breakdown) Insulin increases glucose and triacyglycerol uptake by fat cells, increases lipoprotein lipase activity (clears VLDL and chylomicrons from blood), increases triacylglycerol synthesis (lipogenesis) in adipose tissue and liver form acetyl coa *Lipogenesis: metabolic process through which acetyl-CoA is converted to triglyceride for storage in fat (Insulin increase = triacylglycerol increase) Insulin decreases: *triacylglycerol breakdown (lipolysis) in adipose tissue *Formation of ketone bodies by liver Most important controller of insulin secretion is plasma glucose Above 100 mg/ dL (5.6 mM glucose), insulins secretion directly proportional to plasma glucose Glucose needs to enter B cells and be metabolized, increasing intracellular ATP (leads to calcium release in cell, promotes exocytosis of preformed insulin from intracellular vesicles) So, glucose goes into cell, increases ATP which increases calcium, causes release of insulin Type 1 diabetes; incapable of synthesizing insulin, but synthesize glucagon. This combo increases BS more than if you lost all pancreatic function

Biological Systems

Open systems: can exchange energy (mechanical work or heat) and matter with environment Closed systems: no exchange of matter with environment -> change in internal energy can only come from heat *In a closed biological system, enthalpy, heat, and internal energy are all directly related because there is no change in pressure or volume. Because pressure and volume are fixed, work cannot be done Delta U = Q -W (pressure and volume are constant in living systems) Internal Energy: Sum of different interactions between atoms in system (vibration, rotation, motion, stored stuff, etc) Standard state conditions (physics): 25 deg C, 1 atm, 1 M concentrations Changes in Δ G (free energy) say whether reaction is favorable/unfavorable ΔG = Δ H - T Delta S -> Predicts direction reaction proceeds spontaneously Spontaneous reaction go forward, net loss of free energy, and negative ΔG Nonspontaneous reaction (spontaneous in reverse direction) have net gain of energy and positive Δ G Free energy approaches 0 as reaction proceeds to = (no net change of reactants or products) Catabolic processes RELEASE energy (exergonic)(products lower than reactants) Anabolic processes REQUIRE energy (endergonic) *Even though bond forming is exothermic Enthalpy measures overall change in heat of system during reaction At constant pressure and volume, enthalpy (delta H) and thermodynamic heat exchange (Q) are equal Changes in entropy (delta S) measure degree of disorder or energy dispersion in system (J/K)

Stereochemistry

Optical Isomers: Same chemical formula, differ in spatial arrangement Enantoinmers: Nonidentical, non superimposable mirror images : Opposite absolute configurations *Any molecule with chiral Carbon and no internal plane of symmetry has an enantiomer Absolute configuration (all about priority, R or S, clockwise or counterclockwise): 3D arrangement of groups to Chiral carbon *Relative configuration: change 1 substituent, but everything else stays the same -> same relative configuration (cis and trans, E and Z, D and L *If you changing 1 substituent changes R to S, you can have the same relative configuration but different absolute configuration *Organic chemists use (R) and (S), biochemists use D and L, but they can't be used interchangeable Number of possible stereoisomers = 2^n where n = number of chiral carbons *D and L are based on stereochemistry of glyceraaldehyde, not directly related to + or - designations denoting optical rotations

Lipids

Organic compounds are nonpolar molecules, which are soluble only in nonpolar solvents and insoluble in water because water is polar molecules. Can serve structural, signaling, and energy storage roles Phospholipids and sterols make up vesicles, liposomes, and membranes Structural Lipids: Major component in phospholipid bilayer Each membrane component is amphipathic (hydrophilic, polar head and hydrophobic fatty acid tail) -Fomration of liposomes, micelles, and phospholipid bilayer

Enzyme Classifications (6 categories)

Oxidoreductase: catalyzes oxidation-reduction reactions (transfer of electrons between molecules) -ase ending = breaks things down (look for dehydrogenase or reductase)(oxidase = oxygen is final electron acceptor) -Cofactor that acts as e- carrier: NAD+ or NADP+ -Electron donor = reductant (gets oxidized) Transferase: transfer functional groups -Aminotransferase: converts aspartate and alpha ketoglutarate to glutamate and oxaloacetate by moving amino group -Includes kinases: Catalyze transfer of phosphate group (usually ATP)(kinases add a phosphate, phosphotases take one off) Hydrolase: Catalyze breaking compound by adding water -Usually named only for substate -Phosphatase cleaves phosphate group off -Peptidases break down proteins, nucleases break down amino acids, lipase break down lipids Lyase: Catalyze cleave of molecule into 2 products -Don't require water as substrate and dont act as oxidoreducatses -Can also catalyze reverse and synthesis 2 molecules into one (called synthase) Isomerase: rearrangement of bonds =Some can be classified as oxidoreductases, transferases, lyases -Catalyze reactions between stereoisomers and constitutional isomers Ligase: Catalyze addition or synthesis reactions, usually between larger molecues, often of the same type -Often require ATP -Nucliec acid synthesis -If its smaller molecules it usually done by lyases

Net Results and ATP Yield of CAC

PDH complex takes 1 pyruvate into 1 acetyl-CoA and one NADH (+CO2 + H+) Step 3,4, and 8 of citric acid cycle all produce 1 NADH and step 6 produces 1 FADH2 Step 5 yields 1 ATP 2 Carbons leave as CO2 In the ETC, each NADH = 2.5 ATP and FADH2 = 1.5 ATP Citric acid cycle: Acetyl CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O -> 2 CO2 + CoA-SH + 3 NADH + 3H+ + FADH2 + GTP So, from 1 pyruvate through CAC we produces 4 NADH (10 ATP), 1 FADH2 (1.5 ATP), 1 GTP -> ATP for a total of 12.5 ATP per pyruvate, 25 per glucose Glycolysis yields 2 more ATP and NADH, so we get 7 more ATP Thus, the net yield for one glucose molecule from glycolysis to oxidative phosphorylation is 30-32 ATP NADH, FADH2, and ATP are all products, and thus inhibitors, of the Krebs cycle

Paracellular and transcellular transport

Paracellular goes through gaps, transcellular goes through the actual membrane Gap junctions allow intracellular transport and do not prevent paracellular transport, tight junctions are not used for intracellular transport and do prevent paracellular transport Gap junctions are discontinuous, tight junctions form bands

Oxidative Phosphorylation

Payout site of aerobic respiration: ATP synthesis Protein complex called ATP synthase spans inner mitochondrial membrane that protrudes into matrix *Only 13% of 100 polypeptides needed for oxidative phosphorylation encoded by mDNA -> mitochondrial DNA has SUPER high mutation rate Chemiosmotic Coupling: PMF interacts with part of ATP synthase that spans membrane (called F0 portion, functions as ion channel so protons can travel along gradient back into matrix) Chemiosmotic coupling allows chemical energy to be harnessed to phosphorylate ADP to ATP (F1 portion of ATP synthase takes ADP to ATP) (pH drop?) Conformational coupling: Mechanism that says there is indirect relationship between proton gradient and ATP synthesis instead When PMF dissipated through F0 of ATP synthase, free energy change is -220 kJ/ mol (very exergonic) , which makes since because phosphorylating ADP to ATP is very endergonic If O2 is limited, rate of oxidative phosphorylation decreases and concentrations of NADH and FADH2 increase (accumulation stops citric acid cycle) Regulation = respiratory control In the presence of plenty of O2, rate of oxidative phosphorylation depends on availability of ADP More ADP = less ATP, so ADP accumulation = need for ATP synthesis ADP allosterically activates isocitrate dehydrogenase, increases CAC rate and production of N ADH and FADH2, increase rate of ETC and ATP synthesis Greater proton gradient = greater ATP generation

Glucagon

Peptide hormone secreted by the alpha-cells of the pancreatic islet of lanerhans Primary target = hepatocyte Acts through second messenger Increases liver glycogenolysis (more breakdown of glycogen into glucose) Activates glycogen phsophorylase and inactivates glycogen synthase Increased liver gluconeogenesis Promotes conversion of pyruvate to PEP by pyruvate carboxylase and PEPCK (PEP carboxykianse) Increases conversion of fructose 1,6 bisphosphate to fructose 6 phosphate by fructose 1,6 bisphosphatase Increased liver ketogenesis and decreased lipogenesis (less acetyl-CoA is converted to triglyceride for storage in fat) *increased lipolysis: the breakdown of fats and other lipids by hydrolysis to release fatty acids. Activates hormone sensitive lipase (action in liver, not adipocyte, so glucagon is not considered major fat mobilizing hormone) You eat: Glucose in blood rises, and you counter that by releasing insulin to LOWER blood glucose levels by storing it Insulin causes glucose to undergo glycolysis (converts glucose to ATP) or insulin can cause glycogenesis: formation of glycogen (whole bunch of glucose molecules, stored in the short term in liver and muscles, we can then break it down and use it later) Lipogenesis, caused by insulin, is irreversible. Store glucose as lipids, adipose tissue To counter low glucose, body uses glucagon to increase the amount of glucose in blood by releasing glucose from storage Proteins/ Amino acids, especially basic ones (arginine, lysine, histidine) increase glucagon A hormone secreted by the pancreatic alpha cells that increases blood glucose concentration Prevents Blood glucose levels from dropping by releasing stored glucose Release glucose from glycogen Glycogenolysis: Breaking down glycogen (reversible) amino acids can undergo gluconeogeneisis: bunches amino acid and makes them glucose Glucagon can also turn glucose into ketone bodies (irreversible )-> ketone bodies really only used by heart and brain Type 1 diabetes; incapable of synthesizing insulin, but synthesize glucagon. This combo increases BS more than if you lost all pancreatic function

Phospholipids

Phosphate and alcohol comprise polar head group Joined to hydrophobic fatty acid tail by phosphodiester linkages (1 or more fatty acids attached to backbone to form hydrophobic tail region) Classified by backbone: Glycerol: 3 carbon alcohol form phoshoglycerides / glycerophodpholipids Sphingolipids have sphingosine backbone (note: not all sphingolipids are phsopholipids ) All lipids have long chain fatty acid tail (vary by degree of saturation and length) Fully saturated fatty acids (single bonds only, carbon saturated when it is bound to four things with no pi bonds) -> Butter -> greater Van Der Waals forces and more stable structure (solid at room temp) Unsaturated fatty acid: one or more double bonds (kinks, makes it difficult to stack and solidify) -> olive oil -> tend to be liquid at room temperature *Phosphoplipids with unsaturated fatty acid tails make up more fluid region of bilayer

Phosphofructokinase (PFK-1 and PFK-2)(top right)

Phosphofructokinase-1 is the rate-limiting enzyme and main control point in glcolysis Fructose-6 phosphate is phosphorylated to fructose 1,6-biphsophate using ATP Phosphofructokinase-1 in inhibited by ATP and citrate and activated by AMP (cell turns off glycolysis when it has enough energy/ATP and turns on glycolysis when it needs energy (indicated by high AMP) High levels of citrate imply cell is producing sufficient energy Insulin stimulates PFK-1 and glucagon inhibits PFK-1 (both actions basically turn on glycolysis) *Insulin inhibits gluconeogenesis and glycogenolysis, stimulates glycolysis and glycogenesis *The pancreas releases glucagon when the amount of glucose in the bloodstream is too low. Glucagon causes the liver to convert stored glycogen into glucose, which is released into the bloodstream. High blood-glucose levels, on the other hand, stimulate the release of insulin. *High ATP says we have plenty of energy, stop glycolysis (stop breaking down glucose) Insulin stimulate and glucagon inhibits PFK-1 in hepatocytes by indirect mechanism with PFK-2 and fructose 2,6- bisphosphate Insulin activates PFK-2, converts tiny bit of fructose 6 phosphate to fructose 2,6 bisphophate (F2,6-BP) F2,6-BP activates PFK-1 (making more fructose 1,6 BP, releasing 2 ADP in process) Glucagon inhibits PFK-2, lowering F2,6-BP and thereby inhibiting PFK-1 PFK-2 found mostly in liver By activating PFK-1, cells can override inhibition cause by ATP so glycolysis can continue, even when cell has enough energy So, metabolites of glycolysis can be fed into the production of glycogen, fatty acids, and other storage molecules rather than just being burned to make ATP glucagon may be considered catabolic and insulin anabolic. In conclusion, insulin promotes body gain by stimulating protein and fat synthesis, growth hormone increases protein retention and decrease fat deposition. Growth hormone can alter the sensitivity of tissues to insulin. In contrast, catabolic hormones such as glucagon, epinephrine and glucocorticoids are provided for mobilization of energy reserves to allow the animal to deal with adverse situations.

Pyruvate Dehydrogenase Kinase and Pyruvate Dehydrogenase Phosphatase

Phosphorylation of PDH is facilitated by Pyruvate Dehydrogenase Kinase ATP levels rise, PDH is phosphorylated, acetyl coa production is inhibited KINASE PHOSPHORYLATES AND INACTIVATES Reactivated by Pyruvate Dehydrogenase Phosphatase in response to high ADP

Posttranslational Processing : Phosphorylation Carboxylation Glycosylation Prenylation

Phosphorylation: Add phosphate group (PO4^2-) by protein kinases -> commonly seen with seine, threonine, and tyrosine *Charge of phosphate group is VERY negative *Phosphorylation of amino acid (like serine, threonine, tyrosine) will turn polar amino acid into negatively charged one Carboxylation: Add COOH groups, usually serve as calcium-binding sites Glycosylation: Adding oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination Prenylation: Adding lipid groups to some membrane bound enzymes Chaperones: Special class of proteins that assist in protein folding Proteins also modified by cleavage -Insulin cleaved from larger, inactive peptide to achieve active form In peptides with quaternary structure, subunits come together to form functional protein (hemoglobin) *Clotting factors, like prothrombin require post translational carboxylation of some glutamic acid to function Vitamin K is required for this reaction, so vitamin K deficiency may cause blood disorder

Plane polarized light rotated in clockwise direction is of_ (+ or -) designation

Plane polarized light rotated in clockwise direction is of + designation

Proteins

Polypeptides that range from just a few amino acids in length up to thousands Serve many functions: Enzymes, hormones, membrane pores, receptors, elements of cell structure 4 levels: primary's secondary, tertiary, quaternary

Starches

Polysaccharides that are more digestible by humans because they are alpha-D-glucose monomers Plants store starch as amylose (linear glucose polymer linked via alpha 1,4 glycosidic bonds Another type of starch is amylopectin (also contains alpha 1,6 glycosidic bond branches) Iodine tests for starch B-Amylase cleaves amylose from non-reducing ends (end with acetal) to yield maltose, while alpha-amylase cleaves randomly along the chain to yield shorter chains Amylopectin needs debranching enzymes Amylopectin is more soluble than amylose because it is more branched (increases interactions with other stuff and decreases intermolecular bonding) A 109.5 degree rotation of the anomeric carbon to form beta linkages instead of alpha linkages is enough to make starch into an indigestible substance (cellulose), even though they are both D-glucose polymers

hnRNA

Precursor to mRNA in eukaryotes only Becomes mRNA after splicing out introns and addition of 5' cap, 3' polyA tail

Tertiary Structure

Primarily the result of moving hydrophobic amino acid side chains into the interior of the protein -Secondary structures form first, and then hydrophobic interactions and H bonds cause protein to collapse into proper 3D shape (intermediate states = molten globules) -> SUPER fast process -3D shape determined by H bonding and weak acid-base interactions (create salt bridge) -Determined by hydrophobic (wants to be on the inside) and hydrophilic interactions between R groups -Hydrophillic N-H and C double dond O bonds get pulled in by hydrophobic residues -> form electrostatic interactions and further stabilize with H bonds *Most amino acids on surface have hydrophilic (polar or charged) R groups, and Hydrophobic R groups (like phenylalanine) are never found on the surface: Both of these facts are due to ENTROPY -Disulfide Bond: 2 Cysteine molecule become oxidized (loss of two protons and 2 electrons) to cystine -> create loops, determine how wavy/curly hair is (more disulfide bonds = curlier) If protein loses tertiary structure (denaturation) it loses function Folding and Salvation Layer : Whenever solute dissolves in solvent, nearby solvent molecules form solvation layer around solute -Hydrocarbons more stable in aqueous solution than organic (delta H <0) but when hydrophobic side chain (like on The or Leu) is placed in aqueous solution, water in solvation layer cant form H bonds with side chain, which forces water to rearrange to maximize H bonding, which means negative change in entropy (delta S) ->means decreasing disorder / increasing order -> unfavorable -> non spontaneous (Delta G> 0) Hydrophilic residues (serine or lysine) on exterior increases entropy (Delta S > 0) making process spontaneous overall SO: moving hydrophobic residues away from water and moving hydrophilic residues towards water = protein achieves maximum stability Moving hydrophobic residues to interior increases entropy by allowing water on surface to have more possible configurations (Delta S makes Delta G < 0, stabilizing protein) *Hydrophobic interactions push hydrophobic R groups to interior of protein, increases entropy of surrounding water and creates negative Gibbs free energy Subtypes of tertiary structure: Hydrophobic interactions, acid-base/salt bridges, disulfide links Stabilizing bonds: Van der Waals, H bonds, ionic bonds, covalent bonds

lactose intolerance

Primary LI is hereditary deficiency of lactase Secondary LI can come at any age, caused by damage to intestinal lining where lactase is found Symptoms caused by bacterial fermentation of lactose, which produces a mixture of CH4, H2 and organic acids. Acids are osmotically active and result I movement of water into intestinal lumen

alternative splicing

Primary transcripts of hnRNA may be spliced together in different ways to produce multiple variants of protein : Alternative splicing -Organism can make more proteins from limited genes Function in regulation of gene expression in addition to generating protein diversity -Mutations in splice sites can lead to abnormal proteins

Biosignaling

Process in which cells receive and act on signals; ex. proteins acting as extracellular ligands, transporter for facilitated diffusion, receptor proteins, second messengers Proteins involved can have function in substrate binding or enzyme activity Can take advantage of either existing gradients (ion channels) or second messenger cascades (enzyme linked receptors and G protein coupled receptors)

Glycogenolysis glycogen phosphorylase

Process of breaking down glycogen The rate limiting enzyme is glycogen phosphorylase In contrast to hydrolase, a phosphorylase breaks bonds using an inorganic phosphate of water The glucose 1-phosphate formed by glycogen phosphorylase is converted to glucose 6 phosphate by the same mutase used in glycogen synthesis glycogen phosphorylase breaks a-1,4 glycosidic bonds, releasing glucose 1-phosphate from edge of granule Can't break 1,6 linkages, so it stops about 3 glucoses away from branch point -glycogen phosphorylase is activated by glucagon in liver -> spreads glucose around body In skeletal muscles, its activated by AMP and epinephrine which say that muscle is active and needs glucose -Inhibited by ATP

Flavoproteins

Protein bonded to FAD -contain a modified vitamin B2 (riboflavin). -nucleic acid derivatives (FAD:Flavin adenine dinucleotide or FMN: Flavin mono nucleotide) -electron carriers in mitochondria and chloroplasts -Also involved in modification of other B vitamin to active forms -coenzymes for the oxidation of fatty acids, decarboxylation of pyruvate, and reduction of glutathione Deficiency of riboflavin, key component to flavoproteins = lack of growth, failure to thrive, death

apolipoproteins (apoproteins)

Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins - form the protein component of lipoproteins - receptor molecules - involved in signaling

Protein Isolation

Proteins and other biomolecules are isolated from body tissues or cell cultures by cell lysis and homogenization which is crushing, grinding or blending the tissue of interest into an evenly mixed solution. Centrifugation can then isolate the proteins before another isolation technique must be used -isolation techniques are electrophoresis and chromatography *Chromatogpraphy: the more similar compound is to surroundings, the slower it will move through *Column chromatography: Polar silica and aluminum beads: less polar compound = faster it moves Electrolytic (non spontaneous) cell: Electrophoresis: Electric field moves - charged compounds + charged anode, and + charged compounds will migrate toward - charged cathode Migrational velocity (v) = Electric field strength (E) * net charge (z) / frictional coefficient (f) *Used in electrolytic cell where delta G >0 and E cell < 0 *Anions always move toward the anode (positive charge) and cations always move towards cathode (negative charge) *charged particles towards oppositely charged electrodes Polyacrylamide gel is standard medium for protein electrophoresis Smaller molecules move faster/go farther

Tertiary Structure and Quaternary Structure of Proteins

Proteins can be divided into fibrous (collagen: structure resembles sheets or long strands) and globular proteins (myoglobin: Spherical shape) : Both of these are caused by tertiary and quaternary protein structures, both of which result from protein folding Collagen consists of three helices with carbon backbones that are tightly wrapped around one another in a "triple helix." Which of these amino acids is most likely to be found in the highest concentration in collagen? Because collagen has a triple helix, the carbon backbones are very close together. Thus, steric hindrance is a potential problem. To reduce that hindrance, we need small side chains; glycine has the smallest side chain of all: a hydrogen atom.

Enzymes

Proteins that increase RATE of biological reactions NOT CHANGED during course of the reaction (appear in both reactants and products) Lower activation energy Regulate hosestatic mechanisms pH and temp sensitive, with only optimal activity at specific pH ranges and temps Molecule enzyme acts on = substrate SPECIFIC: Enzyme specificity: Enzyme wil only catalyze single reaction or class or reactions with substrates *An enzyme's specificity is determined by the three dimensional shape of its active site. active site determines which substrate the enzyme will react with. -Urease only catalyzes breakdown of urea Chymotrypsin can cleave peptide bond around amino acids phenylalanine, tryptophan, and tyrosine (all aromatic) in variety of polypeptides Dont affect overall delta G of reaction They are regulated by environmental conditions , activators and inhibitors Some enzymes are kept in an inactivated form called ZYMOGEN (only activated when needed) Important biological catalysts: Dont impact thermodynamics of reaction (Delta H rxn and equilibrium position don't change), but they speed up rate The activation energy required for catalyzed reaction is lower than that of uncatalyzed reaction while delta G and delta H remain same Image: spontaneous, negative delta G Enzymes don't alter free energy overall or change equilibrium They affect rate (kinetics): how quickly reaction gets to equibilirum Remember: Enzymes aren't changed by reaction, so far fewer copies of enzyme are needed compared to about of substrate because one enymze can act on MANY molecules over time Catalysts exert effect by lowering activation energy -> easier for substrate to reach transition state (cut top off the hill so its not so high) -Most are reversible, but it would be VERY unfavorable *SO: Catalysts are characterized by ability to reduce AE of reaction, speeding it up, and they are not used up, Enzymes improve the environment, which lower AE, and they are regenerated at the end Enzymes dont effect thermodynamics (no effect on delta G or H), but they lower energy of transition state, lowering AE Enzymes effect kinetics of reaction: Lowering AE, so equilibrium can be achieved faster (but position of eq doesnt change )

Pyruvate Dehydrogenase Complex enzymes

Pyruvate dehydrogenase (PDH)(Enzyme 1); Needs Vitamin B1 (TPP) and Mg2+ Dihydrolipoyl transacetylase (E2): Molecule transferred to lipoid acid (disulfide group acts a oxidizing agent, creates acetyl group_ Dihydrolipoyl dehydrogenase (E3): FAD reduced to FADH2

Pyruvate Dehydrogenase

Pyruvate from aerobic glycolysis enters mitochondria, where is is converted to acetyl-CoA for entry into citric acid cycle if ATP is needed, or for fatty acid synthesis if ATP is not needed The pyruvate dehydrogenase complex (PDH) reaction is irreversible and cannot be used to cover acetyl coa to pyruvate or glucose PDH activated by insulin in liver, but in the nervous system it doesn't respond to hormones High insulin levels tell liver to not burn glucose for energy, but instead shift fatty acid equilibrium towards production and storage, rather than oxidation Reactants: Pyruvate, NAD+, CoA Products: Acetyl-CoA, NADH, CO2 Large complex: requires cofactors and coenzymes: Thaimine, pyrophosphate, lipoid acid, CoA, FAD< and NAD+ Pyruvate dehydrogenase inhibited by acetyl-CoA (product) During B oxidation, buildup of acetyl cOa causes shift in metabolism so pyruvate is no longer converted to acetyl-CoA (to enter CAC) but rather into oxaloacntate (to enter gluconeogensis) Lipoic acid is a coenzyme for the pyruvate dehydrogenase complex, so deficiencies in lipoic acid would cause a build up of pyruvate and a shift to anaerobic respiration, resulting in the production of lactic acid.

Mechanisms of Transcription: RNA Polymerase

RNA synthesized by DNA dependent RNA polymerase (locates genes by searching promoter regions of DNA) Eukaryotes: RNA polymerase II transcribes mRNA, binding site in promoter region known as TATA box -Transcription factos help RNA polimerase find and bind promoter region, establish where transcription should start *RNA poly does not require primer (unlike DNA poly 3) In eukaryotes, there are three types of RNA polymerases, but only one is involved in transcription of mRNA: RNA poly I: Located in nucleolus and synthesizes most rRNA RNA poly II: Located in nucleus and synthesizes hnRNA (preprocessed mRNA) and some small nuclear RNA (snRNA): Binds to TATA box within promoter region (25 base pairs upstream from first transcribed base) RNA poly III located in nucleus and synthesizes tRNA and some rRNA *When starting transcription, RNA poly II binds to TATA box, located within promoter region of a relevant gene, at about -25 RNA poly travels along template strand in 3' to 5' so construction of transited mRNA can be 5' to 3' *Transcription is 5' to 3', just like DNA synthesis. Synthesis of nucleic acids always in 5 to 3 direction Unlike DNA Poly, RNA poly does not proofread Coding (sense) strand of DNA is not used as template during transcription (complementary to template, identical to mRNA except T replaced with U) First base transcribed from DNA to RNA is +1 base of that gene region Bases to the left (upstream, toward 5' end) are given negative numbers (-1, -2, -3 and so on) Bases to the right (downstream, towards 3' end) have positive numbers No nucleotide - 0 Transcription continues along DNA coding region until RNA polymerase reaches termination sequences/stop signal DNA double helix then reforms, and primary transcript formed = heterogeneous. nuclear RNA (hnRNA) mRNA derived from hnRNA via posttranscriptional modification

Glycogen Synthase

Rate-limiting enzyme of glycogen synthesis, forms alpha-1,4 glycosidic bond in linear glucose chains Stimulated by glucose 6-phosphate and insulin Inhibited by epinephrine and glucagon through protein kinase cascade that phosphorylates and inactivates the enzyme

ATP (adenosine triphosphate)

Readily available form of energy from cell: mid level energy carrier (smaller free energy, about -30 kJ / mol -> small value so no energy is wasted) formed from substrate level phosphorylation (ATP directly) and oxidative phosphorylation (ATP from electon carriers going though ETC) *Adenosine with 3 phosphate groups, generated from ADP and Pi from exergonic reaction or electrochemical gradient Consumed through hydrolysis or transfer of P *If one phosphate removed (ADP is produced), 2 removed = AMP Recycle ATP, ADP and Pi 1000X per day Good energy carrier because of high-energy phosphate bonds (negative charge on phosphate groups have repulsive forces, much more stable after hydrolysis = negative delta G) *High energy compounds, like cAMP (-50.4, second messenger), creatine phosphate (-43.3, direct phosphorylation in muscle) Then, ATP (-30.5 kJ/mol, energy turn over in all cell types) -> free energy of hydrolysis, phosphate to water *Reverse reaction: ADP + Pi -> ATP + H2O has free energy of 30.5 kJ/mol Glucose-6-phosphate (-13.9, intermediate of glycolysis and gluconeogenesis), AMP (-9.2, ATP synthesis *Most ATP produced by mitochondrial ATP synthase (At the end of ETC), but some from glycolysis (indirectly from GTP) in CAC *Can allow non spontaneous reaction to occur or increase rate of spontaneous reaction *Fats are more energy rich (9 kcal/g from fats and 4 kcal/g from carbs, proteins, ketones ATP is used to fuel energetically unfavorable reactions or to activate or inactivate other molecules (ATP cleavage, phosphorylation group transfer) *Inefficient long term storage molecule because it is not energetically dense, and charges make it hard to pack in small space *SUM OF FREE ENERGIES OF INDIVIDUAL REACTIONS = OVERALL FREE ENERGY Phosphoryl group transfers: ATP can provide phosphate group as reactant: Phosphorylation of glucose to form G-6-P

Given that the Keq for the forward reaction is 22.2 under standard conditions, what is the Keqfor the reverse reaction?

The Keq of the reverse reaction is the inverse of the Keq for the forward reaction. Calculating the answer: 1/22.2 = 0.045

Tollen's reagent and Benedict's reagent

Reagents used to detect the presence of reducing sugars. Tollens - utilizes Ag(NH3)2+ as an oxidizing agent. If positive aldehydes reduce Ag+ to metallic silver -Reduced to produce silvery mirror when aldehydes are present Benedicts- when used the aldehyde group of an aldose is readily oxidized which is indicated by a red precipitate of Cu2O -Ketones may react more slowly -Ketones can't be oxidized directly to carboxylic acids, but they can rearrange bonds (tautomerization) to form aldoses under basic conditions -Ketone picks up H (results in enol, which has double bond and OH group) When aldehyde group of aldose is reduced to an alcohol, the compound is considered an alditol. A deoxy sugar on the other hand, contains H that replaces hydroxyl (2-deoxyribose)

Nernst Equation for Membrane Potential

Rearrange equation from image, and we get: (assuming body temp = 310 K) E = 61.5/z log ([ion]outside / [ion] inside) R is ideal gas constant T is temp in K z is charge of ion F is Faraday constant (96500 C/mol e-)

Venturi Effect

Reduction in pressure of a fluid resulting from the speed increase as fluids are forced to flow faster through narrow spaces. Less distance = lower pressure at the edges (high pressure in the middle because its going super fast, so there is less pressure pushing against the walls)

Inducible Systems

Repressor bonded tightly to operator under normal conditions (roadblock) RNA polymerase cant get from promoter to structural gene because repressor is in the way *Allows for gene transcription only when an inducer is present to bind to the otherwise present repressor protein *Inducer-repressor complex cant bind to operator -> structural genes are transcribed *In inducible systems, the repressor normally sits on the operator preventing transcription. When the inducer is present, it binds the repressor causing it to leave the operator and allow transcription to occur. Negative Control: binding reduces activity To remove block inducer must bind repressor so RNA poly can move down gene Think of competitive inhibition: more inducer = more repressor pulled off of operator region = more genes free for transcription Example: LAC operon: Contains gene for lactase Bacteria can digest lactose, but its more energetically expensive than glucose, so they only want to use lactose if it is high and glucose is low. Lac operon induced by presence of lactose, so genes only transcribed when cell needs it Lac operon assisted by binding of catabolite activator protein (CAP) -> transcriptional activator used by E.Coli when glucose is low Lower glucose can signal cyclic AMP (cAMP), which binds to CAP -> conformational change of CAP allows it to bind promoter region of operon, increasing transcription of lactase gene System where binding of molecule increases transcription called positive control mechanism.

Branching Enzyme (Glycosyl a-1,4: a-1,6 transferase)

Responsible for introducing a-1,6 linked branches into granule as it grows Hydrolyzes one of the alpha 1,4 bonds to release a block of oligoglucose (a few glucose molecules together in chain) which is moved and added to different location -> forms a 1,6 bond 1,4 -> keeps branch moving 4ward 1,6 -> puts branch in the mix

Skeletal Muscle Metabolism

Resting: Major fuels = glucose and fatty acids Skeletal muscle is major consumer of fuel In fasting state, resting muscle uses fatty acids derived from free fatty acids circulating in blood Ketone bodies may also be used in prolonged fast Active Muscle: -Short lived energy (2-7 seconds): creatine phosphate (transfers phosphate from ADP to ATP) -Short burst of high intensity excercise can be powered by anaerobic glycolysis drawing on stored muscle glycogen -During moderate/high intensity continuous exercise, oxidation of glucose and fattyacids are important -After 1-3 hours of exercise at this level, glycogen deleted, intensity declines to rate supported by oxidation of fatty acids *Fast twitch muscle have high capacity for anaerobic glycolysis but are quick to fatigue (short term, high intensity) *Slow twitch (red meat): in arm and leg muscles, well vascularized and mostly oxidative, resist fatigue, number of mitochondria increase in trained endurance athletes Cardiac muscle: unlike other tissues, cardiac myocytes prefer fatty acids (ketones during prolonged fasting) -In failing heart, glucose oxidation increases and B oxidation falls Brain: Uses 20% of total O2 and 25% of total glucose -Glucose is primary fuel -In hypoglycemic conditions (<70 mg/ dL), hypothalamic center in brain sense fall in glucose, release glucagon and epi -Fatty acids cant cross blood brain barrier -Glucose from glycogenolysis or gluconeogenesis -In prolonged fasting, brain can use up to 2/3 ketone bodies

Restriction enzymes (EcoRI)

Restriction enzymes (EcoRI) (restriction endonuclease): Enzyme that recognizes specific double stranded DNA sequence -> palindromic, so 5' to 3' of one strand is the same as 5' to 3' in other antiparallel strand -Isolated from bacteria -Once specific sequence is identified, restriction enzyme can cut through backbone of double helix *Sticky ends: Advantageous in facilitating recombination of restriction fragment with vector DNA

Active Transport

Results in the net movement of a solute against its concentration gradient (rolling a ball uphill) Always requires energy Primary active transport: Uses ATP (or similar) to directly power transport -Usually involve transmembrane ATPase -Maintains membrane potential of neurons Secondary Active Transport (coupled transport): No direct coupling to ATP hydrolysis. Instead, secondary active transport harnesses energy released by one particle going down gradient to drive a different particle up its gradient. When both particles flow in the same direction across membrane, its called symport, the particles flow in opposite directions it is called anti port -Kidneys use this, usually driven by sodium, to reabsorb and secrete various solutes in and out of filtrate *Movement of solutes across cell membrane is mediated by concentration gradients

SDS-PAGE electrophoresis

Sodium dodecyl sulfide separates based on molecular mass: Used to eliminate conflation from mass to charge ratios SDS binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein's original charge and denaturing the protein The only variable affecting their velocity is f, the frictional coefficient, which depends on mass SDS page can not reduce disulfide bonds (covalent bonds) requires a stronger reducing agent Protein atomic mass typically expressed in daltons (Da) -> average molar mass of one amino acid is 100 daltons or 100 g/mol SDS solubilizes proteins to give them uniformly negative charges, so the separation is based purely on size.

B-oxidation in mitochondria

Reverse of FA synthesis -> oxidizes and releases (rather than reducing and linking) molecules of acetyl coa Repitiion of 4 steps: Oxidation of FA to form double bond Hydration of DB to form OH group Oxidation of OH group to form carbonyl (B-ketoacid) Splitting B ketoacid into shorter acyl coa and acetyl coa Continues under final two carbons / acetyl coa Each step releasies 1 acetyl coa and reduces NAD+ and FAD (producing NADH and FADH2-> produce ATP in ETC) In muscle and adipose, acetyl coa enters CAC In liver, it cant be converted to glucose, stimulates gluconeogenesis by activating pyruvate carboxylase, so in fasting state, liver makes more acetyl coa from beta oxidation than used in CAC, extra used to make ketone bodies (2 acetyl coa stuck together) Even number of carbons yields 2 acetyl coa in last step Odd numbers yield 1 acetyl coa and 1 propionyl coa (requires addition steps to convert it to succinylcholine coa for CAC *Odd number fatty acids are exception to rule that fatty acids cant be converted to glucose This is all oxidation of Saturated FA In unsaturated fatty acids, 2 more enzymes (Enoyl coa transferase to move cis DB at 3,4 position to trans DB at 2,3 position) and 2,4-dienoyl coa reductase (in polyunsaturated, converts two double bonds to one at 3,4 instead of 2,3 and 4,5) *Unsaturated fatty acids use an isomerase and additional reductase during cleavage

Denaturation

Reverse of folding Protein loses 3D shape (thus they are inactive) Often irreversible Unfolded proteins cant catalyze reactions 2 main causes: Heat and solutes Heat denatures for same reason that tasing reactions temp increases rate: increased average kinetic energy of molecules means more molecular motion When temp gets high enough, extra energy can be enough to overcome hydrophobic interactions that hold protein together (Cause unfolding) Solutes like urea denature by directly interfering with forces that hold protein together -> disrupt tertiary and quaternary structure by breaking disulfide bridges , reducing cystine back to 2 cysteines -Can overcome H bonds and stuff that holds alpha helices and beta sheets intact Detergents (SDS) can solubilize proteins, disrupting noncovalent bonds and promoting denaturation

In humans, which of the following monosaccharides CANNOT be used to produce energy via the glycolytic pathway? A. Glucose B. Galactose C. Ribose D. Fructose

Ribose cannot be metabolized this way. Glycolysis normally metabolizes glucose. It is also possible for galactose to enter glycolysis (entering at the level of glucose-6-phosphate) and for fructose to do the same (as DHAP and G3P).

Immunoglobulins (Ig)(Antibodies)

Rid the body of foreign invaders Proteins produced by B cells Function to neutralize targets int he body (toxins and bacteria) and recruit other cells to eliminate threat V domain: Binds to antigens C domain: Activates Y-shaped proteins: 2 identical heavy chains and two identical light chains -Disulfide links and non covalent bonds hold heavy and light together Antigen binding region at the tip of the Y : Specific polypeptide sequences that bind only ONE SPECIFIC ANTIGENIC SEQUENCE Constant region: Down at the bottom -> recruit and bind other immune cells (like macrophages) *Antigen is what binds at the antigen binding site, t he entire Y shaped molecule is the antibody When antibodies bind to their targets (Antigens) : 3 things can happen: Neutralizing the antigen, making the pathogen or toxin unable to exert effect on body Marking pathogen for destruction by other WBC immediately -> Opsonization Clumping together (agglutination) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

Gene therapy and SCID

SCID: Severe combined immunodeficiency: mutation in gene encoding gamma chain common to interleukin receptors -> Gene therapy can place working copy of gene for gamma chain into virus, and infect/transmit functional gene into cells *retroviral gene therapy Randomly integrated DNA poses risk of activating oncogenes: cancer of white blood cells/leukemia

Membrane Potential

Sarcolemma of muscle cells must maintain membrane potential for muscle contraction to occur The difference in electrical potential across cell membranes is called the membrane potential (Vm). The resting potential for most cells: -40 - -80 mV Potential can rise up to +35 mV during depolarization of the cell Ions passively diffuse through leak channels, so ion transporter/pump regulates concentration *Sodium-Potassium Pump: Na+/K+ ATPase regulates concentration of intracellular and extracellular sodium nd potassium ions Chloride ions also help establish membrane potential Nernst Equation determines membrane potential from intra and extracellular concentration (E = RT/ zF* ln (ion outside / ion inside))

Facilitated Diffusion

Simple diffusion for molecules that are impermeable to the membrane (like large, polar or charged molecules) Unless otherwise stated, semipermeable membrane means small, non polar, lipid-soluble particles (and water) can pass through freely but large, polar, or charged can't (energy barrier too high) Requires integral membrane proteins to serve as transporters or channels for substrates Can involve carrier or channel protein Carrier: Only open to one side of membrane -Binding of substrate molecule to transporter protein induces conformational change: For short time, carrier in in occluded state (not open to either side of phospholipid bilayer) Channels may be open or closed conformation: in open, it acts like a tunnel (rapid transport kinetics)

Which of the following has the lowest ratio of lipid to protein? A. Chylomicrons B. VLDL C. LDL D. HDL

Since lipids are less dense than proteins (fat floats in water, while muscle doesn't), the LOWEST ratio of lipid to protein would correspond to the HIGHEST density. Among the choices, the one with the highest density is HDL. Note:Chylomicrons have the HIGHEST lipid to protein ratio, and lowest density.VLDL has a lower lipid to protein ratio than chylomicrons, but not as low as HDL LDL has a lower lipid to protein ratio than chylomicrons, but not as low as HDL. Order of increasing ratio of lipid to protein: HDL < LDL < VLDL < chylomicrons

Cooperativity

Some enzymes flow sigmoidal (S-shaped curve) kinetics due to cooperativity among substrate binding sites Cooperative enzymes have multiple subunits or active sites 2 States: Low affinity Tensed (T state) or high affinity relaxed (R State) Binding of substrate encourages switching from T to R state , increases chance of substrate binding Loss of substrate can encourage transition from R to T state, and promote dissociation Enzymes showing cooperative kinetics are often regulatory enzymes in pathways (phosphofructokinase -1 in glycolysis) -> also subject to activation and inhibition through allosteric and competitive sites Cooperative binding of hemoglobin acts as transport protein rather than enzyme, also results in sigmoidal binding curve Cooperativity can be quantified using numerical value called Hill's Coefficient: Indicates nature of binding Hill's coefficient > 1, positively cooperative binding occurring, after one ligand is bound, the affinity of the enzyme for further ligands increases If Hills coefficient = 1, the enzyme does not cooperatively bind If <1, negatively cooperate binding occurs such that after one Ligand bound, affinity of enzyme for further ligands decreases

Synthesis of Secretory, Membrane, and Lysosomal Proteins

Some eukaryotic proteins have signal sequences that tell them where to go *Hormones and digestive enzymes told to go to endoplasmic reticulum (ER) so protein can be translated directly into lumen of rough ER, then to Golgi apparatus, and then secreted from vesicle via exocytosis Note: Nascent polypeptide chain means newly synthesized

Structural Proteins: Motor Proteins

Some structural proteins have motor functions in the presence of motor proteins MOTOR PROTEINS ARE ENZYMES: An enzyme is a protein or RNA molecule with catalytic activity -Motor function usually considered nonenzymatic but the ATPase functionality indicates they do have catalytic activity Motile cilia and flagella of bacteria and sperm, contraction of sarcomere in muscle Display enzymatic activity, a sting as ATPases that power conformational change needed for motor function Transient interactions with actin or microtubules (tubulin) Myosin interacts with actin. It is the thick filament in a myofibril Can be involved in cellular transport Single neck and head, movement of neck responsible for power stroke of sarcomere contraction (Sarcomere is small section of myofibril, a single strand , and all of the strands are surrounded by the sarcolemma , a bunch of strands of that whole burrito make up muscle fibers, and a bunch of those burritos make up muscle fascicle )

Osmosis

Specific kind of simple diffusion that concerns water Water moves from region of lower solute concentration to one of higher solute concentration Move from higher water concentration (more dilute) down gradient to region of lower concentration (more concentrated solution) Important when solute is impermeable to membrane: Water moves to try and bring solute concentration to equimolarity -> if concentration of solutes inside cell is higher than outside = hypotonic (cell swells) Hypertonic: Solution more concentrated outside of cell, water moves out (cell shrinks) Isotonic: Solution inside and outside are equal (Note: Isotonicity does not prevent movement, water molecules continue to move, but no water is lost or gained overall) Osmolarity explains why pure water should never be given intravenously for resuscitation. RBC have osmolarity of around 300 mOsm/L while pure water has osmolarity of 0. Water would rush into RBCs and cause them to lyse/burst, so saline or dextrose containing solutions are used

Concentration Gradients

Spontaneous processes do not require energy (negative delta G) proceed through passive transport Nonspontaneous processes that require energy (positive delta G) proceed through active transport Diffusion, facilitated diffusion, and osmosis generally increase in rate as temp increases Active transport may not be affected by temp depending on enthalpy (delta H) Primary motivator in most passive transport is increase in entropy (Delta S) / Primary thermodynamic factor responsible for passive transport is entropy)

Citrate formation

Step 1 of Krebs cycle Acetyl-CoA + OAA → Citryl-CoA → Citrate + CoA (via citrate synthetase)

Citrate Isomerized to Isocitrate

Step 2 of Citric Acid Cycle Achiral citrate is isomerized to one of four possible isomers of Isocitrate Aconitase isomerize citrate to isocitrate Water is lost from citrate

Succinyl-CoA and CO2 Formation

Step 4 of CAC - catalyzed by α-Ketoglutarate dehydrogenase complex -Second and last CO2 lost in cycle -More NADH produced *Dehydrogenases (transfer hydride (H-) ion to E- acceptor) are subtype of oxidoreductases (enzymes that catalyze oxidation reduction reaction)

Succinate Formation

Step 5 in CAC Hydrolysis of thioester = succinate + CoA-SH (and GDP -> GTP) Catalyzed by succicnyl coa synthetase Synthetases require energy to create bonds, but synthase do not Nucleosidediphosphate kinase takes GTP to ADP producing ATP -Only time ATP is produced directly in CAC

Fumarate formation

Step 6: takes place in the mitochondrial inner membrane Only step of the cycle that does not occur in the matrix Succinate oxidized to fumarate catalyzed by succinate dehydrogenase (flavoprotein, covalently bonded to FAD) Each FADH2 eventually leads to production of 1.5 ATP, (compared to NADH which produces 2.5) Step 7: Malate Formation: fumarase catalyzes bond, giving rise to malate Step 8: Maltase dehydrogenase reforms oxaloacetate

Negative control, positive control, repressible, and inducible system

Substrate (inducer) makes repressor inactive: Negative inducible Product makes repressor active: Negative Repressible (when repressor+corepressor complex binds to operator, it turns the system that is normally on, off) Substrate makes activator active: Positive Inducible Product makes activator inactive: Positive Repressible (product inactivates the activator, so it doesn't bind, but no product means that activator binds and is active and transcription occurs) Positive control require binding to increase transcription, negative control require binding to decrease transcription Negative control involves the binding of a repressor to the operator to prevent transcription. In negative inducible operons, a regulatory repressor protein is normally bound to the operator, which prevents the transcription of the genes on the operon. If an inducer molecule is present, it binds to the repressor and changes its conformation so that it is unable to bind to the operator. This allows for expression of the operon. The lac operon is a negatively controlled inducible operon, where the inducer molecule is allolactose. In negative repressible operons, transcription of the operon normally takes place without protein bound. Repressor proteins are produced by a regulator gene, but they are unable to bind to the operator in their normal conformation. However, certain molecules called corepressors are bound by the repressor protein, causing a conformational change to the active site. The activated repressor protein binds to the operator and prevents transcription. The trp operon, involved in the synthesis of tryptophan (which itself acts as the corepressor), is a negatively controlled repressible operon. In positive inducible operons, activator proteins are normally unable to bind to the DNA (normally off). When an inducer is bound by the activator protein, it undergoes a change in conformation so that it can bind to the DNA and activate transcription (binding of protein increases transcription) In positive repressible operons, the activator proteins are normally bound to the pertinent DNA segment (normally on). However, when an inhibitor is bound by the activator, it is prevented from binding the DNA. This stops activation and transcription of the system.

Ribosomal RNA (rRNA)

Synthesized in nucleolus and functions as part of ribosomal machinery used during protein assembly in cytoplasm Many function as ribozymes (enzymes made of RNA instead of peptides) Can help catalyses formation of peptide bonds Splicing out its own introns in nucleus

Krebs Cycle (Citric Acid Cycle)

The Krebs Cycle, also known as the citric acid cycle, takes place in the matrix of the mitochondria. In the Krebs Cycle, each of the two acetyl coenzyme A molecules enter the cycle and combine with oxaloacetate to form citric acid, which then loses two carbons as carbon dioxide. The cycle is now ready to begin again with the second Acetyl CoA. For each Acetyl CoA, the Krebs Cycle produces 1 ATP, 3 NADH, and 1 FADH2. Per glucose, we get 6 NADH, 2 FADH2, and 2 GTP Most likely to inhibit the Krebs cycle: High [NADH]/[NAD+] ratio and high [ATP]/[ADP] ratio -If the cycle is inhibited, the cell does not need energy at that point -High ratio of ATP to ADP indicates the cell has a lot of energy stored and is not likely to need energy immediately -The Krebs cycle generates NADH, so an excess of it ( high [NADH]/[NAD+] ratio) should inhibit the Krebs cycle by Le Chatelier's principle

The movement of sodium and potassium by the sodium-potassium pump is an example of:

The Na-K pump uses ATP to pump Na+ out of a cell and K+ into the cell (3 Na+ out per 2 K+ in).Since it uses ATP, it is an example of primary active transport. Since the movement of sodium and potassium are in opposite directions, symport cannot accurately describe the movement, so its an anti port

Hypothyroidism is associated with a decreased level of lipid metabolism (less lipid metabolism, so products of lipid metabolism would be decrease). What would be expected to have a low serum concentration in hypothyroid patients?

The breakdown products of lipids are acetyl Co-A, malonyl Co-A, and glycerol. With a lower rate of fatty acid breakdown we expect to see a lower concentration of acetyl-CoA. Cholesterol is expected to be seen in increased concentrations because it is recycled and excreted in a manner that depends on the lipid content of the blood (less lipids = less excretion of cholesterol = more cholesterol in circulation)

Kinetics of Monomeric Enzymes: Michaelis-Menten

The concentration of substrate [S] and enzyme [E] affect how quick reactions occurs *Increasing [E] will always increase V max, but [S] depends on how much substrate is present at beginning -High enzyme concentration (relative to substrate) -> quickly form products , quickly reach equilibrium When ll active states are occupied, you kind level off (at saturation, you can't go any faster, enzyme working at maximum velocity (V max: measured in moles of enzyme per second, related to k cat which has units of s^-1) V max = [E] * K cat K cat measures the number of substrate molecules "turned over" or converted to product, per enzyme molecule per second -> values between 101 and 103 v = k cat [E][S] / Km + [S] At very low substrate concentrations Km >>>> [S], the equation can be implied to be : v = (K cat / Km) * [E][S] K cat / Km = catalytic efficiency (large k cat = high turnover or a small km = high substrate affinity will both result in higher catalytic efficient = more efficient enzyme) *Higher Km has lower substrate affinity because it takes more substrate to reach km *Km is just a measure of an enzymes affinity got substrate, defined by substrate concentration at which enzyme is functioning at half of its maximum velocity The only way to increase V max is by increasing increasing enzyme concentration so you can deal with more substrate Image: Michaelis Menten Plot of Enzyme Kinetics : As the amount of substrate increases, enzyme is able to increase its rate until it reaches max. At this point, adding more substrate will not increase rate Plot: Hyperbola When substrate concentration is less than Km, changes in substrate concentration will greatly effect the reaction rate. At high substrate concentrations (above Km), the reaction rate increases more slowly as it approaches V max, w here it becomes independent of substrate concentration

Hexokinase

The enzymes that catalyzes the phosphorylation of glucose to form glucose-6-phosphate in the first step of glycolysis. This is one of the inhibitory steps of this pathway. Hexokinase is feedback-inhibited by glucose-6-P. Called glucokinase in liver and pancreatic B-islet cells Glucokinase is used to trap extra glucose in liver cells as part of a storage mechanism; with low blood glucose, liver cells would be generating new glucose, not storing it. It is also in the pancreas, where it serves as a glucose sensor; if glucose levels are low, it has little activity in this tissue as well.

The formation of ATP is ___________ and the electron transport chain is __________________

The formation of ATP is endergonic and the electron transport chain is exergonic Coupled together, so energy from one powers the other Proteins along inner membrane must transfer electrons from NADH and FADH2 Direction determined by reduction potential Higher reduction potential (oxygen) will be reduced (given electrons), lower reduction potential will be oxidized OXYGEN HAS HIGH REDUCTION POTENTIAL

Gluconeogenesis

The formation of glucose from noncarbohydrate sources, such as amino acids. Production of glucose from other biomolecules, carried out by liver and kidneys Occurs after fasting for over 12 hours Hepatic and renal cells need to have enough energy to drive glucose creation, requires fat stores to undergo B oxidation Liver maintains glucose levels in blood with glycogenolysis or gluconeogenesis. Promoted by epi and glucagon, which want to raise levels of glucose in blood, and inhabiting by insulin (which wants to store glucose) *Insulin lower BS, hormones glucagon, epi, cortisol, and growth hormone act to raise BS by stimulingating glycogenolysis and gluconeogenesis. Important substrates for gluconeogenesis: *Glycerol 3 phosphate (from stored fats, triacylglycerols in adipose tissues) converted to DHAP by glycerol-3-phosphate dehydrogenase *Lactate from anaerobic glycolysis converted to pyruvate by lactate dehydrogenase *Glucogenic amino acids from muscle proteins, like alanine (converted to pyruvate by alanine aminotransferase) Amino acids can be split into glucogenic, ketogenic, or both Glucogenic: Except for leucine and lysine, all can be converted into intermediates that feed into gluconeogenesis Ketogenic: Can be converted into ketone bodies (alternate fuel) Fructose and galactose can be converted into glucose in liver Glucose can be converted to acetyl-CoA through glycolysis and pyruvate dehydrogenase, but acetyl-CoA cant be converted back to glucose Most fatty acids (except odd numbered ones) are metabolized sole to acetyl coa so they aren't major source of glucose either Gluconeogenesis requires acetyl-CoA to occur (to inhibit pyruvate dehydrogenase and stimulate pyruvate carboxylase), it is linked to fatty acid oxidation-> source of acetyl coa cant be glycolysis because this would burn glucose being generated

Which conformation most accurately represents the 3D structure of ribose in aqueous solution?

The lowest energy of ribose (in solution) is the envelope form (A).While the chair form is glucose's predominant conformation, glucose is 6-membered, whereas ribose is 5-membered.The boat form is not a likely conformation of ribose; most ribose molecules will adopt a non-planar conformation to alleviate ring strain.

Differences between RNA and DNA?

The major differences between DNA and RNA are the additional hydroxyl group at the 2′ carbon of the pentose sugar of RNA and whether the strands contain thymine (DNA) or uracil (RNA). Specifically, the additional hydroxyl group in ribose increases the reactivity of RNA, and thereby decreases its stability, compared to DNA There are two chemically distinct forms of nucleic acids within eukaryotic cells. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are polymers There are two families of nitrogen-containing bases found in nucleotides: purines and pyrimidines. Purines contain two rings in their structure. The two purines found in nucleic acids, both DNA and RNA, are adenine (A) and guanine (G). Pyrimidines, on the other hand, contain only one ring in their structure. The three pyrimidines are cytosine (C), thymine (T), and uracil (U). While cytosine is found in both DNA and RNA, thymine is only found in DNA and uracil is only found in RNA.

DNP (2,4-dinitrophenol) is a compound that allows protons to leak across the inner membrane of the mitochondria. After a patient receives a large dose of DNP, which of the following symptoms would be expected?

The patient would experience hyperthermia Disrupting the proton gradient leads to less ATP production, which leads to an increased metabolic rate and an overall rise in body temperature. The proton-motive force is an electrochemical gradient of protons generated by the electron transport chain, in which there are more protons in the intermembrane space then in the mitochondrial matrix. Protons then flow down this gradient through ATP synthase, and generate ATP in the process. Since protons are allowed to leak across the inner membrane, ATP synthesis through ATP synthase will be dramatically lowered and the energy that would have been stored in ATP is now lost as heat energy. Cells cannot use the energy that was lost and in order to meet energy demands, the body will increase overall metabolic rate resulting in hyperthermia, (A).

Tautomerization

The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond For sugar to be reducing, it must have free aldehyde group, but tautomerization allows fructose, which is a ketose, to act as reducing sugar in water Ketose sugars undergo tautomerization, a rearrangement of bonds, to undergo keto-enol shifts. This forms an aldose, which then allows them to act as reducing sugars. A ketone group alone cannot be oxidized. -Maintains ring structure, unlike oxidation

Eukaryotic DNA Replication VS Prokaryotic DNA Replication

The removal of RNA primers is a function of RNase in eukaryotic cells only, as the removal of RNA primers in prokaryotes is instead attributed to DNA polymerase, Helicase is the enzyme responsible for unwinding the DNA (in both eukaryotes and prokaryotes), generating two single-stranded template strands ahead of the polymerase. The first step in DNA replication is to lay down RNA primers for the DNA polymerase to "hook on" to. This is done by primase (in both eukaryotes and prokaryotes). Once the strands are separated and an RNA primer is placed, DNA polymerases are responsible for reading the DNA template and synthesizing the new daughter strand. The DNA polymerase can read the template strand in a 3′ to 5′ direction while synthesizing the complementary strand in the 5′ to 3′ direction. This will result in a new double helix of DNA that has the required antiparallel orientation. Due to this directionality of the DNA polymerase, certain constraints arise. Remember, that two separated parental strands of the helix are also antiparallel to each other. Thus, at each replication fork, one strand is oriented in the correct direction for DNA polymerase; the other strand is antiparallel. The lagging strand is the strand that is copied in a direction opposite the direction of the replication fork. On this side of the replication fork, the parental strand has 5′ to 3′ polarity. DNA polymerase cannot simply read and synthesize on this strand. Because of this, Okazaki fragments are produced on the lagging strand. As the replication fork continues to move forward, it clears additional space that DNA polymerase must fill in. The lagging strand will have a large number of RNA primers added to it as space opens up on the template, and DNA ligase is the enzyme responsible for sealing these DNA molecules together to create one continuous strand of DNA (B).

Michaelis constant (Km)

The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity/ half the enzyme's active sites are bound Large/High Km = less affinity the enzyme has for substrate

Tight Junctions

Tight Junctions: Form watertight seal, preventing paracellular transport of water and solutes Prevent solutes from leaking into space between cells Found in epithelial cells Form physical link between cells as they form single layer Limit permeability enough to create trans epithelial voltage difference based on differing concentrations of ions on either side of epithelium Must not form continuous band or fluid could leak through spaces between tight junctions Found in lining of renal tubules (restrict passage of water and solutes without cellular control)

Amino Acid Composition

To determine primary structure, sequential digestion of protein with enzymes Small proteins use Edman degradation to analyze (uses cleavage to sequence proteins up to 50-70 amino acids) -Removes the N-terminal amino acid -Degredation using Edman proceeds from Amin (N-) terminus Larger proteins digested with synthetic reagent (cyanogen bromide) and chymotrypsin and trypsin is used Protein broken down into primary structure, so we cant find out where disulfide links and salt bridges were

The three-base sequences listed below are DNA sequences, which amino acid is encoded by each after transcription and translation ? GAT ATT CGC CCA

Transcription: Switch it around and complement (GAT becomes TAG becomes ATC), then Replace T with U (ATC becomes AUC) Translation: Take new sequence and find amino acids: AUC -> isoleucine (Ile) GAT: mRNA Codon = AUC (isoleucine: Ile) ATT: mRNA Codon = AAU (asparagine: Asn) CGC: mRNA Codon = GCG (Alanine: Ala) CCA: mRNA Codon = UGG (tryptophan (Trp)

3-phosphoglycerate kinase

Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate Substrate level phosphorylation: ADP directly phosphorylated to ATP using high energy intermediate In contrast to oxidative phosphorylation in mitochondria, substrate level phosphorylation not dependent on O2

Transgenic (gene introduced) and Knockout Mice (gene deleted)

Transgenic mice altered in germ line by introducing cloned gene (transgene) into fertilized ova or into embryonic cells Knock out mice: Gene intentionally deleted Cloned gene may be injected into newly fertilized ovum, rarely the gene may incorporate into nuclear DNA of zygote Useful for studying dominant effects, but not recessive because we cant control how many copies are inserted into genome Embryonic stem cell lines for developing transgenic mice: Altered stem cells injected into developing blastocysts and implanted. Blastocyst composed of 2 types of stem cells: ones with trans gene and original ones Resulting offspring is chimera: patches of cells, including germ cells, from each of 2 lineages Different coat colors Bred to produce mice heterozygous and homozygous for trans gene

How do transport kinetics differ from enzyme kinetics?

Transport: Have both Km and Vmax values Can be cooperative, like some binding proteins Transporters don't have analogous Keq values fro reactions because there is no catalyst

Triacylglycerol (triglyceride) synthesis, oxidation, activation

Triacylglycerols. = storage form of fatty acids (attach three fatty acids as fatty acyl coa to glycerol) Formed by attaching three fatty acids to glycerol 3 phosphate Occurs primarily in liver and a little in adipose tissue In the liver, triglycerides are packed and sent to adipose tissue as VLDL, leaving only a small amount of stored triacylglyceriols Oxidation: FA catabolism (breaking down) via beta oxidation in mitochondrial matrix (can also happen with peroxisomes) Branched may undergo alpha oxidation depending on branch points w-oxidation in ER produces dicarboxylic acids Insulin indirectly inhibits B-oxidation while glucagon stimulate this process Activation: activated by attachment of CoA, catalyzed by fatty-acyl-CoA synthetase (fatty acyl CoA)

Which of the following best characterizes the process of fatty acid synthesis? A. Two reductions followed by a dehydration and bond formation. B. Reduction followed by activation, bond formation, dehydration, and reduction. C. Activation followed by bond formation, reduction, dehydration, and reduction. D. Activation followed by bond formation, oxidation, dehydration, and reduction.

Which of the following best characterizes the process of fatty acid synthesis? A. Two reductions followed by a dehydration and bond formation. B. Reduction followed by activation, bond formation, dehydration, and reduction. C. Activation followed by bond formation, reduction, dehydration, and reduction. D. Activation followed by bond formation, oxidation, dehydration, and reduction. Correct Answer: C Explanation: The steps in fatty acid synthesis are activation (attachment to acyl carrier protein), bond formation (between malonyl-CoA and the growing fatty acid chain), reduction (of a carboxyl group), dehydration, and reduction (of a double bond).

Irreversible Inhibition

active site is made unavailable for prolonged period of time or enzyme is permanently altered *Aspirin: Acetylsalicylic acid irreversibly modifies cyclooxyrgenase-1 so enzyme can no longer bind substrate to make products (prostaglandins: Involved in modulating pain) Prime drug mechanism

Maltose and Maltase

alpha 1,4 glycosidic linkage connecting two glucose molecules Maltase is an enzyme located in on the brush border of the small intestine that breaks down the disaccharide maltose. Maltase catalyzes the hydrolysis (breakdown due to reaction with water) of maltose to the simple sugar glucose

Adaption to high altitudes (Low pO2)

at low oxygen... increased respiration - trying to get more oxygen increased oxygen affinity for hemoglobin (initially) increased rate of glycolysis increased 2,3,BPG in RBC (over 12-24 hour period)- allows an unloading of oxygen in tissues but still allows for 100% saturation in the lungs normalized oxygen affinity for hemoglobin restored by the increased level of 2,3 BPG increase amount of hemoglobin over days/weeks

Desmosomes

bind adjacent cells by anchoring to their cytoskeletons -Formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells -Mostly found at interface between two layers of epithelial tissue -Hemidesmisomes are similar, but their main function is to attach epithelial cells to underlying structures, especially basement membrane Image: Tight junction, desmosomes, then connexon

Calculate the free energy change for the synthesis of ATP from cAMP and Pi *cAMP hydrolyzed to AMP, and free energy of hydrolysis for ATP and ADp is about = 30.5 kJ/mol cAMP + H2O -> AMP free energy change = -50.4 kJ/mol

cAMP + H2O -> AMP free energy change = -50.4 kJ/mol AMP + Pi -> ADP + H2O. free energy = 30.5 kJ/mol ADP + Pi -> ATP + H2O. free energy = 30.5 kJ/mol cAMP + 2 Pi -> ATP + H2O free energy = 10.6 kJ/mol

Sphingolipids What is the difference between a sphingolipid that is a phospholipid and one that is not? The difference is the bond between the backbone and the head group: phosphodiseter bond = phospholipid, glycosidic linkage to sugar = glycolipids

cell surface antigens are this (ABO antigens) sites of biological recognition at the cell surface and can be bonded to various head groups and fatty acids have a *sphingosine or sphingoid* backbone have long chain nonpolar fatty acid tail with a polar head group can be *phosholipids* (because contain *phosphodiester linkage*) or can be a *glycolipid* (because they contain *glycosidic linkages*) *Any lipid linked to sugar can be termed glycolipid 4 classes: 1. Ceramide: Simplest, single H as head group 2. sphingomyelins: Class of sphingolipids that are also phospholipids (sphingophospholipids) -Either have phosphatidylcholine or phosphatidylethanolamine as head group (contain phosphodiester bond -No net charge on head groups -Major component in plasma membrane of cells producing myelin sheaf for axons (oligodendrocytes and Schwann cells) 3. glycosphingolipids --> Sphingolipids with head group composed of sugar bonded by glycosidic linkages -Not phospholipids (no phosphodiester linkage) -Functional group = sugars -Found on outer surface of membrane, can be further classified as cerebrosides or globosides -Cerebrosides have single sugar, globosides have 2 or more -No net charge at physiological pH 4. gangliosides : "gangly" sphingolipids with most complex structure with polar head group composed of oligosaccharides and N-acetylneuraminic acid (Sialic acid, NANA ) molecules at terminus (functional groups are NANA and oligosaccharides) -Negative charge -Glycolipids: glycosidic linkage and no phosphate groups -Cell interaction, recognition, signal transduction Summary: Ceramide has single H atom for head group, sphingomyelins have phosphodiester linkages (phospholipids), cerebrosides have one sugar, globosides have multiple sugars, gangliosides have oligosaccharides and terminal silica acids (NANA)

Irreversible Enzymes of Glycolysis

glucokinase/hexokinase PFK1 pyruvate kinase different enzymes must be used in gluconeogenesis (reverse of glycolysis) Mnemonic: How Glycolysis Pushes Forward the Kinemetic Process: Kinases (H G PFK PK -> Hexokinase, glucokinase, PFK1, Pyruvate kinase)

Glucose transport

glucose can go into most cells it is driven by CONCENTRATION independent of sodium (unlike the absorption from the digestive tract) normal concentration in the periphery is from 4-6mM (around 100 mg/dL or 5.6 mM) 4 glucose transporters : GLUT 1, 2, 3, and GLUT 4 GLUT 2 and 4 are the most significant (only located on specific cells and are highly regulated) Glut 2: Low affinity transporter in hepatocytes and pancreatic cells -After a meal, blood through hepatic portal vein from intestine has lots of glucose, and GLUT 2 grabs the excess glucose for storage. When concentrations drop below Km, glucose bypasses liver and enter peripheral circulation *Km is concentration of substrate when enzyme is active at half of its gas velocity. The lower the Km, the higher the affinity for substatre and vice versa *The Km of GLUT 2 is high (15 mM) so the liver picks up glucose in proportion to its concentration in the blood (1st order kinetics) -> When BG is high, liver stores excess In the B-islet cells of the pancreas, GLUT 2 and the glycolytic enzyme glucokinase serve as sensor for insulin release Glut 4 is in adipose tissue and msucle -Respond to glucose concentration in peripheral blood -Rate of glucose transport increased by insulin, which stimulates movement of more GLUT 4 transporters to the membrane by a mechanism involving exocytosis The Km of GLUT 4 is close to normal (~5 mM)(Km = 5mM so it is pretty low) so the transporters are saturated when BG is a bit higher than normal. *Unlike GLUT2, which cant be saturated under normal/optimal conditions, GLUT 4 is saturated at levels slightly above 5nM GLUT 2 is not responsive to insulin, ut serves as sensor to cause release of insulin in pancreatic B cells, but GLUT 4 is responsive to insulin When a person has high BS, transporters still only permit constant rate of influx because they will be saturated (0 order kinetics), but cells with GLUT 4 transporters can increase their intake of glucose by increasing the number of transporters on the surface Diabetes Mellitus is caused by disruption of insulin/Glut 4 mechanisms. Type 1: No insulin = no stimulation of insulin receptors Type 2: Receptor becomes insensitive to insulin and fails to bring GLUT 4 to surface Both cases: BG rises, leads to increased urination, thirst, ketoacidosis and long term symptoms of blindness, heart attacks, strokes, nerve damage Basal levels of transport occur in all cells with or without insulin, but transport rate increases in adipose tissue and muscles when insulin levels rise Muscles stores glucose as glycogen, adipose requires glucose to form dihydroxyacetone phosphate (DHAP) which is converted to glycerol phosphate to store incoming fatty acids as triacylglyerlols

Glycoside Formation

hemiacetals (or hemiketal) sugars react with alcohol under acidic conditions to form acetals (or ketals). The anomeric hydroyl group is transformed to an alkoxy group yielding a mix of alpha and beta acetals (water is a leaving group). The resulting C-O bond is a glycosidic bond, forms acetals called glycosides Same thing happens with hemiketals forming ketals Breaking glycosidic bond requires hydrolysis

Proenzymes (zymogens)

inactive forms of enzymes Zymogen: Enzyme that is secreted in inactive form and must be activated by cleavage (digestive enzymes)

The discovery of G protein-coupled receptors (GPCRs) that are constitutively active was a large step forward in helping discover of many GPCR families. Such GPCRs are always active, even in the absence of a ligand. In a cell line mutated to have a constitutively active Gq, one would expect to see:

increased levels of intracellular calcium. The Gq protein initiates a mechanism that leads to generation of IP3, which has the ability to open calcium channels in the ER to increase the intracellular calcium. In the family of G protein-coupled receptors, Gq proteins activate the enzyme phospholipase C, which cleaves the membrane phospholipid PIP2 into diacylglycerol and IP3. IP3has the ability to open up the calcium channels in the endoplasmic reticulum to release the stored calcium. A constitutively active Gq protein-coupled receptor would greatly increase the calcium levels inside the cell (A).

Central Dogma of Molecular Biology

information is transferred from DNA to RNA (transcription) and from RNA to protein (translation) Reverse transcription can occur from RNA back to DNA Replication occurs in DNA Double stranded DNA to single stranded RNA Messenger RNA is synthesized (5'-3') and is complementary and antiparallel to DNA template strand Ribosome translates mRNA from 5' to 3' as it synthesizes proteins from amino terminus (N-terminus) to carboxyl terminus (c-terminus) DNA Coding strand is identical to the mRNA strand, except T is replaced with U *The template strand is 3' to 5', so if you make mRNA from template strand, it should be antiparallel (5 to 3) and complementary! (T becomes A, A becomes U, C becomes G....)

Hybridization

joining of complementary base pair sequences Can be DNA-DNA or DNA-RNA recognition Uses 2 single stranded sequences Vital for PCR and southern blotting

G protein-coupled receptors (GPCRs)

large family of integral membrane proteins involved in signal transduction; characterized by their 7 membrane-spanning alpha-helices; Found on extracellular surface utilize heterotrimeric G protein to transmit signals to effector cells (named after their intracellular link to guanine nucleotides (GDP and GTP) Heterotrimeric: Three subunits that comprise G protein: Alpha, beta and gamma subunits together = G protein -Ligand binding increases affinity of receptor for G protein -Binding G protein switches to active state and effects the intracellular signaling pathway *In the inactive form the alpha subunit binds GDP and is in a complex with the beta and gamma subunits. When a ligand binds to the GPCR, the receptor becomes activated and engages G protein Alpha subunit exchanges GDP for GTP, causes alpha subunit to move away from beta-gamma dimer -Activated alpha subunit alters activity of adenylate cyclase (if it is as, it activates, ai inhibits. Once dephosphorylated back to GDP, alpha rebinds with gamma and beta -Alpha activates target protein so it can relay signal Once GTP is hydrolyzed back into GDP, and the repeating process stops Three main types of G proteins: *Gs stimulates adenylate cyclase, increases levels of cAMP in cell *Gi inhibits adenylate cyclase. which decreases levels of cAMP in a cell *Gq activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2, which is cleaved into DAG and IP3, which can open calcium channels in the Endoplasmic reticulum, increasing calcium levels in cell

Regulation of Body Mass

lipids is the primary factor in the gradual change of body mass over time maintaing weight - eating the same amount of energy that is spent on the average day *If energy consumed> than energy spent over time = gain weight if body weight increases so does the BMR: Amount of energy consumed in a given period of time by a resting organism (amount of energy required per day) thus the caloric excess will cause an increase in body mass until equilibrium is reached between the new basal rate and the existing intake body does have a threshold: Larger changes must be made to lose weight than to gain it Diet (energy intake) and exercise (energy expenditure) BMI = mass / height ^2

Signaling Lipids

lipids perform active roles in cellular signaling and as coenzymes: -serve as coenzymes in the ETC and in glycosylation reactions -function as hormones that transmit signals over long distances and as intracellular messengers responding to extracellular signals -those with conjugated double bonds absorb light -act as pigments in plants and animals 3 Important categories: Steroids, prostaglandins, fat soluble vitamins, and then precursors like terpenes *Note: Coenzyme is organic, non-protein factor bound to enzyme and required for its normal activity

Fatty Acids

long chain carboxylic acids Carboxyl carbon = carbon 1 alpha carbon = carbon 2 Found in body as salts, that can form micelles or are esterified to other compounds like membrane lipids *Esterification is the general name for a chemical reaction in which two reactants (typically an alcohol and an acid) form an ester as the reaction product Written as number of carbons: double bonds *saturated fatty acids have no double bonds (max amount of H) *Humans cant synthesize many unsaturated fatty acids *Essentail fatty acids: a-linolenic acid and linoleum acid (both polyunsaturated, important for membrane fluidity) Omega (w) numbering system used (describes last double bond position) Mainly supplied by fats, also from excess carbs and protein (can be stored as energy in triacylglycerol form) Lipid and carb synthesis = contemplate synthesis: dont rely directly on coding nucleic acid, unlike protein and nucleic acid synthesis

Positively Charged (Basic) Side Chains

lysine (terminal primary amino group), arginine (3 N atoms in side chain, positive charge delocalized), histidine (aromatic ring with two nitrogen atoms: Imidazole) Histidine has pKa 6 -> pretty close to 7.4, so at physiological pH, one N is protonated and one is not, but under more acidic conditions both are protonated so there is a positive charge Positively charged nitrogen atoms *Catalytic triad in chymotrypsin makes use of histidine side chains ability to gain proton (histidine residue in active site removes proton from COOH group in aspartic acid residue, which can deprotonate a serine residue

Types of RNA

mRNA carries info from DNA by traveling from nucleus (transcribed) to cytoplasm (translated) tRNA translates nucleic acids to amino acids by pairing anticodon with mRNA codons -> charged with amino acid and added to growing peptide chain rRNA forms structural and catalytic component of ribosome and acts as ribozyme to create peptide bonds between amino acids

Types of RNA: mRNA

mRNA, tRNA, rRNA mRNA is the messenger of genetic info (carries info specifying amino acid sequence to ribosome). -Transcribed from template DNA by RNA polymerase enzymes -Only type of RNA that carries info that is transcribed to proteins, read in 3 nucleotide segments called codons -In eukaryotes, mRNA is monocistronic: each mRNA = 1 protein (different mRNA fro each protein) -mRNA in prokaryotes may be polycistronic -DNA codes for proteins but can't perform any of the important enzymatic reactions that proteins are responsible for in cells mRNA takes intro from DNA to ribosomes where primary protein structure created

Frameshift Mutations

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide The 3 nucleotides of codon referred to as reading frame. Point mutations = 1 nucleotide changed, but frameshift shifts all three Insertion or deletion Usually results in changes in amino acid sequence or premature truncation of the protein Typically more serious

Glycerophospholipids (phosphoglycerides)

phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group Head group determines membrane surface properties -> named according to head group *Phosphatidylcholine have choline head group *phosphatidylethanolamine has ethanol amine head group Head can be +, - or neutral Lots of variety

Native PAGE

polacrylamide gel electrophoresis analyzes proteins in their *native states* limited by the mass to charge and mass to size ratios many different proteins can have the same level of migration native protein can be taken back but only if it is not stained Allows complete protein to be recovered, more accurately determines relative globular size of proteins most useful to compare the molecular size or charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size exclusion chromatography

Ion Channels

proteins that create specific pathways for charged molecules 3 groups, but all permit facilitated diffusion of charged particles *Facilitated diffusion : Passive transport, diffusion down a concentration gradient through a pore created by transmembrane protein -Used when molecules are impermeable to membrane -Integral membrane proteins serve as channels Treatment for heart disease: Calcium channel blockers Treatment for siezues: Sodium channel blockers Treatment for IBSL? Acetylcholine receptor/cation channel blockers Three main types of ion channels: ungated, voltage gated, and ligand gated Ungated: Not regulated (no gates) -> net efflux: ALWAYS OPEN *maintaining the resting membrane potential Voltage gated channels: Gate regulated by membrane potential charge near channel -Voltage gated sodium channels: clos under resting conditions, but membrane depolarization causes protein conformation changes that allow them quickly open then close as voltage increases -Image: action potential of the sinoatrial node: As voltage drops, channels open to bring cell back to threshold and fire another action potential Ligand Gated Channels: -Especially at neuromuscular junction: Binding of specific substance or ligand to the channel causes it to open or close Neurotransmitter: gamma amino butyric acid (GABA) binds to chloride channel and opens it

Polar side chain amino acids

serine threonine asparagine glutamine cysteine POLAR but NOT aromatic Serine and threonine OH group in side chain makes them highly polar and able to H bond Asparagine and glutamine has amide side chains (do not gain or lose charge) Cysteine has thiol (-SH) in side chain Sulfur is larger and less electronegative, so SH bond is weaker than OH bond (thiol prone to oxidation

Fatty acid entry into mitochondria

short- (2-4C) and medium-chain (6-12C) diffuse freely into mitochondria, where they are oxidized Long-chain (14-20C) are oxidized in mitochondria, but are transported in via carnitine shuttle Carnitine acyltransferase I is rate-limiting enzyme of fatty acid oxidation Very long-chain (>20C) are oxidized elsewhere in the cell

Lineweaver-Burk Plot

the double reciprocal graph of the Michaelis-Menten equation Yields Straight line Y: intercept = 1/ V max X intercept = 1/ -Km X axis : 1/ [S] Y axis = 1/V Km and V max can be compared, s o its useful for determining type of inhibition

control points of the citric acid cycle

three checkpoints : Regulated by allosteric activators and inhibitors 1. Citrate synthase ATP, NADH, citrate, succinyl CoA function as allosteric inhibitors of this enzyme 2. isocitrate dehydrogenase inhibited by ATP and NADH ADP and NAD+ activate the enzyme by increasing its affinity for substrates 3. alpha ketoglutarate dehydrogenase complex inhibited by succinyl CoA, ATP, NADH stimulated by ADP and calcium ions Overall, ATP and NADH high levels inhibit CAC, and ADP and NAD+ activate it When lots of energy is consumed, lots of NADH converted to NAD+ and lots of ATP converted to ADP (Active state = NAD+ and ADP levels rise)

Transcription Factors

transcription-activating proteins that search the DNA looking for specific DNA-binding motifs Tend to have 2 recognizable domains: DNA binding domain and activation domain DNA binding domain binds to specific nucleotide sequence in promoter region or to DNA response element (sequence of DNA that binds only to specific transcription factors) ->help recruitment Activation domain: allows for binding of several transcription factors and other important regulatory proteins, like RNA poly and histone acetylates (remodel chromatin)