biochemistry

facilitated diffusion

a type of passive transport diffusion of molecules down a concentration gradient through a pore in the membrane created by this transmembrane protein used for molecules that are impermeable to the membrane (large, polar, or charged) allows integral membrane proteins to serve as channels for these substrates to avoid the hydrophobic fatty acid tails of the phospholipid layer

fluid mosaic model

accounts for the presence of lipids, proteins, and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells.

Fatty acids are synthesized in the cytoplasm from

acetyl-CoA transported out of the mitochondria. • Synthesis includes five steps: activation, bond formation, reduction, dehydration, and a second reduction. • These steps are repeated eight times to form palmitic acid, the only fatty acid that humans can synthesize.

Vitamin E (tocopherols)

act as biological antioxidants. Their aromatic rings destroy free radicals, preventing oxidative damage.

irreversible inhibition

active site is made unavailable for prolonged period of time or enzyme is permanently altered is not easily overcome or reversed is a prime drug mechanism

α-Ketoglutarate dehydrogenase complex

acts similarly to PDH complex, metabolizing α-ketoglutarate to form succinyl-CoA. This enzyme gener-ates the second CO2 and second NADH of the cycle. It is inhibited by ATP, NADH, and succinyl-CoA; it is activated by ADP and Ca2+.

Animal cells specifically used for storage of large triacylglycerol deposits are called

adipocytes.

how many pKa values does amino groups have

all amino acid have at least two groups that can be deprotonated, they all have at least two pKA value. 1. carboxyl group pKa : around 2 2. amino acid pKa: usually around 9-10

Selectins

allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system weakest of CAMs plays role in host defense, including inflammation and white blood cell migration

pentose phosphate pathway (PPP)

also known as the hexose monophos-phate (HMP) shunt, occurs in the cytoplasm of most cells, generating NADPH and sugars for biosynthesis (derived from ribulose 5-phosphate).

Mismatch repair

also occurs during the G2 phase of the cell cycle, using the genes MSH2 and MLH1.

how does salinity effect enzyme activity?

altering the concentration of salt can change enzyme activity in vitro. increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme and in some cases causing denaturation

the isoelectric point for an basic amino acid

amino acid with basic side chains have relatively high isoelectric point above 6

at very acidic pH values (1), how are amino acids charged?

amino acids tend to be positively charged both the carboxyl and amino group get protonated

hydrophobic and hydrophilic amino acids

amino acids with long alkyl side chains- alanine, isoleucine, leucine, valine and phenylalanine- are all strongly hydrophobic and thus more likely to be found in the interior of the protein away from water on the surface of the proteins amino acids with charged side chains -positively charged histidine, arginine and lysine, plus negatively charged glutamate and aspartate- are hydrophilic as are the amides asparagine and glutamine remaining amines are neither particularly hydrophilic nor hydrophobic

membrane-spanning domain

anchors the receptor in the cell membrane

immunoglobulins

antibodies produced by B cells that function to neutralize targets in the body, such as toxins and bacteria and then recruit other cells to help eliminate the threat. Y shaped made up of tow identical heavy chains and light chains disulfide linkages and noncovlanet interactions holds the heavy and light chains together. have antigen- binding regions at the tip of the Y constant region- involved in the recruitment and binding of other cells of the immune system such as macrophage

Dehydrogenases

are a subtype of oxidoreductases (enzymes that catalyze an oxidation-reduction reaction) . transfer a hydride ion (H-) to an electron acceptor, usually NAD+ or FAD . Therefore, whenever you see dehydrogenase in aerobic metabolism, be on the lookout for a high-energy electron carrier being formed!

Both coenzyme Q and cytochrome c

are able to move freely in the inner mitochondrial membrane, this degree of mobility allows these carriers to transfer electrons by physically interacting with the next component of the transport chain .

Phospholipids

are amphipathic and form the bilayer of biological membranes. • They contain a hydrophilic (polar) head group and hydrophobic (nonpolar) tails. • The head group is attached by a phosphodiester linkage and, because it interacts with the environment, determines the function of the phospholipid. • The saturation of the fatty acid tails determines the fluidity of the mem-brane; saturated fatty acids are less fluid than unsaturated ones. Fatty acids form most of the structural thickness of the phospholipid bilayer

Prostaglandins

are autocrine and paracrine signaling molecules that regulate cAMP levels. They have powerful effects on smooth muscle contraction, body temperature, the sleep-wake cycle, fever, and pain.

Fatty acids

are carboxylic acids, typically with a single long chain, although they can be branched.

Transgenic mice

are created by integrating a gene of interest into the germ line or embryonic stem cells of a developing mouse. • Organisms that contain cells from two different lineages (such as mice formed by integration of transgenic embryonic stem cells into a normal mouse blastocyst) are called chimeras. • Transgenic mice can be mated to select for the transgene.

Ketone bodies

are essentially transportable forms of acetyl-CoA . They are produced by the liver and used by other tissues during prolonged starvation

DNA libraries

are large collections of known DNA sequences. • Genomic libraries contain large fragments of DNA, including both coding and noncoding regions of the genome. They cannot be used to make recom-binant proteins or for gene therapy. • cDNA libraries (expression libraries) contain smaller fragments of DNA, and only include the exons of genes expressed by the sample tissue. They can be used to make recombinant proteins or for gene therapy.

Centromeres

are located in the middle of chromosomes and hold sister chro-matids together until they are separated during anaphase in mitosis. They also contain a high GC-content to maintain a strong bond between chromatids.

allosteric site of an enzyme

are non-catalytic region of the enzyme that bind regulators

Terpenes

are odiferous steroid precursors made from isoprene, a five-carbon molecule. • One terpene unit (a monoterpene) contains two isoprene units. • Terpenoids are derived from terpenes via oxygenation or backbone rear-rangement. They have similar odorous characteristics

Glycerophospholipids

are phospholipids that contain a glycerol backbone.

ion channels

are proteins that create specific pathways for charged molecules types: ungated, voltage-gated and ligand- gated

Telomeres

are the ends of chromosomes. They contain high GC-content to prevent unraveling of the DNA. During replication, telomeres are slightly short-ened, although this can be (partially) reversed by the enzyme telomerase.

Triacylglycerols (triglycerides)

are the preferred method of storing energy for long-term use. • They contain one glycerol attached to three fatty acids by ester bonds. The fatty acids usually vary within the same triacylglycerol. • The carbon atoms in lipids are more reduced than carbohydrates, giving twice as much energy per gram during oxidation. • Triacylglycerols are very hydrophobic, so they are not hydrated by body water and do not carry additional water weight.

Free fatty acids

are unesterified fatty acids that travel in the bloodstream

positive charged (basic) side chains

arginine, lysine, histidine have side chains that have positively charged nitrogen atoms lysine has terminal primary amino group arginine has three nitrogen atoms in its side chain; the positive charge is delocalized over all three nitrogen atoms histidine has an aromatic ring with two nitrogen atoms (ring is called imidazole)

The two main methods of energy storage in the body are

as triacylglycerols in adipose tissue or as carbohydrates in glycogen

negative charged (acidic) side chains

aspartic acid (aspartate), glutamic acid (glutamate) at pH 7.4 these amino acid has negative charge have carboxylate (-COO-) group in their side chains rather than amides. aspartate is deprotonated form of aspartic acid glutamate is the deprotonated form of glutamic acid

kinesins and dyneins

associated with microtubules have two head, one attached to tubulin at all times important for vesicle transport kinesins play role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis. bring vesicle to the positive end dyneins are involved in the sliding movement of cilia and flagella, bring vesicle to the negative end

Action of Fatty Acid Synthase

attachment to acyl carrier protein, bond formation, reduction of carboxyl, dehydration, reduction of double bond' Reactions include activation of the growing chain (a) and malonyl-CoA (b) with ACP, bond formation between these activated molecules (c), reduction of a carbonyl to a hydroxyl group (d), dehydration (e), and reduction to a saturated fatty acid (f).

Which of the following is true about glycerophospholipids? A. Glycerophospholipids can sometimes be sphingolipids, depending on the bonds in their head groups. B. Glycerophospholipids are merely a subset of phospholipids. C. Glycerophospholipids are used in the ABO blood typing system. D. Glycerophospholipids have one glycerol, one polar head group, and one fatty acid tail.

b Glycerophospholipids are a subset of phospholipids, as are sphingomyelins. Glycerophospholipids are never sphingo-lipids because they contain a glycerol backbone (rather than sphingosine or a sphingoid backbone), eliminating (A). Sphingolipids are used in the ABO blood typing system, eliminating (C). Glycerophospholipids have a polar head group, glycerol, and two fatty acid tails, not one, as in (D).

What is the function of sodium dodecyl sulfate (SDS) in SDS-PAGE? A. SDS stabilizes the gel matrix, improving resolution during electrophoresis. B. SDS solubilizes proteins to give them uniformly negative charges, so the separation is based purely on size. C. SDS raises the pH of the gel, separating multiunit proteins into individual subunits. D. SDS solubilizes proteins to give them uniformly positive charges, so separation is based purely on pH.

b Sodium dodecyl sulfate is a detergent and will digest proteins to form micelles with uniform negative charges. Because the protein is sequestered within the micelle, other factors such as charge of the protein and shape have minimal roles during separation. In essence, the protein micelles can be modeled as being spheres, dependent only on size.

binding proteins

bind a specific substrate, either to sequester it in the body or hold its concentration at steady state include hemoglobin, calcium binding protein, DNA binding protein

amino acid at basic conditions

both the amino group and the carboxyl group get deprotonated negatively charged under basic conditions

Cardiac muscle uses fatty acid oxidation in

both the well-fed and fasting states.

when the pH of a solution is approximately equal to the pKa of the solute, the solution acts as

buffer

Lipid properties are determined by...

by the degree of saturation in fatty acid chains and the functional groups to which the fatty acid chains are bonded .

Cadherins

calcium-dependent glycoproteins that hold similar cells together

Metabolic rates can be measured using

calorimetry, respirometry, consumption tracking, or measurement of blood concentrations of substrates and hormones.

protein amino acid sequencing

can be automated in a stepwise manner . By combining the information from both techniques, researchers can determine where on a chromosome the gene coding a particular protein resides .

Biological oxidation and reduction reactions

can be broken down into component half-reactions.

beta pleated sheet

can be parallel or antiparallel peptide chain lie alongside one another forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain have pleated or rippled shape to accommodate as many hydrogen bonds as possible R group points above and below the plane of the beta pleated sheet

Nernst equation

can be used to determine the membrane potential from the intra-and extracellular concentrations of the various ions:

LCAT (lecithin-cholesterol acyltransferase)

catalyzes the formation of cholesteryl esters for transport with HDL

CETP (cholesterol ester transfer protein)

catalyzes the transition of IDL to LDL by transferring cholesteryl esters from HDL

Supercoiling

causes torsional strain on the DNA molecule, which can be released by DNA topoisomerases, which create nicks in the DNA molecule.

noncompetitive inhibition

change enzyme conformation by binding to the allosteric site inhibition can not be overcome by adding more substrate due to no interaction between the inhibitor and the substrate. decrease the value of Vmax because there is less enzyme available to rest doesn't alter the Km because any copies fo the enzyme that are still active maintain the same affinity for their substrate

Except for glycine, all amino acids are _____.

chiral thus, most amino acids are optically active

Classes of Lipoproteins

chylomicrons, VLDL, LDL, HDL

The Structure of tRNA

cloverleaf

Tumor suppressor genes

code for proteins that reduce cell cycling or promote DNA repair; mutations of tumor suppressor genes can also lead to cancer.

The Genetic Code

collection of codons of mRNA, each of which directs the incorporation of a particular amino acid into a protein during protein synthesis each codon represents only one amino acid; however, most amino acids are represented by multiple codons .

Protein concentration is determined by

colorimetrically, either by UV spectroscopy or through a color change reaction.

Fructose

comes from honey, fruit, and sucrose (common table sugar). It is trapped in the cell by fructokinase, and then cleaved by aldolase B to form glyceraldehyde and DHAP.

Galactose

comes from lactose in milk. It is trapped in the cell by galactokinase, and converted to glucose 1-phosphate via galactose-1-phosphate uridyltrans-ferase and an epimerase

Adenosine Triphosphate (ATP)

compound used by cells to store and release energy

all transmembrane movement is based

concentration gradients

Metabolism is directed toward

conserving tissues to the greatest extent possible, especially the brain and heart . Digestion of protein compromises muscle—potentially that of the heart—so it is unlikely to occur under normal conditions .

dipeptides and tripeptides

consist of two amino acid residues and three respectively

Nucleosides

contain a five-carbon sugar bonded to a nitrogenous base; nucleo-tides are nucleosides with one to three phosphate groups added. • Nucleotides in DNA contain deoxyribose; in RNA, they contain ribose. • Nucleotides are abbreviated by letter: adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U).

Sphingolipids

contain a sphingosine or sphingoid backbone. • Many (but not all) sphingolipids are also phospholipids, containing a phosphodiester bond; these are termed sphingophospholipids. • Sphingomyelins are the major class of sphingophospholipids and contain a phosphatidylcholine or phosphatidylethanolamine head group. They are a major component of the myelin sheath. • Glycosphingolipids are attached to sugar moieties instead of a phosphate group. Cerebrosides have one sugar connected to sphingosine; globosides have two or more.

Waxes

contain long-chain fatty acids esterified to long-chain alcohols. They are used as protection against evaporation and parasites in plants and animals

Gangliosides

contain oligosaccharides with at least one terminal N-acetylneuraminic acid (NANA; also called sialic acid).

Steroids

contain three cyclohexane rings and one cyclopentane ring. Their oxidation state and functional groups may vary Cholesterol is a steroid important to membrane fluidity and stability; it serves as a precursor to a host of other molecules.

Acetyl-CoA

contains a high-energy thioester bond that can be used to drive other reactions when hydrolysis occurs. can be formed from pyruvate via pyruvate dehydrogenase complex,

Pyruvate Dehydrogenase

converts pyruvate to acetyl-CoA. - stimulated by insulin - inhibited by acetyl-CoA

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.

d Peptidyl transferase is an enzyme that catalyzes the forma-tion 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 (A) and (B). Chaperones maintain a protein's three-dimensional shape as it is formed, as in (C).

Which of the diastereomers of glucose from the previous question are considered to be epimers of glucose? Enantiomers?

d-Glucose's epimers are d-mannose (C-2), d-allose (C-3), and d-galactose (C-4). None of the d-stereoisomers is an enantiomer for glucose; l-glucose is the enantiomer of d-glucose

Oncogenes

develop from mutations of proto-oncogenes, and promote cell cycling. They may lead to cancer, which is defined by unchecked cell prolif-eration with the ability to spread by local invasion or metastasize (migrate to distant sites via the bloodstream or lymphatic system).

DNA sequencing uses

dideoxyribonucleotides, which terminate the DNA chain because they lack a 3′ -OH group. The resulting fragments can be sepa-rated by gel electrophoresis, and the sequence can be read directly from the gel.

Zymogens

digestive enzymes secreted as inactive proteins, converted to active enzymes by removing some of their amino acids

Passive transport

does not require energy because the molecule is moving down its concentration gradient or from an area with higher concentration to an area with lower concentration • Simple diffusion does not require a transporter. Small, nonpolar molecules passively move from an area of high concentration to an area of low concentration until equilibrium is achieved. • Osmosis describes the diffusion of water across a selectively permeable membrane. • Facilitated diffusion uses transport proteins to move impermeable solutes across the cell membrane.

Citrate synthase

doesn't require energy input in order to form covalent bonds, but succinyl-CoA synthetase certainly does

Many oxidation-reduction reactions involve an

electron carrier to transport high-energy electrons.

ATP is used to fuel

energetically unfavorable reactions or to activate or inactivate other molecules .

Covalently Modified Enzymes

enzymes can be activated or deactivated by phosphorylation or dephosphorylation Can also be modified by covalent attachment of sugar groups (glycosylation)

How does pH effect enzyme action?

enzymes depend on pH in order to function properly, not only because pH affects the ionization of the active site, but also because changes in pH can lead to denaturation of the enzyme. enzymes are maximally active within a small pH range; outside of this range, activity drop with change in pH as the ionization of the active site changes and the protein is denatured.idea

Adipose tissue stores lipids under the influence of insulin and releases them under the influence of

epinephrine.

What bonds are broken during saponification?

ester bonds of triacylglycerols are broken to form a glycerol molecule and salts of fatty acids (soap)

Nucleotide excision repair

fixes helix-deforming lesions of DNA (such as thymine dimers) via a cut-and-patch process that requires an excision endonuclease.

Base excision repair

fixes nondeforming lesions of the DNA helix (such as cytosine deamination) by removing the base, leaving an apurinic/apyrimidinic (AP) site. An AP endonuclease then removes the damaged sequence, which can be filled in with the correct bases.

Activity levels for enzymatic samples are determined by

following the process of a known reaction, often accompanied by a color change.

The Final Steps of the Citric Acid Cycle

from succinate to oxaloacetate

Prolonged fasting (starvation) dramatically increases

glucagon and catecholamine secretion. • Most tissues rely on fatty acids. • At maximum, 2/3 of the brain's energy can be derived from ketone bodies.

The enzymes that catalyze irreversible reactions are

glucokinase/hexokinase, PFK-1, and pyruvate kinase

Carbon skeletons of amino acids are used for energy, either through

gluconeogenesis or ketone body formation. Amino groups are fed into the urea cycle for excretion. The fate of a side chain depends on its chemistry.

Glycogen Metabolism

glucose addition to a granule begins with glucose 6-phosphate, which is converted to glucose 1-phosphate. This glu-cose 1-phosphate is then activated by coupling to a molecule of uridine diphosphate (UDP), which permits its integration into the glycogen chain by glycogen synthase. This activation occurs when glucose 1-phosphate interacts with uridine triphosphate (UTP), forming UDP-glucose and a pyrophosphate (PPi).

The brain and other nervous tissues consume

glucose in all metabolic states, except for prolonged fasts, where up to 2/3 of the brain's fuel may come from ketone bodies

The rate-limiting enzyme is

glucose-6-phosphate dehydrogenase, which is activated by NADP+ and insulin and inhibited by NADPH.

Non-polar, non-aromatic side chains

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Carbohydrates can form a protective

glycoprotein coat and also function in cell recognition.

collagen

has characteristic trihelical fiber (three left handed helices woven together to form secondary high handed helix) makes up most of the extracellular matrix of connective tissue provide strength and flexibility

Steroid hormones

have high-affinity receptors, work at low concentrations, and affect gene expression and metabolism.

Unsaturated fatty acids

have one or more double bonds.

Integrins

have two membrane proteins; alpha and beta they transmit signals between the ECM and cytoskeleton plays an important role in cellular signaling impact cellular function by promoting cell division, apoptosis

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

The ratio of free fatty acids to glycerol is 3:1. A triacylglycerol molecule is composed of glycerol and three fatty acids.

enantiomers

The same sugars, in different optical families, are enantiomers (such as d-glucose and l-glucose).

What property of protein-digesting enzymes allows for a sequence to be determined without fully degrading the protein? A. Selectivity B. Sensitivity C. Turnover D. Inhibition

The selective cleavage of proteins by digestive enzymes allows fragments of different lengths with known amino acid endpoints to be created. By cleaving the protein with several different enzymes, a basic outline of the amino acid sequence can be created.

What are the five steps in the addition of acetyl-CoA to a growing fatty acid chain?

The steps in the attachment of acetyl-CoA to a fatty acid chain are attachment to acyl carrier protein, bond formation between molecules, reduction of a carbonyl group, dehydration, and reduction of a double bond.

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain. it is the result of moving hydrophobic amino acid side chain into the interior of the protein determined by hydrophilic and hydrophobic interaction between R groups of amino acids

What type of operon is the trp operon? The lac operon?

The trp operon is a negative repressible system; the lac operon is a negative inducible system.

What are the two major metabolic products of the pentose phosphate pathway (PPP)?

The two major metabolic products of the pentose phosphate pathway are ribose 5-phosphate and NADPH

How does β-oxidation of unsaturated fatty acids differ from that of saturated fatty acids?

There is an additional isomerase and an additional reductase for the β-oxidation of unsaturated fatty acids, which provide the stereochemistry necessary for further oxidation.

Enzymes of DNA Replication

This process involves the action of DNA helicase, gyrase, polymerase, and ligase to create two identical molecules of DNA.

Thyroid storm is a potentially lethal state of extreme hyperthyroidism in which T3 and T4 levels are significantly above normal limits. What vital sign abnormali-ties might be expected in a patient with thyroid storm?

Thyroid storm presents with hyperthermia (high temperature), tachycardia (fast heart rate), hypertension (high blood pressure), and tachypnea (high respiratory rate).

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.

To solve this question, we can use the equation ΔG = ΔG° + RT lnQ. Q, the reaction quotient, is [B][C]^2/[A] for this reaction. Plugging in the variables, we get: ∆G = 0+RT ln [10x10^-3][10x10^-3]^2/[10x10^-3] =RT ln10^-4 = -4 RT ln10 Because both R and T are positive, and natural log values being greater than 0, we know that ΔG must be negative and therefore lower than the original value. A negative ΔG corresponds to a spontaneous reaction.

What purpose do Tollens' reagent and Benedict's reagent serve? How do they differ from each other?

Tollens' reagent and Benedict's reagent are used to detect the presence of reducing sugars. Tollens' reagent is reduced to produce a silvery mirror when aldehydes are present whereas Benedict's reagent is indicated by a reddish precipitate of Cu2O.

Transcription of DNA to hnRNA

Transcription will continue along the DNA coding region until the RNA polymerase reaches a termination sequence or stop signal, which results in the termination of transcription. The DNA double helix then re-forms, and the primary transcript formed is termed heterogeneous nuclear RNA (hnRNA). mRNA is derived from hnRNA via posttranscriptional modifications

What is the difference between a transgenic and a knockout mouse?

Transgenic mice have a gene introduced into their germ line or embryonic stem cells to look at the effects of that gene; they are therefore best suited for study-ing the effects of dominant alleles. Knockout mice are those in which a gene of interest has been removed, rather than added.

What are the three classes of membrane proteins? How are they each most likely to function?

Transmembrane proteins are most likely to serve as channels or receptors. Embedded membrane proteins are most likely to have catalytic activity linked to nearby enzymes. Membrane-associated (peripheral) proteins are most likely to be involved in signaling or are recognition molecules on the extracellular surface.

How do transport kinetics differ from enzyme kinetics?

Transport kinetics display both Km and vmax values. They also can be coopera-tive, like some binding proteins. However, transporters do not have analogous Keq values for reactions because there is no catalysis.

Describe the structure and function of triacylglycerols.

Triacylglycerols, also called triglycerides, are composed of a glycerol backbone esterified to three fatty acids. They are used for energy storage.

True or False: In size-exclusion chromatography, the largest molecules elute first.

True. The small pores in size-exclusion chromatography trap smaller particles, retaining them in the column.

True or False: It is easier to gain weight than to lose weight.

True; the threshold is lower for uncompensated weight gain than it is for uncompensated weight loss. Therefore, it is easier to surpass this threshold and gain weight than to lose weight.

diastereomers.

Two sugars that are in the same family (both are either ketoses or aldoses, and have the same number of carbons) that are not identical and are not mirror images of each other

Osmosis

Water moves from areas of low solute (high water) concentration to high solute (low water) concentration. hypotonic, isotonic , hypertonic solution

Which of the statements regarding waxes is FALSE? A. Waxes generally have melting points above room temperature. B. Waxes are produced only in plants and insects and therefore must be consumed by humans. C. Waxes protect against dehydration and parasites. D. Waxes are esters of long-chain fatty acids and long-chain alcohols.

Waxes are also produced in animals for similar protective functions. Cerumen, or earwax, is a prime example in humans.

Concentration gradients

help to determine appropriate membrane transport mechanisms in cells.

α-1,4 keeps the same branch moving

"4ward"; α-1,6 (one-six) "puts a branch in the mix ."

Mitochondrial Structure

- Outer membrane - Inner membrane (with ATP synthase proteins) - Cristae - Matrix components of the mitochondria are critical in the harvesting of energy. The citric acid cycle takes place in the mitochondrial matrix. the inner mitochondrial membrane is assembled into folds called cristae, which maximize surface area It is the inner mitochondrial membrane that will be essential for generating ATP using the proton-motive force, an electrochemical proton gradient generated by the complexes of the electron transport chain.

Lipids are mobilized from adipocytes by

hormone-sensitive lipase.

Jacob-Monod model of repressors and activators explains

how operons work. • Operons are inducible or repressible clusters of genes transcribed as a single mRNA.

Steps in Translation

1. Initiation 2. Elongation 3. Termination

Fumarase

hydrolyzes the alkene bond of fumarate, forming malate

Succinyl-CoA synthetase

hydrolyzes the thioester bond in succinyl-CoA to form succinate and CoA-SH. This enzyme generates the one GTP generated in the cycle.

ideal temperature for most enzymes

37C, 98.6 F, 310 K

the alpha carbon of amino group contain

4 groups hydrogen, R group, amino and carboxyl group

Which of the following factors determine an enzyme's specificity? A. The three-dimensional shape of the active site B. The Michaelis constant C. The type of cofactor required for the enzyme to be active D. The prosthetic group on the enzyme

A

Which of the following statements about enzyme kinetics is FALSE? A. An increase in the substrate concentration (at constant enzyme concentration) leads to propor-tional increases in the rate of the reaction. B. Most enzymes operating in the human body work best at a temperature of 37°C. C. An enzyme-substrate complex can either form a product or dissociate back into the enzyme and substrate. D. Maximal activity of many human enzymes occurs around pH 7.4.

A An increase in the substrate concentration, while maintaining a constant enzyme concentration, leads to a proportional increase in the rate of the reaction only initially. However, once most of the active sites are occupied, the reaction rate levels off, regardless of further increases in substrate con-centration. At high concentrations of substrate, the reac-tion rate approaches its maximal velocity and is no longer changed by further increases in substrate concentration.

Which of the following characteristics is NOT attributed to antibodies? A. Antibodies bind to more than one distinct antigen. B. Antibodies label antigens for targeting by other immune cells. C. Antibodies can cause agglutination by interaction with antigen. D. Antibodies have two heavy chains and two light chains.

A Antibodies are specific to a single antigen. Each B-cell pro-duces a single type of antibody with a constant region that is specific to the host and a variable region that is specific to an antigen.

Ketose sugars may have the ability to act as reducing sugars. Which process explains this? A. Ketose sugars undergo tautomerization. B. The ketone group is oxidized directly. C. Ketose sugars undergo anomerization. D. The ketone group is reduced directly.

A 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. Anomerization, mentioned in (C), refers to ring closure of a monosaccharide, creating an anomeric carbon

Tumor suppressor genes are most likely to result in cancer through: A. loss of function mutations. B. gain of function mutations. C. overexpression. D. proto-oncogene formation.

A Oncogenes are most likely to result in cancer through acti-vation, (B), while tumor suppressor genes are most likely to result in cancer through inactivation.

The reduction half-reaction in the last step of the electron transport chain is: A. O2 + 4e-+ 4 H+ → 2 H2O B. NADPH → NADP+ + e-+ H+ C. NADP+ + e-+ H+ → NADPH D. Ubiquinone (Q) → Ubiquinol (QH2)

A Reduction is a gain of electrons, which eliminates (B) because it is an oxidation reaction. NADPH, (C), is a product of the pentose phosphate pathway. Ubiquinone, (D), transfers electrons during the course of the electron transport chain, but is not the final electron acceptor. This title belongs to oxygen.

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).

A 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

A 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 glucone-ogenesis 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 Pentose Phosphate Pathway

A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.

Gap Junction

A type of intercellular junction in animals that allows the passage of materials between cells. A connexon (gap junction) is composed of six monomers of connexin and permits travel of solutes between cells

Examples of Nucleosides

Adenosine Deoxythymidine

What is alternative splicing, and what does it accomplish?

Alternative splicing is the ability of some genes to use various combinations of exons to create multiple proteins from one hnRNA transcript. This increases protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes.

Introns stay---- the nucleus; exons will --- the nucleus as part of the mRNA .

in , exit

Which of the two forms of starch is more soluble in solution. Why?

Amylopectin is more soluble in solution than amylose because of its branched structure. The highly branched structure of amylopectin decreases intermolec-ular bonding between polysaccharide polymers and increases interaction with the surrounding solution.

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

An increase in insulin levels will increase lipid storage and decrease lipid mobilization from adipocytes, leading to weight gain in diabetic patients who begin insulin injections.

Why is it preferable to cleave thioester links rather than typical ester links in aerobic metabolism? A. Oxygen must be conserved for the electron transport chain. B. Thioester hydrolysis has a higher energy yield. C. Typical ester hydrolysis cannot occur in vivo. D. Thioester cleavage requires more energy.

B Thioester links release a great deal of energy when hydrolyzed, making them well-suited as respiration reaction drivers. They are particularly useful because they release more energy than typical ester cleavage. It is thioester formation, not hydrolysis, that requires a great deal of energy, making (D) incorrect.

Which fatty acid can be synthesized by humans? A. 12:0 B. 16:0 C. 16:1 D. 18:3

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

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

B 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, (A), appears in both the citric acid cycle and as part of Complex II of the electron transport chain. Isocitrate dehydrogenase, (C), catalyzes the rate-limiting step of the citric acid cycle. Pyruvate dehydrogenase, (D), is one of the five enzymes that make up the pyruvate dehydrogenase complex.

Some enzymes require the presence of a nonprotein molecule to behave catalytically. An enzyme devoid of this molecule is called a(n): A. holoenzyme. B. apoenzyme. C. coenzyme. D. zymoenzyme.

B An enzyme devoid of its necessary cofactor is called an apoenzyme and is catalytically inactive.

Soap bubbles form because fatty acid salts organize into: A. lysosomes. B. micelles. C. phospholipid bilayers. D. hydrogen bonds.

B Fatty acid salt micelles are responsible for the formation of soap bubbles. While phospholipids can form bilayers, as in (C), the fatty acids in soap are free fatty acids, not phospholipids.

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

B The increased permeability of the inner mitochondrial membrane allows the proton-motive force to be dissipated through locations besides the F0 portion of ATP synthase. Therefore, ATP synthase is less active and is forming less ATP, invalidating (A) and (C). The body will attempt to regenerate the proton-motive force by increasing fuel catab-olism, eliminating (D). This increase in fuel use requires more oxygen utilization in the electron transport chain.

Esterification of Glucose

Because carbohydrates have hydroxyl groups they are able to participate in reactions with carboxylic acids and carboxylic derivatives to form esters. Similar to phosphorylation of Glucose Acetic anhydride used as carboxylic acid derivative

Which amino acids contribute most significantly to the pI of a protein? I. Lysine II. Glycine III. Arginine A. I only B. I and II only C. I and III only D. II and III only

C The overall pI of a protein is determined by the relative number of acidic and basic amino acids. The basic amino acids are arginine, lysine, and histidine, and the acidic amino acids are aspartic acid and glutamic acid. Glycine's side chain is a hydrogen atom, so it will have the least contribution of all the amino acids.

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

C Cytochrome c carries electrons from CoQH2-cytochrome c oxidoreductase (Complex III) to cytochrome c oxidase (Complex IV) as part of the electron transport chain. The ETC takes place on the inner mitochondrial membrane.

d-Ribose and d-Arabinose Are

C-2 Epimers

What are the three main classes of cell adhesion molecules? What type of adhesion does each class form?

Cadherin - Two cells of the same or similar type using calcium integrin- One cell to proteins in the extracellular matrix selectin- One cell to carbohydrates, usually on the surface of other cells

Which of the following is a sphingolipid? A. Lecithin B. Phosphatidylinositol C. Cholesterol D. Ganglioside

D Gangliosides, along with ceramide, sphingomyelin, and cerebrosides, are sphingolipids

DNA Strand Polarity

DNA strands run antiparallel to one another; enzymes that replicate and transcribe DNA only work in the 5′ to 3′ direction.

Explain the relationship between the carbonyl carbon, anomeric carbon, and the alpha and beta forms of a sugar molecule.

During hemiacetal or hemiketal formation, the carbonyl carbon becomes chiral and is termed the anomeric carbon. The orientation of the -OH substituent on this carbon determines if the sugar molecule is the α-or β-anomer.

First Law of Thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed.

What is the primary method of transporting free fatty acids in the blood?

Free fatty acids remain in the blood, bonded to albumin and other carrier proteins. A much smaller amount will remain unbonded.

By what histone and DNA modifications can genes be silenced in eukaryotic cells? Would these processes increase the proportion of heterochromatin or euchromatin?

Histone deacetylation and DNA methylation will both downregulate the transcription of a gene. These processes allow the relevant DNA to be clumped more tightly, increasing the proportion of heterochromatin.

Vitamin K is for

Koagulation .

What are the relative benefits of native PAGE compared to SDS-PAGE?

Native PAGE allows a complete protein to be recovered after analysis; it also more accurately determines the relative globular size of proteins. SDS-PAGE can be used to eliminate conflation from mass-to-charge ratios.

Formation of a Recombinant Plasmid Vector

Need ori, ampR and gene (w/ restriction enzyme site)

Bases Commonly Found in Nucleic Acids

Purines Pyrimidines

A Restriction Enzyme (EcoRI) Creating Sticky Ends

Restriction enzymes cut at palindromic sequences, such as GAATTC.

Ribose and Deoxyribose

Ribose has an -OH group at C-2; deoxyribose has an -H.

What are the five histone proteins in eukaryotic cells? Which one is not part of the histone core around which DNA wraps to form chromatin?

The five histone proteins are H1, H2A, H2B, H3, and H4. H1 is the only one not in the histone core.

Plasma Membrane Proteins

The fluid mosaic model also accounts for the presence of three types of mem-brane proteins

What is the preferred fuel for most cells in the well-fed state? What is the exception and its preferred fuel?

The preferred fuel for most cells in the well-fed state is glucose; the exception is cardiac muscle, which prefers fatty acids.

Endocytosis and Exocytosis

What are the two types of active transport?

Order the lipoproteins from greatest percentage of protein to least percentage of protein. Circle the molecules that are primarily involved in triacylglycerol transport.

With respect to protein content, HDL > LDL > IDL > VLDL > chylomicrons. VLDL and chylomicrons are the primary triacylglycerol transporters. HDL and LDL are mostly involved in cholesterol transport.

Protein structure is primarily determined through

X-ray crystallography after the protein is isolated, although NMR can also be used.

Why are some enzymes released as zymogens?

Zymogens are precursors of active enzymes. It is critical that certain enzymes (like the digestive enzymes of the pancreas) remain inactive until arriving at their target site.

pyruvate dehydrogenase complex

a five-enzyme complex in the mitochondrial matrix that forms—and is also inhibited by—acetyl-CoA and NADH

the isoelectric point for an acidic amino acid

amino acid with acidic side chains have relatively low isoelectric point below 6

Order of sites in the ribosome during translation:

ape

Knockout mice

are created by deleting a gene of interest

Chylomicrons

are the transport mechanism for dietary triacylglycerol molecules and are transported via the lymphatic system.

Apoproteins

control interactions between lipoproteins.

Citrate synthase

couples acetyl-CoA to oxaloacetate and then hydrolyzes the resulting product, forming citrate and CoA-SH. This enzyme is regulated by negative feedback from ATP, NADH, succinyl-CoA, and citrate.

Phosphorylation of Glucose

creates a phosphate ester this process is very important reaction in which a phosphate group from ATP is transferred to glucose (and ending with ADP) *hexokinase* *glucoinase* - in liver and pancreatic beta islet cells both enzymes does this reaction

Homogenization

crushing, grinding, or blending the tissue of interest into an evenly mixed solution

If oxygen or mitochondria are absent, the NADH produced in glycolysis is oxidized by

cytoplasmic lactate dehydrogenase. Examples include red blood cells, skeletal muscle (during short, intense bursts of exercise), and any cell deprived of oxygen.

Cholesterol may be obtained through dietary sources or through

de novo synthesis in the liver.

SDS-PAGE

denatures the proteins and masks the native charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel.

Pyruvate dehydrogenase phosphatase

dephosphorylates PDH when ADP levels are high, turning it on.

Relationship of Glucagon and Insulin in Metabolism

feedback diagram of the interaction of insulin and glucagon on plasma glucose concentration, as well as fat and protein metabolism.

proteins can be broadly divided into

fibrous proteins such as collagen that have structure that resemble sheets or long strands and globular proteins such as myoglobin that tend to be spherical

Glycolysis

first step in releasing the energy of glucose, in which a molecule of glucose is broken into two molecules of pyruvic acid

Saturated fatty acids

have no double bonds between carbons

intermediate pH, how are amino acids charged?

if the pH is increased from pH 1 to pH 7.4 (normal pH of human blood), we've moved far above the pKa of the carboxylic acid group. thus carboxyl group will be in its conjugate base form and be deprotonated (-COO-) , but since the pKa is below basic amino group, the amino group will remain fully portioned and in it conjugate acid form (-NH3+) thus the molecule is zwitterions- it has both positive charge and negative charge but overall the molecule is neutral

keratins

intermediate filament proteins found in epithelial cells; contribute to the mechanical integrity of the cell and also function as regulatory proteins; the primary protein that makes up hair and nails

Chylomicrons and VLDL primarily carry triacylglycerols . LDL and HDL primarily carry cholesterol . IDL is

intermediate; it is a transition state between VLDL and LDL, occurring as the primary lipid within the lipoprotein changes from triacylglycerol to cholesterol .

Changes in enthalpy in a closed biological system are equal to changes in

internal energy, which is equal to heat exchange within the environment.

Short-chain fatty acids are absorbed across the

intestine into the blood.

Recombinant DNA

is DNA composed of nucleotides from two different sources.

Proline is unique because

it forms a cyclic amino acid the ring places notable constraints on the flexibility of proline, which limits where it can appear in a protein and can have significant effects on proline's role in secondary structure

Ketone bodies form

ketogenesis) during a prolonged starvation state due to excess acetyl-CoA in the liver.

Acetyl-CoA can be formed from the carbon skeletons of

ketogenic amino acids, ketone bodies, and alcohol.

While the brain normally uses glucose for energy, under conditions such as starvation

ketone bodies can become the brain's major source of energy .

The brain can derive up to two-thirds of its energy from

ketone bodies during prolonged starvation.

What are the roles of the three main types of RNA?

mRNA carries information from DNA by traveling from the nucleus (where it is transcribed) to the cytoplasm (where it is translated). tRNA translates nucleic acids to amino acids by pairing its anticodon with mRNA codons; it is charged with an amino acid, which can be added to the growing peptide chain. rRNA forms much of the structural and catalytic component of the ribosome, and acts as a ribozyme to create peptide bonds between amino acids.

negative feedback

maintain homeostasis; once we have enough of a given product, the pathway is turn off to stop creating more product a high concentration of the product, inhibit enzyme 1, slowing the entire pathway

A degenerate code allows

multiple codons to encode for the same amino acid. • Initiation (start) codon: AUG • Termination (stop) codons: UAA, UGA, UAG

Redundancy and wobble (third base in the codon) allows

mutations to occur without effects in the protein.

ungated channels

no gates, unregulated, ex. potassium channels

Lipids are insoluble in water and soluble in

nonpolar organic solvents.

when antibodies bind to antigen they cause

opsonization, agglutinating

The plasma membrane contains proteins embedded within the

phospholipid bilayer.

Pyruvate dehydrogenase kinase

phosphorylates PDH when ATP or acetyl-CoA levels are high, turning it off.

portions are

polypeptides that range from just a few amino acids in length up to thousands. functions as enzymes, hormones, membrane pores and receptors and elements of cell structure. they are the main actors in cells

Salts of free fatty acids are

soaps and can be synthesized in saponification. Soaps act as surfactants, forming micelles. A micelle can dissolve a lipid-soluble molecule in its fatty acid core, and washes away with water because of its shell of carboxylate head groups.

Physiological concentrations are usually much less than

standard concentrations.

Catabolism of cellular proteins occurs only under conditions of

starvation.

central dogma

states that DNA is transcribed to RNA, which is translated to protein.

feedback regulation

the regulation of a process by its output or end product

Goldman-Hodgkin-Katz voltage equation

where P represents the permeability for the relevant ion. Note that chloride is inverted relative to the other ions because it carries a negative charge

The number of possible stereoisomers of a compound can be calculated by:

where n is the number of chiral carbons in the molecule.

counterregulatory hormones

which include glucagon, epinephrine, cortisol, and growth hormone, act to raise blood sugar levels by stimulating glycogenolysis and gluconeogenesis

feedforward regulation

~ Enzymes regulated by intermediates that precede them

peptides are composed of

~ amino acids subunits ~ Sometimes called residues

The Role of ATP

• ATP is a mid-level energy molecule. • ATP contains high-energy phosphate bonds that are stabilized upon hydrolysis by resonance, ionization, and loss of charge repulsion. • ATP provides energy through hydrolysis and coupling to energetically unfavorable reactions. • ATP can also participate in phosphoryl group transfers as a phosphate donor.

processes that occur 5′ to 3′:

• DNA synthesis • DNA repair • RNA transcription • RNA translation (reading of codons)

• There are three types of RNA with separate jobs in transcription:

• Messenger RNA (mRNA) carries the message from DNA in the nucleus via transcription of the gene; it travels into the cytoplasm to be translated. • Transfer RNA (tRNA) brings in amino acids and recognizes the codon on the mRNA using its anticodon. • Ribosomal RNA (rRNA) makes up the ribosome and is enzymatically active.

Biological systems are considered:

• Open, wherein matter and energy can be exchanged with the environment, or • Closed, wherein only energy can be exchanged with the environment. • This determination is made based on the examination of the entire organism or an isolated process.

Which complex(es) are associated with each of the following? (circle all that apply) • Pumping a proton into the intermembrane space • Acquiring electrons from NADH • Acquiring electrons from FADH2 • Having the highest reduction potential

• Pumping a proton into the intermembrane space: I, III, and IV • Acquiring electrons from NADH: I • Acquiring electrons from FADH2: II • Having the highest reduction potential: IV (reduction potentials increase along the ETC)

Skeletal muscle metabolism differs based on the current activity level and fiber type.

• Resting muscle conserves carbohydrates in glycogen stores and uses free fatty acids from the bloodstream. • Active muscle may use anaerobic metabolism, oxidative phosphorylation of glucose, direct phosphorylation from creatine phosphate, or fatty acid oxidation, depending on fiber type and exercise duration.

Stop codons:

• UAA—U Are Annoying • UGA—U Go Away • UAG—U Are Gone

Substrates of Citric Acid Cycle:

"Please Can I Keep Selling Seashells For Money, Officer?" -Pyruvate -Citrate -IsoCitrate -alpha-Ketoglutarate -Succinyl-CoA -Succinate -Fumarate -Malate -Oxaloacetate

Important Disaccharides

(a) Sucrose (glucose-α-1,2-fructose), (b) Lactose (galactose-β-1,4-glucose), (c) Maltose (glucose-α-1,4-glucose)

Structures of Thyroid Hormones

(a) Triiodothyronine (T3 ); (b) Thyroxine (T4 ) the increase in metabolic rate produced by a dose of thyroxine (T4) occurs after a latency of several hours but may last for several days, while triiodothyronine (T3) produces a more rapid increase in metabolic rate and has a shorter duration of activity. The subscript numbers refer to the number of iodine atoms in the hormone; iodine atoms are represented by purple spheres T4 can be thought of as the precursor to T3; deiodonases (enzymes that remove iodine from a molecule) are located in target tissues and convert T4 to T3

PURe As Gold

(as A and G are purines); think of gold wedding rings . It takes two gold rings at a wedding, just like purines have two rings in their structure .

Inducible systems

(such as the lac operon) are bonded to a repressor under normal conditions; they can be turned on by an inducer pulling the repressor from the operator site.

Repressible systems

(such as the trp operon) are transcribed under normal conditions; they can be turned off by a corepressor coupling with the repressor and the binding of this complex to the operator site.

Resonance in the peptide bond

- This double bond character between the nitrogen atom and the carbonyl carbon adds to the rigidity and stability of the backbone of proteins. - The single bonds on either side of the peptide bond permit free rotation.

Citrate Isomerized to Isocitrate

- citrate binds to aconitase where water is removed then added back to form isocitrate this step is necessary to facilitate the subsequent oxidative decarboxylation.

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

Bradford Protein Assay

- most common method of protein concentration determination - uses a color-change from brown-green to blue

respiratory quotient (RQ)

-Ratio of CO2 produced to O2 consumed -Varies depending on foodstuff consumed

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 -two moles of base to deprotonate one mole of most amino acids -buffering capacity greatest at or near pH of two diss. constants, pKa1 and pKa2; at isoelectric point, capacity is min., vertical line -some have acidic or basic side chains, to find pI, avg two acidic pKa;s if side chain acidic, two basic pKa's if basic -can perform by adding acid to base, sequence is reversed.

cell adhesion molecules (CAMs)

-proteins found on surface of most cells -aid in binding the cell to the extracellular matrix or to other cells types: cadherins, integrins, selections

Column Chromatography

-solution with mixture dripped down colum with solid phase. -more polar=slower down column The sample is added at the top of the column and a solvent is poured over it. The more similar the sample is to the solvent (mobile phase), the more quickly it will elute; the more similar it is to the alumina or silica (stationary phase), the more slowly it will elute—if at all.

Mutarotation

-spontaneous change of configuration about C1 (occurs more rapidly if rxn is catalyzed w/ acid or base) -Exposing hemiacetal rings to water causes them to spontaneously cycle b/w open & closed forms -b/c the substituents on the single bond b/w C1 and C2 can rotate freely, either the α or β anomer can be formed Interconversion between the α-and β-anomers via ring opening and reclosing

What are the three major structural differences between DNA and RNA?

. DNA contains deoxyribose, while RNA contains ribose. DNA contains thymine, while RNA contains uracil. Usually, DNA is double-stranded, while RNA is single-stranded.

In the following phospholipid, determine whether the fatty acids are saturated or unsaturated and label their hydrophobic and hydrophilic regions.

. The hydrophilic region is at the top of this diagram. While you need not be able to recognize it, the head group is phosphatidylcholine in this example. The hydrophobic region is at the bottom and is composed of two fatty acid tails. The tail on the left is saturated; the tail on the right is unsaturated, as evidenced by the kink in its chain

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.

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. Ceramide has a single hydrogen atom for a head group; sphingomyelins have phosphodiester linkages (phospholipids); cerebrosides have one sugar; globosides (not pictured) have multiple sugars; gangliosides have oligosaccharides and terminal sialic acids.

Processing Eukaryotic hnRNA to Form mRNA

1. 5'-cap and 3' poly A tail addition 2. splicing of introns by spliceosome (snRNA and snRNPs in the nucleus) 3. excised intron degraded in the nucleus 4. mRNA is made with only 5'cap, exons, 3'poly A tail 5. mRNA is transported to cytoplasm for translation

Cellulose structure

1. Long, unbranched chain of beta-glucose. 2. Bonds between the sugars are straight, so cellulose chains are straight. 3. Cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils.

β-Oxidation

1. Oxidation of the fatty acid to form a double bond 2. Hydration of the double bond to form a hydroxyl group 3. Oxidation of the hydroxyl group to form a carbonyl (β-ketoacid) 4. Splitting of the β-ketoacid into a shorter acyl-CoA and acetyl-CoA continues until the chain has been shortened to two carbons, creating a final acetyl-CoA.

Reversible inhibition types

1. competitive 2. noncompetitive 3. mixed 4. uncompetitive

If chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine, how many oligopeptides would be formed in enzymatic cleavage of the following molecule with chymotrypsin? Val - Phe - Glu - Lys - Tyr - Phe - Trp - Ile - Met - Tyr - Gly - Ala

4: Val - Phe; Glu - Lys - Tyr; Ile - Met - Tyr; Gly-Ala. A single amino acid on its own is not considered an oligopeptide.

ideal pH most enzymes

7.4 , gastric enzyme= 2, pancreatic enzyme =8.5

Given the following data, calculate the resting membrane potential of this cell:

= 61.5log 11/120.7≈60 log 1/10=−60mV The exact value is -64.0 mV

A eukaryotic cell has been found to exhibit a truncation mutation that creates an inactive RNA polymerase I enzyme. Which type of RNA will be affected by this inactivation? A. rRNA B. tRNA C. snRNA D. hnRNA

A RNA polymerase I in eukaryotes is found in the nucleolus and is in charge of transcribing most of the rRNA for use during ribosomal creation. RNA polymerase II is responsi-ble for hnRNA and snRNA. RNA polymerase III is respon-sible for tRNA and the 5S rRNA.

Enhancers are transcriptional regulatory sequences that function by enhancing the activity of: A. RNA polymerase at a single promoter site. B. RNA polymerase at multiple promoter sites. C. spliceosomes and lariat formation in the ribosome. D. transcription factors that bind to the promoter but not to RNA polymerase.

A 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 poly-merase to transcribe the specific gene for that enhancer more efficiently.

Which of the following DNA sequences would have the highest melting temperature? A. CGCAACCATCCG B. CGCAATAATACA C. CGTAATAATACA D. CATAACAAATCA

A The melting temperature of DNA is the temperature at which a DNA double helix separates into two single strands (denatures). To do this, the hydrogen bonds linking the base pairs must be broken. Cytosine binds to guanine with three hydrogen bonds, whereas adenine binds to thymine with two hydrogen bonds. The amount of heat needed to disrupt the bonding is proportional to the number of bonds. Thus, the higher the GC-content in a DNA segment, the higher the melting point

Which of the following statements regarding polymerase chain reaction is FALSE? A. Human DNA polymerase is used because it is the most accurate. B. A primer must be prepared with a complementary sequence to part of the DNA of interest. C. Repeated heating and cooling cycles allow the enzymes to act specifically and replaces helicase. D. Each cycle of the polymerase chain reaction doubles the amount of DNA of interest.

A The polymerase chain reaction is used to clone a sequence of DNA using a DNA sample, a primer, free nucleotides, and enzymes. The polymerase from Thermus aquaticus is used because the reaction is regulated by thermal cycling, which would denature human enzymes.

Which ion channels are responsible for maintaining the resting membrane potential? A. Ungated channels B. Voltage-gated channels C. Ligand-gated channels D. No ion channels are involved in maintenance of the resting membrane potential

A The resting membrane potential is displayed by cells that are not actively involved in signal transduction. Ungated or "leak" channels permit limited free flow of ions, while the sodium-potassium pump is also active and corrects for this leakage. Ligand-gated and voltage-gated channels are involved in cell signaling and in the pacemaker potentials of certain cells, but cause deviation from—not maintenance of—the resting membrane potential.

Topoisomerases are enzymes involved in: A. DNA replication and transcription. B. posttranscriptional processing. C. RNA synthesis and translation. D. posttranslational processing

A Topoisomerases, such as prokaryotic DNA gyrase, are involved in DNA replication and mRNA synthesis (tran-scription). DNA gyrase is a type of topoisomerase that enhances the action of helicase enzymes by the introduc-tion of negative supercoils into the DNA molecule. These negative supercoils facilitate DNA replication by keeping the strands separated and untangled.

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

A Triglycerides are unlikely to act as coenzymes for a few reasons, including their large size, neutral charge, and ubiq-uity in cells. Cofactors and coenzymes tend to be small in size, such as metal ions like (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

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.

A 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, (B), catalyzes the rate-limiting step of glycogenesis; glucose-6-phosphate dehydro-genase, (C), catalyzes the rate-limiting step of the pentose phosphate pathway; and fructose-1,6-bisphosphatase, >(D), catalyzes the rate-limiting step of gluconeogenesis.

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 layers of the membrane. C. proteins moving within the plane of the membrane. D. proteins exiting the cell through exocytosis.

A 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 mem-brane 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 layers.

Enzymes increase the rate of a reaction by: A. decreasing the activation energy. B. decreasing the overall free energy change of the reaction. C. increasing the activation energy. D. increasing the overall free energy change of the reaction.

A Enzymes increase the rate of a reaction by decreasing the activation energy. They do not affect the overall free energy, ΔG, of the reaction.

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.

A Hormonal controls are coordinated to regulate the met-abolic 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.

What is the function of LCAT? A. LCAT catalyzes the production of cholesteryl esters. B. LCAT catalyzes the production of cholesterol. C. LCAT catalyzes the transfer of cholesteryl esters. D. LCAT catalyzes the transfer of cholesterol.

A 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 live

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

A 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.

What is the fate of long-chain fatty acids that are contained within micelles? A. Transport into chylomicrons released into the lymphatic system B. Transport into chylomicrons released into the circulatory system C. Direct diffusion across the intestine into the lymphatic system D. Direct diffusion across the intestine into the circulatory system

A Short-chain fatty acids are soluble in the intestinal lumen, and thus do not interact with micelles as longer fatty acid chains do. The long-chain fatty acids are taken up by the intestinal cells and packaged into triacylglycerols for transport as chylomicrons. Chylomicrons exit the intestine through lacteals that feed into the lymphatic system, which joins with the bloodstream in the base of the neck through the thoracic duct.

Which of the following statements conflicts with the fluid mosaic model? A. The cell membrane is static in structure. B. Membrane components can be derived from multiple biomolecules. C. Hydrophobic interactions stabilize the lipid bilayer. D. Proteins are asymmetrically distributed within the cell membrane.

A The fluid mosaic model accounts for a dynamic membrane. In this model, membrane components contain both fatty and carbohydrate-derived components, eliminating (B). Further, the membrane is stabilized by the hydrophobic interactions of both fatty acid tails and membrane proteins, which may be found on the cytosolic or extracellular side of the membrane, or may run directly through the membrane; thus, (C) and (D) are also eliminated

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

A 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.

A The movement of any solute or water by diffusion or osmo-sis 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

A 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

In glucose degradation under aerobic conditions: A. oxygen is the final electron acceptor. B. oxygen is necessary for all ATP synthesis. C. net water is consumed. D. the proton-motive force is necessary for all ATP synthesis

A This question is testing our general knowledge of cellular respiration. Notice that all types of cellular respiration (aerobic and anaerobic) start with the degradation of glucose by glycolysis. In aerobic respiration, oxygen is the final electron acceptor, and water is therefore produced at the end of the electron transport chain. While oxygen is needed for aerobic respiration in order to produce the optimal 32 molecules of ATP per glucose, it is not the only method by which ATP is produced. Glycolysis still provides 2 ATP per glucose without the need for oxygen, thus making (B) and (D) incorrect. Water, mentioned in (C), is produced in aerobic metabolism, not consumed.

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.

A 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.

A man collapses while running a marathon and is taken to the emergency room. His blood is found to be somewhat acidic, and further tests show increased lactate dehydrogenase activity. This enzyme is involved in which of the following pathways? A. Anaerobic glycolysis B. β-Oxidation of fatty acids C. Citric acid cycle D. Pentose phosphate pathway

A Under normal conditions, when oxygen is readily available, the pyruvate generated in glycolysis enters the mitochon-drion and is converted into acetyl-CoA by the action of pyruvate dehydrogenase. During strenuous exercise, partic-ularly by individuals in poor physical condition, the oxygen demands of the skeletal muscle may exceed the ability of the heart and lungs to provide oxygen. In this setting, the muscles switch to anaerobic glycolysis, and the pyruvate that is produced is fermented to lactate by the action of lactate dehydrogenase

The Citric Acid Cycle

A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion; the second major stage in cellular respiration.

Of the four types of reversible inhibitors, which could potentially increase Km?

A competitive inhibitor increases Km because the substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor. A mixed inhibitor will increase Km only if the inhibitor preferentially binds to the enzyme over the enzyme-substrate complex.

lactone

A cyclic ester; named according to the number of carbon atoms other than the carbonyl carbon and for the straight-chain form of the compound. Contains a cyclic ester

daltons (Da)

A dalton is an alternative term for molar mass g/ mol . The average molar mass of one amino acid is ~100 daltons, or 100 g/mol

Trehalose

A disaccharide of two glucose molecules, but with a linkage different from maltose. Used as a food additive and sweetener. Example of a disaccharide with an α,α-1,1 linkage between the α-anomeric carbons of two glucose molecules

How many carbons are in a diterpene?

A diterpene has 20 carbon molecules in its backbone. One terpene unit is made from two isoprene units, each of which has five carbons.

body mass index (BMI)

A measure of body fat that is the ratio of the weight of the body in kilograms to the square of its height in meters.

What are the base-pairing rules according to the Watson-Crick model?

A pairs with T (in DNA) or U (in RNA), using two hydrogen bonds. C pairs with G, using three hydrogen bonds.

What are the roles of each site in the ribosome? • A site: • P site: • E site:

A site: binds incoming aminoacyl-tRNA using codon-anticodon pairing P site: holds growing polypeptide until peptidyl transferase forms peptide bond and polypeptide is handed to A site E site: transiently holds uncharged tRNA as it exits the ribosome

epimers

A special subtype of diastereomers are those that differ in configuration at exactly one chiral center. such as d-ribose and d-arabinose, which only differ at C-2

What is the difference between a steroid and a steroid hormone?

A steroid is defined by its structure: it includes three cyclohexane rings and a cyclopentane ring. A steroid hormone is a molecule within this class that also functions as a hormone, meaning that it travels in the bloodstream, is active at low concentrations, has high-affinity receptors, and affects gene expression and metabolism.

Anode in isoelectric focusing

A+ : attracts acids

Glucocorticoids

increase blood glucose in response to stress by mobilizing fat stores and inhibiting glucose uptake • Glucocorticoids increase the impact of glucagon and catecholamines

Chromatin Remodeling by Acetylation

increases space between histones, allowing better access to DNA for transcription factors Transcription factors that bind to the DNA can recruit other coactivators such as histone acetylases. These proteins are involved in chromatin remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone protein Acetylation of histone proteins decreases the posi-tive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA.

Because gluconeogenesis requires acetyl-CoA to occur (to inhibit pyruvate dehydrogenase and stimulate pyruvate carboxylase), gluconeogenesis is

inextricably linked to fatty acid oxidation . The source of acetyl-CoA cannot be glycolysis because this would just burn the glucose that is being generated in gluconeogenesis

The Central Dogma of Molecular Biology

information is transferred from DNA to RNA to protein

How does coupling with ATP hydrolysis alter the energetics of a reaction?

ATP hydrolysis yields about 30 kJ/mol of energy, which can be harnessed to drive other reactions forward. This may either allow a nonspontaneous reaction to occur or increase the rate of a spontaneous reaction.

Explain why ATP is an inefficient molecule for long-term energy storage.

ATP is an intermediate-energy storage molecule and is not energetically dense. The high-energy bonds in ATP and the presence of a significant charge make it an inefficient molecule to pack into a small space. Long-term storage molecules are characterized by energy density and stable, nonrepulsive bonds, primarily seen in lipids.

ATP Synthase Reaction

ATP synthase generates ATP from ADP and inorganic phosphate by allowing high-energy protons to move down the concentration gradient created by the electron transport chain.

uncompetitive inhibition

inhibitor binds only to enzyme-substrate complex locks substrate in enzyme preventing its release (increasing affinity b/w enzyme and substrate so it lowers Km) Lower Km and vmax

Citrate Formation

Acetyl-CoA + OAA → Citryl-CoA → Citrate + CoA (via citrate synthetase) energetically favors the formation of citrate and helps the cycle revolve in the forward direction

How does acetyl-CoA shift the metabolism of pyruvate?

Acetyl-CoA inhibits pyruvate dehydrogenase complex while activating pyruvate carboxylase. The net effect is to shift from burning pyruvate in the citric acid cycle to creating new glucose molecules for the rest of the body. The acetyl-CoA for this regulation comes predominantly from β-oxidation, not glycolysis

. How does acetyl-CoA affect PDH complex activity? Why?

Acetyl-CoA inhibits the PDH complex. As a product of the enzyme complex, a buildup of acetyl-CoA from either the citric acid cycle or fatty acid oxida-tion signals that the cell is energetically satisfied and that the production of acetyl-CoA should be slowed or stopped. Pyruvate can then be used to form other products, such as oxaloacetate for use in gluconeogenesis.

What are the three steps of translation?

initiation, elongation, termination

What is the name for a five-carbon sugar with an aldehyde group? A six-carbon sugar with a ketone group?

Aldopentose; ketohexose

postabsorptive (fasting) state

insulin secretion decreases while glucagon and catecholamine secretion increases. • This state is observed in short-term fasting (overnight). • There is a transition to catabolic metabolism.

postprandial/well-fed (absorptive) state

insulin secretion is high and anabolic metabolism prevails.

Myosin

interact with actin it is a thick filament in a myofibril involved in cellular transport subunit has single head and neck

What is an advantage of analyzing the half-reactions in biological oxidation and reduction reactions?

Analyzing half-reactions can help to determine the number of electrons being transferred. This type of analysis also facilitates balancing equations and the determination of electrochemical potential if reduction potentials are provided.

DNA cloning

introduces a fragment of DNA into a vector plasmid. A restriction enzyme (restriction endonuclease) cuts both the plasmid and the frag-ment, which are left with sticky ends. Once the fragment binds to the plasmid, it can be introduced into a bacterial cell and permitted to replicate, generating many copies of the fragment of interest. • Vectors contain an origin of replication, the fragment of interest, and at least one gene for antibiotic resistance (to permit for selection of that colony after replication). • Once replicated, the bacterial cells can be used to create a protein of inter-est, or can be lysed to allow for isolation of the fragment of interest from the vector.

IDL

is a VLDL remnant in transition between triacylglycerol and cholesterol transport; it picks up cholesteryl esters from HDL.

Deoxyribonucleic acid (DNA)

is a macromolecule that stores genetic informa-tion in all living organisms.

Entropy

is a measure of energy dispersion in a system.

Gene therapy

is a method of curing genetic deficiencies by introducing a func-tional gene with a viral vector.

replisome (replication complex)

is a set of specialized proteins that assist the DNA polymerases.

Structure of Cortisol

is a steroid hormone that promotes the mobilization of energy stores through the degradation and increased delivery of amino acids and increased lipolysis.

Debranching enzyme

is actually made up of two enzymes with different functions: one moves the terminal end of a glycogen chain to the branch point (α-1,4:α-1,4 transferase), and one removes the glucose monomer actually present at the branch point (α-1,6 glucosidase) .

peptide bond formation

is an example of condensation or dehydration reaction because it results in the removal of a water molecules the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid. after the attack the hydroxyl group of the carboxylic acid is kick off and the peptide (amide) bond is formed

Cyanide

is an inhibitor of cytochrome subunits a and a3 . The cyanide anion is able to attach to the iron group and prevent the transfer of electrons . Tissues that rely heavily on aerobic respiration such as the heart and the central nervous system can be greatly impacted .

coenzyme

is an organic, nonprotein factor bound to an enzyme and required for its normal activity .

Equilibrium

is an undesirable state for most biochemical reactions because organisms need to harness free energy to survive.

Heterochromatin

is dense, transcriptionally silent DNA that appears dark under light microscopy.

GLUT 4

is found in adipose tissue and muscle and is stimulated by insulin. It has a low Km

GLUT 2

is found in the liver (for glucose storage) and pancreatic β-islet cells (as part of the glucose sensor). It has a high Km.

Vitamin K (phylloquinone and menaquinones)

is important for formation of prothrombin, a clotting factor. It performs posttranslational modifications on a number of proteins, creating calcium-binding sites.

HDL

is involved in the reverse transport of cholesterol.

Euchromatin

is less dense, transcriptionally active DNA that appears light under light microscopy.

Membrane potential

is maintained by the sodium-potassium pump and leak channels. • The electrical potential created by one ion can be calculated using the Nernst equation. • The resting potential of a membrane at physiological temperature can be calculated using the Goldman-Hodgkin-Katz voltage equation, which is derived from the Nernst equation

Vitamin D (cholecalciferol)

is metabolized to calcitriol in the kidneys and regulates calcium and phosphorus homeostasis in the intestines (increasing calcium and phosphate absorption), promoting bone formation. A deficiency of vitamin D causes rickets.

Vitamin A (carotene)

is metabolized to retinal for vision and retinoic acid for gene expression in epithelial development.

Methionine

is one of only two amino acids that contains a sulfur atom in its side chain. due to the sulfur has a methyl group attached, it considered relatively non polar

alpha- helices

is rodlike structure in which the peptide chain coils clockwise around a central axis. it is stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain the side chains are pointed away from the helix core it is important component of the structure of keratin

ligand-binding domain

is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain result in a second messenger cascade ex:receptor tyrosine kinase RTK.

hnRNA

is synthesized from the DNA template (antisense) strand.

Km

is the concentration of substrate when an enzyme is active at half of its maximum velocity (vmax) . The lower the Km, the higher the enzyme's affinity for the substrate .

proton-motive force

is the electrochemical gradient generated by the electron transport chain across the inner mitochondrial membrane. The intermembrane space has a higher concentration of protons than the matrix; this gradient stores energy, which can be used to form ATP via chemiosmotic coupling.

standard free energy (ΔG°)

is the energy change that occurs at standard concentrations of 1 M, pressure of 1 atm, and temperature of 25°C. where R is the universal gas constant, T is the temperature, and Q is the reaction quotient

ATP synthase

is the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi). • The F0 portion is an ion channel, allowing protons to flow down the gradient from the intermembrane space to the matrix. • The F1 portion uses the energy released by the gradient to phosphorylate ADP into ATP

Saponification

is the ester hydrolysis of triacylglycerols using a strong base, like sodium or potassium hydroxide.

Pinocytosis

is the ingestion of liquid into the cell in vesicles formed from the cell membrane and phagocytosis is the ingestion of larger, solid molecules.

Hybridization

is the joining of complementary base pair sequences. • Polymerase chain reaction (PCR) is an automated process by which mil-lions of copies of a DNA sequence can be created from a very small sample by hybridization. • DNA molecules can be separated by size using agarose gel electrophoresis. • Southern blotting can be used to detect the presence and quantity of various DNA strands in a sample. After electrophoresis, the sample is transferred to a membrane that can be probed with single-stranded DNA molecules to look for a sequence of interest.

secondary structure of proteins

is the local structure of neighboring amino acids. it is the primarily the result of hydrogen bonding between nearly amino acids. alpha helices and beta- pleated sheet the key to the stability of both structures is the formation of intramolecular hydrogen bonds between different residues.

isoelectric point (pI)

is the pH at which the molecule is electrically neutral. The point in the titration of an amino acid with a strong base where all of the carboxylic acid functional groups have been deprotonated - molecule has no net charge between the (R-COO)- and the (R-NH3)+. Maximum number of zwitterions. Dictated by the side group of the amino acid. The more acidic the side group, the lower the pI. Ex: only amino acids with an acidic isoelectric point (all except histidine, arginine, and lysine) will be negatively charged at a basic pH (8) - for electrophoresis where the negatively charged amino acids will run towards the anode.

When an antibody binds to its antigen, what are the three possible outcomes of this interaction?

Antigen-antibody interactions can result in neutralization of the pathogen or toxin, opsonization (marking) of the antigen for destruction, or creation of insoluble antigen-antibody complexes that can be phagocytized and digested by macrophages (agglutination).

Provide an example of disequilibrium that is maintained at the expense of cellular energy

Any excitable cell is maintained in a state of disequilibrium. Classic examples include muscle tissue and neurons. In addition, cell volume and membrane transport are regulated by the action of the sodium-potassium pump, which can maintain a stable disequilibrium state in most tissues.

Osmotic pressure, a colligative property

is the pressure applied to a pure solvent to prevent osmosis and is used to express the concentration of the solution. It is often better conceptualized as a "sucking" pressure in which a solution is drawing water in, proportional to its concentration

citric acid cycle main purpose

is to oxidize carbons in intermediates to CO2 and generate high-energy electron carriers (NADH and FADH2) and GTP.

How is the respiratory quotient expected to change when a person transitions from resting to brief exercise?

As a person begins to exercise, the proportion of energy derived from glucose increases. This transition to almost exclusively carbohydrate metabolism will cause the respiratory quotient to approach 1.

When physicians order a lipid panel to evaluate a patient, which value do they prefer to see over a minimum threshold rather than below a maximum?

As mentioned in the chapter, HDL is often considered "good" cholesterol because it picks up excess cholesterol from blood vessels for excretion. Because of this crucial role, HDL values are checked for being over a minimum value.

What is the relationship between osmotic pressure and the direction of osmosis through a semipermeable membrane?

As osmotic pressure increases, more water will tend to flow into the compart-ment to decrease solute concentration. Osmotic pressure is often considered a "sucking" pressure because water will move toward the compartment with the highest osmotic pressure.

Which of the following is true about cholesterol? A. Cholesterol always increases membrane fluidity in cells. B. Cholesterol is a steroid hormone precursor. C. Cholesterol is a precursor for vitamin A, which is produced in the skin. D. Cholesterol interacts only with the hydrophobic tails of phospholipids.

B Cholesterol is a steroid hormone precursor that has variable effects on membrane fluidity depending on temperature, eliminating (A). It interacts with both the hydrophobic tails and the hydrophilic heads of membrane lipids, nullify-ing (D). It is also a precursor for vitamin D (not vitamin A), which can be produced in the skin in a UV-driven reaction, eliminating (C).

The formation of α-d-glucopyranose from β-d-glucopyranose is called: A. glycosidation. B. mutarotation. C. enantiomerization. D. racemization.

B Mutarotation is the interconversion between anomers of a compound. Enantiomerization and racemization, (C) and (D), are related: enantiomerization is the formation of a mirror-image or optically inverted form of a compound, whereas racemization is moving a solution toward an equal concentration of both enantiomers. Glycosidation, (A), is the addition of a sugar to another compound.

In a single strand of a nucleic acid, nucleotides are linked by: A. hydrogen bonds. B. phosphodiester bonds. C. ionic bonds. D. van der Waals forces.

B Nucleotides bond together to form polynucleotides. The 3′ hydroxyl group of one nucleotide's sugar joins the 5′ hydroxyl group of the adjacent nucleotide's sugar by a phos-phodiester bond. Hydrogen bonding, (A), is important for holding complementary strands together, but does not play a role in the bonds formed between adjacent nucleotides on a single strand.

Peptidyl transferase connects the carboxylate group of 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

B Peptidyl transferase connects the incoming amino termi-nal to the previous carboxyl terminal; the only functional group listed here with a carbonyl and amino group is the amide. Peptide bonds are thus amide linkages, and the correct answer is (B)

A protein collected through affinity chromatography displays no activity even though it is found to have a high concentration using the Bradford protein assay. What best explains these findings? A. The Bradford reagent was prepared incorrectly. B. The active site is occupied by free ligand. C. The protein is bound to the column. D. The protein does not catalyze the reaction of interest.

B Protein activity and concentration are generally correlated. Because we have a high concentration of protein, we expect a high activity unless the protein has been damaged or inactivated in some way. The protein could have been inac-tivated by experimental conditions like detergents, heat, or pH; however, these are not answer choices. Rather, we must consider how the experimental procedure works. Protein elutes off of an affinity column by binding free ligand. In this situation, the binding may not have been reversed and thus the free ligand competes for the active site of the enzyme, lowering its activity.

During saponification: A. triacylglycerols undergo a condensation reaction. B. triacylglycerols undergo ester hydrolysis. C. fatty acid salts are produced using a strong acid. D. fatty acid salts are bound to albumin.

B Saponification is the ester hydrolysis of triacylglycerol using a strong base like sodium or potassium hydroxide to form glycerol and fatty acid salts. This is not a condensation reac-tion, as in (A), but a cleavage reaction. Fatty acids do travel in the body bonded to serum albumin, as in (D), but that is unrelated to the process of saponification.

Which of the following is/are true about sphingolipids? I. They are all phospholipids. II. They all contain a sphingosine backbone. III. They can have either phosphodiester or glycosidic linkages to their polar head groups. A. I only B. III only C. II and III only D. I, II, and III

B 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.

Which of the following best describes the structure of steroids? A. Three cyclopentane rings, one cyclohexane ring B. Three cyclohexane rings, one cyclopentane ring C. Four carbon rings, differing in structure for each steroid D. Three cyclic carbon rings and a functional group

B The basic backbone of steroid structure contains three cyclohexane rings and one cyclopentane ring. Although the oxidation status of these rings varies for different steroids, the overall structure does not, as in (C).

When trypsin converts chymotrypsinogen to chymotrypsin, some molecules of chymotrypsin bind to a repressor, which in turn binds to an operator region 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

B 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

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.

B The hydroxyl group on the anomeric carbon of the β-anomer is equatorial, thereby creating less nonbonded strain than the α-anomer, which has the hydroxyl group of the anomeric carbon in axial position.

A gene encodes a protein with 150 amino acids. There is one intron of 1000 base pairs (bp), a 5′-untranslated region of 100 bp, and a 3′-untranslated region of 200 bp. In the final mRNA, about how many bases lie between the start AUG codon and final termination codon? A. 150 B. 450 C. 650 D. 1750

B The intron will not be a part of the final, processed mRNA, and the untranslated regions of the mRNA will not be turned into amino acids. Translation will begin with codon 1 (which would be AUG). Because there are 150 amino acids, we can surmise that there will be 151 codons. Each codon will use 3 nucleotides, so 150 × 3 = 450 because codon 151 will be the stop codon.

Double-stranded RNA cannot be translated by the ribosome and is marked for degradation in the cell. Which of the following strands of RNA would prevent mature mRNA in the cytoplasm from being translated? A. Identical mRNA to the one produced B. Antisense mRNA to the one produced C. mRNA with thymine substituted for uracil D. Sense mRNA to the one produced

B The mRNA produced has the same structure as the sense strand of DNA (with uracils instead of thymines). Because bonding of nucleic acids is always complemen-tary but antiparallel, the antisense strand of mRNA would be the one that binds to the produced mRNA, creating double-stranded RNA that is then degraded once found in the cytoplasm

A double-stranded RNA genome isolated from a virus was found to contain 15% uracil. What percentage of guanine should exist in this virus's genome? A. 15% B. 35% C. 70% D. 85%

B The percentage of uracil must equal that of adenine due to base-pairing because the genome is double-stranded. This accounts for 30% of the genome. The remaining 70% must be split evenly between guanine and cytosine, so they each account for 35% of the genome.

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.

B 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 tempera-tures. In the absence of enzyme, this peak temperature is generally much hotter. Heating a reaction provides mole-cules 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′

B 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′—GGAUGUCU-CAAAGA—3′. mRNA contains uracil, rather than thymine.

How is cDNA best characterized? A. cDNA results from a DNA transcript with noncoding regions removed. B. cDNA results from the reverse transcription of processed mRNA. C. cDNA is the abbreviation for deoxycytosine. D. cDNA is the circular DNA molecule that forms the bacterial genome.

B cDNA (complementary DNA) is formed from a processed mRNA strand by reverse transcription. cDNA is used in DNA libraries and contains only the exons of genes that are transcriptionally active in the sample tissue.

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

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

Which lipid type is LEAST likely to contribute to membrane fluidity? A. Unsaturated glycerophospholipids B. trans glycerophospholipids C. Cholesterol D. Unsaturated sphingolipids

B Compounds that contribute to membrane fluidity will lower the melting point or disrupt the crystal structure. Cholesterol, (C), and unsaturated lipids, (A) and (D), are known for these functions. trans glycerophospholipids tend to increase the melting point of the membrane and there-fore decrease membrane fluidity

Which of the following correctly shows the amount of ATP produced from the given high-energy carriers? A. FADH2 → 1 ATP B. FADH2 → 1.5 ATP C. NADH → 3 ATP D. NADH → 3.5 ATP

B During oxidative phosphorylation, energy is harvested from the energy carriers FADH2 and NADH in order to form ATP. One molecule of mitochondrial FADH2 is oxidized to produce 1.5 molecules of ATP. Similarly, one molecule of mitochondrial NADH is oxidized to produce 2.5 molecules of ATP in the electron transport chain.

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

B 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, suc-cinate dehydrogenase is located on the inner mitochondrial membrane.

The bulk movement of liquid into a cell through vesicular infoldings is known as: A. phagocytosis. B. pinocytosis. C. exocytosis. D. drinking.

B The endocytosis (bulk uptake through vesicle formation) of fluid is known as pinocytosis. Phagocytosis, (A), is the endocytotic intake of solids, while exocytosis, (C), is a method of releasing vesicular contents. Drinking, (D), does not apply on a cellular level

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

B Adipose tissue and resting skeletal muscle require insu-lin for glucose uptake. Active skeletal muscle, (A), uses creatine phosphate and glycogen (regulated by epinephrine and AMP) to maintain its energy requirements.

After an overnight fast, which of the following processes would be expected to occur at an elevated rate compared with the well-fed state? A. Glycolysis B. Glycogenolysis C. Glycogenesis D. Glycerol synthesis

B After a fast, the liver must contribute glucose into the bloodstream through two main processes: glycogenolysis (early to intermediate fasting) and gluconeogenesis (intermediate to late fasting). The other processes would continue at normal basal levels or have decreased activity after a fast

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

B 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 pan-creas, where it serves as a glucose sensor; if glucose levels are low, it has little activity in this tissue as well. Malate dehy-drogenase, (A), and α-ketoglutarate dehydrogenase, (C), are citric acid cycle enzymes. Phosphofructokinase-1, (D), is a glycolytic enzyme. Other enzymes used in glycolysis, the citric acid cycle, or gluconeogenesis, such as phosphofruc-tokinase-1, would be expected to maintain normal activity after an overnight fast, using glucose derived from glycogen or gluconeogenesis, rather than orally ingested glucose

A man is given antibiotics to treat a urinary tract infection and develops an episode of red blood cell lysis. Further studies show weakness of the plasma membrane and Heinz bodies (collections of oxidized hemoglobin). Which of the following enzymes is most likely defective in this patient? A. Fructose-1,6-bisphosphatase B. Glucose-6-phosphate dehydrogenase C. Hexokinase D. Pyruvate kinase

B Based on the question stem, we can infer that the anti-biotics must have been an oxidative stress on the patient (antibiotics, antimalarial medications, infections, certain foods like fava beans, and other common exposures can induce an oxidative stress). The pentose phosphate pathway is responsible for generating NADPH, which is used to reduce glutathione, one of the natural antioxidants pres-ent in the body. In individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency, NADPH cannot be produced at sufficient levels, and oxidative stresses lead to cell membrane and protein (hemoglobin) damage. Note that you do not need to actually know the disease to answer this question; merely knowing that the enzyme must be from the pentose phosphate pathway, which is involved in mitigating oxidative stress, is sufficient.

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

B Chylomicrons and VLDL are very similar. Both contain apolipoproteins and primarily transport triacylglycerols, eliminating (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 VLDL transport newly synthesized triacylglycerols and originate in the liver

Which complex does NOT contribute to the proton-motive force? A. Complex I B. Complex II C. Complex III D. Complex IV

B Complex II is the only complex of the ETC that does not contribute to the proton gradient. Complexes I and III each add four protons to the gradient; Complex IV adds two protons to the gradient.

Which of the following enzymes is NOT used for lipid digestion in the digestive tract? A. Pancreatic lipase B. Hormone-sensitive lipase C. Cholesterol esterase D. Colipase

B 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.

The ability to exist in both an oxidized and a reduced state is characteristic of: A. adenosine triphosphate (ATP). B. electron carriers. C. regulatory enzymes. D. peptide hormones.

B In order to transport electrons, electron carriers like flavo-proteins must be able to exist in a stable oxidized state and a stable reduced form. ATP can be dephosphorylated but is generally not oxidized or reduced. Regulatory enzymes may also be phosphorylated or dephosphorylated but are not generally oxidized or reduced.

Which of the following is/are function(s) of NADPH in the cell? I. Antimicrobial resistance via bacterial destruction by bleach within lysosomes. II. Involvement in the production of the precursors to steroid hormones. III. Functional carriage of energy across organelle membranes for use within the mitochondria A. I only B. I and II only C. II and III only D. I, II, and III

B NADPH has three primary functions: involvement in biosynthesis of lipids and cholesterol (the precursor to steroid hormones), production of bactericidal bleach in the lysosomes of certain white blood cells, and maintenance of a supply of reduced glutathione for protection against free radical damage. Energy carriage is an important function of NADH, not NADPH.

Which of the following is an ethical concern of gene sequencing? A. Gene sequencing is invasive, thus the potential health risks must be thoroughly explained. B. Gene sequencing impacts relatives, thus privacy concerns may be raised. C. Gene sequencing is very inaccurate, which increases anxiety related to findings. D. Gene sequencing can provide false-negative results, giving a false sense of security.

B One of the primary ethical concerns related to gene sequencing is the issue of consent and privacy. Because genetic screening provides information on direct relatives, there are potential violations of privacy in communicating this information to family members who may be at risk. There are not significant physical risks, eliminating (A), and gene sequencing is fairly accurate, eliminating (C) and (D

Which of the following is NOT a function of the cell membrane? A. Cytoskeletal attachment B. Protein synthesis C. Transport regulation D. Second messenger reservoir

B Ribosomes are the site of protein synthesis within a cell and are not coupled to the cell membrane. The cell membrane functions as a site for cytoskeletal attachment, (A), through proteins and lipid rafts. Transport regulation, (C), is accomplished through channels, transporters, and selective permeability, while the phospholipids act as a reagent for second messenger formation, (D).

What energy state was described in the introduction to this chapter? A. Absorptive B. Postabsorptive C. Starvation D. Vegetative

B Skipping a single meal is not a prolonged fast. However, the increase in hormones that promote gluconeogenesis and glycogenolysis indicates that the absorptive phase has ended.

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

B The brain uses aerobic metabolism of glucose exclu-sively 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 enzyme converts GDP to GTP? A. Nucleosidediphosphate phosphatase B. Nucleosidediphosphate kinase C. Isocitrate dehydrogenase D. Pyruvate dehydrogenase

B The conversion of GDP to GTP is a phosphorylation reac-tion, 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.

How does the inner mitochondrial membrane differ from the outer mitochondrial membrane? A. The inner mitochondrial membrane is more permeable and lacks cholesterol. B. The inner mitochondrial membrane is less permeable and lacks cholesterol. C. The inner mitochondrial membrane is more permeable and has cholesterol. D. The inner mitochondrial membrane is less permeable and has cholesterol.

B The outer mitochondrial membrane is very permeable while the inner membrane is highly impermeable. The inner mitochondrial membrane is unique within the cell because it lacks cholesterol

A respiratory quotient approaching 0.7 indicates metabolism primarily of which macromolecule? A. Carbohydrates B. Lipids C. Nucleic acids D. Amino acids

B The respiratory quotient (RQ) gives an indication of the primary fuel being utilized. An RQ around 0.7 indicates lipid metabolism, 0.8-0.9 indicates amino acid metabo-lism, (D), and 1.0 indicates carbohydrate metabolism, (A). Nucleic acids do not contribute significantly to the respira-tory quotient.

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

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

Where does β-oxidation of fatty acids occur within the cell? A. Cytosol B. Mitochondria C. Smooth endoplasmic reticulum D. Plasma membrane

B β-Oxidation occurs within the mitochondria, along with the electron transport chain. In contrast, fatty acid synthe-sis occurs in the cytosol, (A). Fatty acyl carriers like the carnitine shuttle allow entry into the mitochondrion for breakdown.

Aconitase

isomerizes citrate to isocitrate.

Change in Water Level Due to Osmotic Pressure

Because substances tend to flow, or diffuse, from higher to lower concentration (which results in an increase in entropy), water will diffuse from the compartment containing pure water into the compartment containing the water-solute mixture. This net flow will cause the water level in the compartment containing the solution to rise above the level in the com-partment containing pure water

Branching Enzyme

Branching enzyme is responsible for introducing α-1,6-linked branches into the granule as it grows • Hydrolyzes one of the α-1,4 bonds to release a block of oligoglucose (a few glucose molecules bonded together in a chain), which is then moved and added in a slightly different location. • Forms an α-1,6 bond to create a branch.

The ΔG° of NADH reducing oxygen directly is significantly greater than any individual step along the electron transport chain. If this is the case, why does transferring electrons along the ETC generate more ATP than direct reduction of oxygen by NADH?

By splitting up electron transfer into several complexes, enough energy is released to facilitate the creation of a proton gradient at many locations, rather than just one. The greater the proton gradient is, the greater the ATP genera-tion will be. Direct reduction of oxygen by NADH would release a significant amount of energy to the environment, resulting in inefficient electron transport.

In which of the following reactions is the reactant oxidized? A. FAD → FADH2 B. NAD+ → NADH C. NADPH → NADP+ D. ADP → ATP

C To answer this question, we must remember that reduction is a gain of electrons, while oxidation is a loss of electrons. In the case of the energy-storing molecules of cellular respiration, the high-potential electrons generally come from hydride ions (H-). Because the question is asking us to determine in which reaction the reactant gets oxidized, our task is to select the equation in which the reactant loses hydride ions. From the given choices, the only one that matches our prediction is (C). Another way to look at this question is to notice that NADP+ has a +1 charge, which represents an increase from the zero charge of NADPH, implying than an electron was lost in the conversion from NADPH to NADP+.

2,4-Dienoyl-CoA reductase is used in the oxidation of: A. saturated fatty acids. B. monounsaturated fatty acids. C. polyunsaturated fatty acids. D. cholesterol.

C In order for the enzymes of fatty acid oxidation to operate, there can be, at most, one double bond in the area of enzyme activity, and it must be oriented between carbons 2 and 3. In order to accomplish this in monounsaturated fatty acids, an isomerase is employed. When there are multiple double bonds that fall within the enzymatic binding site, both an isomerase and 2,4-dienoyl-CoA reductase are required for the oxidative enzymes to act on the fatty acid. For this question, simply recognizing that dienoyl refers to having multiple double bonds is sufficient to arrive at the answer

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.

C 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

In the genetic code of human nuclear DNA, one of the codons specifying the amino acid tyrosine is UAC. If one nucleotide is changed and the codon is mutated to UAG, what type of mutation will occur? A. Silent mutation B. Missense mutation C. Nonsense mutation D. Frameshift mutation

C .UAG is one of the three known stop codons, so changing tyrosine to a stop codon must be a nonsense (or truncation) mutation

Which of the following statements about terpenes is FALSE? A. Terpenes are strongly scented molecules that sometimes serve protective functions. B. Terpenes are steroid precursors. C. A triterpene is made of 3 isoprene moieties, and therefore has 15 carbons. D. Terpenes are made by plants and insects.

C A triterpene is made of six isoprene moieties (remember, one terpene unit contains two isoprene units), and there-fore has a 30-carbon backbone.

Aldonic acids are compounds that: A. can be oxidized, and therefore act as reducing agents. HO HO HO HO A. CH2OH HO C. have been oxidized, and have acted as reducing agents. D. have been oxidized, and have acted as oxidizing agents.

C Aldonic acids form after the aldehyde group on a reducing sugar reduces another compound, becoming oxidized in the process.

Which of the following biomolecules is LEAST likely to contain an aromatic ring? A. Proteins B. Purines C. Carbohydrates D. Pyrimidines

C Aromatic rings must contain conjugated π electrons, which require alternating single and multiple bonds, or lone pairs. In carbohydrate ring structures, only single bonds are present, thus preventing aromaticity. Nucleic acids contain aromatic heterocycles, while proteins will generally contain at least one aromatic amino acid (tryptophan, phenylala-nine, or tyrosine).

Which of the following enzymes is NOT involved in DNA replication? A. Primase B. DNA ligase C. RNA polymerase I D. Telomerase

C During DNA replication, the strands are separated by DNA helicase. At the replication fork, primase, (A), creates a primer for the initiation of replication, which is followed by DNA polymerase. On the lagging strand, Okazaki frag-ments form and are joined by DNA ligase, (B). After the chromosome has been processed, the ends, called telo-meres, are replicated with the assistance of the enzyme telo-merase, (D). RNA polymerase I is located in the nucleolus and synthesizes rRNA

For a compound to be aromatic, all of the following must be true EXCEPT: A. the molecule is cyclic. B. the molecule contains 4n + 2 π electrons. C. the molecule contains alternating single and double bonds. D. the molecule is planar.

C For a compound to be aromatic, it must be cyclic, planar, conjugated, and contain 4n + 2 π electrons, where n is any integer. Conjugation requires that every atom in the ring have at least one unhybridized p-orbital. While most examples of aromatic compounds have alternating single and double bonds, compounds can be aromatic if they con-tain triple bonds as well; this would still permit at least one unhybridized p-orbital.

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

C 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 reaction below is an example of one step in: A. aldehyde formation. B. hemiketal formation. C. mutarotation. D. glycosidic bond cleavage

C In solution, the hemiacetal ring of glucose will break open spontaneously and then re-form. When the ring is broken, bond rotation occurs between C-1 and C-2 to produce either the α-or the β-anomer. The reaction given in this question depicts the mutarotation of glucose. (A) is incor-rect because the reactant is an aldehyde, not the product. (B) is incorrect because a hemiketal has an -OH group, an -OR group, and two -R groups. In addition, hemike-tals are formed from ketones, and our starting reactant is an aldehyde. Finally, (D) is incorrect because there is no glycosidic bond in the starting reactant.

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

C 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 con-verted to another -OR group.

Which of the following statements about saturation is FALSE? A. It can describe the number of double or triple bonds in a fatty acid tail. B. It determines at least one of the properties of membranes. C. More saturated fatty acids make for a MORE fluid solution. D. Fully saturated fatty acids have only single bonds.

C More saturated fatty acids make for a less fluid solution. This is because they can pack more tightly and form more noncovalent bonds, resulting in more energy being needed to disrupt the overall structure.

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.

C One common DNA mutation is the transition from cyto-sine 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.

Which of the following is true of amphipathic molecules? A. They form protective spheres in any solvent, with hydrophobic molecules interior and hydrophilic molecules exterior. B. They have two fatty acid chains and a polar head group. C. They are important to the formation of the phospholipid bilayer and soap bubbles. D. They have a glycerol base.

C Phospholipids are amphipathic, as are fatty acid salts. Although amphipathic molecules take spherical forms with hydrophobic molecules interior in aqueous solution, as in (A), the opposite would be true in a nonpolar sol-vent. (B) describes phospholipids and sphingolipids, and (D) describes triacylglycerols and phospholipids; both groups do not include fatty acid salts.

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

C 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 mov-ing 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 downward while the -OH group on C-3 should point upward; (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. affect gene transcription by binding directly to DNA. A. I only B. III only C. I and II only D. I and III only

C 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 as part of the hormone-receptor complex, but the hormone itself does not.

How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis? A. Isoelectric focusing uses a gel with much larger pore sizes to allow for complete migration. B. Isoelectric focusing uses a gel with SDS added to encourage a uniform negative charge. C. Isoelectric focusing uses a gel with a pH gradient that encourages a variable charge. D. The gel is unchanged in isoelectric focusing; the protein mixture is treated before loading.

C The gel in isoelectric focusing uses a pH gradient. When a protein is in a region with a pH above its pI, it is nega-tively charged and moves toward the anode. When it is in a pH region below its pI, it is positively charged and moves toward the cathode. When the pH equals the pI, the migra-tion of the protein is halted

Which of the following proteins is most likely to be found extracellularly? A. Tubulin B. Myosin C. Collagen D. Actin

C The most prevalent extracellular proteins are keratin, elastin, and collagen. Tubulin and actin are the primary cytoskeletal proteins, while myosin is a motor protein.

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

C 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)

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

C 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").

A researcher treats a solution containing animal cells with ouabain, a poisonous substance that interferes with the sodium-potassium ATPase embedded in the cell membrane, and the cell lyses as a result. Which of the following statements best describes ouabain's effects? A. Treatment with ouabain results in high levels of extracellular calcium. B. Treatment with ouabain results in high levels of extracellular potassium and sodium. C. Treatment with ouabain increases intracellular concentrations of sodium. D. Treatment with ouabain decreases intracellular concentrations of sodium.

C This question requires an understanding of osmosis and the action of the sodium-potassium pump. When a cell is placed in a hypertonic solution (a solution having a higher solute concentration than the cell), fluid will diffuse out of the cell and result in cell shrinkage. When a cell is placed in hypotonic solution (a solution having a lower solute con-centration than the cell), fluid will diffuse from the solution into the cell, causing the cell to expand and possibly lyse. The sodium-potassium pump moves three sodium ions out of the cell for every two potassium ions it lets into the cell. Therefore, inhibition of the sodium-potassium pump by ouabain will cause a net increase in the sodium concentra-tion inside the cell and water will diffuse in, causing the cell to swell and then lyse.

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.

C 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 (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.

Which protein properties allow UV spectroscopy to be used as a method of determining concentration? A. Proteins have partially planar characteristics in peptide bonds. B. Globular proteins cause scattering of light. C. Proteins contain aromatic groups in certain amino acids. D. All organic macromolecules can be assessed with UV spectroscopy.

C UV spectroscopy is best used with conjugated systems of double bonds. While the double bond in the peptide bond does display resonance, this is not adequate for UV absorption. However, aromatic systems are conjugated, and phenylalanine, tyrosine, and tryptophan all contain aromatic ring structures.

Which of the following is correct about fat-soluble vitamins? I. Vitamin E is important for calcium regulation. II. Vitamin D protects against cancer because it is a biological antioxidant. III. Vitamin K is necessary for the posttranslational introduction of calcium-binding sites. IV. Vitamin A is metabolized to retinal, which is important for sight. A. III only B. I and II only C. III and IV only D. II, III, and IV only

C Vitamin A is metabolized to retinal, which is important for sight. Vitamin D is metabolized to calcitriol, which is important for calcium regulation. Vitamin E is made up of tocopherols, which are biological antioxidants. Vitamin K is necessary for the introduction of calcium binding sites, such as during the posttranslational modification of prothrombin.

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

C We are asked to identify the type of transport that would allow a large, polar molecule to cross the membrane with-out any energy expenditure. This scenario describes facili-tated 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 of the following RNA molecules or proteins is NOT found in the spliceosome during intron excision? A. snRNA B. hnRNA C. shRNA D. snRNPs

C shRNA (short hairpin RNA) is a useful biotechnology tool used in RNA interference. It is not, however, produced in the nucleus for use in the spliceosome. It targets mRNA to be degraded in the cytoplasm; it is not utilized in splicing of the hnRNA (heterogeneous nuclear RNA). snRNA (small nuclear RNA) and snRNPs (small nuclear ribonucleopro-teins), however, do bind to the hnRNA to induce splicing.

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

C Citrate is produced by citrate synthase from acetyl-CoA and oxaloacetate. This reaction takes place in the mito-chondria. 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 cata-lyzes the rate-limiting step of glycolysis

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

C 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 cyto-plasm 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 mitochon-drial membrane. Once inside, the fatty acid is transferred to a mitochondrial CoA-SH, re-forming fatty acyl-CoA. Through fatty acid oxidation, this fatty acyl-CoA can become acetyl-CoA, which enters the citric acid cycle

Adding heat to a closed biological system will do all of the following EXCEPT: A. increase the internal energy of the system. B. increase the average of the vibrational, rotational, and translational energies. C. cause the system to do work to maintain a fixed internal energy. D. increase the enthalpy of the system.

C 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, thus (C) is correct

Which of the following processes has the following net reaction? 2 acetyl-CoA + 6 NAD+ + 2 FAD + 2 GDP + 2 Pi + 6 H2O → 4 CO2 + 6 NADH + 2 FADH2 + 2 GTP + 6 H+ + 2 CoA-SH A. Pyruvate decarboxylation B. Fermentation C. Tricarboxylic acid cycle D. Electron transport chain

C It is not necessary to have all the net reactions memorized for each metabolic process to answer this question; all we need is to identify a few key reactants and products. In this case, we start with acetyl-CoA and end with CoA-SH. We also notice that in this reaction, NAD+and FAD are reduced to NADH and FADH2, and that CO2is formed. The only metabolic process in which all of the above reactions would occur is the citric acid cycle, also called the tricar-boxylic acid (TCA) or Krebs cycle.

Which of the following is NOT a cell-cell junction in animals? A. Desmosomes B. Gap junctions C. Plasmodesmata D. Tight junctions

C Plasmodesmata are cell-cell junctions that are found in plants, not animals. Gap junctions, tight junctions, des-mosomes, and hemidesmosomes are all found in animals, particularly in epithelia.

Which of the following statements is true about the hydrolysis of ATP? A. The free energy of ATP hydrolysis is independent of pH. B. One mole of creatine phosphate can phosphorylate two moles of ADP. C. The free energy of hydrolysis of ATP is nearly the same as for ADP. D. ATP yields cyclic AMP after two hydrolysis reactions.

C The hydrolysis of ATP is energetically favorable because there are repulsive negative charges that are relieved when hydrolyzed, and the new compounds are stabilized by resonance. This is true of both ATP and ADP. Some of the other answer choices are tempting, though. In (A), ATP hydrolysis relies on pH because a protonated ATP molecule contains less negative charge and therefore experiences less repulsive force. For (B), the energy released by one mole of creatine phosphate upon hydrolysis is not sufficient to phosphorylate two moles of ADP according to Table 12.1; creatine phosphate donates one phosphate group to a molecule of ADP, so one mole of creatine phosphate will phosphorylate one mole of ADP. For (D), the removal of two phosphate groups from ATP yields AMP, not cyclic AMP.

Which of the following statements is FALSE? A. Growth hormone participates in glucose counterregulation. 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.

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

Which of the following is LEAST likely to be the resting membrane potential of a cell? A. -70 mV B. -55 mV C. 0 mV D. +35 mV

C Cell membranes are most likely to have a resting membrane potential that is nonzero because the resting membrane potential creates a state that is capable of responding to stimuli. Signaling molecules and channels would not be as useful with a membrane potential of zero. The values given in the answer choices correspond to different stages of the action potential, but the key information is that a resting potential of 0 mV does not maintain gradients for later activity

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

C 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

Which of the following is true regarding ketolysis? A. Ketolysis occurs only in the brain. B. Ketolysis occurs in the liver. C. Ketolysis generates acetyl-CoA. D. Ketolysis increases glucose metabolism.

C Ketolysis is the breakdown of ketone bodies to acetyl-CoA for energy. This process occurs in the brain and muscle tissues, but cannot occur in the liver, which lacks an enzyme necessary for ketone body breakdown. Ketolysis is not associated with an increase in glucose metabolism because it most often occurs under conditions of starvation.

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

C Lyases are responsible for the breakdown of a single mol-ecule into two molecules without the addition of water or the transfer of electrons. Lyases often form cyclic com-pounds or double bonds in the products to accommodate this.

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 oxi-dation in the citric acid cycle. C. carboxylated to oxaloacetate for entry into gluco-neogenesis. D. reduced to lactate in the process of fermentation.

C Pyruvate is converted primarily into three main intermedi-ates: acetyl-CoA, (B), for the citric acid cycle (via pyruvate dehydrogenase complex); lactate, (D), during fermenta-tion (via lactate dehydrogenase); or oxaloacetate, (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 oxalo-acetate for gluconeogenesis. Acetyl-CoA also stimulates pyruvate carboxylase directly.

With prolonged fasting, the brain can turn to which alternative fuel for energy? A. Fructose B. Lactate C. Ketone bodies D. Fatty acids

C The brain is almost exclusively dependent on glucose for energy; however, in a prolonged fast, ketone bodies can be used for up to 2/ 3 of the brain's energy requirement.

Which of the following best explains why cytosolic NADH can yield potentially less ATP than mitochondrial NADH? A. Cytosolic NADH always loses energy when trans-ferring electrons. B. Once NADH enters the matrix from the cytosol, it becomes FADH2. C. Electron transfer from cytosol to matrix can take more than one pathway. D. There is an energy cost for bringing cytosolic NADH into the matrix.

C The wording of these answer choices is critical. The elec-trons from cytosolic NADH can enter the mitochondrion through one of two shuttle mechanisms: the glycerol 3-phosphate shuttle, which ultimately moves these elec-trons to mitochondrial FAD, and the malate-aspartate shuttle, which ultimately moves these electrons to mito-chondrial NAD+. If the electrons are transferred using the malate-aspartate shuttle, then no energy is lost, making (A) and (D) incorrect. NADH cannot enter the matrix directly, making (B) incorrect. It is the fact that electrons can use more than one pathway—one of which loses energy that could be used for ATP synthesis—that accounts for the potentially decreased yield of ATP from cytosolic NADH.

Structures of Adrenal Catecholamines

Catecholamines are secreted by the adrenal medulla and include epinephrine and norepinephrine, also known as adrenaline and noradrenaline.

What tissue is least able to change its fuel source in periods of prolonged starvation?

Cells that rely solely on anaerobic respiration are the least adaptable to different energy sources. Therefore, red blood cells are the least flexible during periods of prolonged starvation and stay reliant on glucose.

Lipoprotein Structure figure

While free fatty acids are transported through the blood in association with albumin, a carrier protein, triacylglycerol and cholesterol are transported in the blood as lipoproteins: aggregates of apolipoproteins and lipids

Which of the following is digestible by humans and is made up of only one type of monosaccharide? A. Lactose B. Sucrose C. Maltose D. Cellobiose

While maltose and cellobiose both have the same glucose subunits, only maltose is digestible by humans because the β-glycosidic linkages in cellobiose cannot be cleaved in the human body.

How does cholesterol play a role in the fluidity and stability of the plasma membrane?

Cholesterol moderates membrane fluidity by interfering with the crystal structure of the cell membrane and occupying space between phospholipid molecules at low temperatures, and by restricting excessive movement of phospholipids at high temperatures. Cholesterol also provides stability by cross-linking adjacent phospholipids through interactions at the polar head group and hydrophobic interactions at the nearby fatty acid tail.

Cloning Recombinant DNA

Cloning allows production of recombinant proteins, or identification and characterization of DNA by increasing its volume and purity.

competitive inhibition

Competitive inhibition is a process by which a chemical substance has a shape that fits the active site of an enzyme and competes with the substrate, effectively inhibiting the enzyme. can be overcomes by adding substrate so that the substrate to- inhibitor is higher doesn't alter the value of Vmax because if enough substrate is added it will outcompete the inhibitor and be able to run the reaction at maximum velocity. it increase Km because the substrate concentration has to be higher to reach half the maximum velocity in the present of the inhibitor.

What is the purpose of all the reactions that collectively make up the citric acid cycle?

Complete oxidation of carbons in intermediates to CO2 so that reduction reactions can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the electron transport chain.

Elastin

Component of extracellular matrix of connective tissue - stretches and recoils to restore original shape of tissue.

What factors would cause an activity assay to display lower activity than expected after concentration determination?

Contamination of the sample with detergent or SDS could yield an artificially increased protein level, leading to lower activity than expected (because the protein concentration was calculated as higher than its actual value). Alternatively, the enzyme could have been denatured during isolation and analysis.

CUT the PYE

Cytosine, Uracil and Thymine are Pyramidines

How do cytoskeletal proteins differ from motor proteins?

Cytoskeletal proteins tend to be fibrous with repeating domains, while motor proteins tend to have ATPase activity and binding heads. Both types of protein function in cellular motility.

Malate-Aspartate Shuttle

Cytosolic oxaloacetate, which cannot pass through the inner mitochondrial membrane, is reduced to malate, which can. This is accomplished by cytosolic malate dehydrogenase. Accompanying this reduction is the oxidation of cytosolic NADH to NAD+. Once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH. Now that NADH is in the matrix, it can pass along its electrons to the ETC via Complex I and generate 2.5 ATP per molecule of NADH. Recycling the malate requires oxidation to oxaloacetate, which can be transaminated to form aspartate. Aspartate crosses into the cytosol, and can be reconverted to oxaloacetate to restart the cycle

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.

D 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. An enzyme with two subunits occupied must have a higher affinity for the sub-strate than the same enzyme with only one subunit occu-pied

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

D Mismatch repair mechanisms are active during S phase (proofreading) and G2 phase (MSH2 and MLH1), eliminat-ing (B) and (C). Nucleotide and base excision repair mech-anisms are most active during the G1 and G2 phases, also eliminating (A). These mechanisms exist during interphase because they are aimed at preventing propagation of the error into daughter cells during M phase (mitosis).

Which stage of protein synthesis does NOT require energy? A. Initiation B. Elongation C. Termination D. All stages of protein synthesis require energy.

D All three stages of protein synthesis (initiation, elongation, and termination) require large amounts of energy.

Which of the following is NOT a component of all trimeric G proteins? A. Gα B. Gβ C. Gγ D. Gi

D All trimeric G proteins have α, β, and γ subunits—(A), (B), and (C), respectively. Gs, Gi, and Gq are subtypes of the Gα subunit of the trimeric G protein and differ depending on the G protein-coupled receptor's function.

Which of the following statements regarding differences between DNA and RNA is FALSE? A. In cells, DNA is double-stranded, whereas RNA is single-stranded. B. DNA uses the nitrogenous base thymine; RNA uses uracil. C. The sugar in DNA is deoxyribose; the sugar in RNA is ribose. D. DNA strands replicate in a 5′ to 3′ direction, whereas RNA is synthesized in a 3′ to 5′ direction.

D Because we are looking for the false statement, we have to read each choice to eliminate those that are true or find one that is overtly false. Let's quickly review the main differences between DNA and RNA. In cells, DNA is double-stranded, with a deoxyribose sugar and the nitrog-enous bases A, T, C, and G. RNA, on the other hand, is usually single-stranded, with a ribose sugar and the bases A, U, C, and G. (D) is false because both DNA replication and RNA synthesis proceed in a 5′ to 3′ direction.

In the equation below, substrate C is an allosteric inhibitor to enzyme 1. Which of the following is another mechanism necessarily caused by substrate C? A (enzyme 1)-> B(Enzyme 2)-> C A. Competitive inhibition B. Irreversible inhibition C. Feedback enhancement D. Negative feedback

D By limiting the activity of enzyme 1, the rest of the pathway is slowed, which is the definition of negative feedback.

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

D 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 endonu-cleases. 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

Consider a biochemical reaction A → B, which is catalyzed by A-B dehydrogenase. Which of the following statements is true? A. The reaction will proceed until the enzyme con-centration decreases. B. The reaction will be most favorable at 0°C. C. A component of the enzyme is transferred from A to B. D. The free energy change (ΔG) of the catalyzed reaction is the same as for the uncatalyzed reaction.

D Enzymes catalyze reactions by lowering their activation energy, and are not changed or consumed during the course of the reaction. While the activation energy is lowered, the free energy of the reaction, ΔG, remains unchanged in the presence of an enzyme. A reaction will continue to occur in the presence or absence of an enzyme; it simply runs slower without the enzyme

All of the following are true of epimers EXCEPT: A. they differ in configuration about only one carbon. B. they usually have slightly different chemical and physical properties. C. they are diastereomers (with the exception of glyceraldehyde). D. they have equal but opposite optical activities.

D Epimers are monosaccharide diastereomers that differ in their configuration about only one carbon. As with all diastereo-mers, epimers have different chemical and physical proper-ties, and their optical activities have no relation to each other. Enantiomers have equal but opposite optical activities. There-fore, (D) is the only statement that does not apply to epimers.

Which of the following is NOT a difference between heterochromatin and euchromatin? A. Euchromatin has areas that can be transcribed, whereas heterochromatin is silent. B. Heterochromatin is tightly packed, whereas euchromatin is less dense. C. Heterochromatin stains darkly, whereas euchro-matin stains lightly. D. Heterochromatin is found in the nucleus, whereas euchromatin is in the cytoplasm.

D Euchromatin has a classic "beads on a string" appearance that stains lightly, while heterochromatin is tightly packed and stains darkly. Heterochromatin is primarily composed of inactive genes or untranslated regions, while euchroma-tin is able to be expressed. All chromatin is found in the nucleus, not the cytoplasm.

Which of the following is NOT involved in cell migration? A. Dynein B. Flagella C. Actin D. Centrioles

D From the given choices, all of them are involved in cell movement with the exception of (D). Centrioles are com-posed of microtubules, but are involved in mitosis, not cell migration

When glucose is in a straight-chain formation, it: A. is an aldoketose. B. is a pentose. C. has five chiral carbons. D. is one of a group of 16 stereoisomers.

D Glucose is an aldohexose, meaning that it has one aldehyde group and six carbons. Given this information, (A) and (B) can be eliminated. In aldose sugars, each nonterminal carbon is chiral. Therefore, glucose has four chiral centers, not five, as mentioned in (C). The number of stereoisomers possible for a chiral molecule is 2n, where n is the number of chiral carbons. Because glucose has four chiral centers, there are 24 = 16 possible stereoisomers.

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

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

Which of the following is NOT a type of glycolipid? A. Cerebroside B. Globoside C. Ganglioside D. Sphingomyelin

D Glycolipids contain sugar moieties connected to their back-bone. Sphingomyelin is not a glycolipid, but rather a phos-pholipid. This class can either have phosphatidylcholine or phosphatidylethanolamine as a head group and therefore contains a phosphodiester, not glycosidic, bond.

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.

D 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 den-sity 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.

Which of the following is most likely to be found bound to a protein in the body? A. Sodium B. Potassium C. Chloride D. Calcium

D Ions that are not readily accessible in the cytoplasm or extracellular space are likely to be bound to a bind-ing protein. Classically, calcium and magnesium are protein-bound. Without this background knowledge, the question can still be answered. Sodium, (A), and potassium, (B), must exist in their free states to participate in action potentials. Chloride, (C), is readily excreted by the kidney, which would not be true if it were protein-bound. Calcium must be sequestered in both the bloodstream and intracel-lularly because calcium is used for muscle contraction, exo-cytosis (of neurotransmitters and other signals), and many other cellular processes that must be tightly regulated

How does prokaryotic DNA differ from eukaryotic DNA? I. Prokaryotic DNA lacks nucleosomes. II. Eukaryotic DNA has telomeres. III. Prokaryotic DNA is replicated by a different DNA polymerase. IV. Eukaryotic DNA is circular when not restricted by centromeres. A. I only B. IV only C. II and III only D. I, II, and III only

D Prokaryotic DNA is circular and lacks histone proteins, and thus does not form nucleosomes. Both prokaryotic and eukaryotic DNA are replicated by DNA polymerases, although these polymerases differ in identity. Eukaryotic DNA is organized into chromatin, which can condense to form linear chromosomes; only prokaryotes have circular chromosomes. Only eukaryotic DNA has telomeres.

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.

D Prostaglandins are paracrine or autocrine signaling mol-ecules, 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 pos-sibly bruise. Luckily, however, your entire body won't swell as well.

Which process is expected to begin earliest in a prolonged fast? A. Ketone bodies are used by the brain. B. Glycogen storage is halted. C. Proteins are broken down. D. Enzyme phosphorylation and dephosphorylation.

D A prolonged fast is characterized by an increase in glucagon, which accomplishes its cellular activity by phosphory-lating and dephosphorylating metabolic enzymes. Glycogen storage, (B), is then halted, but this requires enzyme regulation by glucagon to occur. Later in the postabsorptive state, protein breakdown, (C), begins. Eventually, in starvation, ketone bodies, (A), are used by the brain for its main energy source.

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 concentra

D In most biochemical pathways, only a few enzymatic reac-tions 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 decar-boxylates 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, (A), should be high because ATP was just burned by the muscle. Acetyl-CoA, (B), is an inhibitor of PDH, causing a shift of pyruvate into the gluconeogenic pathway. A high NADH/ NAD+ ratio, (C), would imply that the cell is already ener-getically satisfied and not in need of energy, which would not be expected in intensely exercising muscle.

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.

D Membrane receptors must have both an extracellular and intracellular domain; therefore, they are considered trans-membrane proteins. In order to initiate a second messenger cascade, they typically display enzymatic activity, although some may act strictly as channels.

After a large, well-balanced meal, all of the following substances would be expected to be elevated EXCEPT: A. fatty acids. B. insulin. C. glucose. D. glucagon

D After a large meal, one would expect blood to contain high levels of nutrients, such as glucose, (C), and fatty acids, (A), as well as regulators telling the body to utilize and store this fuel, like insulin (B). Glucagon is a peptide hormone used to raise blood sugar levels by promoting, among other processes, glycogenolysis and gluconeogenesis. Glucagon should be elevated during a fast

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 irreversibly to provide energy

D Enzymes are not altered by the process of catalysis. A mole-cule that breaks intramolecular bonds to provide activation energy would not be able to be reused.

When insulin is released, it acts to increase the absorption of glucose into skeletal muscle predominantly through which of the following transporters? A. GLUT 1 B. GLUT 2 C. GLUT 3 D. GLUT 4

D GLUT is an abbreviation for glucose transporter and describes a family of sugar transporters with varying distributions and activities. GLUT 4 is found in adipose tissue and muscle, and mediates insulin-stimulated glucose uptake; in fact, it is the only insulin-responsive glucose transporter. Insulin acts via its receptor to translocate GLUT 4 to the plasma membrane. GLUT 4 in skeletal muscle is also stimulated by exercise through an insulin-independent pathway.

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

D 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= 61.5/z log [ion]outside/ [ion]inside . For calcium, z = +2 (Ca2+) and the ratio of [ion outside] to [ion inside] = 10^4. Plugging in, E= 61.5/+2 Log 10^4 = 61.5/+2 x4 =123mV

Which of the following amino acids will provide the most energy when degraded? A. Glycine B. Alanine C. Valine D. Isoleucine

D The energy contribution of an amino acid depends on its ability to be turned into glucose through gluconeogen-esis (glucogenic amino acids), ketone bodies (ketogenic amino acids), or both. All of the amino acids listed in the answer choices are glucogenic; isoleucine is also ketogenic. The energy acquired from an amino acid will also depend on the number of carbons it can donate to these energy-creating processes, which depends on the size of its side chain. Isoleucine has the largest side chain of the answer choices, and will thus contribute the most energy per molecule.

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

D 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 synthe-sized in the liver are transported as VLDL to adipose tissue for storage. Both the adipocytes, (A), and dietary intake, (B), constitute a minor source of triacylglycerols

Which of the following organs does NOT require a constant supply of glucose from the blood for energy during a fast? A. Red blood cells B. Brain C. Pancreas D. Liver

D The liver, like all cells, needs a constant supply of glucose; however, it is able to produce its own glucose through gluconeogenesis (cells in the kidney can also complete low levels of gluconeogenesis). The other cells listed here are absolutely dependent on a glucose source from the blood for energy, although they may also use other fuels in addi-tion to glucose. For example, the brain can utilize ketone bodies during lengthy periods of starvation; however, it still requires at least some glucose for proper function

A biopsy is done on a child with an enlarged liver and shows accumulation of glycogen granules with single glucose residues remaining at the branch points near the periphery of the granule. The most likely genetic defect is in the gene encoding: A. α-1,4 phosphorylase (glycogen phosphorylase). B. α-1,4:α-1,6 transferase (branching enzyme). C. α-1,4:α-1,4 transferase (part of debranching enzyme complex). D. α-1,6 glucosidase (part of debranching enzyme complex).

D The pattern described for this child's glycogen demonstrates appropriate production: there are long chains of glucose monomers, implying that glycogen synthase works. There are also branch points, implying that branching enzyme, (B) works. During glycogenolysis, it seems that the child is able to remove individual glucose monomers and process glycogen down to the branch point itself, which requires glycogen phosphorylase, (A), and α-1,4:α-1,4 transferase, (C). The metabolic problem here is removing the final glucose at the branch point, which is an α-1,6 (not α-1,4) link. This requires (D), α-1,6 glucosidase

Resting membrane potential depends on: I. the differential distribution of ions across the membrane. II. active transport processes. III. selective permeability of the phospholipid bilayer. A. I only B. I and III only C. II and III only D. I, II, and III

D The polarization of the membrane at rest is the result of an uneven distribution of ions between the inside and out-side of the cell. This difference is achieved through active pumping of ions (predominantly sodium and potassium) into and out of the cell and the selective permeability of the membrane, which allows only certain ions to cross

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

D While the transport and lipid binding functions of most lipoproteins are independent of the apolipoprotein compo-nent, the interaction of these lipoproteins with the environ-ment is controlled almost exclusively by apolipoproteins. Lipoproteins cannot exit or enter cells without apolipopro-teins, and are unable to transfer lipids without specialized apolipoproteins or cholesterol-specific enzymes.

RNA primers can later be removed by

DNA polymerase I (prokaryotes) or RNase H (eukaryotes), and filled in with DNA by DNA polymerase I (prokary-otes) or DNA polymerase δ (eukaryotes). DNA ligase can then fuse the DNA strands together to create one complete molecule.

Compare and contrast heterochromatin and euchromatin based on the following characteristics:

Density of chromatin packing-Heterochromatin Dense -Euchromatin Not dense (uncondensed) Appearance under light microscopy ----- Heterochromatin= dark -----Euchromatin = light Transcriptional activity- Heterochromatin = silent ----Euchromatin= active

During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?

Dideoxyribonucleotides lack the 3′ -OH group that is required for DNA strand elongation. Thus, once a dideoxyribonucleotide is added to a growing DNA molecule, no more nucleotides can be added because dideoxyribonucleotides have no 3′ -OH group with which to form a bond.

Absorption of Lipids

Digestion begins in the small intestine (duodenum) and is complete by the end of the small intestine. Digestion of lipids CANNOT begin prior to their reaching the small intestine where the encounter bile and lipase. Triglycerides are broken down to fatty acids, transported across them membrane, then reformed into triglycerides. Enter at the LACTEALS. In order for lipids to travel in blood and lymph, they must 1) bind to a carrier protein (albumin) or 2) be formed into a chylomicron or micelle.

During what stage is there the greatest decrease in the circulating concentration of insulin?

During the postabsorptive state, there is the greatest decrease in insulin levels. The concentrations of the counterregulatory hormones (glucagon, cortisol, epinephrine, norepinephrine, and growth hormone) begin to rise.

Base Pairing of an Aminoacyl-tRNA with a Codon in mRNA

During translation, the codon of the mRNA is recognized by a complementary anti-codon on a transfer RNA (tRNA) the anticodon sequence allows the tRNA to pair with the codon in the mRNA. Because base-pairing is involved, the orientation of this interaction will be antiparallel. For example, the aminoacyl tRNA Ile-tRNAIle has an anticodon sequence 5′—GAU—3′, allowing it to pair with the isoleucine codon 5′—AUC—3′,

Amino Acid Abbreviations

E6V indicate that the sixth amino acid (glutamic acid ,E) has been changed to valine know this by heart

Amino acid composition can be determined by simple hydrolysis, but amino acid sequencing requires sequential degradation, such as the

Edman degradation.

allosteric enzymes

Enzymes that experience changes in their conformation as a result of interactions at sites other than the active site called allosteric sites; conformational changes may increase or decrease enzyme activity alternate between active and inactive form molecules that bind to allosteric site are either allosteric inhibitor or allosteric activator, both cause conformational shift in the protein.

Explain the difference between esterification and glycoside formation

Esterification is the reaction by which a hydroxyl group reacts with either a carboxylic acid or a carboxylic acid derivative to form an ester. Glycoside formation refers to the reaction between an alcohol and a hemiacetal (or hemiketal) group on a sugar to yield an alkoxy group.

What are some examples of transient and covalent enzyme modifications

Examples of transient modifications include allosteric activation or inhibition. Examples of covalent modifications include phosphorylation and glycosylation.

True or False: Motor proteins are not enzymes.

False. An enzyme is a protein or RNA molecule with catalytic activity, which motor proteins do have. Motor function is generally considered nonenzymatic, but the ATPase functionality of motor proteins indicates that these molecules do have catalytic activity.

True or False: Bodily proteins will commonly be broken down to provide acetyl-CoA for lipid synthesis

False. Proteins are more valuable to the cell than lipids, thus they will not commonly be broken down for lipid synthesis.

True or False: All lipids enter the circulation through the lymphatic system.

False. Small free fatty acids enter the circulation directly.

. True or False: The Edman degradation proceeds from the carboxy (C-) terminus.

False. The Edman degradation proceeds from the amino (N-) terminus.

True or False: Body mass can be predicted by the leptin receptor phenotype and caloric intake alone.

False; energy expenditure, genetics, socioeconomic status, geography, and other hormones also play a role in body mass regulation.

Why are fatty acids used to create ketone bodies instead of creating glucose?

Fatty acid degradation results in large amounts of acetyl-CoA, which cannot enter the gluconeogenic pathway to produce glucose. Only odd-numbered fatty acids can act as a source of carbon for gluconeogenesis; even then, only the final malonyl-CoA molecule can be used. Energy is packaged into ketone bodies for consumption by the brain and muscles.

What other molecules can be used to make acetyl-CoA, and how does the body perform this conversion for each?

Fatty acids- Shuttle acyl group from cytosolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo β-oxidation Ketogenic amino acids- Transaminate to lose nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl-CoA Ketones- Reverse of ketone body formation Alcohol- Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol into acetyl-CoA

Why must pyruvate undergo fermentation for glycolysis to continue?

Fermentation must occur to regenerate NAD+, which is in limited supply in cells. Fermentation generates no ATP or energy carriers; it merely regenerates the coenzymes needed in glycolysis.

Describe the role of flippases and lipid rafts in biological membranes.

Flippases are responsible for the movement of phospholipids between the layers of the plasma membrane because it is otherwise energetically unfavorable. Lipid rafts are aggregates of specific lipids in the membrane that function as attachment points for other biomolecules and play roles in signaling.

Alternative Splicing of Eukaryotic hnRNA to Produce Different Proteins

For some genes in eukaryotic cells, however, the primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene. This process is known as alternative splicing, By utilizing alternative splicing, an organism can make many more different proteins from a limited number of genes also known to function in the regulation of gene expression, in addition to generating protein diversity.

Fructose Metabolism

Fructose is found in honey and fruit and as part of the disaccharide sucrose (com-mon table sugar). Sucrose is hydrolyzed by the duodenal brush-border enzyme sucrase, and the resulting monosaccharides, glucose and fructose, are absorbed into the hepatic portal vein. The liver phosphorylates fructose using fructokinase to trap it in the cell. The resulting fructose 1-phosphate is then cleaved into glyceraldehyde and DHAP by aldolase B. Smaller amounts are metabolized in renal proximal tubules

Which enzyme is responsible for trapping fructose in the cell? What enzyme in fructose metabolism results in a product that can feed directly into glycolysis, linking the two pathways?

Fructose is phosphorylated by fructokinase, trapping it in the cell (with a small contribution from hexokinase). Aldolase B produces dihydroxyacetone phosphate (DHAP) and glyceraldehyde (which can be phosphorylated to form glyceraldehyde 3-phosphate), which are glycolytic intermediates, thus linking the pathways.

Compare and contrast GLUT 2 and GLUT 4:

GLUT 2 - TISSUE- liver and pancreas Km- HIGH Saturated at normal glucose levels? No, cant be saturated under normal physiological conditions. Responsive to insulin? No (but serves as glucose sensor to cause release of insulin in pancreatic B-cells) GLUT 4- TISSUE- Adipose tissue, muscle Km- Low Saturated at normal glucose levels? Yes, saturated when glucose levels are only slightly above 5 mM Responsive to insulin? Yes

Insulin Regulation of Glucose Transport in Muscle and Adipose Cells

GLUT 4 is in adipose tissue and muscle and responds to the glucose concentration in peripheral blood. The rate of glucose transport in these two tissues is increased by insulin, which stimulates the movement of additional GLUT 4 transporters to the membrane by a mechanism involving exocytosis

How does insulin promote glucose entry into cells?

GLUT 4 is saturated when glucose levels are only slightly above 5 mM, so glucose entry can only be increased by increasing the number of transporters. Insulin promotes the fusion of vesicles containing preformed GLUT 4 with the cell membrane.

Which enzyme is responsible for trapping galactose in the cell? What enzyme in galactose metabolism results in a product that can feed directly into glycolysis, linking the two pathways?

Galactose is phosphorylated by galactokinase, trapping it in the cell. Galactose-1-phosphate uridyltransferase produces glucose 1-phosphate, a glycolytic intermediate, thus linking the pathways.

Contrast gap junctions and tight junctions.

Gap junctions allow for the intercellular transport of materials and do not prevent paracellular transport of materials. Tight junctions are not used for intercellular transport but do prevent paracellular transport. Gap junctions are in discontinuous bunches around the cell, while tight junctions form bands around the cell.

When creating a DNA library, what are some of the advantages of genomic libraries? What about cDNA libraries?

Genomic libraries include all of the DNA in an organism's genome, including noncoding regions. This may be useful for studying DNA in introns, cen-tromeres, or telomeres. cDNA libraries only include expressed genes from a given tissue, but can be used to express recombinant proteins or to perform gene therapy.

Metabolic Profile of the Postabsorptive (Fasting) State

Glucagon, cortisol, epinephrine, norepinephrine, and growth hormone oppose the actions of insulin. These hormones are sometimes termed counterregulatory hormones because of their effects on skeletal muscle, adipose tissue, and the liver, which are opposite to the actions of insulin. In the liver, glycogen degradation and the release of glucose into the blood are stimulated

Under what physiological conditions should the body carry out gluconeogenesis?

Gluconeogenesis occurs when an individual has been fasting for >12 hours. To carry out gluconeogenesis, hepatic (and renal) cells must have enough energy to drive the process of glucose creation, which requires sufficient fat stores to undergo β-oxidation.

Cyclic Sugar Formation via Intramolecular Nucleophilic Addition

Glucose forms a six-membered ring with two anomeric forms: α (left) and β (right).

Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity from enzymes that cleave side branches? Why?

Glycogen has a higher rate of enzymatic branch cleavage because it contains significantly more branching than amylopectin

What is the structure of glycogen? What types of glycosidic links exist in a glycogen granule?

Glycogen is made up of a core protein of glycogenin with linear chains of glu-cose emanating out from the center, connected by α-1,4 glycosidic links. Some of these chains are branched, which requires α-1,6 glycosidic links.

What are the two main enzymes of glycogenolysis, and what does each accomplish?

Glycogen phosphorylase removes a glucose molecule from glycogen using a phosphate, breaking the α-1,4 link and creating glucose 1-phosphate. Deb-ranching enzyme moves all of the glucose from a branch to a longer glycogen chain by breaking an α-1,4 link and forming a new α-1,4 link to the longer chain. The branchpoint is left behind; this is removed by breaking the α-1,6 link to form a free molecule of glucose.

What are the two main enzymes of glycogenesis, and what does each accomplish?

Glycogen synthase attaches the glucose molecule from UDP-glucose to the growing glycogen chain, forming an α-1,4 link in the process. Branching enzyme creates a branch by breaking an α-1,4 link in the growing chain and moving a block of oligoglucose to another location in the glycogen granule. The oligoglucose is then attached with an α-1,6 link.

G proteins types

Gs stimulates adenylate cyclase, which increases levels of cAMP in the cell. • Gi inhibits adenylate cyclase, which decreases levels of cAMP in the cell. • Gq activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2. PIP2 is then cleaved into DAG and IP3; IP3 can open calcium channels in the endoplasmic reticulum, increasing calcium levels in the cell

the key enzyme in cholesterol biosynthesis is

HMG-CoA reductase

Under what conditions is HMG-CoA reductase most active? In what cellular region does it exist?

HMG-CoA reductase is most active in the absence of cholesterol and when stimulated by insulin. Cholesterol reduces the activity of HMG-CoA reductase, which is located in the smooth endoplasmic reticulum.

DNA strands can be pulled apart (denatured) and brought back together (reannealed)

Heat, alkaline pH, and chemicals like formaldehyde and urea can cause denaturation of DNA; removal of these conditions may result in reannealing of the strands.

For each of the enzymes listed below, list the function of the enzyme and if it is found in prokaryotes, eukaryotes, or both.

Helicase - both - Unwinds DNA double helix Single-stranded DNA-binding protein - both - Prevents reannealing of DNA double helix during replication Primase -both - Places ~10-nucleotide RNA primer to begin DNA replication DNA polymerase III- prokaryotes - Adds nucleotides to growing daughter strand DNA polymerase α - eukaryotes - Adds nucleotides to growing daughter strand DNA polymerase I - prokaryotes - Fills in gaps left behind after RNA primer excision RNase H- eukaryotes - Excises RNA primer DNA ligase - both - Joins DNA strands (especially between Okazaki fragments) DNA topoisomerases- both - Reduces torsional strain from positive supercoils by introduc-ing nicks in DNA strand

Glycosidic Linkage Formation

Hemiacetal (or hemiketal) sugars react with alcohols under acidic conditions to form acetals (or ketals).

Euchromatin and Heterochromatin in an Interphase Nucleus

Heterochromatin is dark, dense, and silent . Euchromatin is light, uncondensed, and expressed . A small percentage of the chromatin remains compacted during interphase and is referred to as heterochromatin the dispersed chromatin is called euchromatin, which appears light under light microscopy Heterochromatin often consists of DNA with highly repetitive sequences.

What property of telomeres and centromeres allows them to stay tightly raveled, even when the rest of DNA is uncondensed?

High GC-content increases hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres.

Fisher Projection

Horizontal lines = wedges/ out of the page vertical lines = dashed/ into the page

Irreversible steps of glycolysis:

How Glycolysis Pushes Forward the Process: Kinases . • Hexokinase • Glucokinase • PFK-1 • Pyruvate Kinase

Succinate Formation

Hydrolysis of the thioester bond on succinyl-CoA yields succinate and CoA-SH, and is coupled to the phosphorylation of GDP to GTP. This reaction is catalyzed by succinyl-CoA synthetase Synthetases, unlike synthases, create new covalent bonds with energy inpu phosphorylation of GDP to GTP is driven by the energy released by thioester hydrolysis. Once GTP is formed, an enzyme called nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, thus producing ATP this is the only time in the entire citric acid cycle that ATP is produced directly; ATP production occurs predominantly within the electron transport chain.

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 protein is present in sufficiently high quantities relative to the substrate, nearly all substrate will be bound despite a low affinity.

Galactose Metabolism

lactose is broken down into galactose and glucose by lactase galactose is phosphorylated by *galactokinase* to trap it inside the tissues/ cells galactose 1 phosphate is converted into glucose 1 phosphate by *galactose 1 phosphate uridyltransferase*

G protein-coupled receptors (GPCRs)

large family of integral membrane proteins involved in signal transduction; characterized by their 7 membrane-spanning alpha-helices; utilize heterotrimeric G protein to transmit signals to effector cells G proteins have intracellular link to guanine nucleotides (GDP and GTP). the binding of a ligand increases the affinity of the receptor for the G protein. the binding of the G protein represents a switch to the active state and affects the intracellular signaling pathway.

What would happen if an amphipathic molecule were placed in a nonpolar solvent rather than an aqueous solution?

In a nonpolar solvent, we would see the opposite of what happens in a polar solvent like water: the hydrophilic, polar part of the molecules would be seques-tered inside, while the nonpolar, hydrophobic part of the molecules would be found on the exterior and exposed to the solvent.

Chargaff's rules:

In double-stranded DNA, purines = pyrimidines: • %A = %T • %G = %C If a sample of DNA has 10% G, what is the % of T? 10% G = 10% C, thus %G + %C = 20% %A + %T = 80%, thus %T = 40% .

Reaction of 2,4-Dienoyl-CoA Reductase

In polyunsaturated fatty acids, a further reduction is required using 2,4-dienoyl-CoA reductase to convert two conjugated double bonds to just one double bond at the 3,4 position, where it will then undergo the same rearrangement as monounsaturated fatty acids (as shown in Figure 11.11) to form a trans 2,3 double bond.

What is wobble, and what role does it serve?

Wobble refers to the fact that the third base in a codon often plays no role in determining which amino acid is translated from that codon. For example, any codon starting with "CC" codes for proline, regardless of which base is in the third (wobble) position. This is protective because mutations in the wobble position will not have any effect on the protein translated from that gene.

Reaction of Enoyl-CoA Isomerase

In unsaturated fatty acids, two additional enzymes are necessary because double bonds can disturb the stereochemistry needed for oxidative enzymes to act on the fatty acid. To function, these enzymes can have at most one double bond in their active site; this bond must be located between carbons 2 and 3. Enoyl-CoA isomerase, , rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons. In monounsaturated fatty acids this single step permits β-oxidation to proceed.

Describe the primary metabolic function of each of the following hormones: • Insulin: • Glucagon: • Cortisol: • Catecholamines: • Thyroid hormones (T3 / T4):

Insulin promotes glucose uptake by adipose tissue and muscle, glucose utilization in muscle cells, and macromolecule storage (glycogenesis, lipogenesis). Glucagon increases blood glucose levels by promoting glycogenolysis, glucone-ogenesis, lipolysis, and ketogenesis. Cortisol increases lipolysis and amino acid mobilization, while decreasing glucose uptake in certain tissues and enhancing the activity of other counterregulatory hormones. Catecholamines increase glycogenolysis in muscle and liver and lipolysis in adipose tissue. Thyroid hormones increase basic metabolic rate and potentiate the activity of other hormones.

What is irreversible inhibition?

Irreversible inhibition refers to the prolonged or permanent inactivation of an enzyme, such that it cannot be easily renatured to gain function.

primary structure of proteins

Is linear sequence of amino acids in polypeptide chain. Written from the amino terminus (N-terminus) to the carboxyl terminus (C-terminus). it is stabilized by the formation of covalent peptide bonds between adjacent amino acids. alone encodes all the information needed for folding at all of the higher structure levels can be determined using sequencing

What enzyme catalyzes the rate-limiting step of the citric acid cycle?

Isocitrate dehydrogenase

α-Ketoglutarate and CO2 Formation

Isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase. Then oxalosuccinate is decarboxylated to produce α-ketoglutarate and CO2 isocitrate dehydrogenase is the rate-limiting enzyme of the citric acid cycle. The first of the two carbons from the cycle is lost here. This is also the first NADH produced from intermediates in the cycle.

What separation methods can be used to isolate a protein on the basis of isoelectric point?

Isoelectric focusing and ion-exchange chromatography both separate proteins based on charge; the charge of a protein in any given environment is determined by its isoelectric point (pI).

From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced? What is the purpose of this process?

It makes sense for carbohydrates to become oxidized while reducing other groups. This is the case because aerobic metabolism requires reduced forms of electron carriers to facilitate processes such as oxidative phosphorylation. Because carbohydrates are a primary energy source, they are oxidized.

Metabolic Profile of the Postprandial (Absorptive) State

Just after eating, blood glucose levels rise and stimulate the release of insulin. The three major target tissues for insulin are the liver, muscle, and adipose tissue

What conditions and tissues favor ketogenesis? Ketolysis?

Ketogenesis is favored by a prolonged fast and occurs in the liver. It is stim-ulated by increasing concentrations of acetyl-CoA. Ketolysis is also favored during a prolonged fast, but is stimulated by a low-energy state in muscle and brain tissues and does not occur in the liver

Ketogenesis and Ketolysis

Ketogenesis: favored by a prolonged fast and occurs in the liver, stimulated by increasing concentrations of acetyl-CoA Ketolysis: favored during prolonged fasting, but is stimulated by low-energy state in muscle and brain tissue and does not occur in the liver

All chiral amino acids used in eukaryotes are?

L-amino acids

What proteins are specific to the formation and transmission of cholesteryl esters, and what are their functions?

LCAT catalyzes the esterification of cholesterol to form cholesteryl esters. CETP promotes the transfer of cholesteryl esters from HDL to IDL, forming LDL.

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

Lipids, including phospholipids, cholesterol, and others, are most plentiful; proteins, including transmembrane proteins (channels and receptors), mem-brane-associated proteins, and embedded proteins, are next most plentiful; carbohydrates, including the glycoprotein coat and signaling molecules, are next; nucleic acids are essentially absent.

Lipoproteins are synthesized primarily by which two organs?

Lipoproteins are synthesized primarily by the intestine and liver.

glycogen in the liver and in skeletal muscle

Liver glycogen is broken down to maintain a constant level of glucose in the blood; muscle glycogen is broken down to provide glucose to the muscle during vigorous exercise .

Which components of membrane lipids contribute to their structural role in membranes? Which components contribute to function?

Membrane lipids are amphipathic: they have hydrophilic heads and hydrophobic tails, allowing for the formation of bilayers in aqueous solu-tion. The fatty acid tails form the bulk of the phospholipid bilayer, and play a predominantly structural role. On the other hand, the functional differences between membrane lipids are determined by the polar head group, due to its constant exposure to the exterior environment of the phospholipid bilayer (remember, this can be either the inside or outside of the cell). The degree of unsaturation of fatty acid tails can also play a small role in function.

Semiconservative Replication

Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand A new double helix is made of one old parent strand and one new daughter strand.

Describe the structure of a micelle

Micelles are collections of lipids with their hydrophobic ends oriented toward the center and their charged ends oriented toward the aqueous environment. Micelles collect lipids within their hydrophobic centers.

Cross-Section of a Micelle

Micelles organize in aqueous solution by forcing hydrophobic tails to the interior, allowing the hydrophilic heads to interact with water in the environment.

What are three primary functions of NADPH?

NADPH is involved in lipid biosynthesis, bactericidal bleach formation in cer-tain white blood cells, and maintenance of glutathione stores to protect against reactive oxygen species.

What is the difference between a nucleoside and a nucleotide?

Nucleosides contain a five-carbon sugar (pentose) and nitrogenous base. Nucle-otides are composed of a nucleoside plus one to three phosphate groups.

Nucleosome Structure

Nucleosomes are composed of DNA wrapped around histone proteins.

What is the key structural difference in the types of lesions corrected by nucleotide excision repair vs. those corrected by base excision repair?

Nucleotide excision repair corrects lesions that are large enough to distort the double helix; base excision repair corrects lesions that are small enough not to distort the double helix.

The Propionic Acid Pathway

Odd fatty acid --> Propionyl-CoA--- (propionyl-CoA carboxylase (biotin))---> Methylmalonyl-CoA ---- (methylmalonyl-CoA mutase (B12)) ---> Succinyl-COA ---> Citric Acid Cycle *exception to the rule that fatty acids cannot be converted to glucose in humans!

What is the difference between an oncogene and a tumor suppressor gene?

Oncogenes (or, more properly, proto-oncogenes) code for cell cycle-promoting proteins; when mutated, a proto-oncogene becomes an oncogene, pro-moting rapid cell cycling. Tumor suppressor genes code for repair or cell cycle-inhibiting proteins; when mutated, the cell cycle is allowed to proceed unchecked. Oncogenes are like stepping on the gas pedal, mutated tumor suppressor genes are like cutting the brakes.

MNEMONIC

One way to remember carotene is to remember that carrots are high in vitamin A, which is why eating carrots is colloquially suggested to improve vision . To remember that vitamin D regulates calcium, remember that it is frequently added to milk in order to aid in the absorption of calcium .

Preferred Fuels in the Well-Fed and Fasting States

Organ : Well-fed : Fasting Liver : glucose, AA : FA Resting Skeletal Muscle: glucose : FA, ketones Cardiac muscle : FA : FA, ketones Adipose tissue : glucose : FA Brain : glucose : glucose (K in prolonged fast) RBC : glucose : glucose

What does PCR accomplish for a researcher? What about Southern blotting?

PCR increases the number of copies of a given DNA sequence and can be used for a sample containing very few copies of the DNA sequence. Southern blotting is useful when searching for a particular DNA sequence because it separates DNA fragments by length and then probes for a sequence of interest.

When lipids leave the stomach, what stages of digestion have been accomplished? What enzymes are added to accomplish the next phase?

Physical digestion is accomplished in the mouth and the stomach, reducing the particle size. Beginning in the small intestine, pancreatic lipase, colipase, cholesterol esterase, and bile assist in the chemical digestion of lipids. In the more distal portion of the small intestine, absorption occurs.

What is a positive control system? What is a negative control system?

Positive control systems require the binding of a protein to the operator site to increase transcription. Negative control systems require the binding of a protein to the operator site to decrease transcription

What are the major posttranslational modifications that occur in proteins?

Posttranslational modifications include proper folding by chaperones, for-mation of quaternary structure, cleavage of proteins or signal sequences, and addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation).

Compare the two types of active transport. What is the difference between symport and antiport?

Primary active transport uses ATP as an energy source for the movement of molecules against their concentration gradient, while secondary active trans-port uses an electrochemical gradient to power the transport. Symport moves both particles in secondary active transport across the membrane in the same direction, while antiport moves particles across the cell membrane in opposite directions.

what role does proline serve in secondary structure?

Proline's rigid structure causes it to introduce kinks in α-helices or create turns in β-pleated sheets.

NSAIDs block prostaglandin production in order to reduce pain and inflammation. What do prostaglandins do to bring about these symptoms?

Prostaglandins regulate the synthesis of cAMP, which is involved in many path-ways, including those that drive pain and inflammation.

Why are proteins analyzed after isolation?

Protein isolation is generally only the first step in an analysis. The protein identity must be confirmed by amino acid analysis or activity. With unknown proteins, classification of their features is generally desired.

What is the overall reaction of the pyruvate dehydrogenase complex?

Pyruvate + CoA-SH + NAD+ → acetyl-CoA + CO2 + NADH + H+

What are the four enzymes unique to gluconeogenesis? Which irreversible glycolytic enzymes do they replace?

Pyruvate carboxylase- Pyruvate kinase Phosphoenolpyruvate carboxykinase (PEPCK)- Pyruvate kinase Fructose-1,6-bisphosphatase- Phosphofructokinase-1 Glucose-6-phosphatase - Glucokinase

What are the reactants of the pyruvate dehydrogenase complex? What are the products?

Pyruvate, NAD+, and CoA are the reactants of the PDH complex. Acetyl-CoA, NADH, and CO2 are the products.

What is the role of each eukaryotic RNA polymerase? • RNA polymerase I: • RNA polymerase II: • RNA polymerase III:

RNA polymerase I synthesizes most rRNA. RNA polymerase II synthesizes mRNA (hnRNA) and snRNA. RNA polymerase III synthesizes tRNA and some rRNA.

When starting transcription, where does RNA polymerase bind?

RNA polymerase II binds to the TATA box, which is located within the pro-moter region of a relevant gene, at about -25.

Except for cysteine, all amino acids have _____.

S absolute configuration. because cysteine has R absolute configuration because the -CH2SH group has priority over the -COOH

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 the nucleus. These receptors are transcription factors that use their DNA-binding domain to attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can then promote increased expression of the relevant gene.

Stimulation of Transcription by an Enhancer and Its Associated Transcription Factors

Signal molecules, such as cyclic AMP (cAMP), cortisol, and estrogen, bind to specific receptors. e receptors are cyclic AMP response element-binding protein (CREB), the glucocorticoid (cortisol) receptor, and the estrogen receptor, respectively; all are transcription factors that bind to their respective response elements within the enhancer. the large distance between the enhancer and promoter regions for a given gene means that DNA often must bend into a hairpin loop to bring these elements together spatially.

Origins of Replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides. Replication forks form on both sides of the origin, increasing the efficiency of replication.

Why does soap appear to dissolve in water, and how is this fact important to cleaning?

Soap appears to dissolve in water because amphipathic free fatty acid salts form micelles, with hydrophobic fatty acid tails toward the center and carboxylate groups facing outward toward the water. Fat-soluble particles can then dissolve inside micelles in the soap-water solution and wash away. Water-soluble com-pounds can freely dissolve in the water.

motor proteins

Specialized proteins that use energy to change shape and move cells or structures within cells. display enzymatic activity, acting as ATPases that power the conformational change necessary for motor function have transient interactions with either actin or microtubules. example: myosin, kinesin and dyneins

Starch Structure

Starches are polymers of 1,4-linked α-d-glucose.

Respiratory Complexes on the Inner Mitochondrial Membrane

Steps 1 and 2 of complex III are drawn as two separate steps here for clarity; however, the same CoQH2-cytochrome c oxidoreductase complex is used for both steps.

A Glycogen Granule

Structure of the cell that stores glycogen and enzymes for glycogen breakdown and synthesis. Glycogen is stored in the cytoplasm as granules. Each granule has a central protein core with polyglucose chains radiat-ing outward to form a sphere

RNA is structurally similar to DNA except:

Substitution of a ribose sugar for deoxyribose • Substitution of uracil for thymine • It is single-stranded instead of double-stranded

RNA polymerase II binds to the

TATA box within the promoter region of the gene (25 base pairs upstream from first transcribed base).

What is the function of a telomere?

Telomeres are the ends of eukaryotic chromosomes and contain repetitive sequences of noncoding DNA. These protect the chromosome from losing important genes from the incomplete replication of the 5′ end of the DNA strand

Disaccharide Formation

Th two monosaccharides in a disaccharide are connected by a glycosidic bond, the bond may be α or β as in cyclic monosaccharides, the structures include glycosidic bondslhat create a 1,4 link between C1 of one monosaccharide and C4 of the second monosaccharide The naturally occurring disaccharides are maltose, lactose, and sucrose

What is the difference between the ETC and oxidative phosphorylation? What links the two?

The ETC is made up of the physical set of intermembrane proteins located on the inner mitochondrial matrix, and they undergo oxidation-reduction reactions as they transfer electrons to oxygen, the final electron acceptor. As electrons are transferred, a proton-motive force is generated in the intermem-brane space. Oxidative phosphorylation is the process by which ATP is gener-ated via harnessing the proton gradient, and it utilizes ATP synthase to do so.

Cholesterol

a fatty substance that travels through the blood and is found in all parts of the body Cholesterol can be produced de novo or absorbed from dietary sources . Hypercholesterolemia, or high cholesterol, is a condition that is strongly correlated with heart disease, in which the combination of these two cholesterol sources is excessive . Accumulation of cholesterol in arterial walls results in atherosclerosis, a hardening of the wall .

R group

a functional group that defines a particular amino acid and gives it special properties. it determines their chemical properties it determine the amino acid functions

How does the aromaticity of purines and pyrimidines underscore their genetic function?

The aromaticity of nucleic acids makes these compounds very stable and unreactive. Stability is important for storing genetic information and avoiding spontaneous mutations.

Why is it necessary that fetal hemoglobin does not bind 2,3-BPG?

The binding of 2,3-BPG decreases hemoglobin's affinity for oxygen. Fetal hemoglobin must be able to "steal" oxygen from maternal hemoglobin at the placental interface; therefore, it would be disadvantageous to lower its affinity for oxygen.

What organ consumes the greatest amount of glucose relative to its percent-age of body mass?

The brain consumes the greatest amount of glucose relative to its percentage of body mass.

Where does the bulk of protein digestion occur?

The bulk of protein digestion occurs in the small intestine.

During protein processing, what is the eventual fate of each of the following components: carbon skeleton, amino group, and side chains?

The carbon skeleton is transported to the liver for processing into glucose or ketone bodies. The amino group will feed into the urea cycle for excretion. Side chains are processed depending on their composition. Basic side chains will be processed like amino groups, while other functional groups will be treated like the carbon skeleton.

Cell Membrane

The cell membrane is a phospholipid bilayer that regulates movement of solutes into and out of the cell.

Why can heat be used as a measure of internal energy in living systems?

The cellular environment has a relatively fixed volume and pressure, which eliminates work from our calculations of internal energy; if ΔU = Q - W and W = 0, ΔU = Q.

What role does the electron transport chain play in the generation of ATP?

The electron transport chain generates the proton-motive force, an electro-chemical gradient across the inner mitochondrial membrane, which provides the energy for ATP synthase to function

semipermeable membrane refers to

a membrane governed by the same permeability rules as biological membranes: small, nonpolar, lipid-soluble particles (and water) can pass through freely, while large, polar, or charged particles cannot .

Gluconeogenesis

The formation of glucose from noncarbohydrate sources, such as amino acids.

How does the human body store spare energy? Why doesn't the human body store most energy as sugar?

The human body stores energy as glycogen and triacylglycerols. Triacylglycer-ols are preferred because their carbons are more reduced, resulting in a larger amount of energy yield per unit weight. In addition, due to their hydrophobic nature, triacylglycerols do not need to carry extra weight from hydration.

What distinguishes the inner mitochondrial membrane from other biological membranes? What is the pH gradient between the cytoplasm and the inter-membrane space?

The inner mitochondrial membrane lacks cholesterol, which differentiates it from most other biological membranes. There is no pH gradient between the cytoplasm and the intermembrane space because the outer mitochondrial membrane has such high permeability to biomolecules (the proton-motive force of the mitochondria is across the inner mitochondrial membrane, not the outer mitochondrial membrane).

Given that the glycogen storage disorder von Gierke's disease affects the last enzyme of gluconeogenesis, predict the associated metabolic derangement that occurs.

The last enzyme in gluconeogenesis is glucose-6-phosphatase so patients with von Gierke's disease are unable to perform gluconeogenesis in addition to glycogenolysis. This means patients will be unable to produce glucose during periods of fasting (resulting in hypoglycemia). Furthermore, given a blocker in the gluconeogenic pathway, a buildup of intermediates (including lactate result-ing in lactic acidosis) would also be expecte

Describe the major metabolic functions of the liver.

The liver is responsible for maintaining a steady-state concentration of glucose in the blood through glucose uptake and storage, glycogenolysis, and glucone-ogenesis. The liver also participates in cholesterol and fat metabolism, the urea cycle, bile synthesis, and the detoxification of foreign substances.

Based on its needs, which of the two shuttle mechanisms is cardiac muscle most likely to utilize? Why?

The malate-aspartate shuttle. Because this mechanism is the more efficient one, it makes sense for a highly aerobic organ such as the heart to utilize it in order to maximize its ATP yield

How is the resting membrane potential maintained?

The membrane potential, which results from a difference in the number of positive and negative charges on either side of the membrane, is maintained primarily by the sodium-potassium pump, which moves three sodium ions out of the cell for every two potassium ions pumped in, and to a minor extent by leak channels that allow the passive transport of ions.

If you were designing a study to assess metabolism, which measurement method would you choose? Defend your answer.

The methods described in the text include chemical analysis, which is objective and can quantify specific metabolic substrates, products, and enzymes; calorim-etry, which is most accurate for basal metabolic rate but also most expensive; respirometry, which provides basic information about fuel sources; and caloric analysis at constant weight (food and exercise logs), which is the least invasive. Any of these answers could be defended

How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?

The parent strand is more heavily methylated, whereas the daughter strand is barely methylated at all. This allows DNA polymerase to distinguish between the two strands during proofreading.

What is the primary thermodynamic factor responsible for passive transport?

The primary thermodynamic factor responsible for passive transport is entropy

What are two potential drawbacks of affinity chromatography?

The protein of interest may not elute from the column because its affinity is too high or it may be permanently bound to the free receptor in the eluent.

Lipids are mobilized from lipoproteins by

lipoprotein lipase

Polypeptides are assembled from _____.

long chains of amino acids

Electron carriers

may be soluble or membrane-bound • Flavoproteins are one subclass of electron carriers that are derived from riboflavin (vitamin B2).

Extracellular ligands can bind to

membrane receptors, which function as channels or enzymes in second messenger pathways.

Polyacrylamide gel electrophoresis (PAGE)

method for analyzing proteins in their native states; compare molecular size or charge of proteins

Electrophoresis

method of separating serum proteins by electrical charge use polyacrylamide gel use electrolytic cells (delta G>0, E cell <0) anions moves toward anode cations moves toward cathode

Endocytosis and exocytosis are

methods of engulfing material into cells or releasing material to the exterior of cells, both via the cell membrane.

digested lipids may form ______ for absorption or be absorbed directly

micelles

Long-chain fatty acids are absorbed as

micelles and assembled into chylomicrons for release into lymphatic system

Proofreading by DNA Polymerase

mispaired nucleotide is removed by DNA polymerase

Fatty acid oxidation occurs in the

mitochondria following transport by the carnitine shuttle. • β-Oxidation uses cycles of oxidation, hydration, oxidation, and cleavage. • Branched and unsaturated fatty acids require special enzymes. • Unsaturated fatty acids use an isomerase and an additional reductase during cleavage.

the citric acid cycle takes place in the

mitochondrial matrix.

Thyroid hormones

modulate the impact of other metabolic hormones and have a direct impact on basal metabolic rate. • T3 is more potent than T4, but has a shorter half-life and is available in lower concentrations in the blood. • T4 is converted to T3 at the tissues.

Amino acids are

molecules that contain two functional groups: an amino group (-NH2) and carboxyl group (-COOH).

Mechanical digestion of lipids occurs primarily in the

mouth and stomach.

If a strand of RNA contained 15% cytosine, 15% adenine, 35% guanine, and 35% uracil, would this violate Chargaff's rules? Why or why not?

no this does not violate Chargaff's rules. RNA is single-stranded, and thus the complementarity seen in DNA does not hold true. For single-stranded RNA, %C does not necessarily equal %G; %A does not necessarily equal %U.

In eukaryotes, DNA is wound around histone proteins (H2A, H2B, H3, and H4) to form

nucleosomes, which may be stabilized by another histone protein (H1). As a whole, DNA and its associated histones make up chromatin in the nucleus.

Gluconeogenesis

occurs in both the cytoplasm and mitochondria, predominantly in the liver. There is a small contribution from the kidneys.

Glycolysis

occurs in the cytoplasm of all cells and does not require oxygen. It yields 2 ATP per molecule of glucose.

Repressible Systems

one type of regulation of transcription system; repressor inactive until it combines with corepressor; the repressor/corepressor complex inhibits transcription; corepressors are often the end products of the biosynthetic pathways they control Continually allow gene transcription unless a corepressor binds to the repressor to stop transcription

voltage gated channels

open and close in response to changes in membrane potential ex: excitable cells such as neurons, sodium- potassium channels close under resting conditions membrane depolarization cause a protein conformation change that allows them to open and close as the voltage increase

Isocitrate dehydrogenase

oxidizes and decarboxylates isocitrate to form α-ketoglutarate. This enzyme generates the first CO2 and first NADH of the cycle. As the rate-limiting step of the citric acid cycle, it is heavily regulated: ATP and NADH are inhibitors; ADP and NAD+ are activators.

Malate dehydrogenase

oxidizes malate to oxaloacetate. This enzyme gener-ates the third and final NADH of the cycle

Pyruvate dehydrogenase (PDH)

oxidizes pyruvate, creating CO2; it requires thiamine pyrophosphate (vitamin B1, TPP) and Mg2+.

Succinate dehydrogenase

oxidizes succinate to form fumarate. This flavoprotein is anchored to the inner mitochondrial membrane because it requires FAD, which is reduced to form the one FADH2 generated in the cycle.

Dihydrolipoyl transacetylase

oxidizes the remaining two-carbon molecule using lipoic acid, and transfers the resulting acetyl group to CoA, forming acetyl-CoA.

Free energy calculations must be adjusted for

pH (ΔG°¹) temperature (37°C, 98.6°F, 310K) concentration

in isoelectric focusing a proton stop moving when

pH = pI .

Enzyme-linked receptors

participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades have three primary protein domains: membrane- spanning domain, ligand- binding domain, catalytic domain.

Membrane Transport Processes

passive and active The movement of solutes across the cell membrane is mediated by concentration gradients.

Biotechnology brings up a number of safety and ethical issues, including

pathogen resistance and the ethics of choosing individuals for specific traits.

The residues in peptides are joined together through

peptide bonds a specialized form of an amide bond, which form between the -COO- group of one amino acid and the NH3+ group of another amino acids forming the functional group -C(O)NH-

No work is performed in a closed biological system because

pressure and volume remain constant.

LDL

primarily transports cholesterol for use by tissues

levels of proteins

primary, secondary, tertiary, quaternary

DNA cannot be synthesized without an adjacent nucleotide to hook onto, so a small RNA primer is put down by

primase.

Biosignaling

process in which cells receive & act on signals

DNA Replication in Prokaryotes and Eukaryotes

prokaryotes - fast eukaryotes - slow

The Composition of Prokaryotic and Eukaryotic Ribosomes

prokaryotes have 50S and 30S large and small sub-units, which assemble to create the complete 70S ribosome. This difference allows us to target antibiotics,

Catecholamines

promote glycogenolysis and increase basal metabolic rate through their sympathetic nervous system activity.

During replication, DNA polymerase

proofreads its work and excises incor-rectly matched bases. The daughter strand is identified by its lack of methylation and corrected accordingly.

BCA assay, Lowry reagent assay, and Bradford protein assay each test for

protein and have different advantages and disadvantages. The Bradford protein assay, which uses a color change from brown-green to blue, is most common.

Actin

protein that makes up microfilaments and the thin filaments in myofibrils has positive side and negative side, this polarity allows tor proteins to travel unidirectionally along an actin filament

tubulin

protein that makes up microtubules important for providing structure, chromosome separation in mitosis and meiosis and intracellular transport with kinesis and dynein. has polarity, the negative end of a microtubule is located adjacent to the nucleus and the positive end is in the periphery of cell

structural proteins

provide physical stability and movement - types : collagen elastin, keratin, actin, tubulin. generally have highly repetitive secondary structure

Overall Reaction of Pyruvate Dehydrogenase Complex

pyruvate + CoA-SH + NAD⁺ → acetyl-CoA + CO₂ + NADH + H⁺

Denaturation and Reannealing of DNA

reannealed (brought back together) if the denaturing condition is slowly removed. If a solution of heat-denatured DNA is slowly cooled, for example, then the two complementary strands can become paired again, Heat, alkaline pH, and chemicals like formaldehyde and urea are com-monly used to denature DNA

Pyruvate dehydrogenase

refers to a complex of enzymes that convert pyruvate to acetyl-CoA It is stimulated by insulin and inhibited by acetyl-CoA

Ketolysis

regenerates acetyl-CoA for use as an energy source in peripheral tissues

Size-exclusion chromatography

relies on porous beads. Larger molecules elute first because they are not trapped in the small pores.

To replicate DNA, it is first unwound at an origin of replication by helicases. This produces two

replication forks on either side of the origin. • Prokaryotes have a circular chromosome that contains only one origin of replication. • Eukaryotes have linear chromosomes that contain many origins of replication.

Active transport

requires energy in the form of ATP or an existing favorable ion gradient • Active transport may be primary or secondary depending on the energy source. Secondary active transport can be further classified as symport or antiport.

Composition of fuel that is actively consumed by the body is estimated by the

respiratory quotient (RQ).

Frameshift mutations

result from nucleotide addition or deletion, and change the reading frame of subsequent codons.

mixed inhibition

results when an inhibitor can bind to either the enzyme or the E-S complex, but has different affinity for each; if it has same affinity = noncompetitive inhibitor; binds to allosteric; alters Km depending on affinity; decreased Vmax

Fatty acid synthesis and β-oxidation are

reverse processes . Both involve transport across the mitochondrial membrane, followed by a series of redox reactions, but always in the opposite direction of one another .

The ribulose 5-phosphate created in the PPP is isomerized to

ribose 5-phosphate, the backbone of nucleic acids . When coupled to a nitrogenous base, it forms a nucleotide that can be integrated into RNA .

Transcription factors

search for promoter and enhancer regions in the DNA. • Promoters are within 25 base pairs of the transcription start site. • Enhancers are more than 25 base pairs away from the transcription start site. • Modification of chromatin structure affects the ability of transcriptional enzymes to access the DNA through histone acetylation (increases accessibil-ity) or DNA methylation (decreases accessibility).

DNA replication is

semiconservative: one old parent strand and one new daughter strand is incorporated into each of the two new DNA molecules.

Chromatography

separates protein mixtures on the basis of their affinity for a stationary phase or a mobile phase.

Isoelectric focusing

separates proteins by their isoelectric point (pI); the protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein.

polar side chains

serine, threonine, asparagine, glutamine, cysteine they are polar but not aromatic serine and threonine both have -Oh group in their side chains which makes them highly polar and able to participate in hydrogen bonding asparagine and glutamine have amide side chains, the amide nitrogen do not gain or lose protons with changes in pH: they do not become charged.

Glyceraldehyde

simplest aldose

Unwound strands are kept from reannealing or being degraded by

single-stranded DNA-binding proteins

Protein digestion occurs primarily in the

small intestine

Chemical digestion of lipids occurs in the

small intestine and is facilitated by bile, pancreatic lipase, colipase, and cholesterol esterase.

oligopeptides are

small peptides, up to 20 residues

electron transport chain

takes place on the matrix-facing surface of the inner mitochondrial membrane.

What effect enzyme activity?

temperature, acidity, alkalinity (pH) and high salinity

Gangliosides are

the "gangly" sphingolipids, with the most complex structure and functional groups (oligosaccharides and NANA) in all directions .

enzyme- catalyzed reaction tend to double in velocity for every 10C increase in temperature until the optimum temperature is reached, then what happens?

the activity falls off sharply as the enzyme will denature at higher temperatures some enzyme that are overheated may regain their function if cooled

ligand-gated channels

the binding of a specific substance or ligand to the channel causes it to open or close ex; neurotransmitter

What is the difference between a sphingolipid that is also a phospholipid and one that is NOT?

the difference is the bond between the sphingosine backbone and the head group. When this is a phosphodiester bond, it's a phospholipid (note the phospho-prefixes). Nonphospholipid sphingolipids include glycolipids, which contain a glycosidic linkage to a sugar.

Between the leading strand and lagging strand, which is more prone to mutations? Why?

the lagging strand is more prone to mutations because it must constantly start and stop the process of DNA replication. Additionally, it contains many more RNA primers, all of which must be removed and filled in with DNA.

The NADH produced in glycolysis is oxidized by

the mitochondrial electron transport chain when oxygen is present

how histidine can acquire a positive charge?

the pKa of the side chain is relatively close to 7.4 at physiologic pH, one nitrogen atom is protonated and other isn't under more acidic conditions, the second nitrogen atom can become protonated, given the side chain a positive charge.

Which mRNA codon is the start codon, and what amino acid does it code for? Which mRNA codons are the stop codons?

the start codon is AUG, which codes for methionine; the stop codons are UAA, UGA, and UAG.

DNA polymerase III (prokaryotes) or DNA polymerases α, δ, and ε (eukaryotes) can

then synthesize a new strand of DNA; they read the template DNA 3′ to 5′ and synthesize the new strand 5′ to 3′. • The leading strand requires only one primer and can then be synthesized continuously in its entirety. • The lagging strand requires many primers and is synthesized in discrete sections called Okazaki fragments.

Succinyl-CoA and CO2 Formation

these reactions are carried out by the α-ketoglutarate dehydrogenase complex, which is similar in mechanism, cofactors, and coenzymes to the pyruvate dehydrogenase (PDH) complex. In the formation of succinyl-CoA, α-ketoglutarate and CoA come together and produce a molecule of carbon dioxide this carbon dioxide represents the second and last carbon lost from the cycle. Reducing NAD+ produces another NADH

A Cysteine has a ______ group

thiol (-SH) group because sulfur is larger and less electronegative than oxygen, the S-H bond is weaker than the O-H bond which leaves cysteine prone to oxidation.

trimeric G proteins cycle

three subunits of the G protein are alpha, beta, gamma. in its inactive form the alpha subunit bind GDP and is in a complex with the β and γ subunits. When a ligand binds to the GPCR, the receptor becomes activated and, in turn, engages the corresponding G protein, as shown in Step 1. Once GDP is replaced with GTP, the α subunit is able to dissociate from the β and γ subunits (Step 2). The activated α subunit alters the activity of adenylate cyclase. If the α subunit is αs, then the enzyme is activated; if the α subunit is αi, then the enzyme is inhibited. Once GTP on the activated α subunit is dephosphorylated to GDP (Step 3), the α subunit will rebind to the β and γ subunits (Step 4), rendering the G protein inactive.

Ribosomes are the factories where

translation (protein synthesis) occurs.

Cell-cell junctions regulate

transport intracellularly and intercellularly • Gap junctions allow for the rapid exchange of ions and other small molecules between adjacent cells. • Tight junctions prevent paracellular transport, but do not provide intercellular transport. • Desmosomes and hemidesmosomes anchor layers of epithelial tissue together.

VLDL

transports newly synthesized triacylglycerol molecules from the liver to peripheral tissues in the bloodstream.

True or False: Fatty acids are synthesized in the cytoplasm and modified by enzymes in the smooth endoplasmic reticulum.

true

true or false: amino acids do not need to have both the amino and carboxyl groups bonded to the same carbon

true ex: the neurotransmitter gamma-aminobutyric acid (GABA) has the amino group on the gamma carbon, three carbons away from the carboxyl group

Aromatic side chains

tryptophan, phenylalanine, tyrosine the largest of these is tryptophan, which has a double ring system that contains a nitrogen atom the smallest is phenylalanine which has benzyl side chain the -OH group on the tryrosine make it a relatively polar

What type of ion channel is active at all times?

ungated channels are always open

Helicase

unwinds the DNA double helix.

Half-reactions

useful information about stoichiometry and thermodynamics.

Dihydrolipoyl dehydrogenase

uses FAD to reoxidize lipoic acid, forming FADH2. This FADH2 can later transfer electrons to NAD+, forming NADH that can feed into the electron transport chain.

Affinity chromatography

uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest.

Ion-exchange chromatography

uses a charged column and a variably saline eluent.

Column chromatography

uses beads of a polar compound, like silica or alumina (stationary phase), with a nonpolar solvent (mobile phase).

migration velocity

v = Ez/f (v = migration velocity; E = electric field strength; z = net charge on molecule; f = frictional coefficient)

Tight junctions form a

watertight seal, preventing paracellular transport of water and solutes .

Osmolarity explains

why pure water should never be given intravenously for resuscitation . Red blood cells have an osmolarity around 300 mOsm/L pure water has an osmolarity of 0 mOsm/L. Water would rush into the red blood cells, causing them to burst . To avoid this, saline or dextrose-containing solutions are used .

peptide bond hydrolysis

~ For enzymes to carry out function need to be relatively stable and don't fall apart ~ Hydrolyzed using acid/base catalyst ~ In living organisms catalyzed by hydrolytic enzymes (cleave at specific points) ~ Break apart by adding H to the amide nitrogen and OH to the carbonyl

Gibbs free energy equation

ΔG = ΔH - TΔS

What conditions does ΔG°′ adjust for that are not considered with ΔG°?

ΔG°′ adjusts only for the pH of the environment by fixing it at 7. Temperature and concentrations of all other reagents are still fixed at their values from stan-dard conditions and must be adjusted for if they are not 1 M.

osmotic pressure (Π)

Π = iMRT

Posttranscriptional modifications include:

• A 7-methylguanylate triphosphate cap is added to the 5′ end. • A polyadenosyl (poly-A) tail is added to the 3′ end. • Splicing is done by snRNA and snRNPs in the spliceosome; introns are removed in a lariat structure, and exons are ligated together. • Prokaryotic cells can increase the variability of gene products from one transcript through polycistronic genes (in which starting transcription in different sites within the gene leads to different gene products). • Eukaryotic cells can increase variability of gene products through alternative splicing (combining different exons in a modular fashion to acquire different gene products).

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

• Beriberi, which is characterized by congestive heart failure or nerve damage . • Wernicke-Korsakoff syndrome, which is characterized by difficulty walking, uncoordinated eye movements, confusion, and memory disturbances .

Checkpoints and Regulation of the Citric Acid Cycle

• Citrate synthase: ATP and NADH function as allosteric inhibitors of citrate synthase, which makes sense because both are products (indirect and direct, respectively) of the enzyme. Citrate also allosterically inhibits citrate synthase directly, as does succinyl-CoA. • Isocitrate dehydrogenase: As we discussed in the beginning of this section, this enzyme that catalyzes the citric acid cycle is likely to be inhibited by energy products: ATP and NADH. Conversely, ADP and NAD+ function as allosteric activators for the enzyme and enhance its affinity for substrates. • α-Ketoglutarate dehydrogenase complex: Once again, the reaction products of succinyl-CoA and NADH function as inhibitors of this enzyme complex. ATP is also inhibitory and slows the rate of the cycle when the cell has high levels of ATP. The complex is stimulated by ADP and calcium ions.

NADH donates electrons to the chain, which are passed from one complex to the next. As the ETC progresses, reduction potentials increase until oxygen, which has the highest reduction potential, receives the electrons.

• Complex I (NADH-CoQ oxidoreductase) uses an iron-sulfur cluster to transfer electrons from NADH to flavin mononucleotide (FMN), and then to coenzyme Q (CoQ), forming CoQH2. Four protons are translocated by Complex I. • Complex II (Succinate-CoQ oxidoreductase) uses an iron-sulfur cluster to transfer electrons from succinate to FAD, and then to CoQ, forming CoQH2. No proton pumping occurs at Complex II. • Complex III (CoQH2-cytochrome c oxidoreductase) uses an iron-sulfur cluster to transfer electrons from CoQH2 to heme, forming cytochrome c as part of the Q cycle. Four protons are translocated by Complex III. • Complex IV (cytochrome c oxidase) uses cytochromes and Cu2+ to transfer electrons in the form of hydride ions (H-) from cytochrome c to oxygen, forming water. Two protons are translocated by Complex IV.

Terminology and 5′ → 3′

• DNA → DNA = replication: new DNA synthesized in 5′ → 3′ direction • DNA → RNA = transcription: new RNA synthesized in 5′ → 3′ direction (template is read 3′ → 5′) • RNA → protein = translation: mRNA read in 5′ → 3′ direction

Posttranslational modifications include:

• Folding by chaperones • Formation of quaternary structure • Cleavage of proteins or signal sequences • Covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

The three-base sequences listed below are DNA sequences. Using Figure 7.5, which amino acid is encoded by each of these sequences, after transcription and translation? • GAT: • ATT: • CGC: • CCA:

• GAT: mRNA codon = AUC; Isoleucine (Ile) • ATT: mRNA codon = AAU; Asparagine (Asn) • CGC: mRNA codon = GCG; Alanine (Ala) • CCA: mRNA codon = UGG; Tryptophan (Trp

Important glycolytic enzymes include:

• Glucokinase, which converts glucose to glucose 6-phosphate. It is present in the pancreatic β-islet cells as part of the glucose sensor and is responsive to insulin in the liver. • Hexokinase, which converts glucose to glucose 6-phosphate in peripheral tissues. • Phosphofructokinase-1 (PFK-1), which phosphorylates fructose 6-phosphate to fructose 1,6-bisphosphate in the rate-limiting step of glycolysis. PFK-1 is activated by AMP and fructose 2,6-bisphosphate (F2,6-BP) and is inhibited by ATP and citrate. • Phosphofructokinase-2 (PFK-2), which produces the F2,6-BP that activates PFK-1. It is activated by insulin and inhibited by glucagon. • Glyceraldehyde-3-phosphate dehydrogenase produces NADH, which can feed into the electron transport chain. • 3-phosphoglycerate kinase and pyruvate kinase each perform substrate-level phosphorylation, placing an inorganic phosphate (Pi) onto ADP to form ATP.

Glycogenolysis is the breakdown of glycogen using two main enzymes:

• Glycogen phosphorylase, which removes single glucose 1-phosphate mole-cules by breaking α-1,4 glycosidic links. In the liver, it is activated by gluca-gon to prevent low blood sugar; in exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for the muscle itself. • Debranching enzyme, which moves a block of oligoglucose from one branch and connects it to the chain using an α-1,4 glycosidic link. It also removes the branchpoint, which is connected via an α-1,6 glycosidic link, releasing a free glucose molecule.

Glycogenesis (glycogen synthesis) is the production of glycogen using two main enzymes:

• Glycogen synthase, which creates α-1,4 glycosidic links between glucose molecules. It is activated by insulin in liver and muscle. • Branching enzyme, which moves a block of oligoglucose from one chain and adds it to the growing glycogen as a new branch using an α-1,6 glycosidic link

The following is a summary of the energy yield of the various carbohydrate metabolism processes:

• Glycolysis generates 2 NADH and 2 ATP. • Pyruvate dehydrogenase generates 1 NADH per molecule of pyruvate. Because each glucose forms two molecules of pyruvate, this complex produces a net of 2 NADH. • The citric acid cycle generates 3 NADH, 1 FADH2, and 1 GTP (6 NADH, 2 FADH2, and 2 GTP per molecule of glucose). • Each NADH yields 2.5 ATP; 10 NADH form 25 ATP. • Each FADH2 yields 1.5 ATP; 2 FADH2 form 3 ATP. • GTP are converted to ATP. • 2 ATP from glycolysis + 2 ATP (GTP) from the citric acid cycle + 25 ATP from NADH + 3 ATP from FADH2 = 32 ATP per molecule of glucose (optimal). Inefficiencies of the system and variability between cells make 30-32 ATP/glucose the commonly accepted range for energy yield

rate-limiting enzymes

• Glycolysis: phosphofructokinase-1 • Fermentation: lactate dehydrogenase • Glycogenesis: glycogen synthase • Glycogenolysis: glycogen phosphorylase • Gluconeogenesis: fructose-1,6-bisphosphatase • Pentose Phosphate Pathway: glucose-6-phosphate dehydrogenase

The liver is the most metabolically diverse tissue.

• Hepatocytes are responsible for the maintenance of blood glucose levels by glycogenolysis and gluconeogenesis in response to pancreatic hormone stimulation. • The liver also participates in the processing of lipids and cholesterol, bile, urea, and toxins.

What are the function and key regulators of the following enzymes? Which ones are reversible? Hexokinase • Function: • Regulation: • Reversible? Glucokinase • Function: • Regulation: • Reversible? Phosphofructokinase-1 (PFK-1) • Function: • Regulation: • Reversible? Glyceraldehyde-3-phosphate dehydrogenase • Function: • Reversible? 3-phosphoglycerate kinase • Function: • Reversible? Pyruvate kinase • Function: • Regulation: • Reversible?

• Hexokinase phosphorylates glucose to form glucose 6-phosphate, "trapping" glucose in the cell. It is inhibited by glucose 6-phosphate. It is irreversible. • Glucokinase also phosphorylates and "traps" glucose in liver and pancreatic cells, and works with GLUT 2 as part of the glucose sensor in β-islet cells. In liver cells, it is induced by insulin. It is irreversible. • PFK-1 catalyzes the rate-limiting step of glycolysis, phosphorylating fructose 6-phosphate to fructose 1,6-bisphosphate using ATP. It is inhibited by ATP, citrate, and glucagon. It is activated by AMP, fructose 2,6-bisphosphate, and insulin. It is irreversible. • Glyceraldehyde-3-phosphate dehydrogenase generates NADH while phos-phorylating glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. It is reversible. • 3-Phosphoglycerate kinase performs a substrate-level phosphorylation, transferring a phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. It is reversible. • Pyruvate kinase performs another substrate-level phosphorylation, transferring a phosphate from phosphoenolpyruvate (PEP) to ADP, forming ATP and pyruvate. It is activated by fructose 1,6-bisphosphate. It is irreversible.

physiological changes that promote a right shift of the oxygen dissociation curve

• High 2,3-BPG • Low pH • High [H+] • High pCO2 These all occur during exercise, giving the mnemonic: "Exercise is the right thing to do ."

NADH cannot cross the inner mitochondrial membrane. Therefore, one of two available shuttle mechanisms to transfer electrons in the mitochondrial matrix must be used.

• In the 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. • In the malate-aspartate shuttle, electrons are transferred from NADH to oxaloacetate, forming malate. Malate can then cross the inner mitochondrial membrane and transfer the electrons to mitochondrial NAD+, forming NADH.

Adaptation to high altitudes (low pO2) involves:

• Increased respiration • Increased oxygen affinity for hemoglobin (initial) • Increased rate of glycolysis • Increased [2,3-BPG] in RBC (over a 12-24 hour period) • Normalized oxygen affinity for hemoglobin restored by the increased level of 2,3-BPG • Increased hemoglobin (over days to weeks)

There are three stages of translation

• Initiation in prokaryotes occurs when the 30S ribosome attaches to the Shine-Dalgarno sequence and scans for a start codon; it lays down N-formylmethionine in the P site of the ribosome. • Initiation in eukaryotes occurs when the 40S ribosome attaches to the 5′ cap and scans for a start codon; it lays down methionine in the P site of the ribosome. • Elongation involves the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site. The now uncharged tRNA pauses in the E site before exiting the ribosome. • Termination occurs when the codon in the A site is a stop codon; a release factor places a water molecule on the polypeptide chain and thus releases the protein. • Initiation, elongation, and release factors help with each step in recruitment and assembly/disassembly of the ribosome.

Insulin and glucagon have opposing activities during most aspects of metabolism.

• Insulin causes a decrease in blood glucose levels by increasing cellular uptake. • Insulin increases the rate of anabolic metabolism. • Insulin secretion by pancreatic β-cells is regulated by blood glucose levels. • Glucagon increases blood glucose levels by promoting gluconeogenesis and glycogenolysis in the liver. • Glucagon secretion by pancreatic α-cells is stimulated by both low glucose and high amino acid levels.

post-transcriptional processing

• Intron/exon splicing • 5′ cap • 3′ poly-A tail

The membrane is not static.

• Lipids move freely in the plane of the membrane and can assemble into lipid rafts. • Flippases are specific membrane proteins that maintain the bidirectional transport of lipids between the layers of the phospholipid bilayer in cells. • Proteins and carbohydrates may also move within the membrane, but are slowed by their relatively large size.

Red blood cells extrude their mitochondria during development

• Maximizing volume available for hemoglobin, the primary oxygen-carrying protein • Stopping the red blood cell from utilizing the oxygen it's supposed to be carrying to oxygen-depleted bodily tissues

Most of gluconeogenesis is simply the reverse of glycolysis, using the same enzymes. The three irreversible steps of glycolysis must be bypassed by different enzymes:

• Pyruvate carboxylase converts pyruvate into oxaloacetate, which is con-verted to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase (PEPCK). Together, these two enzymes bypass pyruvate kinase. Pyruvate carboxylase is activated by acetyl-CoA from β-oxidation; PEPCK is activated by glucagon and cortisol. • Fructose-1,6-bisphosphatase converts fructose 1,6-bisphosphate to fructose 6-phosphate, bypassing phosphofructokinase-1. This is the rate-limiting step of gluconeogenesis. It is activated by ATP directly and glucagon indirectly (via decreased levels of fructose 2,6-bisphosphate). It is inhibited by AMP directly and insulin indirectly (via increased levels of fructose 2,6-bisphosphate). • Glucose-6-phosphatase converts glucose 6-phosphate to free glucose, bypassing glucokinase. It is found only in the endoplasmic reticulum of the liver.

Mechanism of Pyruvate Dehydrogenase

• Pyruvate dehydrogenase (PDH): Pyruvate is oxidized, yielding CO2, while the remaining two-carbon molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP). TPP is a coenzyme held by noncovalent interactions to PDH. Mg2+ is also required. • Dihydrolipoyl transacetylase: The two-carbon molecule bonded to TPP is oxidized and transferred to lipoic acid, a coenzyme that is covalently bonded to the enzyme. Lipoic acid's disulfide group acts as an oxidizing agent, creating the acetyl group. The acetyl group is now bonded to lipoic acid via thioester linkage. After this, dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA. Lipoic acid is left in its reduced form. • Dihydrolipoyl dehydrogenase: Flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions. As lipoic acid is reoxidized, FAD is reduced to FADH2. In subsequent reactions, this FADH2 is reoxidized to FAD, while NAD+ is reduced to NADH.

Point mutations can cause:

• Silent mutations with no effect on protein synthesis. • Nonsense (truncation) mutations that produce a premature stop codon. • Missense mutations that produce a codon that codes for a different amino acid.

What are the three major posttranscriptional modifications that turn hnRNA into mature mRNA?

• Splicing: removal of introns, joining of exons; uses snRNA and snRNPs in the spliceosome to create a lariat, which is then degraded; exons are ligated together • 5′ cap: addition of a 7-methylguanylate triphosphate cap to the 5′ end of the transcript • 3′ poly-A tail: addition of adenosine bases to the 3′ end to protect against degradation

Watson-Crick model.

• The backbone is composed of alternating sugar and phosphate groups, and is always read 5′ to 3′. • There are two strands with antiparallel polarity, wound into a double helix. • Purines (A and G) always pair with pyrimidines (C, U, and T). In DNA, A pairs with T (via two hydrogen bonds) and C pairs with G (via three hydro-gen bonds). RNA does not contain thymine, but contains uracil instead; thus, in RNA, A pairs with U (via two hydrogen bonds). • Purines and pyrimidines are biological aromatic heterocycles. Aromatic compounds are cyclic, planar, and conjugated, and contain 4n + 2 π elec-trons (where n is any integer; Hückel's rule). Heterocycles are ring structures that contain at least two different elements in the ring. • Chargaff's rules state that purines and pyrimidines are equal in number in a DNA molecule, and that because of base-pairing, the amount of ade-nine equals the amount of thymine, and the amount of cytosine equals the amount of guanine. • Most DNA is B-DNA, forming a right-handed helix. Low concentrations of Z-DNA, with a zigzag shape, may be seen with high GC-content or high salt concentration.

Acetyl-CoA can be formed from fatty acids, which enter the mitochondria using carriers.

• The fatty acid couples with CoA in the cytosol to form fatty acyl-CoA, which moves to the intermembrane space. • The acyl (fatty acid) group is transferred to carnitine to form acyl-carnitine, which crosses the inner membrane. • The acyl group is transferred to a mitochondrial CoA to re-form fatty acyl-CoA, which can undergo β-oxidation to form acetyl-CoA.

Body mass regulation is multifactorial with consumption and activity as modifiable factors.

• The hormones leptin, ghrelin, and orexin, as well as their receptors, play a role in body mass. • Long-term changes in body mass result from changes in lipid storage. • Changes in consumption or activity must surpass a threshold to cause weight change. The threshold is lower for weight gain than for weight loss. • Body mass can be measured and tracked using the body mass index (BMI).

The mitochondrial membrane differs from the cell membrane:

• The outer mitochondrial membrane is highly permeable to metabolic molecules and small proteins. • The inner mitochondrial membrane surrounds the mitochondrial matrix, where the citric acid cycle produces electrons used in the electron transport chain and where many other enzymes important in cellular respiration are located. The inner mitochondrial membrane also does not contain cholesterol.

Proteins located within the cell membrane act as transporters, cell adhesion molecules, and enzymes.

• Transmembrane proteins can have one or more hydrophobic domains and are most likely to function as receptors or channels. • Embedded proteins are most likely part of a catalytic complex or involved in cellular communication. • Membrane-associated proteins may act as recognition molecules or enzymes.

Lipids are the primary membrane component, both by mass and mole fraction.

• Triacylglycerols and free fatty acids act as phospholipid precursors and are found in low levels in the membrane. • Glycerophospholipids replace one fatty acid with a phosphate group, which is often linked to other hydrophilic groups. • Cholesterol is present in large amounts and contributes to membrane fluidity and stability. • Waxes are present in very small amounts, if at all; they are most prevalent in plants and function in waterproofing and defense.