MCAT Biology

Three meanings of oxidize

1. attach oxygen (or increase number of bonds to oxygen) 2. remove hydrogen 3. remove electrons

General principles on regulation

1. enzymes that catalyze irreversible reactions frequently sites of regulation 2. increased concentrations of intermediates in a pathway usually serve to decrease activity of that pathway (ex. citrate decreases activity of PFK in glycolysis) 3. each pathway responds to energy state of cell, cellular respiration stimulated by energy deficits (high ADP: ATP ratios, or NAD+:NADH ratios) or inhibited by energy surpluses.

Three meanings of reduce

1. remove oxygen (or decrease number of bonds to oxygen) 2. add hydrogen 3. add electrons

copy-number variations

CNVs, structural variations in genome leading to different copies of DNA sections. Large regions of genome (10^3 to 10^6 base pairs) can be duplicated (increasing copy number) or deleted (decreasing copy number). mechanism by which this occurs may be due to misalignment of repetitive DNA sequences during synapsis of homologous chromosomes in meiosis. .4% of genome can have CNV, are normal part of our genome but also have been associated with cancer and other diseases. Genes involved in immune system function and brain development and activity often enriched in CNVs.

Krebs Stage 2

Citrate is further oxidized to release CO2 and produce NADH from NAD+ with each oxidative decarboxylation. The two carbons that leave as CO2 are not the ones that entered as acetate.

nucleosomes

DNA has the microscopic appearance of being beads on a string. The beads, nucleosomes, are composed of DNA wrapped around an octamer of histones, the octamer composed of two units of each of the histone proteins H2A, H2B, H3, and H4. The string between the beads is a length of double-helical DNA called linker DNA and is bound by single linker histone. histones are mostly basic, since they must be attracted to the acidic exterior of the DNA double helix. basicity is supplied by amino acids arginine and lysine, usually abundant in histones.

watson-crick model (structure of DNA, numbers, bonds)

DNA is a right-handed double helix (corkscrews in clockwise motion) held together by double bonds between bases. Two long polynucleotide chains are bonded together in antiparallel orientation, making DNA double-stranded. H-bonds are between the bases on adjacent chains, A always bonded to T, G always bonded to C. (An H-bond pair always consists of a purine and a pyrimidine, thus each pair takes up the same amount of room in the helix). GC is held together by three hydrogen bonds, AT is held together by two. Two strands are said to be complementary if the bases in each strand can hydrogen bond when the strands are oriented in antiparallel fashion. Talking about length, a double stranded DNA 100 nucleotides long has length 100 base pairs (bp), 1000 long has a kbp (kilobase pair). The ribose/phosphate backbone is on the exterior with the bases on the interior, and hydrophobic interactions between the bases are important in stabilizing the double helix. the bases lie in a plane, perpendicular to the length of the DNA molecule, stacked 3.4 angstroms apart from each other, the helix pattern repeats (completes a full turn) once ever 34 angstroms (every 10 base pairs)

deoxynucleoside triphosphates

DNTP, nucleotides containing three phosphate residues. In specific nucleotides N is replaced by A,G,C,T, or U (N standing for nucleoside).

structure of DNA in the nucleus

Doxyribose -> add base -> nucleoside -> add three phosphates -> nucleotide -> polymerize with loss of two phosphates -> oligonucleotide -> continue polymerization -> single stranded polynucleotide -> two complete chains H-bond in antiparallel orientation -> ds DNA chain -> coiling occurs -> ds helix -> wrap around histones -> nucleosomes -> complete packaging -> chromatin. Each individual double-stranded piece of chromatin is condensed into a chromosome during mitosis and meiosis.

Pathway regulation

Essentially irreversible steps are most likely to be regulated by allosteric regulation. Earlier steps in a long pathway tend to be regulated over later ones.

Active site

Folding is important because it forms the active site, the region in an enzyme's three-dimensional structure that is directly involved in catalysis. The active site for enzymes is generally highly specific in its substrate recognition, including stereospecificity. enzymes that cleave proteins at hydrophobic residues have hydrophobic residues at their active site, and those that cleave polar/hydrophilic substrates will comprise the active site with hydrophilic amino acids.

purines vs. pyrimidines

G and A are purines, C and T are pyrimidines

Amino acids

KNOW ALL 20, study with another set!

Michaelis constant

Km = [S] when V=Vmax/2. Km is unique for eqch enzyme-substrate pair and gives info on the affinity of the enzyme for its substrate. Low Km means not much substrate needed to get reaction to half max, so there is high affinity.

nucleotide

Nucleotides are phosphate esters of nucleosides, with one, two, or three phosphate groups joined to the ribose ring by the 5' hydroxy group. because they contain acidic phosphates, may be referred to by name ending in "ylate" ex. TTP is thymidylate, ATP is adenylate.

Krebs Stage 3

OAA is regenerated so that cycle can continue. Reducing power is stored in 1 NADH, 1 FADH2, and a high=energy phosphate bond is produced directly as GTP (which eventually transfers its high energy phosphate bond to ADP to convert it to ATP). FADH2 is similar to NADH but results in less ATP production.

Fermentation

Under aerobic conditions, pyruvate from glycolysis enters the PDC and Krebs cycle to be oxidized completely to CO2, and the NADH and FADH2 are all oxidized with oxygen as the final electron acceptor. In anaerobic conditions electron transport cannot function and fermentation takes place. All of the limited supply of NAD+ had been reduced to NADH. Fermentation regenerates NAD+ allowing glycolysis to continue in the absence of O2. Uses pyruvate as acceptor of high energy electrons from NADH. The lactate that is produced (or ethanol in yeast/other organisms) builds up and acts as a poison at high concentration so fermentation cannot continue indefinitely

reaction rate

V, for velocity, the amoutn of product formed per unit time, in moles per second. Depends ont he concentration of substrate and enzyme. If there is little substrate, V is directly proportional to the amount of substrate added. At some point there is so much substrate that adding more doesn't increase the reaction rate much and the slope of V vs. [S] starts to level off, eventually plateauing when there is so much substrate that every active site is continuously occupied and the enzyme is saturated (Vmax). Usually concentration of enzyme is kept fixed while substrate concentrations are changed.

prosthetic group

a nonprotein molecule covalently bound to an enzyme as part of the enzyme's active site. ex. PDC contains a thiamine pyrophosphate (TPP) prosthetic group at one of its active sites. The alpha-ketoglutarate deyhdrogenzes complex, which catalyzes the third step in the Krebs cycle also has TPP and catalyzes an oxidative decarboxylation. The thiamine in TPP is vitamin B1. Vitamins often serve as prosthetic groups

recognition pocket

a pocket in the enzyme's structure which attracts certain residues on substrate polypeptides. The enzyme always cuts polypeptides just to one side of the recognition residue ex. chymotrypsin always cuts on carboxyl side of large hydrophobic residues Tyr, Trp, Phe, and Met.

annealing

a.k.a hybridization, the binding of two complementary strands of DNA into a double stranded structure.

Feedback inhibition

a.k.a negative feedback - when the presence of a product goes back and regulates the enzyme that catalyzes the first irreversible step in order to conserve starting material and energy. while positive feedback exists, it is much less common. Thus enzymes act as valves, regulating the flow of substrates into products.

Krebs Cycle

a.k.a tricarboxylic acid cycle (TCA cycle) or citric acid cycle, third stage of cellular respiration. Acyl group from PDC is added to oxaloacetate to form citric acid, which is then decarboxylated and isomerized to regenerate original oxaloacetate. Modest amount ATP, a large amount of NADH, and a small amount of FADH2 are produced. Occurs in the matrix. Requires oxygen though does not use it directly. Third stage of cellular respiration. ` group of reactions that takes 2-carbon acetyl unit from acetyl-CoA and combines it with oxaloacetate and releases two CO2 molecules. NADH and FADH2 generated in the process. Oxaloacetate (4 C) converts to Citrate (6C) upon addition of acetyl-CoA, then decarboxylation of citrate and reduction of NAD+ gives a 5 carbon molecule, then the same step again gives a 4 carbon molecule, then GTP is produced, NADH and FADH2 are produced and we are back at Oxaloacetate.

induced fit model

asserts that the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme.

noncompetitive inhibitor

bind at allosteric site, not at active site. No matter how much substrate you add, inhibitor will not be displaced from its site of action, so does diminish Vmax. Km not altered because substrate can still bind to active site, but inhibitor prevents catalytic activity of enzyme.

enzymes (and types of enzymes)

catalysts with only a kinetic role in test tubes, but with a kinetic and thermodynamic role in the body (selectively promotes unfavorable reactions via reaction coupling, ex. ATP). most are proteins but some are RNA or contain RNA sequences with catalytic activity. Most catalyze their own splicing, and the rRNA in ribosomes helps in peptide-bond formation. Types: hydrolase -- hydrolyzes chemical bonds (includes ATPases, proteases, and others) Isomerase -- rearranges bonds within a molecule to form an isomer Ligase -- forms a chemical bond (ex. DNA ligase) Kinase -- transfers a phosphate group to a molecules from a high energy carrier, such as aTP (ex. PFK) Oxidoreductase -- runs a redox reaction (includes oxidases, reductases, dehydrogenases, and others) Polymerase -- polymerization (ex. add nucleotides to leading strand of DNA by DNA polymerase III) Phosphatase -- removes a phosphate group from a molecule Phosphorylase -- transfers a phosphate group to a molecules from inorganic phosphate (ex. glycogen phosphorylase) Protease -- hydrolyzes peptide bonds (ed. trypsin, chymotrypsin, pepsin, etc.)

Hexokinase

catalyzes the first step in glycolysis, the phosphorylation of glucose to G6P. G6P feedback inhibits hexokinase.

Phosphofructokinase (PFK)

catalyzes the third step of glycolysis: the transfer of a phosphate group from ATP to fructose-6-phosphate to form fructose-1,6-bisphosphate (F1,6bP). This step is thermodynamically very favorable so essentially reversible. Also G6P can go down various pathways but F1,6bP can only react in glycolysis. This step is a committed step. Allosterically regulated by ATP.

feedforward stimulation

common, involves stimulation of enzyme by its substrate, or by a molecule used in the synthesis of the substrate.

chylomicrons

composed of fat and lipoprotein, transported via lymphatic system and blood stream to liver, heart, lungs, and other organs. this dietary fat a.k.a triacylglycerol is hydrolyzed to liberate free fatty acids which then undergo beta-oxidation. degraded by lipases into triglycerides, glycerol and cholesterol rich chylomicron remnants that are taken up by hepatocytes and combined with proteins to make lipoproteins (HDL, LDL, VLDL, etc.) that then re-enter the blood and are a source of cholesterol and triclycerides for other tissues of the body.

intergenic regions

composed of noncoding DNA, may direct the assembly of specific chromatin structures, and can contribute to regulation of nearby genes, but may have no known function. human genome has numerous regions with high transcription rates (rich in genes) separated by long stretches of intergenetic space. Tandem repeats and transposons are major components of intergenic regions.

Four types of enzyme regulation

covalent modification, proteolytic cleavage, association with other polypeptides, and allosteric regulation.

building block of DNA (3 parts)

deoxyribonucleoside 5' triphosphate (DNTP). Deoxyribonucleotides built from a simple monosaccharide (ribose), an aromatic, nitrogenous base (due to ability to accept protons on Ns) (adenine (A), guanine (G), cytosine (C), or thymine (T)), and finally a phosphate group.

Pentose phosphate pathway (PPP)

diverts glucose-6-phosphate from glycolysis in order to form among several other products ribose-5-phosphate which can be used to synthesize nucleotides. This cytoplasmic pathway, sometimes called shunt, is composed of oxidative phase (also generates NADPH) followed by non-oxidative phase producing additional sugar precursors. NADPH shares much structure w/ NADH but has different cellular role and serves as important reducing agent in many anabolic processes. Also aids neutralization of reactive oxygen species. First enzyme in PPP is glucose-6-phophate dehydrogenase (G6PDH), is primary point of regulation and generates NADPH. deficiency in this enzyme limits abilities of red blood cells to eliminate reactive oxygen species which an lead to cell death and potential renal and hepatic complications.

ketogenesis

during periods of starvation, glycogen stores become exhausted and blood glucose falls significantly. To help supply central nervous system with energy when glucose is in short supply, liver generates ketone bodies via ketogenesis in the mitochondrial matrix. ketone bodies include acetone, acetoacetate, and beta-hydroxybutyrate which can be conveted back to acetyl-CoA once they arrive at target organ and enter krebs cycle. In some circumstances ketogenesis can take place when adequate glucose present in blood, but cannot enter clel, ex. when patient suffering from type I diabetes doesn't get insulin for a long time resulting in diabetic ketoacidosis, potentially life-threatening condition. In pseudo-starved state liver begins to generate ketone bodies in attempt to provide body with source of energy causeing patients fatigue, confusion, and fruity-scented breath due to acetone presence in blood. they are often mistaken for intoxicated individuals.

DNA gyrase

enzyme that uses energy of ATP to twist gigantic circular chromosome. functions by breaking DNA and twisting the two sides of the circle around each other resulting in a twisted circle that is composed of ds-DNA. twists created by DNA gyrase are called supercoils, since they are coils of a structure already coiled.

gene

DNA sequence that encodes a gene product, including regulatory regions (ex. promoters and transcription stop sites) and a region that codes for either a protein or a non-coding RNA. the fundamental unit of inheritance.Every gene can be pinpointed to a specific locus on a specific chromsome.

anabolism

building up metabolism, synthesis of macromolecuels

cystine

cysteine involved in a disulfide bond (oxidized cysteine)

NADH

electron carrier, molecule responsible for shuttling energy in the form of reducing power (reduction potential).

protein functions in the body include

enzymes, structural roles, hormones, receptors, channels, antibodies, transporters, etc.

histones

globular proteins around which eukaryotic DNA is wrapped.

genomic variation

human genome has 24 different chromosomes (22 autosomes, two sex chromosomes), 3.2 billion base pairs, codes for 21,000 genes. sequence of human genome reported by human genome project lead by Dr. Francis Collins and independently by Celera Genomics' Dr. J. Craig Venter both in 2001.

nucleoside

ribose with a purine or pyrimidine linked to the 1' carbon in a beta-N-glycosidic linkage. A-ribose = adenosine, G-ribose = guanosine, C-ribose = cytidine, T-ribose = thymidine, and U-ribose = uridine. all have great hydrogen bonding potential.

catabolism

the process of breaking down molecules to supply energy

Enthalpy

∆H = ∆E - P∆V Here E represents the bond energy of products or reactants in a system. Most metabolic reactions are exothermic (which is how homeothermic organisms ex. mammals maintain a constant body temp).

make up of the electron transport chain

five electron carriers named for their redox roles. three are large protein complexes embedded in inner mitochondrial membrane classified as cytochromes due to presence of heme group (porphyrin ring containing tightly-bound iron atom). Other tow are small mobile electron carriers. Chain is organized such that first large carrier (NADH dehydrogenase a.k.a coenzyme Q reductase) receives electrons from NADH and passes them to one of the small carriers ubiquinone (a.k.a coenzyme Q). Ubiquinone then passes electrons to second large membrane-bound complex in the chain cytochrome C reductase which passes electrons to cytochrome C, a small hydrophilic protein bound loosely to the inner mitochondrial membrane. Last member of chain is cytochrome C oxidase, which passes its electrons to O2, the final electron acceptor. Each of the large membrane-bound proteins in the chain pumps protons across the inner mitochondrial membrane into the inter-membrane space creating a large proton gradient, with the pH being much higher inside the matrix than in the rest of the cell. Then ATP synthase embedded in the mitochondrial membrane contains a proton channel spanning the inner membrane, and uses passage of protons to produce ATP from ADP + Pi. The process of electron transport and ATP production is thus coupled to the proton gradient. Together ATP production and electron transport are known as oxidative phosphorylation.

chromatin

fully packed DNA, composed of closely stacked nucleosomes.

Cellular respiration

glucose oxidized to release energy. oxidation of glucose accompanied by reduction of nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD) to NADH and FADH2 (these are high-energy electron carriers) and are later oxidized when deliver electrons to electron transport chain. This generates proton gradient used to generate ATP. FAD and NAD+ can serve as enzymatic cofactors. NAD+ required for activation of adenylate cyclase by cholera toxin, and FAD can associate with a protein to become a flavoprotein (well characterized and commonly involve din redox reactions).

glycolysis

glucose splitting, glucose is partially oxidized while it is split in half into two identical pyruvic acid molecules. First stage of cellular respiration. Glycolysis produces small amount ATP and small amount of NADH. occurs in the cytoplasm and does not require oxygen. All cells from all domains possess the enzyme of this pathway. Produces a net of 2 ATP and 2 NADH. NADH is produced in only one step (when an aldehyde is oxidized to a COOH). ATP is converted to ADP every time a phosphate is added to substrate, and ADP is converted into ATP every time a phosphate comes off a substrate (exception being HPO 2- which gets picked up from medium in step 5).

glycogenolysis

glycogen breakdown. glycogen is polymer of glucose found in muscle and liver cells, main form of carb storage in animals. controlled by hormones that regulate blood sugar level and energy, occurs in response to hormone glucagon when blood sugar levels are low, results in glucose release into blood to initiate glycolysis. Similar process occurs in plants where polymerized glucose in form of starch can be broken down for various cellular processes including glycolysis. both glycogen and starch are glucose polymers with alpha 1,4 and alpha 1,6 glycosidic bonds.

cellular respiration product count

glycolysis: 4 ATP, 2 NADH, -2ATP (so net 2 ATP) per glucose molecule Pyruvate Dehydrogenase: 2 NADH per glucose (one per pyruvate) Krebs Cycle: 6 NADH, 2 FADH2, and 2 GTP per glucose Each NADH molecule oxidized causes 10 protons to be pumped across the membrane, at a cost of 4 protons/ATP synthesized, this yields 2.5 ATP/NADH. FADH2 bypasses NADH dehydrogenase, delivering electrons directly to ubiquinone and thereby causing only 6 protons to be pumped across the membrane, yielding 1.5 ATP/FADH2. Cytosolic NADH produces only 1.5 ATP/NADH due to the cost of transporting it across the mitochondrial membrane.

covalent modification

groups covalently attached to proteins can alter lifespan, cellular location or activity. can change protein subcellular localization, target a protein for degradation, change interactions between proteins and other molecules, activate or inhibit enzyme activity, change enzyme affinity for substrates, etc. typically studied in lab w/ mass spectrometry, western blotting, or eastern blotting. Types include but not limited to: acetylation, formylation, glycosylation, phosphorylation, sulphation

electron transport/oxidative phosphorylation

high energy electrons carried by NADH and FADH2 oxidized by the electron transport chain in the inner mitochondrial membrane. reduced electron carriers dump their electrons at the beginning of the chain and oxygen is reduced to H20 at the end. This liberated energy is used to pump protons out of the innermost compartment of the mitochondria. The protons are allowed to flow back into the mitochondrion, and the energy of this proton flow is used to produce the high-energy triphosphate group in ATP. Goals are to oxidize all the electron carriers reduced in glycolysis, PDC, and the Krebs cycle, and store energy in form of ATP. For each glucose catabolyzed, two NADH created by glycolysis in cytoplasm. These electrons need to be transported into the mitochondria before can go into chain, all other FADH2 and NADH produced in matrix so already in the right place. In prokaryotes, all reduced electron carriers located in cytoplasm bc no membrane-bound organelles at all, they create proton gradient on cell membrane (instead of inner mitochondrial membrane) and use ATP synthase (membrane bound) to produce ATP

transposons (three types, different parts, what they do)

in both prokaryotse and eukaryotes, mobile genetic elements in genomes (transposable elements), thought that many eukaryotic transposons degenerate retroviruses (old and defective). genetic mobility = these short segments can jump around in genome. transposons can cause mutations and chromosome changes (ex. inversions, deletions, rearrangements). Three common types: 1. IS element -- transposase gene flanked by inverted repeat sequences. 2. complex transposons -- contain additional genes, ex. genes for antibiotic resistance 3. composite transposons -- two similar or identical IS elements with central region in between. all transposons contain gene that codes for a protein called transposase. This enzyme has cut and paste activity, catalyzing mobilization of transposon (excision from donor site) and integration into new genetic location (acceptor site). Sometimes transposon sequence completely excised and moved, sometimes duplicated and moved, while still maintaining original location. inverted repeats important for mobilization. Many mobilizations have no affect because transposon inserts into relatively unimportant part of genome, however transposons can cause mutations if they jump into important part of genome.

uncompetitive inhibitor

inhiibtor only able to bind to enzyme-substrate complex (cannot bind before substrate is bound), referred to as uncompetitive inhibitor. Decrease Vmax by limiting amount of available enzyme-substrate complex that can be converted into product. Decreases Km because sequesters enzyme bound to substrate thus increasing the apparent affinity of the enzyme for the substrate by rpeventing dissociation.

Cori cycle

lactate from fermentation is exported from the muscle cell to the liver where oxygen becomes available and it is converted bck into pyruvate while making NADH from NAD+. Then the excess NADH is used to make ATP in oxidative phosphorylation. The pyruvate can enter gluconeogenesis, the Krebs cycle in the liver, or can be sent back to the muscle.

chromosome (eukaryotic vs. prokaryotic)

large piece of linear ds-DNA (double stranded DNA), found in eukaryotes. Humans have 46, 23 of which are inherited form each parent. prokaryotic genomes have a single circular chromosome. Viral genomes may have linear or circular DNA or RNA. Human genome has over 10^9 base pairs, bacterial genomes contain only 10^6 base pairs. largest known genomes in amphibians. Much of size difference in higher eukaryotic genomes is result of repetitive DNA with no known function.

phosphodiester bonds

links nucleotides in the DNA chain covalently between the 3' hydroxy group of one deoxyribose and the 5' phosphate group of the next deoxyribose.

Active site model

lock and key hypothesis, states that the substrate and active site are perfectly complementary.

Proteolytic cleavage

many enzymes and other proteins are synthesized in inactive forms (zymogens) that are activated by cleavage by a protease.

cofactors

metal ions or small molecules (not themselves a protein) required for activity in many enzymes. Majority of vitamins in our diet serve as precursors for cofactors ex. niacin (B3) for NAD+. When a cofactor is an organic molecule, it is called a coenzyme. coenzymes often bind to the substrate during the catalyzed reaction ex. coenzyme A (CoA). various organic and inorganic substances necessary to the function of an enzyme but which never actually interact with the enzyme.

oxidative decarboxylation

molecule is oxidized to release CO2 and produce NADH. ex. pyruvate is changed from a 3-carbon molecule to a 2 carbon molecule where CO2 is given off and NADH is produced.

competitive inhibition

molecules that compete with substrate for binding at active site. structurally resemble the substrate (or transition state, which enzyme active site usually stabilizes). Their inhibition can be overcome by adding more substrate, so Vmax is not affected

Glycogen regulation

must be synthesized and broken down in response to changes in blood glucose and metabolic state. Glycogen synthase (principle enzyme responsible for glycogen generation from glucose-1-phosphate) and glycogen phosphorylase (catabolizes glycogen) reciprocally controlled. Immediately following meal, elevated levels of insulin activate glycogen synthase and inhibit glycogen phosphorylase. This stimulates glycogen synthesis while inhibiting its breakdown. glucagon results in suppression of glycogen synthesis and stimulation of glycogenolysis from liver (but not muscle).

mixed-type inhibition

occurs when an inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex. If enzyme has greater affinity for inhibition in free form, enzyme will have lower affinity for substrate similar to compeititve inhibition (Km increases). If enzyme-substrate complex has greater affinity for inhibitor, enzyme will have apparently greater affinity (Km decreases) for substrate similar to uncompetitive inhibition. If equal affinity both forms, would be a noncompetitive inhibitor.

gluconeogenesis

occurs when dietary source of glucose unavailable and liver has depleted stores of glycogen and glucose, occurs primarily in liver and to lesser extent in kidneys, involves converting non-carb precursor ex. lactate, pyruvate, krebs cycle intermediates, and carbon skeletons of most amino acids, into intermediates in pathway to beocme glucose. 11-step pathway that uses many of same enzymes as glycolysis. pyruvate carboxylase catalyzes conversion of pyruvate to oxaloacetate which an be further converted into phosphoenolpyruvate, second to last product in glycolysis. glycerol backbone of a triglyceride can be converted to glucose during periods of starvation but free fatty acids cannot because acetyl-CoA cannot take part in gluconeogenesis.

reaction coupling

one very favorable reaction is used to drive an unfavorable one. Free energy changes are additive.

structure of the mitochondria

outer membrane and inner membrane, each composed of lipid bilayer. Outer membrane is smooth and contains large pores formed by porin proteins. Inner membrane is impermeable even to very small items like H+ and is densely folded into cristae, which extend into the matrix, the innermost space of the mitochondrion. The space between the two membranes (inter-membrane space) is continuous with the cytoplasm due to large pores in outer membrane. enzymes of Krebs cycle and Pyruvate dehydrogenase complex located in matrix, and those of electron transport chain and ATP synthase involved in oxidative phosphorylation bound to inner mitochondrial membrane.

photoautotrophs and chemoheterotrophs

photoautotrophs -- use energy from light to make their own food ex. plants. chemoheterotrophs -- use energy of chemicals produced by other living things ex. us Plants and animals store chemical energy in reduced molecules ex. carbs and fats, these are oxidized to CO2 and ATP, energy of ATP is used to drive energetically unfavorable reactions in the cell.

heterochromatin and euchromatin

portions of condensed chromasomes that stain darker and are denser, rich in repeats. the lighter regions are less dense and are called euchromatin. density gives a sense of DNA coiling or compactness and these patterns are constant and heritable. lighter regions have higher transcription rates and therefore higher gene activity (looser packing makes DNA accessible to enzymes and proteins).

Why DNA and RNA are called nucleic acid?

possess many acidic phosphate groups

beta-oxidation

process begins at outer mitochondrial membrane with activation of fatty acid. reaction is catalyzed by acyl-CoA synthetase, requires investment of two ATP equivalents to generate fatty acyl-CoA, which is then transported into mitochondrion. Once in matrix, fatty acyl-CoA undergoes repeated series of four reactions which cleave bond between alpha and beta carbons to liberate an acetyl-CoA in addition to generation one FADH2 and NADH. Each round of beta oxidation cleaves two carbon-acetyl-CoA from the molecule however final round cleaves four-carbon fatty acyl-CoA to generate two acetyl-CoA. oxidation of unsaturated fatty acids containing double bonds requires additional steps. for monounsaturated fatty acid, beta oxidation proceeds normally, cleaving tow carbon subunits from fatty acid until double bond encountered. isomerase then moves double bonds and allows oxidation to continue. If fatty acid contains several double bonds, both isomerase and a reductase are required to allow fatty acid to continue through beta oxidation.

proteases

protein-cleaving enzymes, many have serine residue at active site whose OH can act as a nucleophile, attacking the carbonyl carbon of an amino acid residue in a polypeptide chain ex. trypsin, chymotrypsin, and elastase. These enzymes also usually have a recognition pocket near the active site.

Amino acid catabolism

proteins in cells constantly being made then degraded back to amino acids. humans also absorb amino acids from dietary proteins. Free amino acids catabolized via several pathways. Amino group removed and converted into urea for excretion. remaining carbon skeleton (alpha-keto acid) either broken down into water and CO2 or converted to glucose or acetyl-CoA.

pyruvate dehydrogenase complex

pyruvate produced in glycolysis is decarboxylated to form an acetyl group that is then attached to coenzyme A (a carrier that can transfer the acetyl group into the Krebs cycle, basically a long handle with a sulfur at the end, abbreviated CoA-SH) to produce acetyl-coA. Bond between sulfur and acetyl group is very high energy making it easy for acetyl CoA to transfer acetyl fragment into Krebs cycle for further oxidation. A small amount NADH is produced. Second stage of cellular respiration. Occurs in the matrix. Requires oxygen though does not use it directly.

centromere (and kinetochore)

region of the chromosome to which spindle fibers attach during cell division. Fibers attach via kinetochores, multi-protein complexes that act as anchor attachment sites for spindle fibers. Other protein complexes bind centromere after DNA replication to keep sister chromatids attached to each other. Centromeres are made up of heterochromatin, and repetitive DNA sequences. They have p (short) and q (long) arms, and centromere position defines the ratio between the two (metacentric if in the middle, submetacentric if short arms shorter and long arms longer, acrocentric if short arms really short, telocentric if essentially only one arm on each chromatid). centromeres are there to ensure that newly replicated chromosomes are sorted properly during cell division, one copy to each daughter cell. telomerase is turned off in most cells and its inactivity is associated with aging and death.

backbone of DNA

ribose and phosphate portion of the nucleotide (as it is invariant).

PFK and fructose-1,6-bisphosphatase (F-1,6-BPase), PFK-2 and F-2,6-BPase).

serve opposing roles in glycolysis and gluconeogenesis respectively, both allosterically regulated by glycolytic intermediates that activate one enzyme while inhibiting the other. ex. in energy-starved states elevated AMP levels activate PFK while inhibiting F-1,6-BPase, resulting in more glycolysis and less gluconeogenesis. fructose-2,6-bisphosphatase (F-2,6-BP) has concentration set by PFK-2 which sythesizes it and F-2,6-BPase which breaks it down. Insulin and glucagon help control concnentration of intracellular F-2,6-BP by regulating activity of PFK-2 and F-2,6-BPase. Glocagon binds cell surface receptors in the liver resulting in production of cAMP and activation of protein kinase A leading to deactivation of PFK-2 and activation of F-2,6-BPase. Increased F-2,6-BPase activity consumes F-2,6-BP enhancing activity of F-1,6-BPase (enzyme from gluconeogenesis) while decreasing PFK activity. net result is increase in gluconeogenesis and inhibition of glycolsis to allow for restoration of normal blood glucose levels. insulin does the opposite.

chains of nucleotides

several linked together is an oligonucleotide, many is a polynucleotide. Sequences are written using base letters (ACGT) from the 5' to the 3' (the end of the chain with a free 5' phosphate group on the left, the end with a free 3' hydroxy group on the right.)

glycerol phosphate shuttle

shuttle that delivers electrons directly to ubiquinone from cytoplasm, so cytosolic NADH makes only 1.5 ATP instead of 2.5, yielding an overall difference of 2 ATP when eukaryotes do it as opposed to prokaryotes (no membrane to transport it across as all stages are done in the cytoplasm).

residue

single amino acid in a polypeptide chain

Tandem repeats vs. single copy

single copy = there is one copy of a gene in a haploid set of the genome, tandem repeats = regions where short sequences of nucleotides are repeated one after the other, from 3 to over 100 times. human genome has over a thousand regions of tandem repeats, can be unstable, when repeating unit is short (2-3 nucleotides) or when repeat itself is very long. Unstable tandem repeats can lead to chromosome breaks and some have been implicated in disease. Tandem repeats often show variations in length between individuals, useful in DNA fingerprinting. Heterochromatin, centromeres and telomeres all rich in repeats.

single nucleotide polymorphisms (SNPs, pronounced snips).

single nucleotide changes once in every 1,000 base pairs in the human genome. essentially mutations. occur most frequently at noncoding regions of the genome, however some can lead to specific traits or phenotypes ex. 70% of people taste phenylthiocarbamide (PTC) as very bitter and the remaining 30% don't taste it at all. This ability is dominant trait determined by gene on chromosome 7, three SNPs in this gene determine PTC taste sensitivity.

Fatty acid synthase

single peptide with multiple catalytic domains, catalyzes decarboxylation requires NADPH from pentose phosphate pathway. Involved in fatty acid synthesis.

Association with other polypeptides

some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit, ex. some demonstrate continuous rapid catalysis if their regulatory subunit is removed (constitutive activity). Others require association with another peptide to function. Some can bind many regulatory subunits.

fatty acid synthesis

takes place in cytoplasm, involves repeated addition of two-carbon subunits. acetyl-coA is activated in carboxylation reaction (the committed step) and requires investment of ATP, facilitated by acetyl-CoA carboxylase to generate malonyl-CoA. Fatty acid synthase, a single peptide with multiple catalytic domains, then catalyzes decarboxylation reaction where malonyl-CoA provides two carbons to growing fatty acid. synthesis requires NADPH generally obtained from pentose phosphate pathway. Once sixteen-carbon long fatty acid generated, additional enzymes aid in further modification (addition of functional groups and elongation, etc.). No template required, differs from synthesis of polypeptides and nucleic acids in this way. lack of specific enzyme (usually due to genetic mutations) can result in certain fatty acids or amino acids being required in diet, leading to their categorization as essential fatty acids or amino acids.

cooperativity

the binding of one substrate to one subunit allosterically increase the affinity of the other subunits for substrate. conformation pre-substrate binding and w/ low affinity is tense, after conformational change is relaxed. The binding of one substrate molecule to the enzyme complex enhances the binding of more substrate molecules to the same complex. cooperative enzymes must have more than one active site, usually multi-subunit complexes, composed of more than one protein chain held together in a quaternary structure. Also may be single subunit w/ 2 or more active sites. A sigmoidal (S-shaped) curve results from cooperative binding.

telomeres

the ends of linear chromosomes. At DNA level, these regions distinguished by presence of distinct nucleotide sequences repeated 50 to several hundred times. repeated unit is usually 6-8 base pairs long and guanine rich. Many vertebrates have same repeat: 5'-T-T-A-G-G-G-3'. Telomeres composed of both single and double stranded DNA. Single stranded DNA found at very end of chromosome and is about 300 base pairs in length, loops around to form a knot, held together by many telomere-associated proteins, stabilizing end of chromosome. specialized telomere cap proteins distinguish telomeres from double stranded breaks, preventing activation of repair pathways. Telomeres funciton to prevent chromosome deterioration and prevent fusion with neighboring chromosomes. Function as disposable buffers, blocking ends of chromosomes. DNA replication of telomeres represents special challenge to cellular machinery since most prokaryotes have circular genomes their DNA does not contain telomeres. With the help of a special DNA polymerase telomerase, maintains the ends of the linear chromosomes during DNA replication in eukaryotes.

Allosteric regulation

the modification of the active-site activity through interactions of molecules with other specific sites on the enzyme (called allosteric sites).

cholesterol

the presence of cholesterol raises the melting point and lowers the freezing point (makes the membrane less rigid at low temp and more rigid at high temp)

photosynthesis

the process by which plants store energy from the sun in the bond energy of carbohydrates.

melting or denaturation

the separation of two complementary strands of DNA from a double-stranded structure. The temperature at which 50% of DNA molecules are melted is termed Tm

Enzyme kinetics

the study of the rate of formation of products from substrates in the presence of an enzyme.

genome

the sum total of an organism's genetic information

oxidative catabolism

the way we extract energy from glucose. first glycolysis, then the pyruvate dehydrogenase complex (PDC), the Krebs cycle, and electron transport/oxidative phosphorylation. C6H12O6 + 6O2 -> 6CO2 + 6H2O We make the unfavorable synthesis of ATP happen by coupling it to the very favorable oxidation of glucose.

Regulation of Krebs cycle

transformation of pyruvate to acetyl-CoA by PDC regulated in response to concentrations of NAD+ (high = energy deficit), enzymes catalyzing exergonic (irreversible) steps in Krebs cycle also regulated. activity of isocitrate dehydrogenase also changes with energy needs of cell (elevated ATP inhibits enzyme).

Krebs Stage 1

two carbons in the acetate fragment of acetyl-CoA are condensed with the 4-carbon oxaloacetate (OAA) producing citrate.

Giemsa stain

used to stain DNA, produces G-banding patterns. Dark staining regions are more dense than lighter staining regions. chromosome bands are constant and specific to each chromosome, meaning they can be used for diagnostic purposes (where cytologists look at chromosome structure). Banding patterns also linked to DNA replication, lighter staining regions start replication earlier than darker staining regions likely due to accessibility of the DNA. Staining usually is done on chromosomes in metaphase as they are compact and easier to see.

futile cycling

when two pathways serving opposing roles, ex. glycolysis and gluconeogenesis, are agtivated simultaneously causing net loss of energy. Tight regulation resulting in reciprocal control in response to current cellular needs prevents this. comparmentalization, regulation of enzyme quantity, and regulation of enzyme activity all used.