BIO 121 Chapters 9, 12, 13 Exam

Metabolic pathways

Metabolic pathways

• harvest energy from high-energy molecules such as glucose

• cellular respiration is critical and often interacts with other pathways

• comprises thousands of different chemical reactions that may be organized and regulated

Cellular respiration

• occurs through a long series of carefully controlled redox reactions (conserves energy/prevents mini explosions) that use the electrons of high-energy molecules to make ATP

• oxygen atoms are reduced to form water

• glucose + 6 oxygen gas + ADP + inorganic Phosphate —> 6 carbon dioxide + 6 water + ATP

• consists of 4 processes: glycolysis, pyruvate processing, Krebs cycle, and electron transport and oxidative phosphorylation

Glycolysis overview

• a series of 10 reactions that occurs in the cytosol of eukaryotes and prokaryotes

• net yield of 2 NADH, 2 ATP, 2 H2O, and 2 pyruvate for every glucose

• glucose + 2 ATP —> 2 (NADH + H+) + 4 ATP + 2 Pyruvate + 2 H2O

Phosphofructokinase (PFK)

• uses ATP to phosphorylate the end of fructose-6-phosphate to form fructose-1,6-bisphosphate

• increases potential energy

Pyruvate processing

• occurs in the matrix of the mitochondria or the cytosol of prokaryotes

• for eukaryotes, pyruvate is transported from the cytosol to the mitochondrial matrix

• catalyzed by pyruvate dehydrogenase, an enormous enzyme complex which is regulated by a negative feedback loop involving ATP

• 2 pyruvate + 2 NAD+ + 2 Coenzyme A —> 2 acetyl CoA + 2 CO2 + 2 NADH

• Decarboxylation: the carboxyl group on pyruvate (the 3rd carbon) is released as CO2

Kinase

• enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule

Phosphotase

• enzyme that removes phosphate group

Krebs cycle (citric acid cycle)

• also occurs in the matrix of the mitochondria or the cytosol of prokaryotes

• 2 turns of the citric acid cycle for each glucose molecule

• Potential energy is released to reduce coenzymes

• The acetyl group (2C) from acetyl CoA is transferred to oxaloacetate (4C) to form citrate (6C); oxaloacetate is regenerated at the end (cycle)

• 8 reactions

• 2 acetyl coA —> 6 NADH + 6H+ + 2 FADH2 + 2 ATP + 4CO2

Electron transport and oxidative phosphorylation

• electron transport chain consisting of 4 main protein complexes establishes a proton gradient that is used to produce ATP

• uses NADH and FADH2 produced in previous steps to generate the protein gradient, which contributes to the phosphorylation of ADP

• uses O2 (oxygen gas) and produces ATP and water

• occurs across the inner membrane of the mitochondria or the plasma membrane + the periplasm of prokaryotes

• a small amount of energy is released in each reaction; each successive bond/molecule in the ETC holds less potential energy ; after the ETC, most of the chemical energy from glucose is accounted for by a proton electrochemical gradient

• primary goal: make ATP

• secondary goal: regenerate NAD+

Periplasm

• space between the cell wall and the plasma membrane

2 fundamental requirements of cellular life

• energy to generate ATP

• a source of carbon to use as raw materials for synthesizing macromolecules

Catabolic pathways

• involve the breakdown of molecules

• often harvest stored chemical energy to produce ATP

Anabolic pathways

• result in the synthesis of larger molecules from smaller components

• often use energy in the form of ATP

Homeostasis

• maintenance of a stable internal environment under different environmental conditions

Energy investment phase (glycolysis)

• reactions 1 through 5

• uses 2 ATP molecules

• regulation of the metabolic pathway occurs during this phase (reaction 3, regulation of phosphofructokinase)

Energy payoff phase (glycolysis)

• reactions 6 through 10

• NADH is made and ATP is produced by substrate-level phosphorylation

Substrate-level phosphorylation

• 1 way to make ATP

• the ONLY way to produce ATP through glycolysis

• enzyme facilitates the transfer of a phosphate group from a substrate to ADP

Glycolysis regulation

• regulated by feedback inhibition

• high levels of ATP inhibit the third enzyme/step of glycolysis (phosphofructokinase), which have two binding sites for ATP

• when ATP binds to the regulatory site of phosphofructokinase, the reaction rate slows dramatically

Regulation of pyruvate processing

• when products of glycolysis and pyruvate processing are abundant, pyruvate dehydrogenase is phosphorylated, inducing a conformational change in the enzyme and inhibiting its activity

Citric acid cycle regulation

• can be turned off at multiple points via several different mechanisms of feedback inhibitions

• regulated at steps 1, 3, and 4 by ATP and NADH

• reaction rates are high when ATP and NADH are scarce; rates are low when ATP or NAHD are abundant

Oxidation of NADH and FADH2

• oxidized by membrane complexes

• NADH is oxidized when combined with the inner membrane of the mitochondria; in prokaryotes, it is oxidized by the plasma membrane

• molecules in the inner mitochondrial membrane can cycle between oxidized and reduced states

ETC Protein complexes

• most are composed of easily-oxidized proteins

• some accept only electrons, while others accept electrons plus protons; each complex has differing redox potentials

Ubiquinone (coenzyme Q, or simply Q)

• lipid-soluble, non-protein

• critical component of the ETC

• reduced by complexes I and II; moves throughout the hydrophobic interior of the electron transport chain membrane, where it is oxidized by complex III

Redox potential

• ability to accept electrons

• High positive value = more potential to GAIN electrons

• strong negative value = more potential to LOSE electrons

Complex I (ETC)

• NADH dehydrogenase oxidizes NADH

• transfers 2 electrons through proteins containing FMN prosthetic groups and Fe-S cofactors to reduce an oxidized form of Q

• 4 protons pumped out of the matrix to the intermembrane space per pair of electrons

Complex II (ETC)

• Succinate dehydrogenase oxidizes FADH2

• transfers the two electrons through proteins containing Fe-S cofactors to reduce an oxidized form of Q

• this complex is also used in step 6 of the Krebs cycle

• does not produce sufficient energy to pump protons

Complex III

• cytochrome c reductase oxidizes Q

• transfers 1 electron at a time through proteins containing heme prosthetic groups and Fe-S cofactors to reduce an oxidized form of cytochrome c

• 4 protons for each pair of electrons is transported from the matrix to the intermembrane space

Cyt c (cyctochrome c)

• reduced by accepting a single electron from complex III

• moves along the surface of the ETC membrane, where it is oxidized by complex IV

Complex IV

• cytochrome c oxidase oxidizes cyt c

• transfers each electron through proteins containing heme prosthetic groups to reduce oxygen gas, which picks up two protons from the matrix to produce water

• 2 additional protons are pumped out of the matrix of the intermembrane space

ATP Synthesis (ETC)

• fueled by chemiosmosis; uses the established proton gradient to create ATP using ATP synthase

ATP synthase

• located in the inner mitochondrial membrane in eukaryotes, or the plasma membrane in prokaryotes

• creates energy from the proton motive force of the proton gradient to chemical bond energy in ATP

• is a rotary machine that makes ATP as it spins

• consists of 2 components—an ATPase "knob"/F1 unit, and a membrane-bound, proton-transporting base/F0 unit, which is a rotor that turns as protons flow through it—that are connected by a shaft and held in place by a stator

• the spinning F0 unit changes the conformation of the F1 unit so that it phosphorylates ADP to form ATP

Oxidative phosphorylation

• oxidative = FADH2 and NADH are being oxidized

• phosphorylation = ADP —> ATP

• different from substrate-level phosphorylation because instead of potential energy activating the enzyme, kinetic energy activates the enzyme (movement of protons down their gradient)

• yields ~24-28 ATP per glucose

Chemiosmotic hypothesis

• the linkage between electron transport and ATP production by ATP synthase is indirect

• the synthesis of ATP only requires a proton gradient

Aerobic respiration

• O2, which has a very high redox potential, is the final electron acceptor

• most efficient—CO2 (single-carbon compound) is the byproduct

Anaerobic respiration

• some other compound is the final electron acceptor

• has a lower energy yield compared to aerobic respiration because oxygen is super electronegative and has a high redox potential

• less efficient—some other carbon-containing (organic) molecule is the byproduct (ethanol, lactic acid, etc)

• seen in some prokaryotes

Fermentation

• a metabolic pathway that regenerates NAD+ from NADH

• the electron in NADH is transferred to pyruvate

• serves as an emergency backup for aerobic respiration when there is not enough oxygen

• incomplete oxidation of glucose; much less efficient than cellular respiration

• produces 2 ATP per glucose, compared with about 29 ATP per glucose in cellular respiration

Lactic acid fermentation

• fermentation in which the product is lactic acid

• occurs in humans in the absence of oxygen

• muscle cramps = the accumulation of lactic acid

• in humans, lactic acid fermentation results in the production of yogurt, cheese, etc

• produces only 2 ATP (by substrate-level phosphorylation)

Ethanol fermentation

• some yeast cells can perform alcohol fermentation

• pyruvate is converted to acetaldehyde and CO2

• acetaldehyde accepts electrons from NADH

• ethanol and NAD+ are produced

Faculative anaerobes

• organisms that can switch between fermentation and aerobic respiration

• only use fermentation if an electron acceptor is not available

• E.coli, yeast, etc

Glycolysis step 1

• hexokinase uses ATP to phosphorylate glucose, increasing its potential energy

• forms glucose-6-phosphate and ADP

Glycolysis Step 2

• phosphoglucose isomerase converts glucose-6-phosphate to fructose-6-phosphate (an isomer)

Glycolysis Step 3

• Phosphofructokinase uses ATP to phosphorylate the opposite end of fructose-6-phosphate, increasing its potential energy

• forms fructose-1,6-bisphosphate

Glycolysis Step 4

• fructose-bis-phosphate aldolase cleaves fructose-1,6-bisphosphate into 2 different 3-carbon sugars (DAP and G3P)

Glycolysis Step 5

• triose phosphate isomerase converts dihydroxyacetone phosphate (DAP) to glyceraldehyde-3-phosphate (G3P)

• reaction is fully reversible, but DAP-to-G3P reaction is favored because G3P can be immediately used as a substrate for step 6

Glycolysis Step 6

• glyceraldehyde-3-phosphate (G3P) dehydrogenase catalyzes a 2-step reaction

• first oxidizes G3P using the NAD+ coenzyme to produce NADH

• Energy from this reaction is used to attach an inorganic phosphate to the oxidized product to form 1,3-bisphosphoglycerate

Glycolysis Step 7

• phosphoglycerate kinase transfers a phosphate from 1,3-bisphosphoglycerate to ADP to make 3-phosphoglycerate and ATP (PRODUCES ATP—1 for each 3-carbon intermediate)

Glycolysis Step 8

• phosphoglycerate mutase rearranges the phosphate in 3-phosphoglycerate to form 2-phosphoglycerate

Glycolysis Step 9

• enolase removes a water molecule from 2-phosphoglycerate to form a C=C double bond and produce phosphoenolpyruvate

Glycolysis Step 10

• remaining phosphate groups are added to 2 ADP molecules to form 2 ATP and pyruvate

• pyruvate kinase transfers a phosphate fro phosphoenolpyruvate to ADP to make pyruvate and ATP

Electron Transport Chain Theoretical Yield

• 1 NADH = 3 ATP

• 1 FADH2 = 2 ATP (lower because complex II, where FADH2 is oxidized, has a lower redox potential than complex I, where NADH is oxidized)

ETC Actual Yield

• 1 NADH = ~2.25 ATP

• 1 FADH2 = ~1.25 ATP

Meiosis

• reduction division

• the number of chromosomes in the daughter cell(s) are halved —> 4 daughter cells

• integral to sexual reproduction; creates genetic variation and diversity

• Interphase (G1, S, G2), Meiosis I, and Meiosis II

Gametogenesis

• production of gametes

• uses meiosis in animals

• spermatogenesis = creation of sperm

• oogenesis = creation of eggs

Traits

• characteristics that are inherited

• specified by genes

Genes

• specific segments of DNA at a specific location (locus) on chromosomes

• code for proteins or RNA that produce an organism's inherited traits

• may occur in several varieties (alleles) that may code for different variants of the same trait

Karyotype

• identifies the number and types of chromosomes present in a species

• Karyotyping: technique to view chromosomes

Homologous chromosomes (homologs)

• chromosomes of the same type (size and shape)

• not identical

Homologous pairs

• a pair of homologs

• contain the same genes in the same position along the chromosome (but not identical!!)

Ploidy

• each species has a haploid number (n), which indicates the number of DISTINCT TYPES of chromosomes present (sex chromosomes count as a single type)

• indicates the number of complete chromosome sets it contains

• in humans, n = 23

Diploid

• organisms or cells that have a paternal and maternal chromosome

• 2n; contains 2 homologs of each chromosome, and 2 alleles of each gene

Haploid

• organisms or cells containing only one of each type of chromosome, with just one allele of each gene

Polyploid

• organisms or cells containing 3 or more versions of each type of chromosome

Sex chromosomes

• determine the sex of the individual

• in many animals, X and Y are the sex chromosomes; there are sex-determining regions within these chromosomes

• also contain homologous regions that do not determine sex

Autosomes

• non-sex chromosomes

S phase (meiosis)

• DNA in each chromosome in the diploid (2n) parent cell is replicated

• when replication is complete, each chromosome has two identical sister chromatids, which remain attached along most of their life (still considered a single chromosome)

Meiosis I

• homologs separate so that one homolog goes to one daughter cell and the other homolog goes to the other daughter cell

• each daughter cell has one set of chromosomes; 1 cell (2n) —> 2 cells (n)

• sister chromatids stay together, while non-sister chromatids separate

Meiosis II

• sister chromatids separate

• reduction division; 2 cells (n) —> 4 cells (n), each with a single chromosome of the homologous pair

• equivalent to mitosis in a haploid cell

Spindle apparatus

• made up of microtubules

• coordinate chromosome movement

Meiosis in animal life cycles

• meiosis reduces chromosome number in half—in animals, these products of meiosis are gametes (sperm or eggs)

• gametes fuse by fertilization, which restores diploidy; resulting diploid cell is called a zygote and represents the start of a new organism

Early prophase I

• nuclear envelope begins to break down

• chromosomes condense—as they condense, sister chromatids stay joined along their entire length by cohesins

• spindle apparatus begins to form

• nucleolus disappears

• synapsis occurs

Synapsis

• the pairing process in which homologous pairs come together

• held together by proteins called the synaptonemal complex

Bivalent

• structure that results from synapsis

• consists of two homologs

Tetrad

• structure containing 4 sister and nonsister chromatids

Late prophase I

• nuclear envelope breaks down

• centromeres of homologs become attached to microtubules from opposite poles of the spindle apparatus

• chiasma formation and homologous recombination (crossing over) occur

• synaptonemal complex eventually disassembles in late prophase I, leaving homologs held together only at chiasmata

Chiasma formation

• synaptonemal complex dissociates except for at certain points called chiasmata, where DNA exchange (crossing over) between homologous non-sister chromatids occurs

Homologous recombination (crossing over)

• KEY event in meiosis; carefully regulated

• breaks are made in the DNA and reattached

• occurs between homologous segments of non-sister chromatids

• spindle fibers partially separate chromosomes during crossing over

• produces chromosomes with a combination of maternal and paternal alleles

Metaphase I

• tetrads line up at the metaphase plate

• alignment of the homologs is random and independent of the alignment of other homologs (independent assortment)

Anaphase I

• paired homologs separate and migrate to the opposite ends of the cell

• sister chromatids of each chromosome remain together

• non-sister chromatids separate

Telophase I (interkinesis)

• homologs finish moving to opposite sides of the spindle

• spindle fibers partially disassemble

• other steps are not the same for all organisms—chromosomes may decondense, nucleolus/nuclear envelope may reappear

Prophase II

• spindle apparatus forms

• one spindle fiber attaches to the centromere of each sister chromatid and moves the pairs of sister chromatids back and forth

Metaphase II

• replicated chromosomes line up at the metaphase plate

Anaphase II

• sister chromatids separate

• resulting daughter chromosomes begin moving to opposite sides of the cell

Telophase II

• chromosomes arrive at opposite sides of the cell

• a nuclear envelope forms around each haploid set of chromosomes

• chromosomes decondense

• nucleolus reappears

• spindle completely disappears

Similarities between mitosis and meiosis

• Begins after a cell has passed through the G1, S, and G2 phases of the cell cycle

• cell division

Differences between mitosis and meiosis

• homologous pairs form a tetrad

• at metaphase plate, there are tetrads instead of individual replicated chromosomes (sister chromatids)

• crossing over occurs in meiosis

• meiosis is a reduction division

• produces genetically distinct haploid daughter cells rather than genetically identical diploid daughter cells

Mutations

• original source of genetic variation

• produce different versions of genes—can be positive or negative

Genetic diversity

• variation in gene pool of a species

• produced by mutations and meiosis/sexual reproduction

• sources include crossing over (creating new combinations of alleles that did not exist in the parents) and independent assortment (creating more possible combinations of genetic material)

Fertilization (genetic diversity)

• each gamete is genetically unique

• even in self-fertilization where gametes from the same individual combine, the offspring will be genetically different from the parent

• outcrossing: where gametes from two individuals combine, increasing the genetic diversity of the offspring even further

Nondisjunction

• occurs when both homologs or both sister chromatids move to the same pole in the parent cell, leading to abnormal products of meiosis

• results in gametes that contain an extra chromosome (n+1) or lack one chromosome (n-1)

Trisomy

• result of fertilization of a n + 1 gamete

Monosomy

• result of fertilization of an n-1 gamete

Aneuploid

• cells with too many or too few chromosomes

Nondisjunction

• disjunction of the chromatids did not occur properly; may have different outcomes depending on where the nondisjunction occurred (Meiosis I vs Meiosis II)

• nondisjunction in meiosis I affects all gametes, while nondisjunction in meiosis II affects only 2

Oogenesis in humans

• primary oocytes enter meiosis I during female embryonic development and arrest in prophase I until sexual maturity is reached

• meiosis is not completed until ovulation, years later

Purifying selection

• natural selection against deleterious alleles; favors sexual reproduction

• over time, purifying selection should steadily reduce the numerical advantage of asexual reproduction—in asexual reproduction, a damage gene will be inherited by all of that individual's offspring, while in sexual reproduction, offspring will likely lack deleterious alleles present in the parent

The changing-environment hypothesis

• if a new strain of disease-causing agent evolves all of the asexually produced offspring are likely to be susceptible to that new strain, but if the offspring are genetically varied, then it is likely that some offspring will have combinations of alleles that enable them to fight off the new disease and eventually produce offspring of their own

• supported by studies involving roundworms and tracking the rate of outcrossing between populations that were introduced to a pathogen and populations that were not

• therefore, sexual reproduction may be an adaptation that increases the fitness of individuals in certain environments

Binary Fission

• Asexual cell division for unicellular organisms

• Purpose: reproduction; division of one cell reproduces the entire organism

• Occurs in bacteria, archaea, and protists

• bacterial chromosome replication —> segregation (proteins bind to chromosomes and separate them) —> other proteins (tubulin homologs) divide the cytoplasm —> PG (peptidoglycan?) is synthesized

Mitosis

• a type of cell division where the daughter cells are identical to the parent cell (clones—same genetic content)

• purpose: reproduction, growth and development, and tissue renewal within multicellular organisms; essential for the development of the zygote into the adult organism

• number of chromosomes is conserved in division

Haploid cells

• contain one copy of each chromosome

Diploid cells

• contain two copies of each chromosome