Biology I: Chapters 9-14

A process that results in the partial degradation of sugars or other organic fuel without the use of oxygen.

Oxygen is consumed as a reactant along with the organic fuel.

Done by most eukaryotic and prokaryotic organisms.

Some prokaryotes use substances other than oxygen as reactants in a similar process called anaerobic respiration.

Technically includes aerobic and anaerobic processes but refers mostly to aerobic respiration.

C6H12O6+ 6O2 -> 6CO2 + 6H2O + Energy (ATP+Heat)

Process is exergonic (negative ^G change, spontaneous)

Includes: oxidation and reduction

~Also called: Oxidation-Reduction Reactions

~Transfer of one or more electrons from one reactant to another.

• ~The loss of electrons from one substance is called OXIDATION.
• ~The addition of electrons to another substance is called REDUCTION

• ~Reducing Agent: Electron donor
• ~Oxidixing Agent: Electron acceptor

~Oxidation and Reduction ALWAYS go hand in hand

~Not all redox reactions involve the complete transfer of electrons from one substance to another

~Oxygen is one of the most potent oxidizing agents because it's so electronegative

~Energy MUST be added to pull an electron away from an atom

• Electron Donor
• &
• Electron Acceptor

• An electron carrier, functioning as an oxidizing agent during respiration
• A coenzyme
• Can cycle easily between oxidized (NAD+) and reduced (NADH) states

• In cristae of mitrochondrion
• Consists of a number of molecules (mostly proteins) built into the inner membrane of the mitochondria of eukaryotic cells
• Respiration uses an ETC to break the fall of electrons to oxygen into several energy-releasing steps
• Thousands in each mitochondrion
• Does not generate ATP

• Occurs in the cytosol
• Begins the degradation process by breaking glucose into two molecules of pyruvate
• Carbon (6-carbon sugar) is split into two 3-carbon sugars, then oxidized, then rearranged to form two molecules of pyruvate
• Two phases: energy investment phase (ATP spent) and energy payoff phase (ATP gained)

• Functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate
• Catabolic - Oxidizing acetyl CoA and using energy to synthesize ATP

• Mode of ATP synthesis powered by the redox reactions of the electron transport chain
• Adds an inorganic phosphate to ADP

Mode of ATP synthesis that occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP,

• Acetyl Coenzyme A
• Pyruvate converted to Acetyl CoA in step linking glycolysis and the citric acid cycle

• 4 ATP Molecules
• 2 during glycolysis
• 2 during citric acid cycle

3 CO2 (Each completing cycle alone; 3 Calvin Cycles)

Three times (3 CO₂)

• Proteins
• Most of the remaining electron carriers between ubiquinone and ozygen in ETC

• Protein complex
• The enzyme that makes ATP from ADP and inorganic phosphate
• Works like an ion pump running in reverse
• Populates inner membrane of the mitochondrion or prokaryotic plasma membrane
• Uses the energy of an existing ion gradient to power ATO synthesis

• Process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work
• Example: the synthesis of ATP
• The flow of H+ across a membrane

The potential energy stored in the form of a proton electrochemical gradient, generated by the pumping H+ across a biological membrane during chemiosmosis

Glucose -> NADH -> ETC -> Proton-Motive Force -> ATP

*ETC: Electron Transport Chain

• A way of harvesting chemical energy w/o using either oxygen or any ETC (w/o cellular respiration)
• Alcohol and Lactic Acid

• Pyruvate converted to Ethanol in two steps
• Step 1: Release CO2 from pyruvate, which is converted to the 2-carbon compound acetaldehyde
• Step 2: Acetaldehyde is reduced by NADH to ethanol (regenerates supply of NAD+ needed for glycolysis)
• Many bacteria carry out AF under anaerobic (w/o air) conditions

• Pyruvate reduced directly by NADH to form lactate w/ no release of CO2
• Certain fungi/bacteria used by dairy industry to make cheese and yogurt
• Used by human muscle cells to make ATP when oxygen is scarce (during strenuous exercise)

Without air

Cellular Respiration

• -Both use glycolysis to oxidize glucose and other organic fuels to pyruvate
• -Cellular respiration produces much more ATP
• -Fermentation Final Electron Acceptor: Pyruvate
• -Cellular Respiration Final Electron Acceptor: O2

• The body uses small molecules to build other substances
• Small molecules may come directly from food, from glycolysis, or from the citrci acid cycle

• The conversion from solar to chemical energy
• Most plants, algae, some prokaryotes, and some unicellular eukaryotes

• Autotrophs: Sustain themselves w/o eating anything derived from other organisms (plants)
• Heterotrophs: Obtain their organic material from other organisms; Consumers (humans)

• Plants
• Organisms that use light as a source of energy to synthesize organic substances

• All green parts of a plant have chloroplasts
• Found mainly in the mesophyll (tissue in the interior of the leaf)
• Has an envelope of two membranes surrounding a dense fluid called the stroma

Leaves (in most plants)

• The tissue in the interior of the lead
• Has about 30-40 chloroplasts, 2-4um by 4-7um

• Microscopic pores
• Oxygen exits the leaf through the stomata

• A envelope of two membranes surrounding a dense fluid
• Contains membrane system made up of sacs, called thylakoids, which segregates the stroma from the thylakoid space inside the sacs

• Sacs that segregate the stroma from the thylakoid space inside these sacs
• In some places, they are stacked in columns called grana (singular granum)
• Chlorophyll found here

• Columns of thylakoids
• Singular: granum

• The green pigment that gives leaves their color
• Found in the thylakoid

• 6CO₂ + 6H₂O + Light Energy -> C₆H₁₂O₆ + 6O₂
• 6CO₂ + 12H₂O + Light Energy -> C₆H₁₂O₆ + 6O₂+6H₂O

• 1- Light Reactions (photo)
• 2- The Calvin Cycle (synthesis)

• The steps of photosynthesis that convert solar energy to chemical energy
• Water is split (providing electrons & protons)
• O₂ released
• No sugar produced

Process in which ATP is generated by using chemiosmosis to power the addition of a phosphate group to ADP

• Anabolic - Building carbs from smaller molecules and consuming energy
• Incorporates CO₂ from the air into organic molecules already present in the chloroplast (called Carbon Fixation)
• The fixed carbon is then reduced to carbohydrates by the addition of electrons
• 3 Phases: Carbon Fixation, Reduction, Regeneration of the CO₂ Acceptor

The initial incorporation of carbon into organic compounds

• The distance between the crests of electromagnetic waves
• Range from less than a nanometer to more than a kilometer

• The entire range of radiation
• Less than a nanometer-More than a kilometer
• Segment most important to life: 380nm-750nm

• 380nm-750nm
• Called visible light

• 380nm-750nm
• Segment of the electromagnetic spectrum most important to life
• Can be detected as various colors by the human eye

• Discrete particles
• Not tangible objects, but act like objects in that each of them has a fixed quantity of energy

• The amount of energy is inversely related to wavelength of light
• The shorter the wavelength of light, the greater the energy of each photon of that light

Visible Light

A graph plotting a pigment's light absorption versus wavelength

The key light-capturing pigment that participates directly in the light reactions

The accessory pigment

• Separate group of accessory pigments
• Hydrocarbons that are various shades of yellow and orange because they absorb violet and blue-green light
• May broaden the spectrum of colors that can drive photosynthesis
• Some function as photoprotectors - Absorb and disspate excessive light energy that would otherwise damage chlorophyll or interact with oxygen, forming reactive oxidative molecules that are dangerous to the cell

• Profiles the relative effectiveness of different wavelengths of radiation in driving the process
• Prepared by illuminating chloroplasts with light of different colors, then plotting wavelength against some measure of photosynthetic rate

The colors corresponding to the absorbed wavelengths disappear from the spectrum of the transmitted and reflected light (but energy cannot disappear)

Green

• Composed of a reaction-center complex surrounded by several light-harvesting complexes
• Photosystem I and Photosystem II
• Each photosystem functions in the chloroplast as a unit
• Converts light energy to chemical energy, which will ultimately be used for the synthesis of sugar

• An organized association of proteins holding a special pair of chlorophyll a molecules
• Contains a molecules capable of accepting electrons and becoming reduced (primary electron acceptor)

• Consists of various pigment molecules (may include chlorophyll a, b, and multiple carotenoids) bound to proteins
• Enables a photosystem to harvest light ove a larger surface area and a larger portion of the spectrum than any single pigment alone

A molecule capable of accepting electrons and becoming reduced

The solar-powered transfer of an electron from the reaction-center chlorophyll a pair to the primary electron acceptor

As soon as the chlorophyll electron is excited to a higher energy level, the primary electron acceptor captures it

• Functions 1st in light reactions
• P680

• Functions 2nd in light reactions
• P700

• A flow of electrons through the photosystems and other molecular components built into the thylakoid membrane
• Occurs during the light reactions of photosynthesis
• Generates ATP and NADPH

• Uses photosystem I only
• No production of NADPH or oxygen
• Generate ATP
• Occurs in photosynthetic bacteria with one photosystem (PSII or PSI)
• Can occur in photosynthetic organisms with both photosystems

• in Mitochondrion: Chemical Energy (from food) transfer to ATP
• in Chloroplasts: Light energy transforms to Chemical Energy of ATP

• Glyceraldehydr 3-Phosphate
• The carbohydrate produced directly from the Calvin Cycle
• 3-Carbon Sugar
• For the net synthesis of one molecule of G3P, the cycle must take place 3 times (3 CO₂)

• 9 ATP
• 6 NADPH

• 18 ATP
• 12 NADPH

6 (6CO₂)

• Plants that use the Calvin Cycle for the initial steps that incorporate CO₂ into organic material, producing 3-Phosphoglycerate
• Examples: Rice, Wheat, Soybeans

• Plants in which the Calvin Cycle is preceded by reactions that incorporate CO₂ into a 4-carbon product
• Examples: Sugarcane, Corn

• Plants that use crassulacean acid metabolism*
• Examples: Pineapple

*An adaptation for photosynthesis in arid conditions

An adaptation for photosynthesis in arid conditions

Arranged into tightly packed sheaths around the veins of the leaf

• A process that occurs in the light and consumes O₂ while producing CO₂
• Uses ATP
• Produces no sugar
• Decreases photosynthesis output

Reproduction of cells

• The life of the cell from the time it is first formed during division of a parent cell until its own division into two daughter cells
• Crucial Function: Passing identical genetic material to cellular offspring

• A cell's genetic info
• Prokaryotic genomes - single DNA molecule
• Eukaryotic genomes - a number of DNA molecules

• Structures containing DNA molecules
• # in Human Somatic Cells: 46 (2 sets of 23)
• # in Human Gametes: 23 (one set)

• The units of info that specify an organism's inherited traits
• Program the specific traits that emerge as we develop from fertilized eggs into adults
• Written in the language of DNA

• The entire complex of DNA and proteins that is the building material of chromosomes
• Varies in its degree of condensation during cell division

All body cells except the reproductive cells

• 46 chromosomes
• Two sets of 23 (one set inherited from each parent)

• Reproductive Cells
• Sperm and Eggs
• One set of chromosomes (half as many somatic)
• In humans: one set of 23 chromosomes
• The vehicles that transmit genes from one generation to the next

• Joined copies of the original chromosome
• Initially attached all along their lengths by protein complexes called cohesins

Protein complexes that initially attach sister chromatids along their lengths

The attachment of sister chromatids to each other

• The division of the genetic material in the nucleus
• Usually followed by cytokinesis (the division of the cytoplasm)

• Mitotic (M) Phase
• Interphase (Sub-phases: G1 Phase, S Phase, G2 Phase)
• Prophase
• Prometaphase
• Metaphase
• Anaphase
• Telophase
• Cytokinesis

• Accounts for 90% of the cell cycle
• Includes sub-phases: G1 Phase, S Phase, and G2 Phase
• A cell grows by producing proteins and cytoplasmic organelles such as mitochondria and endoplasmic reticulum

• Sub-phase of interphase
• Duplication of the chromosomes occurs entirely

• Consists of fibers made of microtubules and associated proteins
• Begins to form in the cytoplasm during prophase
• Includes: The centrosomes, The spindle microtubules, and the asters

• A nuclear envelope (double membrane) encloses the nucleus
• Two centrosomes have formed by duplication of a single centrosome
• Each centrosome contains two centrioles

• The chromatin fibers become more tightly coiled
• The nucleoli disappear
• Each duplicated chromosome appears as two identical sister chromatids joined at their centromeres
• The mitotic spindle begins to form
• The centrosomes move away from each other

• The nuclear envelope fragments
• The microtubules extending from each centrosome can now invade the nuclear area
• The chromosomes have become even more condensed
• Each of the two chromatids of each chromosome now has a kinetochore (specialized protein structure at center of centromere)
• Some of the microtubules attach to kinetochores, becoming "kinetochore microtubules," which kerl the chromosomes back and forth

• The centrosomes are now at opposite poles of the cell
• The chromsomes have all arrived at the metaphase plate (a plane equidistant between spindle's two poles)
• For each chromosome, the kinetochores of the sister chromatids are attached to kinetochore microbtubules coming from opposite poles

• Shortest stage of mitosis
• Begins when the cohesin proteins are cleaved, allowing the two sister chromatids of each pair to part suddenly (each chromatid becomes a full-ledged chromosomes)
• The two liberated sister chromosomes begin moving toward opposite ends of the cell
• The cell elongates as the nonkinetochore microtubules lengthen
• By the end of this stage, the two ends of the cell have equivalent (and complete) collections of chromosomes

• Two daughter nuclei form in the cell
• Nuclear envelopes arise from the fragments of the parent cell's nuclear envelope
• Nucleoli reappear
• The chromosomes become less condensed
• Any remaining spindle microtubules are depolymerized
• Mitosis is complete

The division of the cytoplasm is usually well under way by the late telophase, so the two daughter cells appear shortly after the end of mitosis

• A subcellular region containing material that functions throughout the cell cycle to organize the cell's microtubules
• A pair of centrioles at center

• A radial array of short microtubules
• Extends from each centrosome

A structure made of proteins that have assembled on specific sections of DNA at each centromere

• A plane midway between the spindle's two poles
• Imaginary plate

• A shallow groove in the cell surface near the old metaphase plate
• The 1st sign of cleavage
• Deepens until the parent cell is pinched in two, producing two separate cells
• Animal cells, not plant cells

• Process by which cytokinesis occurs
• 1st Sign: Cleavage Furrow

• Produced in plant cells when vesicles from the Golgi move along microtubules to the middle of the cell, where they coalesce (come together)
• Enlarges until its surrounding membrane fuses with the plasma membrane along the perimeter of the cell

• "Division in Half"
• Refers to the process and asexual reproduction of single-celled eukaryotes (bacteria)

• A cyclically operating set of molecules in the cell that both triggers and coordinates key events in the cell cycle
• Proceeds on its own, according to a built in "clock"
• Regulated at certain checkpoints by internal and external adjustment

• A control point in the cell cycle where stop and go-ahead signals can regulate the cycle
• Three important checkpoints found in G1, G2, and M Phases

• Protein
• Cyclically fluctuating concentration in the cell

• Enzymes that activate or inactivate other proteins by phosphorylating them
• Activity rises and falls with changes in the concentration of its cyclin partner

• G1 Checkpoint
• If a cell receives a go-ahead signal at the G1 checkpoint, it will usually complete the G1, S, G2, and M phases and divide
• If a cell does not receive a go-ahead signal at the G1 checkpoint, it may exit the cycle, switching into a nondividing state called the G₀ phase

• Nondividing state
• The result of not receiving a go-ahead signal at G1 checkpoint
• Most cells of human body at this phase

• A protein released by certain cells that stimulates other cells to divide
• Different cell types respond specifically to different growth factors or combinations of growth factors

A phenomenon in which crowded cells stop dividing

• To divide, cells must be attached to a substratum
• Signaled to the cell cycle control system via pathways involving plasma membrane proteins and elements of the cytoskeleton linked to them

• Most do not cause serious problems
• Most can be removed by surgery
• A mass of abnormal cells within otherwise healthy tissue that remains at the original site (too few genetic and cellular changes to survive at another site)

• A mass of abnormal cells within otherwise healthy tissue whose genetic and cellular changes enable them to spread to new tissues and impair the functions of one or more organs
• "Cancer"

Spread of cancer cells to locations distant from their original site

• Transmission of traits from one generation to the next
• Also called inheritance

Differences between members of the same species

Scientific study of heredity and hereditary variation

• A gene's specific location along the length of a chromosome
• Plural: loci

• A single individual is the sole parent and passes copies of all its genes to its offspring without the fusion of gametes
• Example: Single-celled eukaryotic organisms,
• Some multicellular organisms

• Two parents give rise to offspring that have unique combinations of genes inherited from the two parents
• Offspring vary genetically  from their siblings and parents
• Variations not replicas

• The generation-to-generation sequence of stages in the reproductive history of an organism
• Conception to own reproduction

46 Chromosomes

• Each chromosome has two pairs
• 23 x 2 = 46

• Ordered display of chromosomes
• Starts with longest

• Also called homologs
• A pair of chromosomes of the same length, centromere position, and staining pattern
• Possesses genes controlling the same inherited characteristics
• Exception: X and Y Chromosomes

XX

XY

• Sex chromosome
• Males: XY
• Females: XX

• Also called homologous chromosomes
• A pair of chromosomes of the same length, centromere position, and staining pattern
• Possesses genes controlling the same inherited characteristics
• Exception: X and Y Chromosomes

Chromosomes that are not sex chromosomes

• Any somatic cell with two chromosome sets
• Has a diploid number of chromosomes, abbreviated 2n
• Humans: Diploid # = 46 (2n=46)

• Any gamete with one chromosome set
• Has a haploid number of chromosomes, abbreviated n
• Humans: Haploid # = 23 (n=23)

• The union of gametes
• Result: Zygote, fertilized egg

• Fertilized egg
• Diploid because it contains two haploid sets (paternal and maternal copy of chromosomes)

Gametes

• In germ cells, in the gonads
• Ovaries and Testes

• Type of cell division involved in gamete formation
• Occurs in germ cells (in the gonads)
• Reduces the number of sets of chromosomes from two to one in the gametes, counterbalancing the doubling that occurs at fertilization
• Meiosis I and Meiosis II

• Plants and some species of algae
• Includes both diploid and haploid stages that are multicellular
• Sporophyte: Muticellular Diploid Stage
• Gametophyte: Muticellular Haploid Stage
• The sporophyte generation produces a gametophyte as its offspring, and the gametophyte produces the next sporophyte

• Two
• Meiosis I and Meiosis II

4 daughter cells, each with only half as many chromosomes as the parent cells

• Meiosis I: Prophase I, Metaphase I, Anaphase I, Telophase I, Cytokinesis
• Meiosis II: Prophase II, Metaphase II, Anaphase II, Telophase II, Cytokinesis

• Centrosome movement, spindle formation, and nuclear envelope breakdowns
• Chromosomes condense progressively
• Each chromosome pairs with its homolog, aligned gene by gene, and crossing over occurs
• Each homologous pair has one or more X-shaped regions called chiasmata, where crossovers have occured
• Microtubules from one pole or the other will attach to the two kinetochores (one at the centromere of each homolog)
• The homologous pairs will then move toward the metaphase state

• Pairs of homologous chromosomes are now arranged at the metaphase plate, each pair facing its own pole
• Both chromatids of one homolog are attached to kinetochore microtubules from one pole

• Breakdown of proteins that are responsible for sister chromatid cohesion along chromatid arms allows homologs to separate
• Homologs move toward opposite poles
• Sister chromatid cohesion persists at the centromere, causing chromatids to move as a unit toward the same pole

• Each half of the cell has a complete haploid set of duplicated chromosomes
• Cytokinesis usually occurs simultaneously with telophase I, forming two haploid daughter cells
• In animal cells, a cleavage furrow forms
• In some species, chromosomes condense and nuclear envelopes form
• No chromosome duplication occurs between Meiosis I and Meiosis II

• Spindle apparatus forms
• Chromosomes move toward metaphase II plate

• The chromosomes are positioned at the metaphase plate
• Because of crossing over in meiosis I, the two sister chromatids of each chromsome are not genetically identical
• The kinetochores of sister chromatids are attached to microtubules extending from opposit poles

• Breakdown of proteins holding the sister chromatids together at the centromere allows the chromatids to separate
• The chromatids move toward oppiste poles as individual chromosomes

• Nuclei form, the chromosomes begin decondensing, and cytokinesis occurs
• The meiotic division of one parent cell produces four daughter cells (each w/ haploid set of chromosomes)
• The four daughter cells are genetically distinct from each other and the parent cell

• Zipper-like structure
• The formation of which holds one homolog tightly to the other

During - The DNA breaks are closed up so that each broken end is joined to the corresponding segment of the nonsister chromatid

• Independent Assortment of Chromosomes
• Crossing Over

• A heritable feature that varies among individuals
• Example: Flower color

• Each variant for a character
• Example: Purple or white color for flowers

Organisms produce offspring of the same variety over many generations of self-pollination

• The crossing of two true-breeding varieties
• P Generation: true-breeding parents
• F1 Generation: hybrid offspring of P Generation
• F2 Generation: offspring from F1 Generation

Two true-breeding parents

Hybrid offspring of P Generation

Offspring of F1 Generation

Alternative versions of a gene

• Alternative versions of genes account for variations in inherited characters.
• For each character, an organism inherits two copies (two alleles) of a gene, one from each parent.
• If the two alleles at a locus differ, than one (the dominant allele) determines the organisms appearance; the other (the recessive allele) has no noticeable effect on the organisms appearance
• The two alleles for a heritable character segregate during gamete formation and end up in different gametes (The Law of Segregation)

• States that the two alleles for a heritable character segregate during gamete formation and end up in different gametes
• An egg or a sperm gets only one of the two alleles that are present in the somatic cells of the organism making the gamete

A diagrammatic device for predicting the allele composition of offspring from a cross between individuals of known genetic makeup

Name for an organism that has a pair of identical alleles for a character

• Name for an organism that has two different alleles for a gene
• Not true-breeding

Name for an organism that has a pair of identical recessive alleles for a character

• An organism's appearance or observable traits
• Example: PP and Pp (purple vs white colored petals) have the same phenotype, which is the purple petals

• An organism's genetic makeup
• Example: PP and Pp (purple vs white colored petals) have different genotypes, PP vs Pp

• Breeding an organism of unknown genotype with a recessive homozygote
• Can reveal the genotype of the unknown organism

• Monohybrid: An organism is heterozygous for one particular character
• Monohybrid Cross: A cross between two heterozygous organisms with a single differing character

• Dihybrid: An organism heterozygous for two characters
• Dihybrid Cross: A cross between two heterozygous organisms with two differing characters

• Two or more genes assort independently - each pair of alleles segregates independently of each other pair of alleles - during gamete formation
• Only applies to genes located on different chromosomes or to genes that are very far apart on the same chromosome

0-1

To determine the probability that two or more independent events will occur together in some specific combination: Multiply the probability of one event by the probability of the other event

The probability that any one of two or more mutually exclusive events will occur is calculated by adding their individual probablities

• Neither allele is completely dominant
• Example: Red and White flower mate - Produce Pink offspring

• The phenotype of the heterozygote and the dominant homozygote are indistinguishable
• Example: Red and White flower mate - Produce dominant colored offspring

• Two alleles each affect the phenotype in separate, distinguishable ways
• Example: Red and White flower mate - Produce Red and White speckled offspring

• An inherited disorder in humans
• Brain cells cannot metabolize certain lipids because a crucial enzyme does not work properly
• Symptoms: Seizures, blindness, degeneration of motor/mental performances, and death

• Multiple phenotypic characters
• Most genes have this property

Phenotypic expression of a gene at one locus alters that of a gene at a second locus

Example: human skin color

• An additive affect of two or more genes on a single phenotypic character
• Example: Height. Over 180 genes affect height

Characters that have many factors, both genetic and environmental, influence phenotype

A family tree describing the traits of parents and children across generations

Heterozygotes that may transmit the recessive allele for a genetic disorder to their offspring

• Most common lethal genetic disease in the US
• 1/2500 people
• Can cause death by 5 years old
• Abnormally high concentration of extracellular chloride, which causes mucus coating certain cells to become thicker and stickier

• Most common inherited disorder among people of African descent
• 1/400 African-Americans
• Red blood cells sickle-shaped

Techniques that can determine whether the developing fetus has Tay-Sachs disease