Photosynthesis: Chloroplasts, Pigments, and Reactions

• Photosynthesis synthesizes organic molecules from inorganic molecules using light energy, performed by plants, algae, and cyanobacteria.
• During photosynthesis, water converts to oxygen, carbon dioxide converts to glucose; CO2 enters from the environment, O2 is released.

Chloroplast Structure and Function

• Chloroplasts specialize in photosynthesis within plants and many protists.
• The thylakoid membrane contains chlorophyll and other pigments which absorb solar energy.
• The stroma, a semifluid matrix, is where glucose is built.

Pigments and Light Absorption

• Pigments in thylakoids absorb solar energy, reflecting specific wavelengths of light.
• Chlorophyll, the main photosynthetic pigment, reflects green light.
• Pigments are within photosystems which are within thylakoid membranes which are within chloroplasts which are within cells.

Stages of Photosynthesis

• Light reactions (in the thylakoid membrane): Light energy converts to ATP and NADPH, water splits to release O2.
• Calvin Cycle reactions (in the stroma): ATP and NADPH energy drives glucose and carbohydrate synthesis from CO2 and water.

Calvin Cycle

• The Calvin cycle reactions are the second stage of photosynthesis.

Light Wavelengths in Photosynthesis

• Photosynthesis uses a small fraction of the sun's total energy.

Carotenoids

• Carotenoids are accessory pigments in photosynthesizers.
• Accessory pigments expand the range of light wavelengths a photosynthesizer can use.

Photosystems

• Two types of photosystems: PS II & PS I which are named in order of discovery.
• Pigment complexes in photosystems gather solar energy.
• Solar energy energizes electrons, which then move down an electron transport chain.

ATP and NADPH Formation

• ATP forms when electrons moving between molecules drive hydrogen ions across a gradient, flowing through ATP synthase.
• NADPH forms when electrons reach Photosystem 1, hop to another pigment, and are accepted by NADP+.
• Oxygen is released because Photosystem 2 loses electrons.
• Water splitting replaces lost electrons from PS II; hydrogens from water contribute to the hydrogen ion gradient inside the thylakoid membrane.

Electron Transport Chain (ETC)

• The electron transport chain consists of organized enzymes and proteins that pass electrons in a series.
• Energy is released at each step in the ETC, creating an H+ gradient which is an efficient transfer of electrons for energy.

Glucose Formation

• Glucose forms during Calvin cycle reactions in the stroma, powered by ATP & NADPH.
• The Calvin cycle's end product is glucose (C6H12O6).
• Calvin cycle steps:
  • Carbon dioxide fixation: CO2 attaches to RuBP, forming a 6-carbon molecule that splits into two 3-carbon molecules (3PG).
  • Carbon dioxide reduction: 3PG converts to G3P using NADPH and ATP; G3P can become glucose.
  • Regeneration of 1st substrate (RuBP): G3P & ATP reform RuBP.

Fixation

• Fixation is the conversion of something from an inorganic to a usable state.

Cellular Respiration

• Cellular respiration converts food energy into cellular energy.

Oxidation and Reduction

• Oxidation: removal of hydrogen atoms, loss of electrons.
• Reduction: addition of hydrogen atoms, gain of electrons.
• In cellular respiration, hydrogens and electrons are removed from glucose to make CO2, and oxygen accepts them to form water.

Coenzymes

• Coenzymes are non-protein enzymes that join with hydrogen and electrons.
• Key coenzymes in cellular respiration: NAD+ → NADH, FAD → FADH2.

Stages of Cellular Respiration

• The stages include:
  • Glycolysis
  • Preparatory reaction
  • Citric acid cycle
  • Electron transport chain

Glycolysis

• Glycolysis breaks down glucose, starting with food and producing glucose, It occurs in the cytoplasm.
• During glycolysis, 1 glucose (6 carbon) breaks down into 2 pyruvates (3C).
• Energy investment: 2 ATP transfer phosphates to glucose, activating them.
• Energy harvesting: Substrate-level ATP synthesis produces 4 ATP, with a net gain of 2 ATP and 2 NADH.
• Other cellular respiration stages occur in mitochondria (except in bacteria).
• Eukaryotes net 38 ATP; bacteria net only 2 ATP.

Products of Cellular Respiration Stages

• Glycolysis net yield: 2 pyruvate, 2 ATP, and 2 NADH per glucose.
• Preparatory reaction (mitochondrial matrix): Pyruvate splits and oxidizes; NAD+ reduces to NADH (2 per glucose molecule), producing acetyl-CoA (2 per glucose molecule) and releasing CO2 (2 per glucose molecule). 2 CO2, 2 NADH, 2 Acetyl-CoA
• Citric acid cycle (Krebs cycle; mitochondrial matrix): Acetyl CoA transfers acetyl group to a C4 molecule, producing citric acid (6C); acetyl group oxidizes to CO2. NAD+ → NADH and FAD → FADH2 and ATP is synthesized. Two cycles per glucose molecule.
  • Inputs: 2 acetyl-CoA
  • Outputs: 4 CO2, 6 NADH, 2 FADH2, 2 ATP
• Electron transport chain: path of e- & H+. NADH & FADH2 deliver electrons and electrons go through the transport chain, H+ get shuttled out (via active transport), forming a H+ concentration gradient.

Carbon Dioxide Release

• 2 CO2 molecules are released during the preparatory reaction.
• The remaining CO2 molecules are released in the citric acid cycle.

Final Electron Acceptor

• Oxygen is the final electron acceptor in the electron transport chain.

Total Reduced Coenzymes

• The first three stages produce 10 NADH and 2 FADH2 for every glucose molecule.

Fate of Reduced Coenzymes

• The reduced coenzymes (NADH and FADH2) go on to deliver electrons to the electron transport chain.

Krebs Cycle Combinations

• During the citric acid cycle (Krebs), acetyl co-A (2 carbons) combines with a four-carbon molecule to make a six-carbon compound.

Electron Travel

• H+ travels with the electrons, forming a H+ concentration gradient.

ATP Production

• H+ concentration is higher in the outer compartment; H+ follows its gradient through ATP synthases to the interior, forming ATP.
• Finally, oxygen accepts electrons and combines with H+, forming water.

Photosynthesis and Aerobic Respiration

• Photosynthesizers use solar energy for food production.
• Aerobic respiration balances photosynthesis.

Mitotic Cell Division Functions

• Functions include:
  • Growth
  • Tissue repair
  • Asexual reproduction (e.g., amoebas)
  • Zygote development
• Cell division involves:
  • Cell growth: duplication of contents.
  • Cell division: parent cell separating into two daughter cells.

Chromosome Composition

• During cell division:
  • DNA replicates and packages into chromosomes (DNA & proteins).
  • At other times, DNA & proteins exist as thin chromatin threads.
  • Sister chromatids are joined at the centromere (identical DNA).

DNA-Associated Proteins

• Proteins associated with DNA in eukaryotes are histones.
• Histone-DNA units are nucleosomes.

Human Chromosome Count

• Humans have 46 chromosomes (23 pairs).

Cell Cycle Parts

• The cell cycle sequence of 2 stages:
  • Interphase (DNA is condensing)
    • G1: Cell growth and activity; organelles double. Divide or not? G0 (cells that are not in active division)
    • S: DNA replication (synthesis)
    • G2: Synthesis of proteins for cell division
  • M (Mitotic) stage (nucleus & cytoplasm divides)
    • Cell division occurs
    • Division of nucleus (mitosis)
    • Division of cytoplasm (cytokinesis)
• Begins with new cell, ends when 2 daughter cells arise

DNA Replication Timing

• DNA replication and chromosome duplication occur in the S stage of interphase.

Mitosis and Cytokinesis

• Mitosis is division of the nucleus, producing two nuclei with the same number and kind of chromosomes as the parent.
• Cytokinesis is division of the cytoplasm.

Spindle Apparatus

• Microtubules from opposite poles attach to different sister chromatids and separate them.
• The centrosome is a region near the nucleus that organizes spindle microtubules.

Mitosis Stages

• Mitosis proceeds in 4 stages:
  • Prophase: Chromosomes condense, microtubules form bipolar spindle, nuclear envelope breaks up, and microtubules attach to chromosomes.
  • Metaphase: Duplicated chromosomes line up midway between the spindle poles.
  • Anaphase: Microtubules separate sister chromatids of each chromosome and pull them to opposite spindle poles.
  • Telophase: Chromosomes reach spindle poles, a new nuclear envelope forms around each set of chromosomes, forming two new nuclei with the same chromosome number as the parent.

Cytokinesis in Animal vs. Plant Cells

• Animal cell cytokinesis: A cleavage furrow and contractile ring form.
• Plant cell cytokinesis: A cell plate forms between spindle poles instead of a cleavage furrow.

Cell Cycle Control

• The cell cycle is controlled at checkpoints which ensures they go in order and only when previous stage completed successfully.
• Checkpoints include:
  • G1 checkpoint: makes sure organelles are doubled
  • G2 checkpoint: makes sure that DNA is duplicated
  • Mitotic stage checkpoint: make sure mitosis is running correctly

Contact Inhibition

• Cells stop dividing when they touch each other.

Telomeres significance

• With each cell division, telomeres (repeating DNA sequences at the end of the chromosome) shorten.

Apoptosis

• Apoptosis is programmed cell death.

Cancer

• Cancer is uncontrolled cellular reproduction.
• Cancerous cells:
  • May be immortal
  • Don't contribute to body function.
  • Have abnormal nuclei with abnormal chromosome numbers.
  • Don't undergo apoptosis.
  • Form tumors (no contact inhibition, no signal inhibition).
  • Undergo metastasis
• Types of cancer classified by location:
  • Carcinoma: epithelial tissue that lines organs.
  • Sarcoma: muscle or connective tissue.
  • Leukemia: blood.
• Benign tumors are contained; malignant tumors are invasive and spread.
• Metastasis: Spreading of a malignant tumor.

Sexual vs. Asexual Reproduction

• Asexual reproduction produces genetically identical copies of a parent (clones).
• Sexual reproduction introduces variation in the combinations of traits among offspring, leading to more variation and evolutionary change.

Meiosis

• Meiosis occurs only in cells for sexual reproduction (eggs and sperms)
• Functions:
  • Reduces chromosome number by nuclear division
  • Shuffles chromosomes to create variety via crossing over and independent assortment

Homologous Chromosomes

• Humans have 23 pairs of homologous chromosomes (diploid): 22 autosomal pairs, 1 sex pair (XX, XY).
• Have the same genes for the same traits, and are the same size and same shape.
• Pairs separate in gamete formation (meiosis), forming haploid sperm/eggs.

Genes and Alleles

• Genes: regions in an organism's DNA that encode information about heritable traits.
• Alleles: different forms of the same gene.
• Offspring of sexual reproducers inherit new combinations of alleles, the basis of traits

Somatic Cells

• Mitosis for growth, repair & development: diploid to diploid.
• Somatic cells are diploid.
• Meiosis: diploid to haploid.
• Produces gametes
• Meiosis occurs in germ cells.
• Egg and sperm join to form diploid zygote.
• Fertilization
• Diploid: cell has 2 sets of chromosomes.
• Haploid: cell has only one set of chromosomes.

Gametes

• Gametes (sperm and egg cells) are haploid and act as sex cells produced during meoisis; carrying genetic information from each parent.
• Zygotes are diploid first cells of a new organism which is formed when 2 gametes combine and divide by mitosis to grow and develop into a complete organisms.

Nuclear Divisions

• In meiosis I (1st division), duplicated homologous chromosomes are separated from its partner (1 to 2).
  • Prophase I: Chromosomes condense, homologous chromosomes pair up (synapsis), and crossing over occurs.
  • Metaphase I: Homologous chromosome pairs line up in the center of the cell.
  • Anaphase I: Homologous chromosomes are pulled appart to opposite poles while sister chromatids remain together.
  • Telophase I: Two new cells form, each haploid, but with duplicated chromosomes (chromatids still connected).
• In meiosis II (2nd division), sister chromatids are separated (2 to 4).
  • Prophase II: Chromosomes condense again in each haploid cell.
  • Metaphase II: Chromosomes line up individually in the center of the cell.
  • Anaphase II: Sister chromatids are finally separated to opposite poles.
  • Telophase II: 4 haploid gametes result, each with a unique combination of chromosomes.
• Result of Meiosis:
  • 4 haploid cells (gametes) with genetic diversity due to crossing over and independent assortment

Variation in Traits

• Crossing-over:
  • During synapsis in Prophase I, chromatids from homologous chromosomes may exchange genetic material.
  • Increases variability of the gametes
• Chromosome number stays constant which generates diversity.
• All possible combinations of haploid chromosomes occur (random assortment of chromosomes during Metaphase I).

Synapsis

• Synapsis is the process during Prophase I where homologous chromosomes pair up and align closely.

Key Differences Between Meiosis I and Meiosis II

• Differences in Meiosis I and Mitosis are:
• Chromatids separate vs. paired chromosomes separate
• Synapsis, crossing over and independent assortment in meiosis I
• Meiosis II compared is the same as Mitosis where chromatids separate.
  • Meiosis only occurs in "sex" cells in sexually reproducing organisms while Mitosis occurs in body (somatic cells).

Nondisjunction

• Nondisjunction: error in meiosis where chromosomes fail to separate properly.
• Meiosis I when both members of a pair go into the same daughter cell
• Meiosis II when sister chromatids fail to separate

Chromosomal Disorders

• Down syndrome: extra copy of chromosome #21 (trisomy)
• Klinefelter syndrome (XXY): extra X (trisomy)
• Turner syndrome (XO) female - missing all or part of 2nd X chromosome (monosomy)

Chromosome Abnormalities

• Trisomy: 3 instead of 2 chromosomes
• Monosomy: only 1 chromosome

Blending Theory: What is it

• People knew that sperm and eggs transmitted information about traits, leading to the blending theory
• Variation in traits persists

Genes Locus and Alleles

• Genes:
  • Heritable units of information about traits
  • Parents transmit genes to offspring
  • Each gene has a specific locus on a chromosome
  • Alleles are different molecular forms of a gene

Homozygous and Heterozygous

• An individual with nonidentical alleles of a gene is heterozygous for that gene
• An individual with identical alleles of a gene is homozygous for that gene
• An allele is dominant if its effect masks the effect of a recessive allele paired with it
• Capital letters (A) signify dominant alleles: lowercase letters (a) signify recessive alleles
• Genotype: the particular alleles an individual carries
• Phenotype: An individual's observable traits (the expression of the gene)

Generations

• P stands for parents, F for filial (offspring)
• F1: First generation offspring of parents
• F2: Second generation offspring of parents

Mendel and Pea Plant genetics

• Mendel was a monk with training in plant breeding and mathematics - considered to be the founder of modern genetics
• Used the pea plant in his experiments
• Normally self-pollinating
• True breeding (differnet alleles not normally introduced)
• Can be experimentally cross-pollinated - excellent for genetic manipulation
• Small, easy to grow, can self-fertilize, easily distinguisable traits

One-Trait Experiment

• Crossed true-breeding purple pea plants with true-breeding white pea plants
• F1 results: 100% flowers were all purple
• Blending theory not supported
• Purple beats white
• Mendel then crossed 2 plants from the F1 generation
• F2 results: 75% were purple, 25% were white; phenotypic ratio was 3:1

Mendel Law of Segregation

• Genes can exist in more than one form
• Organisms inherit two alleles for each trait
• When sex cells are produced (by meiosis), allele pairs separate leaving each cell with a single allele for each trait
• When the two alleles of a pair are different, one is dominant and the other is recessive
• Relates to meiosis
  • Diploid cells have pairs of genes on pairs of homologous chromosomes
  • The two genes of each pair separate during meiosis, and end up in different gametes
  • Experiment Based Theory

Punnett Squares

• Probability: a measure of the chance that a particular outcome will occur
• Punnett square: a grid used to calculate the probability of genotypes and phenotypes in offspring
• Shows all possible combinations of egg and sperm

Two Trait Experiment

• Mendel crossed tall plants with green pods (TTGG) with short plants with yellow pods (ttgg)
• Two-trait experiment: If one trait impacted another
• F1 generation: all plants are tall with green pods
• F2 phenotype ratio is 9:3:3:1 (four phenotypes) inheritance of one trait does not affect the inheritance of another
• 9 of the 16 offspring would be tall and green
• 3 of them would be green but short
• 3 of them would be tall with yellow pods
• 1 would be short with yellow pods

Independent Assortment

• Mendel's law of independent assortment with Genes are sorted into gametes independently of other genes
• All possible combinations of factors can occur in the gametes which was proved by supplied by Mendel's 2-trait (dihybrid) crosses
• Independent assortment on meiosis
  • Homologous chromosome pairs sort independently during metaphase one

Incomplete and Codominance

• Incomplete dominance: one allele is not fully dominant over its partner; the hetereozygote's phenotype is somewhere between the two homozygotes
• Codominance: Two nonidentical alleles of a gene are fully expressed in heterozygotes; neither is dominant or recessive

Polygenetic Inheritance

• Polygenic inheritance: when multiple genes work together to control a trait
• Continuous variation: traits with a range of small differences governed by MORE than one set of alleles (polygenic)
• Example: All blue eyed people do not have the same shade of blue

Environment Effecting Phenotype

• Expression of some genes is affected by environmental factors such as temperature, altitude, or chemical exposure
• The result may be variation in traits

Pleiotropy

• Single genes can have more than one effect

Photosynthesis converts light energy into chemical energy, synthesizing organic molecules. Chloroplasts, containing chlorophyll, are vital for this process. The process occurs in two stages: light reactions and the Calvin cycle, each playing a critical role in energy conversion and sugar production.