Biology Lecture Review: Photosynthesis, Cell Reproduction, and Genetics
Lecture 8 – Photosynthesis Review
What is photosynthesis?
Defined as the process that converts light energy into chemical energy.
Utilizes sunlight, carbon dioxide (CO₂), and water (H₂O).
Produces glucose and oxygen (O₂) in the chloroplasts of plants and algae.
Definitions of key terms:
Photoautotroph: Organisms that use light energy to synthesize organic molecules.
Chemoautotroph: Organisms that utilize chemicals (not light) to create organic molecules.
Heterotroph: Organisms that must consume food for energy, as they cannot produce their own.
Examples of organisms by category:
Photoautotrophs:
Examples include plants, algae, and cyanobacteria.
Chemoautotrophs:
An example includes bacteria found at deep-sea vents.
Heterotrophs:
Examples include animals, fungi, and most bacteria.
Chloroplast structure:
Thylakoids: Flat membrane sacs where light reactions of photosynthesis occur.
Grana: Stacks of thylakoids.
Stroma: The fluid-filled region surrounding the grana, where the Calvin cycle takes place.
Molecule found in the thylakoid membrane:
Chlorophyll pigments, specifically chlorophyll a and chlorophyll b.
Photosynthesis equation:
The overall chemical reaction is given by:
6CO₂ + 6H₂O + ext{light}
ightarrow C₆H₁₂O₆ + 6O₂
Relationship between photosynthesis and cellular respiration:
Photosynthesis produces glucose and oxygen, which are used by cellular respiration.
In turn, respiration releases carbon dioxide and water, which are utilized in photosynthesis.
They function as reverse processes to each other.
Light and photosynthetic pigments:
Pigments, such as chlorophyll, are crucial as they absorb light energy.
Chlorophyll absorbs primarily red and blue light, reflecting green light.
The absorption of light excites electrons, initiating the process of photosynthesis.
Major photosynthetic pigments in plants:
Chlorophyll a: The main pigment involved in the light reactions.
Chlorophyll b: An accessory pigment that broadens the spectrum of light absorption.
Carotenoids: These pigments absorb blue-green light and provide photoprotection for the plant.
Photosystems:
Defined as protein-pigment complexes located in the thylakoid membranes that capture light energy and excite electrons.
There are two types of photosystems:
Photosystem II (PSII)
Photosystem I (PSI)
Primary electron acceptor in a photosystem:
The primary electron acceptor resides in the reaction-center complex, accepting electrons from the pigment molecules.
Fates of H⁺ and electrons during light reactions:
Electrons obtained from split water molecules are used to replace lost electrons in Photosystem II.
The protons (H⁺) generated contribute to forming a proton gradient essential for ATP production.
Oxygen (O₂) is released as a byproduct into the atmosphere.
Three stages of the Calvin cycle:
Carbon Fixation: Carbon dioxide (CO₂) is attached to ribulose bisphosphate (RuBP) by the enzyme rubisco.
Reduction: ATP and NADPH are used to reduce molecules to form glyceraldehyde-3-phosphate (G3P).
Regeneration: Ribulose bisphosphate (RuBP) is regenerated using ATP, allowing the cycle to continue.
During carbon fixation:
Carbon dioxide (CO₂) is consistently attached to RuBP with the aid of the enzyme rubisco.
End product of the Reduction stage of the Calvin cycle:
Glyceraldehyde-3-phosphate (G3P), which is then utilized to synthesize glucose.
RuBP at the end of the Calvin cycle:
RuBP is regenerated, ensuring continuity of the Calvin cycle.
Lecture 9 – Cell Reproduction
Cell Cycle and Division:
Cell Cycle: A sequence of events encompassing cell growth, DNA replication, and cellular division.
Cell Division: The specific process by which two daughter cells are created from a parent cell.
Functions of Cell Division:
Essential for the processes of growth, repair, replacement, and reproduction.
Definition of a Genome:
The genome represents the complete set of DNA contained within a cell or organism.
Difference between Somatic Cells and Gametes:
Somatic Cells: These are diploid body cells containing two sets of chromosomes.
Gametes: They are haploid sex cells that only contain one set of chromosomes.
Sister Chromatids Defined:
Identical copies of a chromosome that are joined at a region known as the centromere.
Centromere:
A structural region where sister chromatids are attached and where spindle fibers connect during cell division.
DNA Packaging Process:
DNA wraps around proteins known as histones, forming structures called nucleosomes, which coil into chromatin.
Two Phases of the Cell Cycle:
Interphase: The phase where the cell grows and DNA replication occurs.
M phase: This phase is responsible for cell division (mitosis and cytokinesis).
Stages of Interphase:
G1 Phase: The cell experiences growth and engages in metabolic activity.
S Phase: The stage of DNA replication, where the genetic material is duplicated.
G2 Phase: The phase focused on preparation for mitosis.
Stages of Mitosis:
Prophase: Chromosomes condense, and the nuclear envelope begins to decompose.
Metaphase: Chromosomes align at the cell's equatorial plane.
Anaphase: Sister chromatids are separated and pulled to opposite poles of the cell.
Telophase: Two nuclei begin to form, marking the end of mitosis.
End products of Mitosis:
Result in two genetically identical diploid daughter cells.
Cytokinesis Process:
This is the division of the cytoplasm resulting in the formation of two separate cells.
Differences in Cytokinesis between Plants and Animals:
Animals: Involve the formation of a cleavage furrow.
Plants: A cell plate forms to separate the daughter cells.
Definition and Function of Checkpoints:
Checkpoint: Regulatory points that ensure proper cell division.
G1 Checkpoint: Evaluates the cell size, nutrients availability, and checks for DNA damage.
G2 Checkpoint: Confirms the completion of DNA replication.
M Checkpoint: Assesses chromosome alignment before segregation.
Positive vs Negative Regulators of the Cell Cycle:
Positive Regulators: Promote progression of the cell cycle (e.g., cyclins, cyclin-dependent kinases [CDKs]).
Negative Regulators: Halt the cell cycle when issues are detected (e.g., tumor suppressor gene p53).
Proto-oncogenes and Tumor-suppressor Genes in Cancer:
Proto-oncogenes: These genes promote cell growth; mutations can cause proto-oncogenes to become oncogenes, leading to cancer.
Tumor-suppressor Genes: These genes prevent uncontrolled cell growth; their loss can lead to cancer development.
Binary Fission Defined:
It is a form of asexual reproduction found in prokaryotic organisms, where the cell splits to form two new cells.
Asexual vs Sexual Reproduction:
Asexual reproduction: Involves one parent and produces genetically identical offspring.
Sexual reproduction: Involves two parents and generates genetically diverse offspring.
Diploid and Haploid Cells:
Diploid (2n): Cells with two complete sets of chromosomes.
Haploid (n): Cells with one set of chromosomes.
Homologous Chromosomes:
Chromosome pairs that are of similar size and contain the same gene locations; one originates from each parent.
Crossing Over and Associated Structures:
Refers to the exchange of genetic material between homologous chromosomes.
Chiasmata: The points at which chromatids exchange segments of DNA during crossing over.
Tetrads: Formed pairs of homologous chromosomes.
Stages of Meiosis:
Meiosis I: In this stage, homologous chromosomes separate to form two haploid cells.
Meiosis II: The sister chromatids separate, resulting in the creation of four haploid gametes.
Differences between Metaphase of Mitosis and Metaphase I of Meiosis:
In mitosis, individual chromosomes line up in the center, while during meiosis I, homologous pairs align at the equatorial plane.
End Products of Meiosis I and II:
Meiosis I: Yields two haploid cells.
Meiosis II: Results in four haploid cells.
Comparison of Life Cycles:
Haploid-dominant: Life cycle where most life stages are haploid (e.g., fungi).
Diploid-dominant: Organisms primarily exist in diploid form (e.g., humans).
Alternation of Generations: A life cycle that includes both haploid multicellular stages and diploid multicellular stages (e.g., plants).
Lecture 10 – Mendel and Inheritance
Gregor Mendel’s Contribution to Genetics:
He established foundational laws of inheritance through experiments with pea plants.
Demonstrated that traits are governed by discrete units called genes.
Dichotomous Traits:
Traits that exhibit two contrasting forms, such as tall versus short.
True Breeding Plants:
These plants produce offspring that are genetically identical to themselves for a specific trait.
Generational Terms:
P Generation: The original parental generation used in breeding experiments.
F1 Generation: The first filial generation resulting from crossbreeding the P generation.
F2 Generation: The generation that results from the self-pollination of the F1 generation.
Allele Definition:
An allele is a variant form of a gene.
Dominant vs. Recessive Alleles:
Dominant Allele: An allele that is expressed phenotypically if present.
Recessive Allele: An allele that is expressed phenotypically only when two copies are present (homozygous condition).
Genotype vs. Phenotype:
Genotype: Represents the genetic composition.
Phenotype: Refers to observable physical traits.
Homozygous vs. Heterozygous:
Homozygous: Organisms with two identical alleles for a specific gene.
Heterozygous: Organisms with two different alleles for a specific gene.
Punnett Squares:
These diagrams are used to predict the ratios of genotypes and phenotypes for different inheritance patterns, including the following:
Complete dominance
Incomplete dominance
Codominance
Multiple alleles
Sex-linked inheritance.
Mendel’s Laws of Inheritance:
Law of Segregation: States that alleles separate during the formation of gametes.
Law of Independent Assortment: Specifies that genes located on different chromosomes segregate independently of one another.
Epistasis Defined:
A phenomenon in which one gene influences the expression of another gene.
Chromosomal Theory of Inheritance:
A theory that posits genes are situated on chromosomes, a concept introduced by Sutton and Boveri.
Non-disjunction:
The failure of chromosomes to separate correctly during cell division, resulting in abnormal gametes.
Aneuploidy and Its Consequences:
Refers to having an abnormal number of chromosomes; can lead to conditions such as Down syndrome.
Polyploidy and Its Consequences:
Involves the presence of extra sets of chromosomes; very common in plant species and may lead to the emergence of new species.
Barr Body:
An inactivated X chromosome found in female mammals, which serves to equalize gene dosage between males and females.
Chromosome Structural Alterations:
Includes changes such as duplication, deletion, inversion, and translocation of chromosome segments.
Lecture 11 – DNA Structure and Function
DNA Replication Defined:
The process of duplicating DNA before cell division occurs.
Key Scientists in DNA Research:
Miescher: Initially discovered DNA.
Griffith: Conducted experiments that demonstrated transformation.
Avery, McLeod, McCarty: Established that DNA is the genetic material.
Hershey & Chase: Confirmed that DNA is the carrier of genetic information.
Chargaff: Developed the base pairing rules that govern nucleotide pairing.
Watson & Crick / Franklin / Wilkins: Described the double-helix structure of DNA.
Structure of a Nucleotide:
Composed of a 5-carbon sugar, a phosphate group, and a nitrogenous base.
Organization of DNA:
Organized as a double helix structure with a sugar-phosphate backbone and nitrogenous bases oriented towards the interior.
Nitrogenous Base Pairing:
The base pairing rules state that adenine (A) pairs with thymine (T), while cytosine (C) pairs with guanine (G).
Antiparallel Nature of DNA:
The two strands of DNA run in opposite directions (5’ to 3’ and 3’ to 5’).
Semiconservative Replication:
This method of replication ensures that each new DNA molecule consists of one old strand and one new strand.
Origin of Replication:
Refers to the starting point in the DNA where replication begins.
Replication Fork:
This is the area where the DNA is unwound during replication, forming a Y-shaped structure.
Key Enzymes and Proteins Involved in DNA Replication:
Helicase: Responsible for unwinding the DNA strands.
Single-Stranded Binding Proteins (SSB): Keep the separated strands apart to prevent re-annealing.
Topoisomerase: Alleviates the twisting strain created ahead of the replication fork.
Primase: Synthesizes RNA primers necessary for DNA polymerization.
DNA Polymerase III: Enzyme that synthesizes new DNA strands by adding nucleotides.
DNA Polymerase I: Fills in the gaps left after RNA primers are removed.
DNA Ligase: Connects Okazaki fragments on the lagging strand to create a continuous DNA molecule.
Nuclease: Enzyme involved in the repair of DNA by excising mismatched or damaged sections.
Leading vs. Lagging Strands:
Leading Strand: Synthesized continuously in the direction of the replication fork.
Lagging Strand: Synthesized in fragments known as Okazaki fragments.
Okazaki Fragments:
These are short segments of DNA synthesized on the lagging strand during replication.
DNA Error Repair Mechanisms:
Included proofreading, mismatch repair, and nuclease excision repair processes to maintain DNA integrity.
Types of Mutations:
Point Mutation: A change in a single nucleotide.
Frameshift Mutation: Insertion or deletion of nucleotides that shifts the reading frame.
Silent Mutation: A mutation that does not affect the amino acid sequence.
Missense Mutation: A substitution mutation that results in a different amino acid.
Nonsense Mutation: A mutation that creates a premature stop codon.
Telomeres:
Repetitive nucleotide sequences located at the ends of chromosomes, providing protection and stability.
Telomere Shortening:
Telomeres shorten with each cell division; telomerase extends the length of telomeres mainly in stem cells and cancer cells.
Lecture 12 – Genes and Proteins
Central Dogma of Molecular Biology:
The flow of genetic information is described as DNA → RNA → Protein.
Degeneracy of the Genetic Code:
The phenomenon whereby multiple codons can encode the same amino acid.
Transcription vs. Translation:
Transcription: The process of converting DNA into messenger RNA (mRNA).
Translation: The process of synthesizing proteins based on the sequence of the mRNA.
Location of Processes:
Transcription: Occurs in the nucleus for eukaryotes and cytoplasm for prokaryotes.
Translation: Takes place at the ribosome.
mRNA vs tRNA:
mRNA (messenger RNA): Carries the genetic code from DNA to the ribosome.
tRNA (transfer RNA): Brings specific amino acids to the ribosome during protein synthesis.
Codon Definition:
A codon is a sequence of three nucleotides in mRNA that codes for a specific amino acid.
Genetic Code Composition:
The genetic code consists of 64 codons that correspond to 20 different amino acids.
DNA vs RNA Base Pairing:
In DNA: A pairs with T, C pairs with G.
In RNA: A pairs with U (uracil), C pairs with G.
Steps of Transcription in Prokaryotes:
Initiation: RNA polymerase attaches to the promoter region of DNA.
Elongation: RNA nucleotides are added to the growing RNA chain.
Termination: The completed mRNA strand is released from the DNA.
Consensus Sequences:
Specific promoter sequences that facilitate RNA polymerase binding.
Transcription in Eukaryotes:
Initiation: RNA polymerase bind with transcription factors to the promoter.
Elongation: The FACT complex moves histones to allow elongation.
Termination: Pre-mRNA is released once transcription is complete.
Differences between Eukaryotes and Prokaryotes:
Eukaryotes contain a nucleus, have introns and exons, and require RNA processing.
Prokaryotes have no nuclei, lack introns, and have operons for gene expression.
FACT Complex:
A protein complex involved in the removal of nucleosomes during transcription to allow RNA polymerase access to DNA.
RNA Processing Steps:
Involves adding a 5’ cap, a poly-A tail, and the removal of introns.
Introns and Exons:
Introns: Non-coding regions of the gene.
Exons: Coding regions that remain in the mature RNA.
RNA Splicing:
A process facilitated by the spliceosome, which removes introns and joins exons together.
Translation Process in Prokaryotes and Eukaryotes:
Initiation: Recognizes the start codon (AUG) to begin translation.
Elongation: tRNA brings amino acids, and the polypeptide chain is elongated.
Termination: Translation stops when a stop codon is reached, releasing the completed protein.
Codon-Anticodon Interaction:
A codon is the three-base sequence in mRNA, while an anticodon is the complementary three-base sequence found in tRNA.
Types of Mutations:
Point Mutation: Change at a single nucleotide.
Silent Mutation: No change in amino acid sequence.
Missense Mutation: Results in a different amino acid.
Nonsense Mutation: Leads to a premature stop codon.
Frameshift Mutation: Changes resulting from insertion or deletion of nucleotides.
Operons Defined:
Clusters of genes under a single promoter in prokaryotic organisms, allowing coordinated regulation.
Operon Regulation:
Regulators such as repressors, activators, and inducers modulate the operon functions.
Epigenetic Regulation:
Methylation: Often turns genes off.
Acetylation: Typically promotes gene expression.
Gene Expression in Eukaryotes:
Involves complex processes, including DNA bending, the interaction of enhancers, transcription factors, and mediator proteins.
Differential Gene Expression:
The expression of different sets of genes in distinct cell types, leading to cell specialization.
Alternative Splicing:
A process where one gene can give rise to multiple protein products through various splicing configurations.
Lecture 13 – Evolution
Darwin & Wallace:
Both independently proposed natural selection as the primary mechanism driving evolution.
Adaptation Defined:
A trait that enhances an organism's fitness and chances of survival in a given environment.
Natural Selection Mechanism:
Describes the differential survival and reproduction of individuals with advantageous traits, leading to evolutionary change.
Requirements for Natural Selection:
There must be variation in traits among individuals in a population.
More offspring are produced than the environment can support, leading to competition.
Traits that confer an advantage in survival and reproduction must be hereditary.
Evidence for Evolution (Four Types):
Fossils: Provide historical evidence and document changes over time.
Comparative Anatomy: Analyses homologous and analogous structures among species.
Embryology: Studies similar developmental stages in different organisms.
Molecular Biology: Examines DNA and protein comparisons for genetic relationships.
Homologous vs. Analogous Structures:
Homologous Structures: Same structural elements but different functions, indicating common ancestry.
Analogous Structures: Seraphic function but different structural origins, often resulting from convergent evolution.
Vestigial Structures:
Reduced or non-functional structures remaining from a common ancestor (e.g., human appendix).
Convergent Evolution:
Occurs when different species evolve similar traits due to similar environmental pressures (e.g., wings of bats and insects).
Misconceptions about Evolution:
Evolution is not goal-directed, not simply a theory, and does not involve changes in individual organisms over their lifetimes; evolution occurs at the population level.
Species, Hybrid, Gene Pool Definitions:
Species: A group of organisms that can interbreed and produce fertile offspring.
Hybrid: The offspring resulting from the mating of two different species.
Gene Pool: The total collection of alleles in a population.
Allopatric Speciation Explained:
Occurs when a population is geographically isolated, leading to the formation of a new species.
Sympatric Speciation:
A new species forms in the same geographic area without physical barriers between them.
Pre-zygotic and Post-zygotic Barriers:
Pre-zygotic Barriers: Prevent mating or fertilization from occurring (e.g., temporal, behavioral isolation).
Post-zygotic Barriers: Occur after fertilization and can result in hybrid inviability or sterility.
Genetic Drift & Gene Flow:
Bottleneck Effect: A significant reduction in population size, leading to changes in allele frequencies.
Founder Effect: Occurs when a small group establishes a new population with different allele frequencies.
Gene Flow: The migration of individuals between populations affects allele frequencies.
Hardy-Weinberg Principle:
Expressed with the equation: p² + 2pq + q² = 1. This principle predicts allele and genotype frequencies in a population that is not evolving.
Selection Types:
Stabilizing Selection: Favors intermediate phenotypes.
Directional Selection: Favors one extreme phenotype.
Diversifying Selection: Favors extreme phenotypes over intermediate ones.
Relative Fitness Defined:
The contribution of an individual to the gene pool of the next generation relative to others.
Intrasexual vs Intersexual Selection:
Intrasexual Selection: Competition among the same sex (e.g., males competing for mates).
Intersexual Selection: Mate choice, typically where one sex selects mates of the other sex based on certain traits.
Handicap Principle:
Suggests that costly traits may signal to potential mates the genetic fitness of an individual (e.g., extravagant peacock tails).
Week 14 – Biotechnology and Viruses
Genetic Manipulation Techniques:
Methods include DNA/RNA extraction, Polymerase Chain Reaction (PCR), gel electrophoresis, and blotting techniques.
Cloning Types:
Molecular Cloning: Involves the cloning of DNA fragments.
Cellular Cloning: Cloning of whole somatic cells.
Reproductive Cloning: Cloning of an entire organism.
Plasmid Definition:
Circular DNA molecules often used as vectors in genetic engineering experiments.
Genetically Modified Organism (GMO):
An organism that has had foreign DNA inserted into its genome through genetic engineering.
Transgenic Organism:
Organisms that contain DNA from another species, utilized in medicine or agriculture.
Gene Therapy:
A technique for correcting defective genes in patients for therapeutic benefits.
Virus Definition:
Characterized as a non-living particle that must infect a host cell to replicate.
Viral Shapes:
Common viral shapes include helical (e.g., Tobacco Mosaic Virus), icosahedral (e.g., adenovirus), enveloped (e.g., influenza virus), and complex (e.g., bacteriophage).
Viral Genome:
Viruses can possess either DNA or RNA, which may be single-stranded or double-stranded, and their genome size varies significantly.
Steps of Viral Infection:
The viral cycle includes the following stages: attachment, entry, replication, assembly, and release.
Lytic vs. Lysogenic Cycle:
Lytic Cycle: The virus actively replicates and causes lysis of the host cell.
Lysogenic Cycle: The viral DNA integrates into the host genome and may remain dormant until induced to replicate.
Retrovirus Defined:
A type of RNA virus that uses reverse transcriptase to reverse transcribe its RNA into DNA, which then integrates into the host's genome.
Vaccine Definition:
A preparation that stimulates the immune system to recognize and combat specific pathogens.
Plant Virus Transmission Methods:
Transmission can occur through mechanical damage or via vectors such as insects.