Cellular Energetics and Division

BIO FINAL EXAM REVIEW 24 questions ATP * Energy required * Cellular Respiration: The main pathway for ATP production involves the breakdown of glucose and other organic molecules through processes like glycolysis, the Krebs cycle, and the electron transport chain. * Oxidative Phosphorylation: This process, which occurs in the mitochondria, uses the energy released during the electron transport chain to create a proton gradient that drives the synthesis of ATP. * Photophosphorylation (in plants and some bacteria): In photosynthetic organisms, light energy is used to drive the phosphorylation of ADP to ATP, a process called photophosphorylation. * Energy release * When ATP is needed to power cellular activities, it is broken down (hydrolyzed) into ADP and inorganic phosphate, releasing the stored energy. PHOTOSYNTHESIS/RESPIRATION * What organelles are involved in each? * Photosynthesis: the chloroplasts * Respiration: mitochondria * Equation for each – to determine reactants and products * Photosynthesis: 6CO2 + 6H2O (plus light energy) → C6H12O6 + 6O2 * Respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy (ATP) * What is redox? * Short for reduction-oxidation reaction; a chemical reaction in which electrons are lost from one substance (oxidation) and added to another (reduction) * Photosystem II * In photosystem II (PSII), sunlight energy is captured and used to split water molecules. This process, also known as water oxidation, releases electrons that are then transferred to plastoquinone. The splitting of water also produces protons, which contribute to the formation of a proton gradient across the thylakoid membrane, ultimately leading to the production of ATP. PSII is the first step in the light-dependent reactions of photosynthesis * Photosystem I * In Photosystem I (PSI), light energy excites electrons, which are then transferred to a protein called ferredoxin. This process is part of the light-dependent reactions of photosynthesis, where PSI acts as an electron acceptor from plastocyanin and uses light energy to transfer electrons to ferredoxin on the stromal side of the thylakoid membrane RESPIRATION * Summarize the three steps of Respiration- Glycolysis, Oxidation of pyruvate/Kreb’s cycle and Oxidative Phosphorylation. * Glycolysis - occurs in the cytosol of the cell. Glycolysis begins cellular respiration by breaking down glucose into 2 molecules of a 3-carbon compound called pyruvate * Pyruvate oxidation/the citric acid cycle - take place within the mitochondria. Together pyruvate oxidation and the reactions of the citric acid cycle complete the breakdown of glucose to carbon dioxide. Thus the CO2 you exhale is generated in the mitochondria of your cells during this second stage of respiration * Oxidative phosphorylation - involves electron transport and a process known as chemiosmosis. NADH and a related electron carrier, FADH2, shuttle electrons to electron Transport chains embedded in the inner mitochondrial membrane. Most of the ATP produced by cellular respiration is generated by oxidative phosphorylation, which uses the energy released by redox reactions to make ATP. The electrons are finally passed to oxygen, which becomes reduced to H2O. * Chemiosmosis - an energy-coupling mechanism that uses the energy of hydrogen ion (H+) gradients across membranes to drive cellular work, such as the phosphorylation of ADP; powers most ATP synthesis in cells * Which process produces the most ATP? * oxidative phosphorylation * Why do organisms need oxygen? * because it's essential for cellular respiration, the process that converts food into energy. Oxygen acts as the final electron acceptor in this process, allowing the body to efficiently produce the energy-carrying molecule ATP. https://biomanbio.com/HTML5GamesandLabs/PhotoRespgames/photoresp.html PHOTOSYNTHESIS * Where does gas exchange in a leaf occur? * The stomata - tiny pores on the surface of leaves and stems that allow for gas exchange (carbon dioxide and oxygen) and water vapor release * Where are chloroplasts located? * The leaves/plant cells - within the cells of land plants and red and green algae, specifically in the green tissues of these organisms * Structure and function of chloroplast. * Chloroplasts are organelles in plant cells and some algae responsible for photosynthesis, converting light energy into chemical energy in the form of sugar. They have a complex structure, including an outer and inner membrane, thylakoids, and a fluid-filled space called the stroma. Chloroplasts also contain their own DNA and ribosomes. * What does a plant do with the sugar it produces? * Plants utilize the sugar they produce through photosynthesis in several ways. They use it for energy through cellular respiration, build cell walls with it (using it to make cellulose), store it as starch for later use, and even use it to create other sugars like fructose for fruits * Light reactions and Light independent reactions…..location, reactants, products, and the relationship between them. * Light-dependent reactions (also called light reactions) occur in the thylakoid membranes of chloroplasts, using light energy and water to produce ATP, NADPH, and oxygen. * Light-independent reactions (also known as the Calvin cycle or dark reactions) occur in the stroma, using ATP and NADPH from the light reactions, along with carbon dioxide, to produce sugars. * What is carbon fixation? * Carbon fixation - the incorporation of carbon from atmospheric CO2 into an organic compound. During photosynthesis in a C3 plant, carbon is fixed * What is the source of oxygen in the atmosphere? (Yes plants but be specific) * The oxygen in Earth's atmosphere primarily comes from the process of photosynthesis performed by cyanobacteria and other photosynthetic organisms, like plants, algae, and phytoplankton. These organisms convert carbon dioxide and water into oxygen as a byproduct of their metabolism. * Pigments – reflected vs absorbed * During photosynthesis, plants primarily absorb blue (around 420-450 nm) and red (around 620-680 nm) wavelengths of light. Green light (around 495-570 nm) is generally not absorbed as strongly, and is reflected, causing plants to appear green. * Chlorophyll, the main pigment responsible for capturing light energy, strongly absorbs blue and red light https://media.hhmi.org/biointeractive/click/photosynthesis/?_gl=1*yqejb5*_ga*NDMxNDEwMjQ5LjE3NDg1NDIzMjc.*_ga_H0E1KHGJBH*czE3NDg1NDIzMjckbzEkZzAkdDE3NDg1NDIzMjgkajU5JGwwJGgw https://quizlet.com/245726026/photosynthesis-review-diagram/ MITOSIS/MEIOSIS (30 questions) * Asexual reproduction * The creation of genetically identical offspring, generated by a single parent, without the participation of egg and sperm * sexual reproduction * The creation of genetically uniques offspring by the fusion of two haploid sex cells (gametes), forming a diploid zygote * What are the functions of cell division? * Cell division, a fundamental process in biology, serves vital functions in both single-celled and multicellular organisms. In single-celled organisms, it's a primary means of reproduction, while in multicellular organisms, it's crucial for growth, development, and repair of tissues and damaged cells * GROWTH, REPAIR, REPRODUCE * Prokaryote vs eukaryote DNA * Prokaryotic DNA is typically a single, circular chromosome, found in the cytoplasm within a region called the nucleoid * while eukaryotic DNA is linear and organized into multiple chromosomes within a membrane-bound nucleus * Organization of DNA * In both mitosis and meiosis, DNA is organized into chromosomes, which are then further condensed. Mitosis produces two identical daughter cells, maintaining the same number of chromosomes as the parent cell, while meiosis results in four unique daughter cells, each with half the number of chromosomes, crucial for sexual reproduction. * Structure of a duplicated chromosome * Structure of a duplicated chromosome * Cell cycle vs mitosis vs cytokinesis (plant vs animal) * CELL CYCLE - AN ORDERED SEQUENCE OF EVENTS (INCLUDING INTERPHASE AND THE MITOTIC PHASE) THAT EXTENDS FROM THE TIME A EUKARYOTIC CELL IS FIRST FORMED FROM A DIVIDING PARENT CELL UNTIL ITS OWN DIVISION INTO 2 CELLS * MITOSIS - THE DIVISION OF A SINGLE NUCLEUS INTO 2 GENETICALLY IDENTICAL NUCLEI. MITOSIS AND CYTOKINESIS MAKE UP THE MITOTIC (M) PHASE OF THE CELL CYCLE * Cytokinesis - the process where the cytoplasm of a cell divides, resulting in the formation of two separate daughter cells. * Prophase - the first stage of mitosis, during which the chromatin condenses to form structures (sister chromatids) visible with a light microscope and the mitotic spindle begins to form, but the nucleus is still intact * Prometaphase - the second stage of mitosis, during which the nuclear envelope fragments and the spindle microtubules attach to the kinetochores of the sister chromatids * Metaphase - the third stage of mitosis, during which all the cell’s duplicated chromosomes are lined up at an imaginary plane equidistant between the poles of the mitotic spindle * Anaphase - the fourth stage of mitosis, beginning when sister chromatids separate from each other and ending when a complete set of daughter chromosomes arrives at each of the two poles of the cell * Telophase - the fifth and final stage of mitosis, during which daughter nuclei form at the two poles of a cell. Telophase usually occurs together with cytokinesis * Distinguish between replicated chromosomes, chromosomes, and sister chromatids. * Chromosome: A single, long DNA molecule, tightly wound around proteins, forming a compact structure. It contains the genes that determine an organism's traits. * Replicated Chromosome: Before a cell divides, each chromosome is duplicated. This means the DNA is copied, resulting in two identical copies called sister chromatids. * Sister Chromatids: The two identical copies of a replicated chromosome. They are connected at a central region called the centromere and are held together by protein complexes called cohesins. * Stages of the Cell cycle * G1 phase: The cell grows, replicates its organelles, and prepares for DNA replication. It is the longest phase of the cell cycle for most cells. * S phase: The cell duplicates its DNA, ensuring that each daughter cell receives a complete set of genetic information. * G2 phase: The cell continues to grow and synthesizes proteins and other molecules needed for cell division. * M phase: This phase involves mitosis (nuclear division) and cytokinesis (cell division). Mitosis ensures that each daughter cell receives an identical copy of the original cell's DNA. Cytokinesis physically divides the cytoplasm and cell membrane, resulting in two separate daughter cells * Labeling the significant events of mitosis * Control of cell division * The cell cycle control system is a set of molecules that both triggers and coordinates key events in the cell cycle. * Checkpoints of cell division. * G1 Checkpoint: This checkpoint occurs at the end of the G1 phase, before the cell enters the S phase (DNA replication). It assesses whether the cell is large enough, has sufficient nutrients, and if the DNA is undamaged. If any of these conditions are not met, the cell cycle can be halted, and the cell may attempt to repair the DNA or enter a quiescent state. * G2 Checkpoint: This checkpoint occurs at the end of the G2 phase, before the cell enters mitosis. It checks whether DNA replication has been completed correctly and if there is any DNA damage. If DNA damage is detected, the cell cycle can be arrested, and the cell will attempt to repair the damage or undergo apoptosis (programmed cell death). * M Checkpoint (Spindle Checkpoint): This checkpoint occurs during metaphase, the second phase of mitosis. It monitors whether all chromosomes are correctly attached to the spindle fibers and aligned at the metaphase plate. If chromosomes are not properly attached, the cell cycle will be halted, and the cell will try to fix the problem. * These checkpoints are crucial for maintaining genomic integrity and preventing the formation of cancerous cells. If a checkpoint fails, the cell can be arrested, attempt to repair the damage, or undergo programmed cell death. * Mitosis vs meiosis products * Mitosis produces two genetically identical daughter cells, each with the same number of chromosomes as the original parent cell (diploid). This process is essential for growth, repair, and development in the body * Meiosis, a specialized cell division process, produces four haploid gametes (sperm and egg cells) from a single diploid cell. These gametes are essential for sexual reproduction, ensuring genetic diversity and the restoration of diploid chromosome numbers during fertilization * Autosomes vs Sex Chromosomes * autosomes are chromosomes (numbered 1-22) that are the same in both males and females, while sex chromosomes (X and Y) differ between the sexes. * Haploid vs diploid. Germ cells, Gametes, Somatic * Somatic: Somatic cells are any cells in a multicellular organism that are not involved in reproduction. This means they exclude sperm, egg cells, and any cells that develop into these gametes. * Gametes (sperm and egg cells) are haploid, containing a single set of chromosomes (n = 23 for humans). They are produced through meiosis, which reduces the chromosome number by half, ensuring genetic diversity in offspring. * A haploid cell is a type of cell that contains a single set of chromosomes. This means it has only one member of each homologous chromosome pair * Diploid cells are cells that contain two complete sets of chromosomes, one set inherited from each parent. This is represented as 2n. * Germ cells are specialized cells that give rise to gametes, which are the reproductive cells (sperm and egg) in organisms. These cells are crucial for sexual reproduction as they carry genetic information to the next generation. * Sources of Genetic diversity * Mitosis: During mitosis, the sister chromatids of each chromosome are separated, resulting in two daughter cells that are genetically identical to the parent cell. * Meiosis: * Crossing Over: During prophase I of meiosis, homologous chromosomes exchange genetic material, creating new combinations of alleles. * Independent Assortment: The random alignment of homologous chromosomes during metaphase I allows for the production of gametes with different combinations of chromosomes from each parent. * Random Fertilization: The fusion of two genetically different gametes (egg and sperm) during fertilization further increases genetic diversity by creating new combinations of genes in the zygote. * Reduction to Haploid: Meiosis I and II reduce the chromosome number from diploid to haploid, ensuring that each gamete receives only one set of chromosomes. Cell Size Lab MEIOSIS https://www.sciencefacts.net/mitosis-vs-meiosis.html * Significant Events of Meiosis including synapsis/crossing over and random assortment. * Synapsis - In meiosis, synapsis is the pairing of homologous chromosomes that occurs during prophase I. This pairing, often assisted by a protein complex called the synaptonemal complex, ensures that the homologous chromosomes align precisely. This precise alignment is crucial for the subsequent process of crossing over, where genetic material is exchanged between non-sister chromatids. * Crossing over - Crossing over, also known as genetic recombination, is the exchange of genetic material between non-sister chromatids of homologous chromosomes during meiosis. It results in new combinations of genes on chromosomes, contributing to genetic diversity in gametes and offspring. * random assortment - Random assortment, also known as independent assortment, in meiosis refers to the random distribution of homologous chromosomes during meiosis I, leading to diverse combinations of genes in the resulting gametes. This process contributes significantly to genetic variation among offspring. * Karyotyping * Karyotyping is the process of pairing and ordering all the chromosomes of an organism, thus providing a genome-wide snapshot of an individual's chromosomes. Karyotypes are prepared using standardized staining procedures that reveal characteristic structural features for each chromosome. * Homologous Chromosomes * paired chromosomes, one inherited from each parent, that contain the same genes but may have different alleles. They are crucial for ensuring proper chromosome segregation during meiosis, a type of cell division that produces gametes (sperm and egg cells). * Significant events * Meiosis involves two successive nuclear divisions (meiosis I and II) that reduce the chromosome number by half. Key events include chromosome pairing and crossing over in prophase I, homologous chromosome separation in anaphase I, and sister chromatid separation in anaphase II, leading to four haploid daughter cells * Nondisjunction: Down Syndrome, Turner Syndrome, Edwards Syndrome, Klinefelters Syndrome * Nondisjuncion - Nondisjunction is failure of paired chromosomes to move to opposite poles of the spindle during mitosis or meiosis. If nondisjunction occurs during meiosis, the resulting embryo inherits an extra chromosome (trisomy) or lacks a chromosome (monosomy). DISORDER CHROMOSOMES DESCRIPTION Klinefelter Syndrome one or more extra sex chromosomes (i.e., XXY) a male is born with an extra X chromosome Turner Syndrome 45 chromosomes occurs when females only have one X chromosome Down Syndrome Trisomy 21, extra chromosome 21 an extra chromosome 21 Edward Syndrome 3 copies of chromosome 18 occurs when there is an extra copy of chromosome 18 * Gene mutations vs. chromosome mutations. * Gene Mutations: * Definition: Changes in the DNA sequence within a single gene. * Examples: Point mutations (single base changes), frameshift mutations (insertions or deletions that shift the reading frame), and expansions of repeat sequences. * Impact: Can alter the protein produced by the gene, potentially leading to a variety of effects, from no change at all (silent mutations) to altered or non-functional proteins. * Inheritance: Germline mutations (occurring in reproductive cells) can be inherited by offspring. * Examples of Genetic Disorders: Huntington's disease, cystic fibrosis. * Chromosomal Mutations: * Definition: Changes to the number or structure of chromosomes. * Examples: Deletions, duplications, inversions, translocations, and aneuploidy (having extra or missing chromosomes). * Impact: Can significantly alter the genetic material, often leading to more severe consequences. * Inheritance: Can be inherited from germline mutations. * Examples of Genetic Disorders: Down syndrome (trisomy 21), Edward's syndrome (trisomy 18) * Types of each mutation. Chapter 9 PATTERNS OF INHERITANCE * Blending Theory * A discredited theory in biology that suggests traits from parents mix together in their offspring, resulting in an intermediate trait * Why did Mendel use peas? * They were easy to grow, had visible characteristics, and were relatively quick to reproduce, allowing him to study multiple generations in a short time. Additionally, pea plants could be self-pollinated or cross-polinated, giving mendel control over their fertilization * Mendel’s Experiments and Conclusions (Monohybrid Ratios and Dihybrid ratios) * Monohybrid cross - an experimental mating of individuals that are heterozygous for the character being followed (or the self-pollination of a heterozygous plant) * Dihybrid cross - an experimental mating of individuals that are each heterozygous for both of the 2 characters (of the self-pollination of a plant that is heterozygous for both characters) * True Breeding, Cross Breeding, Hybridization, P, F1, F2 * True breeding - referring to organisms for which sexual reproduction produces offspring with inherited traits identical to those of the parents. The organisms are homozygous for the characters under consideration. * Hybrid - offspring that results from the mating of individuals from two different species or from two true-breeding varieties of the same species; an offspring of two parents that differ in one or more inherited traits; an individual that is heterozygous for one or more pairs of genes * Cross breeding - a matting of 2 sexually reproducing individuals; often used to describe a genetics experiment involving a controlled mating (a “genetic cross”) * P generation - the parent individuals from which offspring are derived in studies of inheritance; P stands for parental * F1 generation - the offspring of 2 parental (P generation) individuals; F1 stands for first filial * F2 generation - the offspring of the F1 generation; F2 stands for second filial * Allele * An alternative version of a gene * Genotype * The genetic makeup of an organism * Phenotype * The expressed traits of an organism * Homozygous * Having 2 identical alleles for a given gene * Heterozygous * Having 2 different alleles for a given gene * Test Cross * The mating between an individual of unknown genotype for a particular character and an individual that is homozygous recessive for that same character. The testcross can be used to determine the unknown genotype (homozygous dominant versus heterozygous) * Law of Independent Assortment * A general rule of inheritance (originally formulated by Gregor Mendel) that when gametes form during meiosis, each pair of alleles for a particular character segregates independently of other pairs; also known as Mendel’s second law of inheritance * Dominant/Recessive * Dominant allele - the allele that determines the phenotype of a gene when the individual is heterozygous for that gene * Recessive allele - an allele that has no noticeable effect on the phenotype of a gene when the individual is heterozygous for that gene * Codominant/Incomplete Dominance/Polygenic Inheritance * Codominant inheritance - two alleles for a specific trait are both expressed in the phenotype of a heterozygous individual, rather than one masking the other * Incomplete dominance - a genetic phenomenon where neither allele for a trait completely masks the other in a heterozygous individual, resulting in a blended phenotype that is intermediate between the 2 homozygous phenotypes * Polygenic inheritance - a type of inheritance where a trait is controlled by multiple genes, rather than a single gene. This results in a wide range of phenotypes for the trait, often following a bell-shaped curve distribution * Blood Typing * A method of classifying blood based on the presence or absence of specific inherited antigens on the surface of red blood cells * Crosses involving multiple traits * Solve genetics problems * Dominant, Recessive, and Sex-Linked Disorders. * Carrier * An individual who is heterozygous for a recessively inherited disorder and who therefore does not show symptoms of that disorder but who may pass on the recessive allele to offspring * Linked Genes * Genes that are located close together on the same chromosome and are therefore usually inherited together * Sex determination in humans only * Pedigree * A family genetic tree representing the occurrence of heritable traits in parents and offspring across a number of generations. A pedigree can be used to determine genotypes of matings that have already occurred CHAPTER 10 Replication and PROTEIN SYNTHESIS (Questions 28) * DNA Structure/Function * Double helix * Deoxyribonucleic acid * Thymine and cytosine - a single-ring nitrogenous base found in DNA * Adenine and guanine - a double ring nitrogenous base found in DNA * Semiconservative model - type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand * Dna polymerase - a large molecular complex that assembles dna nucleotides into polynucleotides using a preexisting strand of dna as a template * Dna ligase - an enzyme, essential for DNA replication, that catalyzes the covalent bonding of adjacent DNA polynucleotide strands. DNA ligase is used in genetic engineering to paste a specific piece of DNA containing a gene of interest into a bacterial plasmid or other vector * RNA types and their function * Uracil - a single-ring nitrogenous base found in RNA * RNA polymerase - a large molecular complex that links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template * Promoter - a specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins * Terminator - a special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule and then to depart from the gene. * mRNA - the type of ribonucleic acid that encodes genetic information from DNA and conveys it to ribosomes, where the information is translated into amino acid sequences * RNA splicing - the removal of introns and joining of exons in eukaryotic RNA, forming an mRNA molecule with a continuous coding sequence; occurs before mRNA leaves the nucleus * tRNA - a type of ribonucleic acid that functions as an interpreter in translation. Each tRNA molecule has a specific anticodon, picks up a specific amino acid, and conveys the amino acid to the appropriate codon on mRNA * Anticodon - on a tRNA molecule, a specific sequence of 3 nucleotides that is complementary to a codon triplet on mRNA * Replication including enzymes * DNA helicase - an enzyme that plays a crucial role in DNA replication and other processes involving nucleic acids * Protein Synthesis: Transcription including RNA processing, Translation and enzymes. * Transcription - the synthesis of RNA on a DNA template * Translation - the synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids * Codon - a 3 - nucleotide sequence in mRNA that specifies a particular amino acid or polypeptide termination signal; the basic unit of the genetic code * Ribosomes - a cell structure consisting of RNA and protein organized into 2 subunits and functioning as the site of protein synthesis in the cytoplasm. In eukaryotic cells, the ribosomal subunits are constructed in the nucleolus * Ribosomal RNA (rRNA) - the type of ribonucleic acid that, together with proteins, makes up ribosomes; the most abundant type of RNA in most cells * Start codon - on mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information * P site - one of a ribosom’s binding sites for tRNA during translation. The P site holds the tRNA carrying the growing polypeptide chain. ( P stands for prptidyl tRNA) * A site - one of a ribosomes binding sites for tRNA during translation. The A site holds the tRNA that carries the next amino acid in the polypeptide chain (A stands for aminoacyl tRNA) * Stop codon - in mRNA, one of three triplets (UAG, UAA, UGA) that signal gene translation to stop * Mutations * Silent mutation - a mutation in a gene that changes a codon to one that codes for the same amino acid as the original codon. The amino acid as the original codon. The amino acid sequence of the resulting polypeptide is thus unchanged * Missense mutation - a change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide. In a missense mutation, a codon is changed from encoding one amino acid to encoding a different amino acid * Nonsense mutation - a change in the nucleotide sequence of a gene that converts an amino-acid-ecoding codon to a stop codon. A nonsense mutation results in a shortened polypeptide * Frameshift mutation - a change in the genetic material that involves the insertion of deletion of one or more nucleotides in a gene, resulting in a change in the triplet grouping of nucleotides EXTRA PHOTOSYNTHESIS NOTES 7.1 Photosynthesis powers most life on Earth. Plants, algae, and some photosynthetic protists and bacteria are photoautotrophs, the producers of food consumed by virtually all heterotrophic organisms. 7.2 Photosynthesis occurs in chloroplasts in plant cells. Chloroplasts are surrounded by a double membrane and contain stacks of thylakoids and a thick fluid called stroma. 7.3 Scientists traced the process of photosynthesis using isotopes. Experiments using both heavy and radioactive isotopes helped determine the details of the process of photosynthesis. 7.4 Photosynthesis is a redox process. In photosynthesis, H2O is oxidized and CO2 is reduced. 7.5 Photosynthesis occurs in two stages, which are linked by ATP and NADPH. The light reactions occur in the thylakoids, producing ATP and NADPH for the Calvin cycle, which takes place in the stroma. 7.6 Visible radiation absorbed by pigments drives the light reactions. Certain wavelengths of visible light are absorbed by chlorophyll and other pigments. Carotenoids also function in photoprotection from excessive light. 7.7 Photosystems capture solar energy. Thylakoid membranes contain photosystems, each consisting of light-harvesting complexes and a reaction-center complex. A primary electron acceptor receives photoexcited electrons from reaction-center chlorophyll a. 7.8 Two photosystems connected by an electron transport chain convert light energy to the chemical energy of ATP and NADPH. Electrons shuttle from photosystem II to photosystem I, providing energy to make ATP, and then reduce NADP+ to NADPH. Photosystem II regains electrons as water is split and O2 released. 7.9 The light reactions take place within the thylakoid membranes. In photophosphorylation, the electron transport chain pumps H+ into the thylakoid space. The concentration gradient drives H+ back through ATP synthase, powering the synthesis of ATP. 7.10 ATP and NADPH power sugar synthesis in the Calvin cycle. The steps of the Calvin cycle include carbon fixation, reduction, release of G3P, and regeneration of RuBP. Using carbon from CO2, electrons from NADPH, and energy from ATP, the cycle constructs G3P, which is used to build glucose and other organic molecules. 7.11 Other methods of carbon fixation have evolved in hot, dry climates. In C3 plants, a drop in CO2 and rise in O2 when stomata close divert the Calvin cycle to photorespiration. C4 plants and CAM plants first fix CO2 into four-carbon compounds that provide CO2 to the Calvin cycle even when stomata close on hot, dry days. 7.13 Rising atmospheric levels of carbon dioxide may affect plants in various ways. Scientists study the effects of rising CO2 levels using laboratory growth chambers and field studies. Long-term field projects enable scientists to assess the effects of CO2 levels on natural ecosystems. 7.14 Reducing both fossil fuel use and deforestation may moderate climate change. CO2 and other gases in the atmosphere create the greenhouse effect. An international agreement reached at the Paris climate conference of 2015 seeks to reduce greenhouse gas emissions and limit global warming.

https://quizlet.com/245726026/photosynthesis-review-diagram/

MITOSIS/MEIOSIS (30 questions)
* Asexual reproduction
   * The creation of genetically identical offspring, generated by a single parent, without the participation of egg and sperm
*  sexual reproduction
   * The creation of genetically uniques offspring by the fusion of two haploid sex cells (gametes), forming a diploid zygote
* What are the functions of cell division?
   * Cell division, a fundamental process in biology, serves vital functions in both single-celled and multicellular organisms. In single-celled organisms, it's a primary means of reproduction, while in multicellular organisms, it's crucial for growth, development, and repair of tissues and damaged cells
   * GROWTH, REPAIR, REPRODUCE
* Prokaryote vs eukaryote DNA
   * Prokaryotic DNA is typically a single, circular chromosome, found in the cytoplasm within a region called the nucleoid
   * while eukaryotic DNA is linear and organized into multiple chromosomes within a membrane-bound nucleus
* Organization of DNA        
   * In both mitosis and meiosis, DNA is organized into chromosomes, which are then further condensed. Mitosis produces two identical daughter cells, maintaining the same number of chromosomes as the parent cell, while meiosis results in four unique daughter cells, each with half the number of chromosomes, crucial for sexual reproduction.
* Structure of a duplicated chromosome
   * Structure of a duplicated chromosome
* Cell cycle vs mitosis vs cytokinesis (plant vs animal)
   * CELL CYCLE - AN ORDERED SEQUENCE OF EVENTS (INCLUDING INTERPHASE AND THE MITOTIC PHASE) THAT EXTENDS FROM THE TIME A EUKARYOTIC CELL IS FIRST FORMED FROM A DIVIDING PARENT CELL UNTIL ITS OWN DIVISION INTO 2 CELLS
   * MITOSIS - THE DIVISION OF A SINGLE NUCLEUS INTO 2 GENETICALLY IDENTICAL NUCLEI. MITOSIS AND CYTOKINESIS MAKE UP THE MITOTIC (M) PHASE OF THE CELL CYCLE
   * Cytokinesis - the process where the cytoplasm of a cell divides, resulting in the formation of two separate daughter cells.
   * Prophase - the first stage of mitosis, during which the chromatin condenses to form structures (sister chromatids) visible with a light microscope and the mitotic spindle begins to form, but the nucleus is still intact
   * Prometaphase - the second stage of mitosis, during which the nuclear envelope fragments and the spindle microtubules attach to the kinetochores of the sister chromatids
   * Metaphase - the third stage of mitosis, during which all the cell’s duplicated chromosomes are lined up at an imaginary plane equidistant between the poles of the mitotic spindle
   * Anaphase - the fourth stage of mitosis, beginning when sister chromatids separate from each other and ending when a complete set of daughter chromosomes arrives at each of the two poles of the cell
   * Telophase - the fifth and final stage of mitosis, during which daughter nuclei form at the two poles of a cell. Telophase usually occurs together with cytokinesis
* Distinguish between replicated chromosomes, chromosomes, and sister chromatids.
   * Chromosome: A single, long DNA molecule, tightly wound around proteins, forming a compact structure. It contains the genes that determine an organism's traits. 
   * Replicated Chromosome: Before a cell divides, each chromosome is duplicated. This means the DNA is copied, resulting in two identical copies called sister chromatids. 
   * Sister Chromatids: The two identical copies of a replicated chromosome. They are connected at a central region called the centromere and are held together by protein complexes called cohesins.
* Stages of the Cell cycle
   * G1 phase: The cell grows, replicates its organelles, and prepares for DNA replication. It is the longest phase of the cell cycle for most cells. 
   * S phase: The cell duplicates its DNA, ensuring that each daughter cell receives a complete set of genetic information. 
   * G2 phase: The cell continues to grow and synthesizes proteins and other molecules needed for cell division. 
   * M phase: This phase involves mitosis (nuclear division) and cytokinesis (cell division). Mitosis ensures that each daughter cell receives an identical copy of the original cell's DNA. Cytokinesis physically divides the cytoplasm and cell membrane, resulting in two separate daughter cells
* Labeling the significant events of mitosis
* Control of cell division
   * The cell cycle control system is a set of molecules that both triggers and coordinates key events in the cell cycle.
* Checkpoints  of cell division. 
   * G1 Checkpoint: This checkpoint occurs at the end of the G1 phase, before the cell enters the S phase (DNA replication). It assesses whether the cell is large enough, has sufficient nutrients, and if the DNA is undamaged. If any of these conditions are not met, the cell cycle can be halted, and the cell may attempt to repair the DNA or enter a quiescent state. 
   * G2 Checkpoint: This checkpoint occurs at the end of the G2 phase, before the cell enters mitosis. It checks whether DNA replication has been completed correctly and if there is any DNA damage. If DNA damage is detected, the cell cycle can be arrested, and the cell will attempt to repair the damage or undergo apoptosis (programmed cell death). 
   * M Checkpoint (Spindle Checkpoint): This checkpoint occurs during metaphase, the second phase of mitosis. It monitors whether all chromosomes are correctly attached to the spindle fibers and aligned at the metaphase plate. If chromosomes are not properly attached, the cell cycle will be halted, and the cell will try to fix the problem. 
   * These checkpoints are crucial for maintaining genomic integrity and preventing the formation of cancerous cells. If a checkpoint fails, the cell can be arrested, attempt to repair the damage, or undergo programmed cell death.
* Mitosis vs meiosis products
   * Mitosis produces two genetically identical daughter cells, each with the same number of chromosomes as the original parent cell (diploid). This process is essential for growth, repair, and development in the body
   * Meiosis, a specialized cell division process, produces four haploid gametes (sperm and egg cells) from a single diploid cell. These gametes are essential for sexual reproduction, ensuring genetic diversity and the restoration of diploid chromosome numbers during fertilization
* Autosomes vs Sex Chromosomes
   * autosomes are chromosomes (numbered 1-22) that are the same in both males and females, while sex chromosomes (X and Y) differ between the sexes.
* Haploid vs  diploid.  Germ cells, Gametes, Somatic
   * Somatic: Somatic cells are any cells in a multicellular organism that are not involved in reproduction. This means they exclude sperm, egg cells, and any cells that develop into these gametes.
   * Gametes (sperm and egg cells) are haploid, containing a single set of chromosomes (n = 23 for humans). They are produced through meiosis, which reduces the chromosome number by half, ensuring genetic diversity in offspring.
   * A haploid cell is a type of cell that contains a single set of chromosomes. This means it has only one member of each homologous chromosome pair
   * Diploid cells are cells that contain two complete sets of chromosomes, one set inherited from each parent. This is represented as 2n.
   * Germ cells are specialized cells that give rise to gametes, which are the reproductive cells (sperm and egg) in organisms. These cells are crucial for sexual reproduction as they carry genetic information to the next generation.
* Sources of Genetic diversity
   * Mitosis: During mitosis, the sister chromatids of each chromosome are separated, resulting in two daughter cells that are genetically identical to the parent cell. 
   * Meiosis: 
   * Crossing Over: During prophase I of meiosis, homologous chromosomes exchange genetic material, creating new combinations of alleles. 
   * Independent Assortment: The random alignment of homologous chromosomes during metaphase I allows for the production of gametes with different combinations of chromosomes from each parent. 
   * Random Fertilization: The fusion of two genetically different gametes (egg and sperm) during fertilization further increases genetic diversity by creating new combinations of genes in the zygote. 
   * Reduction to Haploid: Meiosis I and II reduce the chromosome number from diploid to haploid, ensuring that each gamete receives only one set of chromosomes.
Cell Size Lab
 
 
MEIOSIS
https://www.sciencefacts.net/mitosis-vs-meiosis.html 
* Significant Events of Meiosis including synapsis/crossing over and random assortment.
   * Synapsis - In meiosis, synapsis is the pairing of homologous chromosomes that occurs during prophase I. This pairing, often assisted by a protein complex called the synaptonemal complex, ensures that the homologous chromosomes align precisely. This precise alignment is crucial for the subsequent process of crossing over, where genetic material is exchanged between non-sister chromatids. 
   * Crossing over - Crossing over, also known as genetic recombination, is the exchange of genetic material between non-sister chromatids of homologous chromosomes during meiosis. It results in new combinations of genes on chromosomes, contributing to genetic diversity in gametes and offspring.
   * random assortment - Random assortment, also known as independent assortment, in meiosis refers to the random distribution of homologous chromosomes during meiosis I, leading to diverse combinations of genes in the resulting gametes. This process contributes significantly to genetic variation among offspring. 
* Karyotyping
   * Karyotyping is the process of pairing and ordering all the chromosomes of an organism, thus providing a genome-wide snapshot of an individual's chromosomes. Karyotypes are prepared using standardized staining procedures that reveal characteristic structural features for each chromosome.
* Homologous Chromosomes
   * paired chromosomes, one inherited from each parent, that contain the same genes but may have different alleles. They are crucial for ensuring proper chromosome segregation during meiosis, a type of cell division that produces gametes (sperm and egg cells).
* Significant events
   * Meiosis involves two successive nuclear divisions (meiosis I and II) that reduce the chromosome number by half. Key events include chromosome pairing and crossing over in prophase I, homologous chromosome separation in anaphase I, and sister chromatid separation in anaphase II, leading to four haploid daughter cells
* Nondisjunction: Down Syndrome, Turner Syndrome, Edwards Syndrome, Klinefelters Syndrome
   * Nondisjuncion - Nondisjunction is failure of paired chromosomes to move to opposite poles of the spindle during mitosis or meiosis. If nondisjunction occurs during meiosis, the resulting embryo inherits an extra chromosome (trisomy) or lacks a chromosome (monosomy).

DISORDER
	CHROMOSOMES
	DESCRIPTION

Klinefelter Syndrome

one or more extra sex chromosomes (i.e., XXY)
	a male is born with an extra X chromosome

Turner Syndrome

45 chromosomes 
	occurs when females only have one X chromosome

Down Syndrome

Trisomy 21, extra chromosome 21
	an extra chromosome 21

Edward Syndrome

3 copies of chromosome 18
	occurs when there is an extra copy of chromosome 18

* Gene mutations  vs. chromosome mutations.
   * Gene Mutations: 
   * Definition: Changes in the DNA sequence within a single gene. 
   * Examples: Point mutations (single base changes), frameshift mutations (insertions or deletions that shift the reading frame), and expansions of repeat sequences. 
   * Impact: Can alter the protein produced by the gene, potentially leading to a variety of effects, from no change at all (silent mutations) to altered or non-functional proteins. 
   * Inheritance: Germline mutations (occurring in reproductive cells) can be inherited by offspring. 
   * Examples of Genetic Disorders: Huntington's disease, cystic fibrosis. 
   * Chromosomal Mutations: 
   * Definition: Changes to the number or structure of chromosomes. 
   * Examples: Deletions, duplications, inversions, translocations, and aneuploidy (having extra or missing chromosomes). 
   * Impact: Can significantly alter the genetic material, often leading to more severe consequences. 
   * Inheritance: Can be inherited from germline mutations. 
   * Examples of Genetic Disorders: Down syndrome (trisomy 21), Edward's syndrome (trisomy 18)
* Types of each mutation. 
 
Chapter 9 PATTERNS OF INHERITANCE
* Blending Theory
   * A discredited theory in biology that suggests traits from parents mix together in their offspring, resulting in an intermediate trait 
* Why did Mendel use peas? 
   * They were easy to grow, had visible characteristics, and were relatively quick to reproduce, allowing him to study multiple generations in a short time. Additionally, pea plants could be self-pollinated or cross-polinated, giving mendel control over their fertilization
* Mendel’s Experiments and Conclusions (Monohybrid Ratios and Dihybrid ratios)
   * Monohybrid cross - an experimental mating of individuals  that are heterozygous for the character being followed (or the self-pollination of a heterozygous plant)
   * Dihybrid cross - an experimental mating of individuals that are each heterozygous for both of the 2 characters (of the self-pollination of a plant that is heterozygous for both characters)
* True Breeding, Cross Breeding, Hybridization, P, F1, F2
   * True breeding - referring to organisms for which sexual reproduction produces offspring with inherited traits identical to those of the parents. The organisms are homozygous for the characters under consideration. 
   * Hybrid - offspring that results from the mating of individuals from two different species or from two true-breeding varieties of the same species; an offspring of two parents that differ in one or more inherited traits; an individual that is heterozygous for one or more pairs of genes
   * Cross breeding - a matting of 2 sexually reproducing individuals; often used to describe a genetics experiment involving a controlled mating (a “genetic cross”)
   * P generation - the parent individuals from which offspring are derived in studies of inheritance; P stands for parental
   * F1 generation - the offspring of 2 parental (P generation) individuals; F1 stands for first filial
   * F2 generation - the offspring of the F1 generation; F2 stands for second filial
* Allele
   * An alternative version of a gene
* Genotype
   * The genetic makeup of an organism
* Phenotype
   * The expressed traits of an organism
* Homozygous
   * Having 2 identical alleles for a given gene
* Heterozygous
   * Having 2 different alleles for a given gene
* Test Cross
   * The mating between an individual of unknown genotype for a particular character and an individual that is homozygous recessive for that same character. The testcross can be used to determine the unknown genotype (homozygous dominant versus heterozygous)
* Law of Independent Assortment
   * A general rule of inheritance (originally formulated by Gregor Mendel) that when gametes form during meiosis, each pair of alleles for a particular character segregates independently of other pairs; also known as Mendel’s second law of inheritance
* Dominant/Recessive
   * Dominant allele - the allele that determines the phenotype of a gene when the individual is heterozygous for that gene
   * Recessive allele - an allele that has no noticeable effect on the phenotype of a gene when the individual is heterozygous for that gene
* Codominant/Incomplete Dominance/Polygenic Inheritance
   * Codominant inheritance - two alleles for a specific trait are both expressed in the phenotype of a heterozygous individual, rather than one masking the other
   * Incomplete dominance - a genetic phenomenon where neither allele for a trait completely masks the other in a heterozygous individual, resulting in a blended phenotype that is intermediate between the 2 homozygous phenotypes
   * Polygenic inheritance - a type of inheritance where a trait is controlled by multiple genes, rather than a single gene. This results in a wide range of phenotypes for the trait, often following a bell-shaped curve distribution
* Blood Typing
   * A method of classifying blood based on the presence or absence of specific inherited antigens on the surface of red blood cells
* Crosses involving multiple traits
* Solve genetics problems
* Dominant, Recessive, and Sex-Linked Disorders.  
* Carrier
   * An individual who is heterozygous for a recessively inherited disorder and who therefore does not show symptoms of that disorder but who may pass on the recessive allele to offspring 
* Linked Genes
   * Genes that are located close together on the same chromosome and are therefore usually inherited together
* Sex determination in humans only
* Pedigree
   * A family genetic tree representing the occurrence of heritable traits in parents and offspring across a number of generations. A pedigree can be used to determine genotypes of matings that have already occurred
 
CHAPTER 10 Replication and PROTEIN SYNTHESIS (Questions 28)
* DNA Structure/Function
   * Double helix 
   * Deoxyribonucleic acid
   * Thymine and cytosine - a single-ring nitrogenous base found in DNA
   * Adenine and guanine - a double ring nitrogenous base found in DNA
   * Semiconservative model - type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand
   * Dna polymerase - a large molecular complex that assembles dna nucleotides into polynucleotides using a preexisting strand of dna as a template
   * Dna ligase - an enzyme, essential for DNA replication, that catalyzes the covalent bonding of adjacent DNA polynucleotide strands. DNA ligase is used in genetic engineering to paste a specific piece of DNA containing a gene of interest into a bacterial plasmid or other vector 
* RNA types and their function
   * Uracil - a single-ring nitrogenous base found in RNA
   * RNA polymerase - a large molecular complex that links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template
   * Promoter - a specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins
   * Terminator - a special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule and then to depart from the gene.
   * mRNA - the type of ribonucleic acid that encodes genetic information from DNA and conveys it to ribosomes, where the information is translated into amino acid sequences
   * RNA splicing - the removal of introns and joining of exons in eukaryotic RNA, forming an mRNA molecule with a continuous coding sequence; occurs before mRNA leaves the nucleus
   * tRNA - a type of ribonucleic acid that functions as an interpreter in translation. Each tRNA molecule has a specific anticodon, picks up a specific amino acid, and conveys the amino acid to the appropriate codon on mRNA
   * Anticodon - on a tRNA molecule, a specific sequence of 3 nucleotides that is complementary to a codon triplet on mRNA
* Replication including enzymes
   * DNA helicase - an enzyme that plays a crucial role in DNA replication and other processes involving nucleic acids 
* Protein Synthesis: Transcription including RNA processing, Translation and enzymes.
   * Transcription - the synthesis of RNA on a DNA template
   * Translation - the synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids
   * Codon - a 3 - nucleotide sequence in mRNA that specifies a particular amino acid or polypeptide termination signal; the basic unit of the genetic code
   * Ribosomes - a cell structure consisting of RNA and protein organized into 2 subunits and functioning as the site of protein synthesis in the cytoplasm. In eukaryotic cells, the ribosomal subunits are constructed in the nucleolus
   * Ribosomal RNA (rRNA) - the type of ribonucleic acid that, together with proteins, makes up ribosomes; the most abundant type of RNA in most cells
   * Start codon - on mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information
   * P site - one of a ribosom’s binding sites for tRNA during translation. The P site holds the tRNA carrying the growing polypeptide chain. ( P stands for prptidyl tRNA)
   * A site - one of a ribosomes binding sites for tRNA during translation. The A site holds the tRNA that carries the next amino acid in the polypeptide chain (A stands for aminoacyl tRNA)
   * Stop codon - in mRNA, one of three triplets (UAG, UAA, UGA) that signal gene translation to stop
* Mutations
   * Silent mutation - a mutation in a gene that changes a codon to one that codes for the same amino acid as the original codon. The amino acid as the original codon. The amino acid sequence of the resulting polypeptide is thus unchanged
   * Missense mutation - a change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide. In a missense mutation, a codon is changed from encoding one amino acid to encoding a different amino acid
   * Nonsense mutation - a change in the nucleotide sequence of a gene that converts an amino-acid-ecoding codon to a stop codon. A nonsense mutation results in a shortened polypeptide
   * Frameshift mutation - a change in the genetic material that involves the insertion of deletion of one or more nucleotides in a gene, resulting in a change in the triplet grouping of nucleotides

EXTRA PHOTOSYNTHESIS NOTES
7.1 Photosynthesis powers most life on Earth. Plants, algae, and some photosynthetic protists and bacteria are photoautotrophs, the producers of food consumed by virtually all heterotrophic organisms.
7.2 Photosynthesis occurs in chloroplasts in plant cells. Chloroplasts are surrounded by a double membrane and contain stacks of thylakoids and a thick fluid called stroma.
7.3 Scientists traced the process of photosynthesis using isotopes. Experiments using both heavy and radioactive isotopes helped determine the details of the process of photosynthesis.
7.4 Photosynthesis is a redox process. In photosynthesis, H2O is oxidized and CO2 is reduced.
7.5 Photosynthesis occurs in two stages, which are linked by ATP and NADPH. The light reactions occur in the thylakoids, producing ATP and NADPH for the Calvin cycle, which takes place in the stroma.
7.6 Visible radiation absorbed by pigments drives the light reactions. Certain wavelengths of visible light are absorbed by chlorophyll and other pigments. Carotenoids also function in photoprotection from excessive light.
7.7 Photosystems capture solar energy. Thylakoid membranes contain photosystems, each consisting of light-harvesting complexes and a reaction-center complex. A primary electron acceptor receives photoexcited electrons from reaction-center chlorophyll a.
7.8 Two photosystems connected by an electron transport chain convert light energy to the chemical energy of ATP and NADPH. Electrons shuttle from photosystem II to photosystem I, providing energy to make ATP, and then reduce NADP+ to NADPH. Photosystem II regains electrons as water is split and O2 released.
7.9 The light reactions take place within the thylakoid membranes. In photophosphorylation, the electron transport chain pumps H+ into the thylakoid space. The concentration gradient drives H+ back through ATP synthase, powering the synthesis of ATP.
7.10 ATP and NADPH power sugar synthesis in the Calvin cycle. The steps of the Calvin cycle include carbon fixation, reduction, release of G3P, and regeneration of RuBP. Using carbon from CO2, electrons from NADPH, and energy from ATP, the cycle constructs G3P, which is used to build glucose and other organic molecules.
7.11 Other methods of carbon fixation have evolved in hot, dry climates. In C3 plants, a drop in CO2 and rise in O2 when stomata close divert the Calvin cycle to photorespiration. C4 plants and CAM plants first fix CO2 into four-carbon compounds that provide CO2 to the Calvin cycle even when stomata close on hot, dry days.
7.13 Rising atmospheric levels of carbon dioxide may affect plants in various ways. Scientists study the effects of rising CO2 levels using laboratory growth chambers and field studies. Long-term field projects enable scientists to assess the effects of CO2 levels on natural ecosystems.
7.14 Reducing both fossil fuel use and deforestation may moderate climate change. CO2 and other gases in the atmosphere create the greenhouse effect. An international agreement reached at the Paris climate conference of 2015 seeks to reduce greenhouse gas emissions and limit global warming.

Transcript for:Cellular Energetics and Division

Transcript for:
Cellular Energetics and Division