1. Chapter 4- A Tour of the Cell
1.1. Microscopes:
1.1.1. Light: visible light is passed through a specimen and then through a glass lense
1.1.2. Electron: focuses a beam of electrons through a specimen or onto its surface
1.1.3. Scanning Electron: Study the detailed architecture of cell surfaces
1.1.4. Transmission Electron: Used to study the details of internal cell structure
1.2. Chromosomes: carrying genes made of DNA
1.3. ribosomes: tiny structures that make proteins according to instructions from the genes
1.4. Cytoplasm: Interior
1.5. Nucleoid: region where the cell's DNA is located
1.6. flagella: propel through its liquid environment
1.7. Nucleus: Cell's DNA
1.8. Endomembrane System:
1.8.1. Nuclear envelope
1.8.2. Endoplasmic reticulum
1.8.2.1. Smooth
1.8.2.2. Rough
1.8.3. Golgi apparatus
1.8.3.1. Finishes
1.8.3.2. sorts
1.8.3.3. ships
1.8.4. Lysosomes
1.8.4.1. Break down body
1.8.5. Vacuoles
1.8.5.1. large vesicles that have a variety of functions
1.8.5.1.1. Central: helps the cell grow in size by absorbing water and enlarging
1.8.6. Plasma membrane
1.9. Central Power Stations:
1.9.1. Mitochondria: Organelles that carry out cellular respiration in nearly all eukaryotic cell: converting chemical energy of foods to chemical energy of the molecule ATP
1.9.2. Mitochondrial matrix: contains mitochondria DNA and ribosomes as well as enzymes that catalyze some of the reactions of cellular respiration
1.10. Chloroplast: convert solar energy to chemical energy
1.10.1. Stroma: thick fluid inside inner membrane
1.10.1.1. Thylakoids: interconnected sacs
1.10.1.1.1. Granum: solar power packs
1.11. Cytoskeleton:
1.11.1. Microfilaments
1.11.1.1. Intermediate Filaments
1.11.1.1.1. Microtubules
1.12. Three types of cell junctions
1.12.1. Tight: tightly pressed together against each other and knit together by proteins
1.12.1.1. Anchoring: fastening cells together into strong sheets
1.12.1.1.1. Gap: Channels that allow small molecules to flow through protein lined pores between cells
2. Chapter 5: The Working Cell
2.1. Membrane structure:
2.1.1. Attachment to the cytoskeleton and extracellular matrix
2.1.2. Signal transduction
2.1.3. Transport
2.1.4. Intercellular Junctions
2.1.5. Cell-cell recognition
2.1.6. Enzymatic activity
2.2. Phospholipids key ingredient
2.3. Diffusion: particles to spread out evenly in an available space
2.3.1. Concentration gradient
2.3.2. Passive transport: cell doesn't have to do work when molecules diffuse across membrane
2.3.3. Osmosis: diffusion of water across a selectively permeable membrane
2.3.4. Tonicity: ability of a surrounding solution to cause a cell to gain or lose water
2.3.5. Hypotonic: A solution with a solute concentration lower than that of the cell
2.3.6. Hypertonic: solution with a higher solute concentration
2.3.7. Osmoregulation: control of water balance
2.3.8. active transport: cell must expend energy to move a solute against its concentration gradient
2.3.8.1. exocytosis (outside)
2.3.8.2. Endocytosis (inside)
2.3.8.3. Phagocytosis: cellular eating
2.3.8.4. Pinocytosis: cellular drinking
2.4. Energy:
2.4.1. Kinetic: energy of motion
2.4.1.1. Thermal
2.4.2. Potential: matter possesses as a result of its location
2.4.3. Chemical
2.4.4. First law of thermodynamic: energy cannot be created or destroyed but it can be transfer and transformed
2.4.5. Second law of thermodynamics: energy conversions increase the disorder of the universe
2.5. Inhibitor: regulates enzyme active
2.5.1. Competitive
2.5.2. Noncompetitive
2.5.3. Feedback
3. Chapter 6- How Cells Harvest Chemical Energy
3.1. Cellular respiration: C6H1206+602----->6C02+6H20+ATP
3.1.1. Three main stages:
3.1.1.1. Glycolysis
3.1.1.2. Citric acid cycle
3.1.1.2.1. Acetyl COA stokes the furnace
3.1.1.2.2. NADH, ATP and C02 are generated during redox reactions
3.1.1.2.3. Further redox reactions generate FADH2 and more NADH
3.1.1.3. Oxidative phosphorylation
3.1.1.3.1. Substrate-level: how ATP is formed
3.1.1.3.2. Electron transport chain: oxygen is the final acceptor
3.1.1.3.3. Chemiosmosis: uses energy stored in a hydrogen ion gradient across a membrane to drive ATP synthesis
3.2. Redox reactions
3.2.1. Oxidation: loss of electrons
3.2.2. Reduction: gaining of electrons
3.3. Fermentation: cells can produce ATP without oxygen
3.3.1. Lactic acid
3.3.2. Alcohol
4. Chapter 7- Photosynthesis: Using Light to Make Food
4.1. Autotrophs: self eaters
4.1.1. Heterotrophs: Other
4.2. Photosynthesis: light energy and convert it to chemical energy
4.2.1. Occurs in the Chloroplast:
4.2.1.1. Concentrated in the mesophyll the green tissue in the leaf
4.2.1.2. CO2 enters tiny pores in the stomata
4.2.2. Chlorophyll: light absorbing pigment
4.2.3. 6C02+6H20-----> C6H1206+602
4.2.4. Redox reaction
4.2.5. Linked by ATP and NADPH
4.2.5.1. Light reactions: convert light energy to chemical energy and release 02
4.2.5.1.1. Electromagnetic spectrum: full range of electromagnetic wavelengths from the very short gamma rays to very long radio waves.
4.2.5.1.2. Photosynthetic pigments: visible light in the chloroplast
4.2.5.2. Electron acceptor NADP+ reducing it to NADPH
4.2.5.3. Calvin cycle: occurs in the stroma and is called carbon fixation
4.2.6. Photosystem: light harvesting complexes surrounding a reaction center complex
4.2.6.1. Photosystem I
4.2.6.2. Photosystem II
4.2.7. Calvin Cycle;
4.2.7.1. Carbon fixation
4.2.7.2. Reduction
4.2.7.3. Release of one molecule of G3P
4.2.7.4. Regeneration of RuBP
5. Chapter 8- The Cellular Basis of Reproduction and Inheritance
5.1. Cell division: Reproduction of a cell through duplication of the genome and division of the cytoplasm
5.1.1. Growth factor: protein secreted by certain body cells that stimulates other cells to divide
5.2. Chromosomes: structures that contain most of the cell's DNA
5.2.1. Chromatin: fibers composed of roughly equal amount of DNA and protein molecules
5.2.2. Sister Chromatids: two copies
5.2.3. Centromere: "waist" is where the two sister chromatids join together
5.2.4. Alterations can cause birth defects and cancer
5.2.4.1. Deletion: lost
5.2.4.2. Duplication:
5.2.4.3. Inversion: reverse orientation
5.3. Reproduction
5.3.1. Asexual: creation of genetically identical offspring by a single parent
5.3.2. Sexual: Requires the fertilization of an egg by a sperm
5.3.3. Binary fission: dividing in half
5.4. Cell cycle:
5.4.1. Interphase I: spends most of its time here
5.4.2. 3 Phases:
5.4.2.1. G1: first gap: cell grows
5.4.2.2. S: continues to grow as it copies its chromosomes
5.4.2.3. G2: Completes preparations for cell division
5.4.3. M: cell actually divides
5.4.3.1. Mitosis
5.4.3.1.1. Prophase:
5.4.3.1.2. Prometaphase
5.4.3.1.3. Metaphase
5.4.3.1.4. Anaphase:
5.4.3.1.5. Telophase
5.4.3.2. Cytokinesis
5.4.3.2.1. Cleavage furrow
5.4.3.2.2. Cell plate
5.5. Meiosis
5.5.1. Crossing over: exchange of corresponding segments between non sister chromatids of homologous chromosomes
5.5.1.1. Chiasma: X shaped regions
5.5.2. Somatic cell 46 chromosomes
5.5.3. Homologous chromosome: two chromosomes of such a matching pair
5.5.3.1. Diploid
5.5.3.1.1. Haploid: single chromosome
5.5.4. Locus: location of particular gene
5.5.5. Sex chromosomes: determine someones sex
5.5.5.1. 22 remaining pairs: autosomes
5.5.6. Gametes: egg and sperm
5.5.6.1. Fertilization: when egg and sperm meet
5.5.6.1.1. Resulting in a zygote
5.5.7. Prophase I: two cells haploid
5.5.8. Metaphase I
5.5.9. Anaphase I
5.5.10. Telophase I and Cytokinesis
5.5.11. Then under goes the stages again: four cell haploid
6. Chapter 9- Patterns of Inheritance
6.1. Heredity: transmission of traits from one generation to the next
6.1.1. Genetics: Scientific study
6.1.2. Character: a heritable feature that varies among individuals
6.1.2.1. Trait: each variant
6.2. Self fertilize
6.2.1. Cross fertilize: fertilization of one plant by pollen from a different plant
6.2.1.1. cross
6.3. True breeding: varieties for which self-fertilization produced offspring all identical to the parent
6.3.1. Hybrids: offspring of two different varieties
6.3.1.1. F1 generation
6.3.1.1.1. F2 generation
6.3.2. Parental plants: P generation
6.4. Monohybrid cross: crossing something that differs in only one character
6.5. Mendel's law of segregation:
6.5.1. There are alternative versions of genes that account for variations in inherited characters
6.5.2. For each character an organism inherits two alleles one from each parent:
6.5.2.1. Homozygous: Two identical alleles
6.5.2.2. Heterozygous: two different alleles
6.5.3. If the alleles of an inherited pair differ, then one determines the organism's appearance and its called the dominant allele. The other has no noticeable effete on the organism's appearance and its called the recessive allele.
6.5.4. A sperm or egg carries only one allele for each inherited character because allele paris separate from each other during the production of gametes: Law of segregation
6.6. Phenotype: Physical traits
6.7. Genotype: Genetic makeup
6.8. Dihybrid cross: mating of parental varieties differing in two characters
6.8.1. Test cross: mating between an individual of unknown genotype and a homozygous recessive individual
6.9. Dominance
6.9.1. Incomplete: A type of inheritance in which the phenotype of a heterozygote is intermediate between the phenotypes of the two types of homozygotes
6.9.2. Complete: the dominate allele has the same phenotypic effect whether present in one or two copies
7. Chapter 10- Molecular Biology of the Gene
7.1. Genetic material:
7.1.1. Molecular biology: study of heredity at the molecular level
7.1.2. Bacteriophages: bacteria eaters
7.2. Nucleotides:
7.2.1. Polynucleotide:
7.2.1.1. RNA base: Uracil
7.3. DNA: deoxyribonucleic acid
7.3.1. Thymine
7.3.2. Cytosine
7.3.3. Adenine
7.3.4. Guanine
7.4. DNA: double helix
7.4.1. Base pair
7.4.2. Hydrogen bond
7.5. Origin of replication:
7.5.1. DNA polymerases: add nucleotides only to the 3' end of the strand.
7.5.2. Okazaki fragments:
7.5.3. DNA ligase: links the pieces together into a single DNA strand
7.6. Central Dogma: Chain of command
7.6.1. Transcription: synthesis of RNA under the direction of DNA
7.6.1.1. RNA Polymerase: RNA nucleotides linked
7.6.1.1.1. Promoter: start
7.6.1.2. Phases:
7.6.1.2.1. Initiation: attachment of RNA polymerase to the promoter
7.6.1.2.2. Elongation: RNA grows longer
7.6.1.2.3. Termination: RNA polymerase reaches a sequence of bases in the DNA template. end of the gene and detaches
7.6.2. Translation: synthesis of protein under the direction of RNA
7.6.2.1. Initiation
7.6.2.1.1. P site: holds the growing polypeptide
7.6.2.1.2. A site: is vacant and ready for the next amino acid bearing tRNA
7.6.2.2. Elongation
7.6.2.2.1. Codon recognition
7.6.2.2.2. Peptide Bond formation
7.6.2.2.3. Translocation
7.6.2.3. Termination
7.7. Codons: Non overlapping three base words
7.7.1. Intron: noncoding regions
7.7.2. Exons: gene that is expressed
7.8. Genetic code: set of rules that relate codons in RNA to amino acids in proteins
7.8.1. Universal
7.9. mRNA: encodes amino acid sequences conveys genetic messages from DNA to the translation machinery of the cell
7.9.1. tRNA: Interpreter
7.10. RNA splicing: cutting and pasting
7.11. Mutations: any change
7.11.1. Silent: changes a codon to one that encodes for the same amino acid as the original codon
7.11.2. Missense: change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide
7.11.3. Nonsense:change an amino acid codon into a stop codon
8. Chapter 11- How Genes Are Controlled
8.1. Gene Regulation: the turning on and off of genes can help organisms respond to environmental changes
8.1.1. Gene expression: genetic information flows from genes to proteins from genotype to phenotype
8.2. Promoter: site where the transcription enzyme attaches and initiates transcription
8.2.1. Operator: acts as a switch
8.2.2. Repressor: turns off transcription
8.2.3. Regulatory gene: codes for the repressor
8.2.4. operons: genes with related functions along with control sequences
8.2.4.1. Activators turn on by binding to DNA
8.3. Chromosome structure:
8.3.1. Differentiation: must become specialized in structure and function
8.3.2. DNA packing:
8.3.2.1. Histones: small proteins
8.3.2.2. Nucleosome: DNA wound around a protein core of eight histone molecules
8.4. X chromosome inactivation: initiated early in embryonic development when one of the X chromosomes in each cell is inactivated at random
8.4.1. Barr body: an inactivated X in each cell of a female condenses into a compact object
8.5. Enhancers: the binding of activator proteins to DNA control sequences
8.5.1. transcription factors
8.5.2. Alternative RNA splicing: organism can produce more than one type of polypeptide from a single gene
8.6. microRNAs: that can bind to complementary sequences on mRNA molecules
8.6.1. Forms a complex with protein
8.6.2. Bind to any mRNA molecule with the complementary sequence
8.6.2.1. Complex either degrades the target mRNA
8.6.2.2. OR blocks its translation
8.6.3. RNAi:
8.7. Signal transduction pathway: series of molecule changes that converts a signal on a target cell's surface to a specific response inside the cell
8.8. Clone: organism produced through asexual reproduction from a single parent
8.8.1. Nuclear transplantation
8.8.2. Embryonic stem cells: are harvested from the blastocyst
8.8.2.1. Adult stem cell: able to give rise to many but not all cell types in the organism
8.9. Regeneration: regrowth of lost body parts
8.10. Mutations in genes
8.10.1. Oncogenes: can cause cancer when present in a single copy in the cell
8.10.2. Proto-oncogenes: a normal gene that has the potential to become an oncogene
8.10.3. Tumor-suppressor: gene whose product inhibits cell division thereby preventing uncontrolled cell growth
8.10.4. Carcinogens: cancer causing agents factors that alter DNA and make cells cancerous
9. Chapter 12- DNA Technology and Genomics
9.1. Cloning:
9.1.1. Biotechnology: Manipulation of organisms or their components to make useful products
9.1.1.1. DNA technology
9.1.1.1.1. Recombinant: formed when scientists combine nucleotide sequences from to different species
9.1.2. Plasmids: used to manipulate genes
9.1.2.1. Key tools for cloning: production of multiple identical copies of gene-carrying piece of DNA
9.2. Restriction enzymes: cutting tools
9.3. Restriction site: DNA sequence recognized by a particular restriction enzyme
9.3.1. Restriction fragments
9.4. Genetically modified organisms: have acquired one or more genes by artificial means
9.4.1. Raises concern about human and environmental health
9.5. Gene therapy may one day treat disease?
9.5.1. alteration of an afflicted individual's genes for therapeutic purposes
9.5.2. The normal gene is cloned converted to RNA version and then inserted into the RNA genome of a harmless retrovirus vector
9.5.3. Bone marrow cells are taken from the patient and infected with the virus
9.5.4. The virus inserts a DNA version of its genome including the normal human gene into the cells DNA
9.5.5. The engineered cells are then injected back into the patient
9.6. DNA profiling: the analysis of DNA samples to determine whether they came from the same individual
9.6.1. DNA samples are isolated from the crime scene, suspects, victims, or stored evidence
9.6.2. Selected markers from each DNA sample are amplified producing an adequate supply for testing
9.6.3. Amplified DNA markers are compared providing which samples were derived from the same individual
9.6.3.1. Polymerase chain reaction: technique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the lab.
9.6.3.1.1. Reaction mixture is heated to separate the DNA strands
9.6.3.1.2. The mixture is cooled to allow primers to form hydrogen bonds with the ends of target sequences
9.6.3.1.3. DNA polymerase adds nucleotides in the 5'--->3' direction
9.6.3.2. Primers
9.6.4. Gel electrophoresis: sorts DNA molecules by size
9.6.4.1. STR analysis: method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome
9.6.4.1.1. Genomics: studying a complete set of genes and their interactions
10. Chapter 1- Biology: Exploring Life
10.1. What is life?
10.1.1. 1. Order 2. Reproduction 3. Growth and development 4. Energy processing 5. Response to the environment 6. Regulation 7. Evolutionary adaption
10.1.2. Life's Hierarchy of organization
10.1.2.1. 1. Biosphere 2. Ecosystem 3. Community 4. Population 5. Organism 6. Organ system 7. Organ 8. Tissue 9. Cell 10. Organelle 11. Molecule
10.1.3. Cells:
10.1.3.1. Eukaryotic: nucleus
10.1.3.2. Prokaryotic: no nucleus
10.2. Evolution:species living today are descendants of ancestral species
10.2.1. Genes
10.2.2. DNA
10.2.3. Natural Selection: Individuals in a population vary in their traits many of which are passed on from parents to offspring. A population can produce from more offspring than the environment can support. Individuals with heritable traits best suited to the environment are more likely to survive and reproduce than are less well-less suited individuals.
10.3. Three Domains of life
10.3.1. Bacteria
10.3.2. Archaea
10.3.3. Eukarya
10.4. The process of science
10.4.1. Inductive reasoning: this kind of reasoning derives generalizations from a large number of specific observations
10.4.2. Hypothesis: Proposed explanation for a set of observations
10.4.3. Deductive reasoning: Logic flows from general premises to the specific results we should expect if the premises are true
10.4.4. Theory: much more broader in scope than a hypothesis.
11. Chapter 2- The Chemical Basis of Life
11.1. Elements, Atoms, and Compounds
11.1.1. Matter: anything that occupies space and has mass
11.1.1.1. Liquid
11.1.1.2. Gas
11.1.1.3. Solid
11.1.2. Element: A substances that cannot be broken down into other substances by ordinary chemical means (92 elements that occur in nature)
11.1.3. Compound: Substance consisting of two or more different elements combined in a fixed ratio
11.1.4. Atoms: Smallest unit of matter that still retains the properties of an element
11.1.4.1. Proton: Subatomic particle with a single positive electrical charge
11.1.4.2. Electron: Subatomic particle with a single negative charge
11.1.4.3. Neutron: Electrically neutral (has no charge)
11.1.4.4. Nucleus: atoms central core
11.1.4.5. Mass number: the sum of the number of protons and neutrons in its nucleus
11.1.4.6. Atomic mass: (weight) approximately equal to its mass number- the sum of its protons and neutrons
11.1.4.7. Isotopes: same number of protons different number of neutrons
11.1.4.7.1. Radioactive: one in which the nucleus decays spontaneously giving off particles and energy.
11.2. Ion: atom of molecule with an electrical charge resulting from a gain or loss of one or more electrons
11.2.1. Ionic bond: two ions with opposite charges attract each other and the attraction holds.
11.2.2. Hydrogen bond: A type of weak chemical bond formed when the partially positive hydrogen atom participating in a polar covalent bond in one molecule is attracted to the partially negative atom participating in a polar covalent bond in another molecule
11.2.2.1. heat
11.2.2.2. temperature
11.3. Chemical Bonds: Two atoms with incomplete outer shells react, each atom will share donate or receive electrons so that both partners end up with completed outer shells.
11.3.1. Electron shell: Electrons move around the nucleus only at certain energy levels
11.3.2. Covalent bond: Two atoms share one or more pairs of outer-shell electrons
11.3.2.1. two or more atoms held together form a molecule
11.3.2.2. electronegativity: an atom's attraction for shared electrons
11.3.2.3. Nonpolar covalent bonds: electrons are shared equally between two atoms of similar electronegativity
11.3.2.4. Polar covalent: Differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom making it slightly negative and the other atom slightly positive.
11.3.2.5. Polar molecule: Contains polar covalent bonds and having an unequal distribution of charges
11.4. Chemical reaction: The breaking and making of chemical bonds leading to changes in the composition of matter
11.4.1. reactants
11.4.2. Product
12. Chapter 3- The Molecules of Cells
12.1. Life's molecular diversity
12.1.1. Organic compounds: carbon-based molecules
12.1.2. Hydrocarbons: compounds composed of only carbon and hydrogen
12.1.2.1. Examples:
12.1.2.1.1. Methane
12.1.2.1.2. Propane
12.1.3. Isomers: compounds with the same formula but different structural arrangements
12.1.4. Functional groups: affect a molecule's function by participating in chemical reactions in characteristic ways
12.1.4.1. Hydroxyl group: consists of hydrogen atom bonded to an oxygen atom which in turn is bonded to the carbon skeleton
12.1.4.2. Carbonyl group: a carbon atom is linked by a double bond to an oxygen atom and also bonded to a hydroxyl group
12.1.4.3. Carboxyl group: carbon double-bonded to an oxygen atom and also bonded to a hydroxyl group
12.1.4.4. Amino group: Has a nitrogen bonded to two hydrogens and the carbon skeleton
12.1.4.5. Phosphate group: consists of a phophorus atom bonded to four oxygen atoms
12.1.4.6. Methyl group: consists of carbon bonded to three hydrogens.
12.1.5. Polysaccharides: are macromolecules
12.1.5.1. Strach
12.1.5.2. Glycogen
12.1.5.3. Cellulose : most abundant organic compound
12.1.6. Lipids: they do not mix well with water- hydrophobic
12.1.6.1. fats: glycerol and fatty acids
12.1.6.2. Unsaturated fatty acid
12.1.6.3. Saturated fatty acid
12.1.6.3.1. Examples:
12.1.6.3.2. Corn oil
12.1.6.3.3. Olive oil
12.1.6.3.4. vegetable oil
12.1.6.4. Trans fat: fat that is not good for you: associated with health risks
12.1.6.5. Important: phospholipids and steroids
12.1.7. Protein: polymer of amino acids
12.1.7.1. Peptide bond: the covalent bond between two amino acid units in a polypeptide formed by a dehydration reaction
12.1.7.2. Polypeptide: a polymer of amino acids linked by peptide bonds
12.1.7.2.1. Denaturation: Polypeptide chains unravel losing their specific shape and their function
12.1.7.3. Primary Structure
12.1.7.4. Secondary Structure
12.1.7.5. Tertiary Structure
12.1.7.6. Quaternary Structure
12.2. Nucleic acids
12.2.1. DNA
12.2.1.1. RNA
12.2.2. Nucleotides