Biology 101

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Biology 101 by Mind Map: Biology 101

1. Chapter 1- Biology: Exploring Life

1.1. What is life?

1.1.1. 1. Order 2. Reproduction 3. Growth and development 4. Energy processing 5. Response to the environment 6. Regulation 7. Evolutionary adaption

1.1.2. Life's Hierarchy of organization 1. Biosphere 2. Ecosystem 3. Community 4. Population 5. Organism 6. Organ system 7. Organ 8. Tissue 9. Cell 10. Organelle 11. Molecule

1.1.3. Cells: Eukaryotic: nucleus Prokaryotic: no nucleus

1.2. Evolution:species living today are descendants of ancestral species

1.2.1. Genes

1.2.2. DNA

1.2.3. 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.

1.3. Three Domains of life

1.3.1. Bacteria

1.3.2. Archaea

1.3.3. Eukarya

1.4. The process of science

1.4.1. Inductive reasoning: this kind of reasoning derives generalizations from a large number of specific observations

1.4.2. Hypothesis: Proposed explanation for a set of observations

1.4.3. Deductive reasoning: Logic flows from general premises to the specific results we should expect if the premises are true

1.4.4. Theory: much more broader in scope than a hypothesis.

2. Chapter 2- The Chemical Basis of Life

2.1. Elements, Atoms, and Compounds

2.1.1. Matter: anything that occupies space and has mass Liquid Gas Solid

2.1.2. Element: A substances that cannot be broken down into other substances by ordinary chemical means (92 elements that occur in nature)

2.1.3. Compound: Substance consisting of two or more different elements combined in a fixed ratio

2.1.4. Atoms: Smallest unit of matter that still retains the properties of an element Proton: Subatomic particle with a single positive electrical charge Electron: Subatomic particle with a single negative charge Neutron: Electrically neutral (has no charge) Nucleus: atoms central core Mass number: the sum of the number of protons and neutrons in its nucleus Atomic mass: (weight) approximately equal to its mass number- the sum of its protons and neutrons Isotopes: same number of protons different number of neutrons Radioactive: one in which the nucleus decays spontaneously giving off particles and energy.

2.2. Ion: atom of molecule with an electrical charge resulting from a gain or loss of one or more electrons

2.2.1. Ionic bond: two ions with opposite charges attract each other and the attraction holds.

2.2.2. 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 heat temperature

2.3. 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.

2.3.1. Electron shell: Electrons move around the nucleus only at certain energy levels

2.3.2. Covalent bond: Two atoms share one or more pairs of outer-shell electrons two or more atoms held together form a molecule electronegativity: an atom's attraction for shared electrons Nonpolar covalent bonds: electrons are shared equally between two atoms of similar electronegativity 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. Polar molecule: Contains polar covalent bonds and having an unequal distribution of charges

2.4. Chemical reaction: The breaking and making of chemical bonds leading to changes in the composition of matter

2.4.1. reactants

2.4.2. Product

3. Chapter 3- The Molecules of Cells

3.1. Life's molecular diversity

3.1.1. Organic compounds: carbon-based molecules

3.1.2. Hydrocarbons: compounds composed of only carbon and hydrogen Examples: Methane Propane

3.1.3. Isomers: compounds with the same formula but different structural arrangements

3.1.4. Functional groups: affect a molecule's function by participating in chemical reactions in characteristic ways Hydroxyl group: consists of hydrogen atom bonded to an oxygen atom which in turn is bonded to the carbon skeleton Carbonyl group: a carbon atom is linked by a double bond to an oxygen atom and also bonded to a hydroxyl group Carboxyl group: carbon double-bonded to an oxygen atom and also bonded to a hydroxyl group Amino group: Has a nitrogen bonded to two hydrogens and the carbon skeleton Phosphate group: consists of a phophorus atom bonded to four oxygen atoms Methyl group: consists of carbon bonded to three hydrogens.

3.1.5. Polysaccharides: are macromolecules Strach Glycogen Cellulose : most abundant organic compound

3.1.6. Lipids: they do not mix well with water- hydrophobic fats: glycerol and fatty acids Unsaturated fatty acid Saturated fatty acid Examples: Corn oil Olive oil vegetable oil Trans fat: fat that is not good for you: associated with health risks Important: phospholipids and steroids

3.1.7. Protein: polymer of amino acids Peptide bond: the covalent bond between two amino acid units in a polypeptide formed by a dehydration reaction Polypeptide: a polymer of amino acids linked by peptide bonds Denaturation: Polypeptide chains unravel losing their specific shape and their function Primary Structure Secondary Structure Tertiary Structure Quaternary Structure

3.2. Nucleic acids

3.2.1. DNA RNA

3.2.2. Nucleotides

4. Chapter 4- A Tour of the Cell

4.1. Microscopes:

4.1.1. Light: visible light is passed through a specimen and then through a glass lense

4.1.2. Electron: focuses a beam of electrons through a specimen or onto its surface

4.1.3. Scanning Electron: Study the detailed architecture of cell surfaces

4.1.4. Transmission Electron: Used to study the details of internal cell structure

4.2. Chromosomes: carrying genes made of DNA

4.3. ribosomes: tiny structures that make proteins according to instructions from the genes

4.4. Cytoplasm: Interior

4.5. Nucleoid: region where the cell's DNA is located

4.6. flagella: propel through its liquid environment

4.7. Nucleus: Cell's DNA

4.8. Endomembrane System:

4.8.1. Nuclear envelope

4.8.2. Endoplasmic reticulum Smooth Rough

4.8.3. Golgi apparatus Finishes sorts ships

4.8.4. Lysosomes Break down body

4.8.5. Vacuoles large vesicles that have a variety of functions Central: helps the cell grow in size by absorbing water and enlarging

4.8.6. Plasma membrane

4.9. Central Power Stations:

4.9.1. Mitochondria: Organelles that carry out cellular respiration in nearly all eukaryotic cell: converting chemical energy of foods to chemical energy of the molecule ATP

4.9.2. Mitochondrial matrix: contains mitochondria DNA and ribosomes as well as enzymes that catalyze some of the reactions of cellular respiration

4.10. Chloroplast: convert solar energy to chemical energy

4.10.1. Stroma: thick fluid inside inner membrane Thylakoids: interconnected sacs Granum: solar power packs

4.11. Cytoskeleton:

4.11.1. Microfilaments Intermediate Filaments Microtubules

4.12. Three types of cell junctions

4.12.1. Tight: tightly pressed together against each other and knit together by proteins Anchoring: fastening cells together into strong sheets Gap: Channels that allow small molecules to flow through protein lined pores between cells

5. Chapter 5: The Working Cell

5.1. Membrane structure:

5.1.1. Attachment to the cytoskeleton and extracellular matrix

5.1.2. Signal transduction

5.1.3. Transport

5.1.4. Intercellular Junctions

5.1.5. Cell-cell recognition

5.1.6. Enzymatic activity

5.2. Phospholipids key ingredient

5.3. Diffusion: particles to spread out evenly in an available space

5.3.1. Concentration gradient

5.3.2. Passive transport: cell doesn't have to do work when molecules diffuse across membrane

5.3.3. Osmosis: diffusion of water across a selectively permeable membrane

5.3.4. Tonicity: ability of a surrounding solution to cause a cell to gain or lose water

5.3.5. Hypotonic: A solution with a solute concentration lower than that of the cell

5.3.6. Hypertonic: solution with a higher solute concentration

5.3.7. Osmoregulation: control of water balance

5.3.8. active transport: cell must expend energy to move a solute against its concentration gradient exocytosis (outside) Endocytosis (inside) Phagocytosis: cellular eating Pinocytosis: cellular drinking

5.4. Energy:

5.4.1. Kinetic: energy of motion Thermal

5.4.2. Potential: matter possesses as a result of its location

5.4.3. Chemical

5.4.4. First law of thermodynamic: energy cannot be created or destroyed but it can be transfer and transformed

5.4.5. Second law of thermodynamics: energy conversions increase the disorder of the universe

5.5. Inhibitor: regulates enzyme active

5.5.1. Competitive

5.5.2. Noncompetitive

5.5.3. Feedback

6. Chapter 6- How Cells Harvest Chemical Energy

6.1. Cellular respiration: C6H1206+602----->6C02+6H20+ATP

6.1.1. Three main stages: Glycolysis Citric acid cycle Acetyl COA stokes the furnace NADH, ATP and C02 are generated during redox reactions Further redox reactions generate FADH2 and more NADH Oxidative phosphorylation Substrate-level: how ATP is formed Electron transport chain: oxygen is the final acceptor Chemiosmosis: uses energy stored in a hydrogen ion gradient across a membrane to drive ATP synthesis

6.2. Redox reactions

6.2.1. Oxidation: loss of electrons

6.2.2. Reduction: gaining of electrons

6.3. Fermentation: cells can produce ATP without oxygen

6.3.1. Lactic acid

6.3.2. Alcohol

7. Chapter 7- Photosynthesis: Using Light to Make Food

7.1. Autotrophs: self eaters

7.1.1. Heterotrophs: Other

7.2. Photosynthesis: light energy and convert it to chemical energy

7.2.1. Occurs in the Chloroplast: Concentrated in the mesophyll the green tissue in the leaf CO2 enters tiny pores in the stomata

7.2.2. Chlorophyll: light absorbing pigment

7.2.3. 6C02+6H20-----> C6H1206+602

7.2.4. Redox reaction

7.2.5. Linked by ATP and NADPH Light reactions: convert light energy to chemical energy and release 02 Electromagnetic spectrum: full range of electromagnetic wavelengths from the very short gamma rays to very long radio waves. Photosynthetic pigments: visible light in the chloroplast Electron acceptor NADP+ reducing it to NADPH Calvin cycle: occurs in the stroma and is called carbon fixation

7.2.6. Photosystem: light harvesting complexes surrounding a reaction center complex Photosystem I Photosystem II

7.2.7. Calvin Cycle; Carbon fixation Reduction Release of one molecule of G3P Regeneration of RuBP

8. Chapter 8- The Cellular Basis of Reproduction and Inheritance

8.1. Cell division: Reproduction of a cell through duplication of the genome and division of the cytoplasm

8.1.1. Growth factor: protein secreted by certain body cells that stimulates other cells to divide

8.2. Chromosomes: structures that contain most of the cell's DNA

8.2.1. Chromatin: fibers composed of roughly equal amount of DNA and protein molecules

8.2.2. Sister Chromatids: two copies

8.2.3. Centromere: "waist" is where the two sister chromatids join together

8.2.4. Alterations can cause birth defects and cancer Deletion: lost Duplication: Inversion: reverse orientation

8.3. Reproduction

8.3.1. Asexual: creation of genetically identical offspring by a single parent

8.3.2. Sexual: Requires the fertilization of an egg by a sperm

8.3.3. Binary fission: dividing in half

8.4. Cell cycle:

8.4.1. Interphase I: spends most of its time here

8.4.2. 3 Phases: G1: first gap: cell grows S: continues to grow as it copies its chromosomes G2: Completes preparations for cell division

8.4.3. M: cell actually divides Mitosis Prophase: Prometaphase Metaphase Anaphase: Telophase Cytokinesis Cleavage furrow Cell plate

8.5. Meiosis

8.5.1. Crossing over: exchange of corresponding segments between non sister chromatids of homologous chromosomes Chiasma: X shaped regions

8.5.2. Somatic cell 46 chromosomes

8.5.3. Homologous chromosome: two chromosomes of such a matching pair Diploid Haploid: single chromosome

8.5.4. Locus: location of particular gene

8.5.5. Sex chromosomes: determine someones sex 22 remaining pairs: autosomes

8.5.6. Gametes: egg and sperm Fertilization: when egg and sperm meet Resulting in a zygote

8.5.7. Prophase I: two cells haploid

8.5.8. Metaphase I

8.5.9. Anaphase I

8.5.10. Telophase I and Cytokinesis

8.5.11. Then under goes the stages again: four cell haploid

9. Chapter 9- Patterns of Inheritance

9.1. Heredity: transmission of traits from one generation to the next

9.1.1. Genetics: Scientific study

9.1.2. Character: a heritable feature that varies among individuals Trait: each variant

9.2. Self fertilize

9.2.1. Cross fertilize: fertilization of one plant by pollen from a different plant cross

9.3. True breeding: varieties for which self-fertilization produced offspring all identical to the parent

9.3.1. Hybrids: offspring of two different varieties F1 generation F2 generation

9.3.2. Parental plants: P generation

9.4. Monohybrid cross: crossing something that differs in only one character

9.5. Mendel's law of segregation:

9.5.1. There are alternative versions of genes that account for variations in inherited characters

9.5.2. For each character an organism inherits two alleles one from each parent: Homozygous: Two identical alleles Heterozygous: two different alleles

9.5.3. 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.

9.5.4. 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

9.6. Phenotype: Physical traits

9.7. Genotype: Genetic makeup

9.8. Dihybrid cross: mating of parental varieties differing in two characters

9.8.1. Test cross: mating between an individual of unknown genotype and a homozygous recessive individual

9.9. Dominance

9.9.1. Incomplete: A type of inheritance in which the phenotype of a heterozygote is intermediate between the phenotypes of the two types of homozygotes

9.9.2. Complete: the dominate allele has the same phenotypic effect whether present in one or two copies

10. Chapter 10- Molecular Biology of the Gene

10.1. Genetic material:

10.1.1. Molecular biology: study of heredity at the molecular level

10.1.2. Bacteriophages: bacteria eaters

10.2. Nucleotides:

10.2.1. Polynucleotide: RNA base: Uracil

10.3. DNA: deoxyribonucleic acid

10.3.1. Thymine

10.3.2. Cytosine

10.3.3. Adenine

10.3.4. Guanine

10.4. DNA: double helix

10.4.1. Base pair

10.4.2. Hydrogen bond

10.5. Origin of replication:

10.5.1. DNA polymerases: add nucleotides only to the 3' end of the strand.

10.5.2. Okazaki fragments:

10.5.3. DNA ligase: links the pieces together into a single DNA strand

10.6. Central Dogma: Chain of command

10.6.1. Transcription: synthesis of RNA under the direction of DNA RNA Polymerase: RNA nucleotides linked Promoter: start Phases: Initiation: attachment of RNA polymerase to the promoter Elongation: RNA grows longer Termination: RNA polymerase reaches a sequence of bases in the DNA template. end of the gene and detaches

10.6.2. Translation: synthesis of protein under the direction of RNA Initiation P site: holds the growing polypeptide A site: is vacant and ready for the next amino acid bearing tRNA Elongation Codon recognition Peptide Bond formation Translocation Termination

10.7. Codons: Non overlapping three base words

10.7.1. Intron: noncoding regions

10.7.2. Exons: gene that is expressed

10.8. Genetic code: set of rules that relate codons in RNA to amino acids in proteins

10.8.1. Universal

10.9. mRNA: encodes amino acid sequences conveys genetic messages from DNA to the translation machinery of the cell

10.9.1. tRNA: Interpreter

10.10. RNA splicing: cutting and pasting

10.11. Mutations: any change

10.11.1. Silent: changes a codon to one that encodes for the same amino acid as the original codon

10.11.2. Missense: change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide

10.11.3. Nonsense:change an amino acid codon into a stop codon

11. Chapter 11- How Genes Are Controlled

11.1. Gene Regulation: the turning on and off of genes can help organisms respond to environmental changes

11.1.1. Gene expression: genetic information flows from genes to proteins from genotype to phenotype

11.2. Promoter: site where the transcription enzyme attaches and initiates transcription

11.2.1. Operator: acts as a switch

11.2.2. Repressor: turns off transcription

11.2.3. Regulatory gene: codes for the repressor

11.2.4. operons: genes with related functions along with control sequences Activators turn on by binding to DNA

11.3. Chromosome structure:

11.3.1. Differentiation: must become specialized in structure and function

11.3.2. DNA packing: Histones: small proteins Nucleosome: DNA wound around a protein core of eight histone molecules

11.4. X chromosome inactivation: initiated early in embryonic development when one of the X chromosomes in each cell is inactivated at random

11.4.1. Barr body: an inactivated X in each cell of a female condenses into a compact object

11.5. Enhancers: the binding of activator proteins to DNA control sequences

11.5.1. transcription factors

11.5.2. Alternative RNA splicing: organism can produce more than one type of polypeptide from a single gene

11.6. microRNAs: that can bind to complementary sequences on mRNA molecules

11.6.1. Forms a complex with protein

11.6.2. Bind to any mRNA molecule with the complementary sequence Complex either degrades the target mRNA OR blocks its translation

11.6.3. RNAi:

11.7. Signal transduction pathway: series of molecule changes that converts a signal on a target cell's surface to a specific response inside the cell

11.8. Clone: organism produced through asexual reproduction from a single parent

11.8.1. Nuclear transplantation

11.8.2. Embryonic stem cells: are harvested from the blastocyst Adult stem cell: able to give rise to many but not all cell types in the organism

11.9. Regeneration: regrowth of lost body parts

11.10. Mutations in genes

11.10.1. Oncogenes: can cause cancer when present in a single copy in the cell

11.10.2. Proto-oncogenes: a normal gene that has the potential to become an oncogene

11.10.3. Tumor-suppressor: gene whose product inhibits cell division thereby preventing uncontrolled cell growth

11.10.4. Carcinogens: cancer causing agents factors that alter DNA and make cells cancerous

12. Chapter 12- DNA Technology and Genomics

12.1. Cloning:

12.1.1. Biotechnology: Manipulation of organisms or their components to make useful products DNA technology Recombinant: formed when scientists combine nucleotide sequences from to different species

12.1.2. Plasmids: used to manipulate genes Key tools for cloning: production of multiple identical copies of gene-carrying piece of DNA

12.2. Restriction enzymes: cutting tools

12.3. Restriction site: DNA sequence recognized by a particular restriction enzyme

12.3.1. Restriction fragments

12.4. Genetically modified organisms: have acquired one or more genes by artificial means

12.4.1. Raises concern about human and environmental health

12.5. Gene therapy may one day treat disease?

12.5.1. alteration of an afflicted individual's genes for therapeutic purposes

12.5.2. The normal gene is cloned converted to RNA version and then inserted into the RNA genome of a harmless retrovirus vector

12.5.3. Bone marrow cells are taken from the patient and infected with the virus

12.5.4. The virus inserts a DNA version of its genome including the normal human gene into the cells DNA

12.5.5. The engineered cells are then injected back into the patient

12.6. DNA profiling: the analysis of DNA samples to determine whether they came from the same individual

12.6.1. DNA samples are isolated from the crime scene, suspects, victims, or stored evidence

12.6.2. Selected markers from each DNA sample are amplified producing an adequate supply for testing

12.6.3. Amplified DNA markers are compared providing which samples were derived from the same individual Polymerase chain reaction: technique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the lab. Reaction mixture is heated to separate the DNA strands The mixture is cooled to allow primers to form hydrogen bonds with the ends of target sequences DNA polymerase adds nucleotides in the 5'--->3' direction Primers

12.6.4. Gel electrophoresis: sorts DNA molecules by size STR analysis: method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome Genomics: studying a complete set of genes and their interactions