Biology : Ultimate Review Guide

Unit 1 : Experimental Design

Types of Data

• Qualitative—characteristics that cannot be easily counted or measured (color, texture, and smell)

• Quantitative—characteristics that are counted or measured (temperature, weight, length, and time)

Parts of an Experiment

• Hypothesis—predicted outcome of experiment, proposed explanation

• Independent Var.—variable that is intentionally changed

• Dependent Var.—variable that is observed or measured

• Controlled Var.—variable that is kept constant between groups

• Control Groups—groups used as a baseline/comparison for “normal”

Graphing

• Line Graph—data points are related to each other; data points are continuous

• Bar Graph—data points are unrelated to each other; data points are discrete

Statistics

• Mean—average value

• Median—middle value when listed from least to greatest

• Mode— most common value

Unit 2 : Cells

Characteristics of Living Cells

1. All living things grow and develop

2. All living things have one or more cells

3. All living things reproduce

4. All living things use energy

5. All living things have DNA

6. All living things sense and respond to stimuli

Cell Theory

1. All living things have one or more cells

2. The cell is the basic unit of life

3. All cells come from other pre-existing cells

Notable Scientists

• Robert Hooke—first to discover cells, named them “cells”

• Anton von Leeuwenhoek—discovered many single cell organisms. discovered that not only plants have cells

• Matthias Schleiden—determined that all plants are made of cells

• Theodor Schwann—determined that all animals have cells

• Rudolph Virchow—determined that all cells come from other pre-existing cells

Eukaryotic Cell Structures & Organelles

• Cell Membrane—thin, flexible protective barrier that covers the cell’s surface and acts as a barrier; determines what goes in and out of the cell. all cells have a cell membrane

• Nuclear Envelope—double membrane surrounding the nucleus. defines and protects the nucleus. all eukaryotes have a nuclear envelope

• Centriole—one of two structures that make up a centrosome. participates in cell division. only animal cells have centrioles

• Centrosome—structure located near the nucleus that forms the spindle during cell division. made up of two centrioles. only animal cells have centrosomes

• Nucleoplasm—fluid material inside the nucleus. all eukaryotes have nucleoplasm

• Endomembrane System—all organelles whose membranes are physically continuous or are transferred in segments as vesicles. includes the nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vesicles, and vacuoles. all eukaryotes have an endomembrane system

• Mitochondria—organelle in all eukaryotes (including plants) that converts the energy stored in glucose into energy stored in ATP does the process of cellular respiration. all eukaryotes have mitochondrias

• Lysosome—small organelles filled with hydrolytic enzymes that break down materials that are not needed by the cell. only animal cells have lysosomes. plant cells do not have them because they cant store wastes in the large central vacuole.

• Cytoplasm—the fluid and most of the organelles in a cell EXCEPT the nucleus. all cells have cytoplasms

• Cytosol—the fluid inside the cell. all cells have cytosol

• Cytoskeleton—network of fiber extending throughout the cytoplasm that organizes the structures and activities of the cell.

  • Types of Cytoskeletons

    • Microfilaments—smallest fibers; maintains cell shape; forms the cleavage furrow during cytokinesis

    • Intermediate Filaments—medium sized fibers; contributes to cell shape

    • Microtubules—largest fibers; involved in cell division (separates the chromatids) and motility

• Free Ribosome—makes proteins. free ribosomes make proteins that will be used within the cell. they float freely in the cytoplasm. all cells (prokaryotes and eukaryotes) have free ribosomes

• Bound Ribosome—makes proteins. bound ribosomes make proteins that will either be in the cell membrane or will be secreted from the cell. they are attached to the rough endoplasmic reticulum. all eukaryotes have bound ribosomes

• Nucleolus—dense region in the nucleus where ribosome production begins. all eukaryotes have nucleoli

• Golgi Apparatus—warehouse for receiving, sorting, shipping, modifying, and storing proteins that will be secreted from the cell. all eukaryotes have the golgi apparatus

• Smooth Endoplasmic Reticulum—folded membranes that do NOT have ribosomes attached. has various functions depending on the cell type. functions include: production of lipids, metabolizing carbohydrates, detoxifying drugs and poisons, and storing calcium ions. all eukaryotes have a smooth endoplasmic reticulum

• Rough Endoplasmic Reticulum—folded membranes where ribosomes attach if the ribosome is making a secreted protein. newly made proteins are threaded in the RER where they fold and may get carbohydrates attached. the RER transports the proteins as they are being made. all eukaryotes have a rough endoplasmic reticulum.

• Nuclear Pore—small holes in the nuclear envelope that eukaryotes use to move some materials in and out of the nucleus. all eukaryotes have nuclear pores

• Vesicles—transport sacs that move materials throughout the cell. vesicles bud off of the rough endoplasmic reticulum to deliver material to the Golgi Apparatus and vesicles also bud off of the Golgi Apparatus to deliver material to the cell membrane. vesicles can also move materials into the cell during endocytosis. all eukaryotes have vesicles

• Vacuole—sac-like structures that store materials such as water, salts, proteins, and carbohydrates. all eukaryotes have vacuoles. animals have small, temporary vacuoles. plants have large, permanent central vacuoles.

Phospholipid Structure

• phosphate group (“head”)—hydrophilic

• lipid (“tail”)—hydrophobic

Types of Microscopes

• Compound Light Microscopes

  • Benefits: uses light, cheap, easy to use, can view living specimens

  • Limitations: magnification is limited, can’t see very small objects

• Scanning Electron Microscope

  • Benefits: uses electrons, allows us to see the 3D surface of an object.

  • Limitations: expensive, requires a lot of training, specimens are killed

• Transmission Electron Microscope

  • Benefits: uses electrons, allows us to see the internal structures of a cell.

  • Limitations: expensive, requires a lot of training, specimens are killed

Types of Cells

• Eukaryotic—cells with membrane bound organelles, may be multicellular or unicellular.

• Prokaryotic—cells without membrane bound organelles, all prokaryotes are unicellular.

Plant Cell Structures & Functions

• Large Central Vacuole—large, sac like structure in plant cells that stores water and other inorganic materials. contributes to turgor pressure (pressure that allows plant cells to be rigid)

• Chloroplasts—organelles that performs photosynthesis, converting sunlight, carbon dioxide, and water into glucose

• Cell Wall—rigid structure outside of a plant cell membrane that gives extra support and protection to the plant cell.

Prokaryote Structure

• Nucleoid Region—non-membrane bounded region in a prokaryotic cell where DNA in concentrated

• Ribosomes—produces proteins (NOT membrane bound and NOT technically organelles. ribosomes are subcellular structures that ALL cells have)

• Capsule—sticky layer of sugars or proteins that surrounds the cell wall, protecting the cell and enabling it to adhere to various surfaces.

• Cell Membrane—thin, flexible protective barrier that covers the cell’s surface and acts as a barrier; determines what goes in and out of the cell. all cells have a cell membrane

• Cell Wall—rigid structure outside of the cell membrane that gives the prokaryote protection from pressure. almost all prokaryotes have cell walls.

• Flagellum—motility structure

• Plasmid—extrachromosomal DNA; carries accessory genes

Endosymbiont Theory—a theory about where mitochondria and chloroplasts come from. the theory is that an ancient ancestor to the eukaryote engulfed and oxygen-using prokaryote, forming an endosymbiont. over time, eukaryotic cells became dependent on the eukaryote for nutrients and protection.

• Evidence: mitochondria and chloroplasts are both double membrane bound, they both have their own DNA and ribosomes, and they can both divide independently from the nucleus.

Organelle—any membrane enclosed structure with specialized functions in the cytoplasm of a eukaryotic cell.

Homeostasis—maintenance of a stable internal environment

Chromosome—discrete units of DNA and the associated proteins. eukaryotes have linear chromosomes stored in the nucleus. prokaryotes have a single, circular chromosome in the nucleoid region.

Chromatin—granular, loose form of DNA present in a resting cell. individual chromosomes cannot be seen (but they are present…they just haven’t condensed. the chromatin condenses into individual chromosomes during cell division)

Apoptosis—programmed cell death initiated by lysosomes.

Contractile Vacuole—some unicellular eukaryotes do not have cell walls and could burst due to osmosis of water into the cell. contractile vacuoles pump water out of the unicellular eukaryotes.

Unit 3 : Macromolecules

Molecular Interactions

• Ionic Bond: bond formed when one or more electrons are transferred from one atom to another. The bond is held together by the attraction of a positively charged cation to a negatively charged anion.

• Covalent Bond: bond formed when atoms share a pair of electrons

• Hydrogen Bond: attractions between hydrogens and negative charged poles of OTHER molecules. hydrogen bonds are attractions between two different molecules.

• Van Der Waals Forces: temporary and random attractions between nonpolar molecules

Water’s Polarity

• Water is polar because oxygen has a higher affinity for electrons. therefore, the electrons are around the oxygen side of the molecules, making it have a partial negative charge. The hydrogen side, then, has a partial positive charge.

• Oxygen and hydrogen do not share the electron equally

• Cohesion: the attraction between molecules of the same substance. Contributes to the high surface tension of water.

• Adhesion: the attraction between molecules of different substances. contributes to the formation of a meniscus in a graduated cylinder.

• High Heat Capacity: water can absorb a lot of heat without increasing in temperature. allows water to have an insulating effect on Earth

• High Heat of Vaporization: water can absorb a lot of heat before changing into a gaseous state. allows sweat to cool us down

• Solid Water is less Dense than liquid water: this allows ice to float and keeps lakes and oceans from becoming permanently frozen.

• Water is an excellent solvent: it likes to interact with any charged or partially charged molecules. can dissolve polar covalent compounds and ionic compounds

Characteristics of Carbon

• has 4 valence electrons and can form up to 4 covalent bonds.

• can bond to other carbons, making backbones for organic molecules with infinite combinations

• carbon chains can vary in length, be branched or unbranched, have double bonds between carbons, and form rings.

4 Classes of Macromolecules

• Carbohydrates: sugars or polymers of sugars

  • elements: C, H, and O in a 1:2:1 ratio

  • monomer: monosaccharide (simple sugar)

  • polymer: polysaccharide (complex sugar)

  • Functions

    • short term energy storage

      • ex: glucose, glycogen, starch

    • structure

      • ex: chitin, cellulose

• Proteins: polymers of amino acids

  • elements: C, H, O, N, and S

  • monomer: amino acid

  • functions: numerous functions, including enzymes, transport, defense, communication, structure, movement, etc

• Lipids: non-polar, hydrophobic macromolecules

  • elements: mostly C and H

  • monomer: no true monomer

  • Types and Functions

    • fats and oils: long term energy storage (lipids can store more energy in a smaller amount of space than carbohydrates)

    • phospholipids: structure. phospholipids are the major components of cell membrane.

    • steroids: mediate physiological reactions

2 Types of Nucleic Acids

• Deoxyribonucleic Acid (DNA): hereditary material for the cell

• Ribonucleic Acid (RNA): involved in protein synthesis

Amino Acid Structure

• Amino group and carboxyl group connected by an R group’

Protein Folding

• Primary Structure: the amino acid sequence of a protein. made up of covalent bonds called peptide bonds

• Secondary Structure: hydrogen bonds in the backbone of a protein. does not involve the R groups of the amino acids. can be an a helix or a B pleated sheet

• Tertiary Structure: covalent, ionic, or hydrogen bonds between the R groups of different amino acids. gives a protein its overall shape

• Quaternary Structure: if a protein requires more than one chain to be functional, quaternary structure is how the multiple chains fit together.

Enzyme Functions

• enzymes speed up reactions by lowering the activation energy of a reaction. all biological reactions require an input of energy to start the reaction. enzymes lower that amount of energy, allowing the reaction to go more quickly.

Definitions

• Electronegativity: the affinity of an atom for electrons. oxygen has a high electronegativity and therefore has a high affinity for electrons.

• organic chemistry: chemistry involving carbon chains

• monomer: small subunits that when linked together form a polymer

• polymer: large molecules made up of small monomers linked together

• dehydration reaction: chemical reaction that joins monomers to form a polymer. also known as a condensation reaction. forms polymers

• hydrolysis reaction: chemical reaction that breaks monomers from polymers. breaks apart polymers

• monosaccharide: monomer of a carbohydrate. glucose is a monosaccharide.

• polysaccharide: polymer of a carbohydrate. glycogen, starch, chiting, and cellulose are polysaccharides

• amino acid: monomer of a protein

• Nucleotide: monomer of a nucleic acid

• carbohydrates

  • starch: energy storage polysaccharides in plants

  • glycogen: energy storage polysaccharide in animals

  • cellulose: structural polysaccharide in plants (part of their cell wall)

  • chitin: structural polysaccharide in some animals and fungi

  • glucose: energy storage monosaccharide for plants and animals

• lipids

  • fats

    • structure: glycerol and three fatty acid chains

    • function: long term energy storage

  • phospholipid

    • structure: glycerol, two fatty acid chains and a phosphate group

    • function: structure, most prevalent compound of a membrane

  • steroid

    • structure: four ring structure

    • function: mediates physiological reactions

  • all three of these are HYDROPHOBIC

Saturation

• saturated: when fatty acid chains do NOT have any double bonds between carbons

• unsaturated: when there is at least one double bond between carbons in a fatty acid chain

Denaturation

• the unfolding of a protein. it is caused by changes in temperature, pH, or salt concentration. when a protein unfolds, it cannot perform its function

Activation Energy

• the energy required to start a biological reaction. it is lowered but NOT eliminated by the presence of an enzyme

Active Site

• where the substrates (reactants) bind to an enzyme. the shape of the active site is critical to an enzyme’s function.

Enzyme

• a biological catalyst that speeds up reactions by lowering the activation energy required for the reaction to occur. enzyme are always proteins

Catalyst

• a substance that lowers the activation energy for a reaction to occur. enzymes are biological catalysts

Substrate

• reactants for enzymes. they bind to the active site of the enzyme, where the reaction occurs.

Unit 4 : Cell Transport

lipid bilayer

• the organization of phospholipids in a membrane, with the hydrophilic phosphate group head facing outward and the hydrophobic lipid tail facing inward.

fluid mosaic model

• describes the structure of cell membranes. cell membranes are made of many different types of molecules (phospholipids, proteins, glycoproteins, glycolipids, and cholesterol). unless they are anchored, they are free to move around in the cell membrane.

passive transport

• transport of material that does NOT require energy. always moves material with the concentration gradient, from a greater concentration to a lesser concentration.

• diffusion: movement of particles from a greater concentration until they are equal. SMALL, NONPOLAR MOLECULES can diffuse directly across the cell membrane when they are moving WITH the concentration gradient.

• facilitated diffusion: diffusion of molecules through protein channels, SMALL, POLAR MOLECULES need protein channels to travel across the cell membrane when they are moving WITH the concentration gradient because the cell membrane in non-polar and does not like to interact with polar molecules.

• osmosis: diffusion of water through a semi-permeable membrane.

active transport

• transport of material requiring the use of energy. moves materials against the concentration gradient, from a lower concentration to a higher concentration.

• ion pumps: protein channels that move ions (charged particles) against the concentration gradient. requires energy

• endocytosis: how cells bring large molecules (such as proteins) into a cell. the cell engulfs the material and brings it inside the cell in a vesicle. requires energy because it moves large amounts of cytoplasm and cell membrane.

  • phagocytosis: engulfing really large material or cells

  • pinocytosis: engulfing smaller but still large enough not to be able to move through the membrane

• exocytosis: how cells release large molecules (such as proteins) out of a cell. vesicles fuse with the cell membrane, expelling the material from the cell. requires energy because it moves large amounts of cytoplasm and cell membrane.

concentration gradient

• going from higher concentration to a lower concentration

dynamic equilibrium

• when concentration of particles is equal on both sides of the membrane, but particles continue to move but there is no net change in concentration

most likely transport for the following molecules

• large molecules

  • into: endocytosis

  • out of: exocytosis

• polar molecules

  • with gradient: facilitated diffusion

  • against gradient: active transport

• small, nonpolar molecules

  • with gradient: simple diffusion directly through the membrane

  • against gradient: active transport

selectively permeable membrane

• a membrane that allows for the transport of some materials through it but not others

how cells respond to being in different types of solutions

• hypertonic: when placed in hypertonic solutions, plant and animal cells shrivel

• isotonic: when place in isotonic solutions, animal cells and plant cells behave normally

• hypotonic: when placed in a hypotonic solution, animal cells swell and may burst, whereas plant cells are protected by their cell walls.

role of vesicle sin cell transport

• vesicles are used in both endocytosis and exocytosis. in endocytosis, engulfed material is brought into the cell in vesicles. in exocytosis, vesicles fuse to the cell membrane to expel material out of the cell.

definitions

• hypotonic: when comparing two solutions, hypotonic solutions are the solutions with the lower amount of solute.

• isotonic: when comparing two solutions, isotonic solutions have equal concentration of solute

• hypertonic: when comparing two solutions, hypertonic solutions are the solutions with the higher amount of solute (hypertonic solutions are more concentrated)

• osmotic pressure: during osmosis, water will always move to the side of the membrane that is hypertonic (contains more solute). this puts pressure on that side of the membrane.

Unit 5 : Cellular Energy

atp

• structure: adenosine + ribose + 3 phosphates bonded with 3 high-energy bonds

• function: energy storage molecule that the cell can directly use to power cellular functions

glucose

• formula: C₆H₁₂O₆

• function: short term energy storage monosaccharide. but the cell cannot use it directly to power cell functions

atp cycle

• ADP + P → energy from cellular respiration → ATP → energy for cellular work → ADP + P

electron carriers

• NADH: carries two high energy electrons in cellular respiration. drops off the electrons at the electron transport train

• FADH₂: carries two high energy electrons in cellular respiration. drops off the electrons at the electron transport chain

• NADPH: carries two high energy electrons in photosynthesis. drops off the electrons in the Calvin Cycle (light independent reaction)

definitions

• metabolism: the totality of all chemical reactions in the cell

• catabolism: cellular reactions that break large molecules into smaller molecules. releases energy. cellular respiration is an example of catabolism

• anabolism: cellular reactions that combine smaller molecules to make larger molecules. requires an input of energy. photosynthesis is an example of anabolism

Unit 6 : Cellular Respiration

definition

• cellular respiration: the process by which cells break down glucose and other food molecules in the presence of oxygen that releases energy

stages

1. glycolysis: occurs in the cytoplasm and is anaerobic (does NOT require oxygen)

2. citric acid cycle (krebs cycle): occurs in the mitochondrial matrix and is aerobic (requires oxygen)

3. electron transport chain: occurs in the mitochondrial inner membrane is aerobic

equation

• C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP + heat

reactions

• glycolysis breaks down glucose and we get 2 NADH, a net gain of 2 ATP, and 2 pyruvate (or pyruvic acid)

  • makes 2 atp

• citric acid cycle converts pyruvate into CO2 and we get (per glucose) 8 NADH, 2 FADH₂, 6CO₂ and 2 atp

  • makes 2 atp

• electron transport chain uses the energy stored in NADH and FADH₂ to ultimately make a lot of ATP. final electron acceptor is oxygen.

  • makes approximately ~32 atp

• active transport in the ETC: ion pumps pushing H⁺ ions against the concentration gradient from the matrix to the intermembrane space. the energy for these pumps come from the electrons dropped off by NADH and FADH₂

• passive transport in the ETC: facilitated diffusion: H⁺ ions diffuse through atp synthase back into the matrix. as they diffuse, ATP synthase spins and makes atp

  • fermentation recycles NAD⁺ from NADH when there is no oxygen. lactic acid fermentation is done by muscle cells and produces lactic acid as waste. alcoholic fermentation is done by yeast and produces ethanol and CO₂ as waste.

• under aerobic conditions, cellular respiration produces 36 atp per glucose. under anaerobic conditions, fermentation produces 2 atp per glucose. cellular respiration produces 18 times more atp than fermentation

definitions

• aerobic: requires oxygen

• anaerobic: does not require oxygen

• phosphorylation: the addition of a phosphate group (to adp)

• oxidative phosphorylation: the process in the electron transport chain when the oxidation of NADH and FADH₂ ultimately provides the energy to phosphorylate ADP.

• coenzyme A: allows acetate to enter the citric acid cycle

Unit 7 : Photosynthesis

definition

• photosynthesis is a process used by plants and other organisms to convert light energy, normally from the sun, into chemical energy stored in carbohydrates

carbon fixation

• converting gaseous carbon in carbon dioxide into solid carbon during photosynthesis. this occurs during the light independent reactions (calvins cycle)

equation

• CO₂ + H₂O + photons → C₆H₁₂O₆

reactions

• light dependent reactions:

  • occurs in the thylakoid membrane in chloroplasts. requires light energy. the ultimate source of energy for all life comes from light energy from the sun. requires H₂O. water is broken apart by photostem II in order to supply electrons for the light dependent reaction to occur. produces O₂ as a waste product of breaking apart H₂O.

  • function: produces atp and NADPH for the light independent reactions (calvin cycle)

• light independent reactions (AKA calvin cycle)

  • occurs in the chloroplast stroma. requires atp and NADPH produced in the light dependent reaction. requires CO₂ from the atmosphere.

  • function: ultimately produces C₆H₁₂O₆. carbon fixation occurs during the light independent reactions.

comparing photosynthesis and cellular respiration

• the reactants of cellular respiration are the products of photosynthesis and vice versa.

• they utilize different energy types (photosynthesis converts light energy to chemical energy. cellular respiration converts one type of chemical energy into another type of chemical energy).

• cellular respiration is catabolic—it breaks down a larger molecule (C₆H₁₂O₆) into smaller molecules (CO₂)

• photosynthesis is anabolic—it makes larger molecules (C₆H₁₂O₆) from smaller molecules (CO₂)

definitions

• heterotroph (“other-feeders”)

  • they live off organic compounds produced by other organisms

  • consumers-dependent upon photoautotrophs either directly or indirectly

• autotroph (“self-feeders”)

  • they sustain themselves without feeding on anything derived from other living beings

  • producers-ultimate source of all organic compounds for non-autotrophic organisms

• chlorophyll: pigment in the chloroplast; found in the photosystems. absorbs energy from light energy.

• photon: a packet of light energy

• pigment: substances that absorb visible light; when pigments absorb visible light, electrons in the pigment molecule go to a high energy state.

• thylakoid: membrane bound compartments inside of chloroplasts. the thylakoid membrane is the site of the light dependent reactions.

• stroma: the part of the chloroplast that is outside of the thylakoids. this is where the light independent reactions (calvin cycle) occurs.

• photo-phosphorylation: when ADP is phosphorylated in the photosynthesis to produce ATP. the source of the energy to attach the phosphate group to ADP is from the light.

Unit 8 : Cell Division/Cycle

reasons why the cell can’t be large

• dna overload: if a cell get’s too large, it’s amount of dna will not be sufficient to control all the activities of the cell

• surface area to volume ratio: as a cell gets larger, the cell volume will ALWAYS increase FASTER than the surface area. the surface area, however, controls how nutrients move into the cell and wastes move out of the cell. as the cell gets larger, the cell membrane will be unable to get enough nutrients into the cell nor enough wastes out of the cell

importance of normal cell division

• for unicellular organisms, cell division is asexual reproduction

• for multicellular organisms, cell division is used for:

  • organismal growth and development

  • tissue regeneration (healing and repair)

stages of interphase

• G₁ (first gap phase): cell growth occurs and normal cell function occurs

• S (synthesis phase): chromosomes are duplicated

• G₂ (second gap phase): the cell checks to see if anything else needs to be done prior to mitosis. if anything else needs to be copied, it copies it. it also checks to make sure all of the dna has been copied.

• M (mitotic phase): consists of two processes: mitosis and cytokinesis

• INTERPHASE is the first 3 stages of the cell cycle: G₁, S and G₂. interphase is the longest part of the cell cycle and it’s length differs for different types of cells. during interphase, individual chromosomes are NOT visible. the dna is in a chromatin state.

what is G₀

• G₀ is opting out of the cell cycle. if a cell has no need to divide ever again, it may go into G₀. most cells cannot come back out of G₀, but a few can

phases of mitosis

• prophase

  • chromosomes condense. (the dna duplicates in S phase, but does not condense until prophase of mitosis)

  • centrosomes move to opposite ends of the cell

  • the nucleolus disappears

  • the nuclear envelope disappears

  • the spindle forms

  • kinetochore proteins bind the centromeres of each chromosome.

  • kinetochore microtubules bind the kinetochores of each chromosome

• metaphase

  • the microtubules push and pull the chromosomes until they are lined up at the center of the cell.

• anaphase

  • kinetochore microtubules pull sister chromatids apart to opposite sides of the cell

  • non-kinetochore microtubules push against each other starting the process of cytokinesis

• telophase

  • there are 2 nuclei (until cytokinesis is complete)

  • sister chromatids are on opposite sides of the cell. they go back to a chromatin state.

  • the nuclear envelopes reform

when does cytokinesis occur?

• cytokinesis is the division of the cell nucleus and often begins as early as the end of anaphase, but almost always overlaps with telophase.

chromosomes

• number in a human somatic cell: 46 (two of each type of chromosome-diploid)

• number in a human gamete: 23 (one of each type of chromosome-haploid)

regulations on cell division

• external regulators: factors that respond to events outside the cell that direct cells to speed up or slow down the cell cycle.

  • example of external regulator: contact inhibition (when cells come into contact with other cells, they stop dividing)

• internal regulators: factors from inside the cell that directs cells to speed up or slow down the cell cycle

  • example of internal regulator: cyclins (a family of proteins within the cell that controls the timing of the cell cycle)

definitions

• cancer: uncontrolled cell division (caused by p-53)

• homeostasis: maintenance of a stable, internal environment

• chromosome: discrete units of genetic material composed of DNA and proteins. contains the genetic information of the cell. human somatic cells have 46 chromosomes. human gametes have 23 chromosomes

• chromatin: granular form of dna found in resting cells (cells that are in interphase)

• mitosis: division of the cell nucleus

• cytokinesis: division of the cell cytoplasm

• interphase: time between cell divisions. comprised of G₁, S, and G₂. longest part of the cell cycle. dna is in a chromatin state

• cleavage furrow: part of cytokinesis in animal cells. the pinching between the two new cells being formed

• cell plate: part of cytokinesis in plant cells. the formation of a new cell wall between two new plant cells

• spindle: structure formed by centrosomes and microtubules during mitosis which draws the duplicated chromosomes apart as the cell divides

• centriole: one of two structures that makes up a chromosome

  • plant cells do NOT have centrioles

• centrosome: structure that facilitates cell division made up of two centrioles. plant cells do not have these

• centromere: the part of the duplicated chromosome that links sister chromatids

• chromatid: one of two strands of replicated dna in a duplicated chromosome. sister chromatids are identical to each other

• histone: protein around which dna is wrapped in a chromosome. helps to organize dna

• tetrad: homologous chromosome pair

• homologous chromosome pairs: each somatic cell has 2 of each chromosome. a homologous pair is when both of the same chromosome find each other; they have the same genes but may have different alleles for that gene.

• autosome: chromosomes that do not control the gender of the individual. humans have 32 pairs of autosomal chromosomes

• sex chromosome: chromosomes that control the gender of the organism. humans have 1 pair of sex chromosomes (XX for females, XY for males)

• gamete: cell used for sexual reproduction. egg (ova) for females; sperm for males. gametes are haploid and are produced by meiosis

• somatic cell: cells that are not used for sexual reproduction. most cells in humans. somatic cells are diploid and are produced by mitosis

• diploid: having 2 of each type of chromosomes. diploid number for humans is 46

• haploid: having one of each type of chromosome. the haploid number for humans is 23

• karyotype: an image of the number and appearance of chromosomes in a eukaryotic cell

• contact inhibition: external regulator in cell division; when cells come into contact with other cells, they stop dividing

• cyclins: internal regulator in cell division; a family of proteins within the cell that controls the timing of the cell cycle

• fertilization: when a sperm and an egg fuse

• zygote: diploid cell formed upon cell division

• meiosis: cellular reproduction that halves the number of chromosomes and ensures genetic diversity of gametes

• crossing over: when homologs pair up in prophase I, sister chromatids wrap around each other wand may “swap” alleles

• independent assortment: random lining up of homologs on the metaphase plate in metaphase I. ensures genetic diversity as it shuffles up the alleles.

• importance of cell division

  • mitosis: used for organismal growth, development, and tissue regeneration

  • meiosis: produces gametes (halves the number of chromosomes and produces genetic diversity in gametes)

• phases of mitosis

  • prophase: nuclear envelope disappears; chromosomes condense; nucleolus disappears; spindle forms

  • metaphase: chromosomes line up on the metaphase plate

  • anaphase: sister chromatids are pulled apart

  • telophase: nuclei reform; chromosomes go back to a chromatin state

ways mitosis differs from meiosis

• mitosis goes from 1 (2N) cell to 2 (2N) cells; meiosis goes from 1 (2N) cell to 4 (1N) cells.

• the daughter cells in mitosis are genetically identical; the daughter cells in meiosis are genetically different

• cells undergoing mitosis go through a single division; cells undergoing meiosis go through 2 divisions

• homologous chromosomes pair up in meiosis; they do not pair up in mitosis

• somatic cells undergo mitosis; only sex cells undergo meiosis

regulations on cell division

• internal: cyclins and p53

• external: contact inhibition and growth factors

asexual reproduction versus sexual reproduction

• asexual reproduction: 1 aparent with identical offspring. Good: faster, more offspring. Bad: much less genetic variation (relies on mutations)

• sexual reproduction: 2 parents with offspring that a mix of genes from each parent. Good: much more genetic variation. Bad: slower, fewer offspring

phases of meiosis

• meiosis I: splits homologous chromosomes (tetrads)

  • prophase I: homologous chromosomes pair up; crossing over occurs

  • metaphase I: homologous chromosomes line up on the meta phase plate (how they line up is random→independent assortment)

  • anaphase I: homologous chromosomes are pulled apart

  • telophase I and cytokinesis: end up with 2 1N cells (homologs were separated)

• between meiosis I and meiosis Ii there is no telophase

• meiosis II: separates sister chromatids

  • prophase II: sister chromatids start to move to the center of the cell

  • metaphase II: sister chromatids line up at the metaphase plate

  • anaphase II: sister chromatids are pulled apart

  • telophase II and cytokinesis: end up with 4 1N cells since sister chromatids were separated

Unit 9 : Genetics

gregor mendel

• austrian monk; father of genetics

mendel’s 3 laws of genetics

• law of dominance and recessiveness: intraits with multiple alleles, one allele masks or covers up another

• law of segregation: in meiosis, the diploid parent cell’s alleles separate (segregate) during meiosis

• law of independent assortment: the segregation of one trait’s alleles has no effect on the segregation of another trait’s alleles

punnet squares

• monohybrid, dihybrid, incomplete dominance (non-dominance), codominance (think blood types), sex-linked traits

4 exceptions to mendel’s principles

• phenotype can be affected by more than genotype

• not all genes show a pattern of dominance and recessiveness

• for some genes, there are more than two alleles

• many times, traits are controlled by more than one gene

pedigree

• be able to read an interpret a pedigree

definitions

• trait: characteristic due to a genotype (think of these as being the physical characteristics)

• allele: variation of a gene

• gene: a segment of dna that encodes for a protein

• generations: P = parental generation, F1 = first generation of offspring, F2 = second generation of offspring

• hybrid: heterozygous

• true breeding: homozygous

• dominant allele: the allele that if present in even 1 copy is whose trait we’ll see in an organism

• recessive allele: the trait that must be present in 2 copies in order to see the trait in on an organism

• homozygous: having 2 identical alleles for the same trait

• heterozygous: having 2 different alleles for the same trait

• genotype: allele combinations for a trait (Tt)

• phenotype: the physical characteristic that results from a genotype

• probability: the likelihood that an event will occur

Unit 10 : DNA Structure & Replication

structure of a nucleotide

1. phosphate group

2. 5 C sugar (dna-deoxyribose, RNA-ribose)

3. nitrogenous base (dna: A,T,G,C rna: A,U,G,C)

differences between dna and rna

1. 5 C sugar: dna-deoxyribose; rna-ribose

2. DNA-double stranded; RNA-single stranded

3. DNA-thymine; RNA-uracil

4 dna bases and 4 rna bases

• DNA: adenine, thymine, cytosine, guanine

• RNA: adenine, uracil, cytosine, guanine

base pairing rules for DNA and RNA

• DNA: adenine bonds to thymine; cytosine bonds to guanine

• RNA: adenine bonds to uracil; cytosine bonds to guanine

chargaff’s rule

• in a given sample of DNA, the amount of A=T and C=G

purines vs. pyrimidines

• purines: double ring structure, adenine and guanine

• pyrimidines: single ring structure, cytosine and thymine (also uracil in rna)

  • purines always bond to pyrimidines

rosalind franklin

• used x-ray crystallography to determine the structure of dna

watson and crick

• credited with discovering the structure of dna

structure of dna

• sugar phosphate backbone; nitrogen bases form the “rungs”

• all the bonds are covalent EXCEPT the hydrogen bonds holding the nitrogen bases together in the center

where replication occurs

• the nucleus

template for replication

• dna (both strands)

enzyme required for replication

• dna polymerase (main enzyme; polymerizes dna nucleotides and proofreads)

• helicase (unwinds dna double helix), primase (makes an rna primer)

final product of replication

• exact copy of dna

error rate of replication

• 1 in 10,000,000,000 bases

definitions

• helix: spiral

• complementary base pairs: in dna, A bonds with T and C bonds with G

• replication: copying dna

• semi-conservative replication: at the end of replicatIon, each new DNA strand is made up of two strands; one is an old, template strand and one is a new strand

• mutagen: anything that causes a mutation (example: UV light, some chemicals, radiation)

Unit 10.5 : Translation & Transcription

two parts of gene expression

1. transcription (making an mRNA copy of a DNA gene)

2. translation (making a protein from an mRNA copy of a gene)

how many amino acids do we have

• 20

3 types of RNA and their functions

• mRNA (messenger RNA): carries a copy of DNA instructions for a gene to the cytoplasm

• rRNA (ribosomal RNA): RNA molecules in a ribosome

• tRNA (transfer RNA): brings over an amino acid to a growing protein chain

where transcription occurs

• cytoplasm

template for transcription

• DNA ( a single gene at a time)

enzyme required for transcription

• RNA polymerase

final product of transcription

• mRNA copy of a gene

modifications that must be made to RNA before sending it to a ribosome

• introns (interrupting sequences) must be removed

• extrons (expressed sequences) must be spliced together

• a cap and a tail must be added

where translation occurs

• cytoplasm

template for translation

• mRNA

structure required for translation

• ribosome

final product of translation

• protein

amino acid sequence from a DNA sequence

• how the ribosome knows where to start making the protein

  • the start codon (AUG)

• what determines the amino acid (codon or anticodon)

  • the codon

codons versus anticodons

• codons are found in the mRNA; anticodons are found on the tRNA. codons are used to determine the amino acids

AUG

• start codons, encodes for methionine

definitions

• transcription: making an mRNA copy of a DNA gene

• translation: making a protein from an mRNA

• amino acid: monomer of a protein

• codon: triplet of nucleotides that usually encodes for a specific amino acid (exception: 3 stop codons)

• start codon: AUG, also encodes for methionine

• stop codon: 3 stop codons, they do not code for a specific amino acid

• promoter: binding site for RNA polymerase, tells the cell where the gene begins on the chromosome

• terminator: sequence of nucleotides at the end of a gene that signals where the gene ends. RNA polymerase falls off here

• intron: interrupting sequence of nucleotides the is cut out of mRNA before the mRNA leaves the nucleus. does not contribute to the production of a protein

• exon: expresses sequence of nucleotides that contributes to the production of a protein

Unit 11 : Evolution

georges couvier

• produced “catastrophism” in which he said a series of catastrophes account for the different strata of fossils

jean-baptiste lamarck

• proposed “inheritance of acquired characteristics”, an incorrect theory for a mechanism of evolution. believed that through the use and disuse, organisms can pass on non-heritable characteristics to their offspring. NOT a part of modern evolutionary theory

charles darwin

• proposed “natural selection” as a mechanism of evolution. IS a part of modern evolutionary theory

james hutton

• proposed “uniformitarianism” in which he said that geological processes are generally slow and take a long time. all theories about geology, must take into account that these processes are slow. said that the earth is much older than many had previously suggested.

charles lyell

• popularized hutton’s work

thomas malthus

• proposed that war, famine, and disease help to control population growth in people. darwin extended that idea to understanding competition for resources for all organisms

adaptation example—darwin’s finches

• inherited characteristics that increase an organism’s chance for survival and reproduction

adaptation

• they arise through mutation (randomly) but are selected for by the environment (not randomly)

• both physical and behavioral

survival of the fittest

• the ability of an individual to survive and reproduce in its specific environment

types of evidence for evolution

• fossils, homology, direct observation, biogeography

principle of superposition

• in geology, the oldest fossils are the most simple and are the deepest. the youngest fossils are the most complex and are found in the youngest strata.

examples of homologous structures, vestigial structures, and analogous structures

• homologous structures: structures that may have different mature forms in different organisms but develop from the same embryonic tissues. comes from common descent

• vestigial structures: homologous organs/structures of many animals that are so reduced in size that they are just vestiges, or traces, of homologous organs in other species

• analogous structures: structures that share similar function but NOT common ancestry

modern definition of evolution

• a change in the relative frequency of alleles in a population over time

two sources of genetic variation

• in sexually reproducing organisms: mutation and gene shuffling in sexual reproduction. (gene shuffling is a more important source of variation)

4 mechanisms that change relative frequency

1. mutation—any change in the sequence of nucleotides

2. natural selection—the process in which individuals that have certain heritable traits survive and reproduce at a higher rate in their particular environment than other individuals because of those favorable traits

3. migration (gene flow)—the transfer of genes from one population to another

4. genetic drift—variation in the relative frequency owing to the chance disappearance of particular genes as individuals die or do not reproduce. (most clearly seen in small populations)

evolution of single gene traits versus polygenic traits

• natural selection of single gene traits can be easily graphed as a bar graph. natural selection of polygenic traits (traits that are controlled by more than one gene) are graphed by a bell curve

directional selection, stabilizing selection, and disruptive selection

• directional selection: organisms in a population on one or the other end of the bell curve have the highest fitness. the entire bell curve shifts in that direction

• stabilizing selection: organisms in a population in the center of a bell curve have the highest fitness. the entire bell curve stays centered in the same area but narrow

• disruptive selection: organisms in a population on both ends of the bell curve have the highest fitness. the curve splits into two different bell curves.

definitions

• conserved genes/proteins: genes or proteins that are similar/the same across many different but related species

• evolution: change in relative frequency of alleles in a population over time

• population: a group of individuals of the same species that interbreed

• theory: a well-substantiated explanation of same aspect of the natural world that is acquired through the scientific method, and repeatedly confirmed through observation and experimentation

• inheritance of acquired characteristics: lamarck’s theory for a mechanism of evolution. incorrect theory for a mechanism for evolution. stated that through use and disuse, organisms can pass on non-heritable characteristics to their offspring. NOT a part of modern evolutionary theory

• adaptation: inherited characteristics that increase an organism’s chance for survival and reproduction

• descent with modification: each living species has descended, with changes, from other species over time

• artificial selection: also called selective breeding; the process by which humans breed other animals and plants for particular traits

• natural selection: the process in which individuals that have certain heritable traits survive and reproduce at a higher rate in their particular environment than other individuals because of those favorable traits

• fitness: the ability of an individual to survive and reproduce in its specific environment

• fossil: the preserved remains or traces of animals, plants, and other organisms from the remote past

• homology: similarity resulting from common ancestor

• homologous structure: structures that have different mature forms in different organisms but develop from the same embryonic tissues; arise from common descent

• embryology: study of organisms’ embryos; evidence for evolution

• vestigial structure: homologous organs/structures of many animals are so reduced in size that they are just vestiges, or traces, of homologous organs in other species

• convergent evolution: the independent evolution of similar features in different lineages

• analogous structures: structures that share similar function but NOT common ancestry

• gene pool: consists of all genes, including all the different alleles, that are present in a population

• relative frequency: the number of times the allele occurs in a gene pool, compared with the number of times other alleles for the same gene occur; usually expressed as a percentage