Biology BASIS 8 : PreComp

^{good luck on bio; it’s gonna be hard}

Experimental Design

Types of Data

• Qualitative: characteristics that cannot be easily counted/measured

• Quantitative: characteristics that are counted/measured

Parts of an Experiment

• Hypothesis: predicted outcome of experiment, proposed explanation

• Independent Var.: variable that is intentionally changed

• Dependent Var.: variable that is observed/measured

• Controlled Var.: variables that are kept constant between groups

• Control Group: group used as a comparison for “normal”

Graphing

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

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

Statistics

• Mean: average

• Median: middle when in numerical order

• Mode: most common

Cells

Statistics

• Mean: average

• Median: middle when in numerical order

• Mode: most common

Characteristics of Living Things

1. All living things grow and develop

2. All living things have 1+ 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 all living things

3. All cells come from other preexisting cells

Notable Scientists

• Robert Hooke: discovered cells

• Anton von Leeuwenhoek: discovered many single-cell organisms & that not only plants have cells

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

• Theodor Schwann: determined that all animals are made of cells

• Rudolph Virchow: determined that all cells come from existing cells

Organelles

• Cell Membrane: thin, flexible protective barrier that covers the cells surface and acts as a barrier; determine what goes in and out. 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 and 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 that converts the energy stored in glucose into energy stored in ATP. does the process of cellular respiration. all eukaryotes have mitochondria

• 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 can store waste in the large central vacuole

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

• Cytoskeleton: network of fiber extending throughout the cytoplasm that organizes the structures of the cell.

  • 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 sister chromatids) and motility

  • all eukaryotic cells have cytoskeleton

• Free Ribosome: make proteins. free ribosomes make proteins that will be used within the cell. they float freely in the cytoplasm. all cells (prokaryote and eukaryote) have free ribosomes

• Bound Ribosome: make 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 (including steroids and some hormones), 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 vud off of the golgi apparatus to deliver material to the cell membrane; vesicles can also move materials into the cell during endocytosis. all eukaryotic cells 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 Microscope

  • Benefits: uses light, cheap, easy to use, views living specimens.

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

• Scanning Electron Microscope

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

  • Limitations: expensive, requires a lot of training, kills specimens

• Transmission Electron Microscope

  • Benefits: uses electrons, allows us to see internal cell structure

  • Limitations: expensive, requires a lot of training, kills specimens

Types of Cells

• Eukaryotic: cells with membrane bound organelles (unicellular/multicellular)

• Prokaryotic: cells without membrane bound organelles (all unicellular)

Plant Cells

• Structures & Functions

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

  • Chloroplasts: organelles that perform photosynthesis, converting sunlight, carbon dioxide, and water into glucose

  • Cell Wall: rigid structure outside of a plant cell membrane that give extra support and protection to the plant cell

Prokaryote Cells

• Structure & Functions

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

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

  • 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 cells surface and acts as a barrier; determines what goes in and out of the cell. all cells have a cell membrane—prokaryotes and eukaryotes

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

  • Flagellum: motility structure

  • Plasmid: extrachromosomal DNA; carries accessory genes

Endosymbiont Theory

• The endosymbiont theory is a theory about where mitochondria and chloroplasts come from. the theory is that an ancient ancestor to the eukaryote engulfed an oxygen-using prokaryote, forming an endosymbiont. over time, eukaryotic cells became dependent on the endosymbiont for energy conversion and the endosymbiont 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

Definitions

• 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 havent 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 these unicellular eukaryotes.

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 oppositely charged ions

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

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

• Van der Waals Forces: temporary and random attractions between non-polar molecules.

Waters 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 electrons equally

• The polarity of water makes it form hydrogen bonds with other water molecules. These hydrogen bonds give water the following characteristics.

  • 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 Organic 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

      • Examples: glucose, glycogen, & starch

    • structure

      • Examples: chitin and cellulose

• Proteins—polymers of amino acids

  • Elements: C, H, O, N, and S

  • Monomer: amino acids

    • Structure: amino group and carboxyl group connected by R group

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

• Nucleic Acids—polymers of nucleotides

  • Elements: C, H, O, N, and P

  • Monomer: nucleotides

  • Polymers: either RNA or DNA

  • Functions: stores and transmits hereditary info and carries the instructions for making proteins

    • 2 types

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

      • Ribonucleic Acid (RNA)—involved in protein production

• Lipids—non polar, hydrophobic macromolecules

  • Elements: mostly C and H

  • Monomer: no true monomer

  • Types and Functions:

    • Fats and Oils: long term energy storage

    • Phospholipids: structure. phospholipids are the major components of cell membranes

    • Steroids: mediate physiological reactions

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 α helix or a β 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 Function

• 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 energy, allowing the reaction 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. (remember, oxygen is the final electron acceptor in the electron transport chain in cellular respiration.)

• 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. glucsoe is a monosaccharide

• Polysaccharide: polymer of a carbohydrate. Glycogen, starch, chitin, and cellulose are polysaccharides.

• Amino Acid: monomer of a protein

• Nucleotide: monomer of a nucleic acid.

• Carbohydrates

  • Starch: energy storage polysaccharide in plants

  • Glycogen: energy storage polysaccharide in animals

  • Cellulose: structure polysaccharide in plants (part of 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 component of a membrane

  • Steroid

    • Structure: four ring structure

    • Function: mediates physiological reactions

  • ALL LIPIDS 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: unfolding of a protein. 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 enzymes function.

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

• Catalyst: a substance that lowers the activation energy to occur. enzymes are biological catalysts.

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

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 WITH the concentration gradient, from a higher to a lower concentration.

  • Diffusion: movement of particles from a greater concentration to a lesser one 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 is non-polar and does not like to interact with polar molecules.

  • Osmosis: diffusion of water through a semipermeable 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/cells

    • Pinocytosis: engulfing smaller but still large enough to not 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 a 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

  • 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 membrane

    • Against gradient: active transport

• Selectively Permeable Membrane: a membrane that allows for the transport of some materials but not others

• How Cells Respond in Different Types of Solutions

  • Hypertonic

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

  • Isotonic

    • when placed in an isotonic solution, animal cells and plant cells behave normally

  • Hypotonic

    • when placed in a hypotonic solution, animal cells swell and may burst

    • when placed in a hypotonic solution, plant cells are protected by their cell walls

• Role of Vesicles in 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 2 solutions, hypotonic solutions are the solutions with the lower amount of solute

• Isotonic: when comparing 2 solutions, isotonic solutions have equal concentrations of solute.

• Hypertonic: when comparing 2 solutions, hypertonic solutions are the solutions with the higher amount of solute

• Osmotic Pressure: during osmosis, water will always move to the side of the membrane that is hypertonic. this puts pressure on that side of the membrane

Cellular Energy

• ATP—adenosine triphosphate

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

• Glucose—C₆H₁₂O₆

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

• ATP Cycle

  • energy for cellular work → ADP + P → energy from cellular resp.→ ATP

• Electron Carriers

  • NADH: carries 2 high energy electrons in cellular respiration. drops off the electrons at the electron transport chain.

  • FADH₂: carries 2 high energy electrons in cellular respiration. drops off the electrons at the electron transport chain.

  • NADPH: carries 2 high energy electrons in photosynthesis. drops off the electrons in the calvin cycle (light independent reactions)

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 combines smaller molecules to make larger molecules. requires an input of energy. photosynthesis is an example of anabolism.

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 cytoplasm and is anaerobic

  • 2. Citric Acid Cycle: occurs in mitochondrial matrix and is aerobic

  • 3. Electron Transport Chain: occurs in the mitochondrial inner membrane and is aerobic

• Equation: C₆H₁₂O₆ → 6CO₂ + 6H₂O + ATP + heat

• Reactions

  • Glycolysis breaks down glucose and we get 2 NADH, a net gain of 2 ATP and 2 pyruvate

    • 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 ~32 ATP

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

  • Passive Transport in 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 18x more ATP than fermentation.

Definitions

• Aerobic: requires oxygen

• Anaerobic: doesnt 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

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 (calvin cycle)

• Equation: CO₂ + H₂O + photons → C₆H₁₂O₆ + O₂

• Reactions

  • Light Dependent Reactions

    • occurs in the thylakoid membrane in chloroplasts

    • requires light energy

    • 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 produces in the light independent reaction

    • requires CO₂ from the atmosphere

    • Function: ultimately produces C₆H₁₂O₆

    • Carbon fixation occurs during the light independent reactions

• Comparing photosynthesis & cellular respiration

  • reactions of cellular resp. are the products of photosynthesis and vice versa

  • they utilize different energy types

  • cellular resp. is catabolic—it breaks down a larger molecule into smaller molecules

  • photosynthesis is anabolic—it makes larger molecules from smaller molecules

Definitions

• Heterotroph

  • “other-feeders”

    • live off organic compounds produced by other organisms

    • consumers—dependent upon photoautotrophs either directly or indirectly

• Autotroph

  • “self-feeders”

    • 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 choroplast; 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 photosynthesis to produce ATP. the source of the energy to attach the phosphate group to ADP is from light.