SCIENTIFIC METHOD

2 TYPES OF SCIENTIFIC INQUIRY

• Discovery science: uses verifiable observations and measurements to describe science
• Hypothesis-based science: uses data from discovery science to explain science. Requires proposing/testing hypothesis.

HYPOTHESIS, THEORY, LAW

• Hypothesis: proposed explanation for set of observations
• Theory: supported by large and usually growing body of evidence
• Law: universal constants

2 TYPES OF LOGIC USED IN SCIENCE

• Deductive reasoning: conclusion must necessarily follow from premises (Sherlock Holmes)
• Living things use ATP; ATP stores energy; Living things use energy
• Inductive reasoning: makes generalizations based on individual occurrences
• Sparrows have feathers; Penguins have feathers; All birds have feathers
• Good hypothesis must be testable and falsifiable

DESIGN OF EXPERIMENT

• Independent variable: the factor that is being altered
• Dependent variable: what’s being measured
• Experimental group: group that experiences altered independent variable Experimental group: group that experiences altered independent variable Experimental group: group that experiences altered independent variable
• Control group: group used to see if effect occurred in experimental

SCIENTIFIC METHOD

• Observation – Hypothesis – Predictions – Experiment – Conclusions

CONCLUSIONS

• Reject or accept hypothesis, but can never prove hypothesis

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PRINCIPLES OF LIFE

PROPERTIES OF LIFE

All living things exhibit…

• Order: complex organization of living things
• Regulation: ability to maintain internal environment consistent with life – homeostasis
• Growth & Development: consistent growth/development controlled by DNA
• Energy Processing: acquiring energy and transforming it to form useful for organism – metabolism
• Response to Environment: ability to respond to environmental stimuli
• Reproduction: perpetuate the species – like begets like – asexual & sexual
• Evolutionary Adaptation: acquisition of trains that best suit organism to its environment

Life’s level of organization define the scope of biology

• Life emerges through organization of various levels
• Each new level, novel properties emerge: emergent properties

Upper tier is global perspective of life

• Biosphere: all environments on earth that support life (Earth)
• Ecosystem: all organisms living in particular area (FL coast)
• Community: array of organisms living in particular ecosystem (All organisms on FL coast)
• Population: all individuals of a species within a specific area (Group of Brown Pelicans)

Middle tier characterized by the organism (Brown Pelican) an individual living thing, which is composed of

• Organ systems: have specific functions; composed of organs (Nervous system)
• Organs: provide specific functions for organism (Brain)
• Tissues: made of groups of similar cells (Nervous tissue)

Lower tier: life emerges at level of the cell

• Cells: living entities distinguished from environment by membrane (Nerve cell)
• Organelles: membrane-bound structure with specific functions (Nucleus)
• Molecules: cluster of atoms (DNA)

• All living things composed of cells
• Structure dictates function
• Evolution

• Smallest unit of life – all properties of life present in cells
• Have membrane & DNA

DNA: genetic material of all cells

• Genes are found in DNA
• Chemical structure of DNA accounts for function
• Diversity of life results from differences in DNA structure
• Unity of life

2 distinct groups of cell types

• Prokaryotic: simple/small; no nucleus/organelles; examples are bacteria & archaea
• Eukaryotic: organelles separated by membranes; have nucleus; examples are plants, animals, fungi

• By studying bio structure you determine what it does and how it works
• Molecular level: enzymes, DNA, RNA
• Organism level: teeth, fins

Basis for diversity & unity of life

• Diversity many different organism on planet
• Unity: all living things are related

Descent with modification – natural selection

• Leads to adaptation

Natural selection: major mechanism of evolution (Darwin). 2 major components are…

• Variation: individuals within population inherit difference characteristics and vary from other individuals
• Differential Reproduction: particular population of individuals produce more offspring than will survive to produce
  offspring of their own

Natural selection is editing mechanism

• Results from exposure to heritable variations to environmental factors that favor some individuals over others
• Survival of the fittest

3 groups of life

• Bacteria: prokaryotic, most are unicellular & microscopic (multiple kingdoms)
• Archaea: like bacteria, prokaryotic, unicellular & microscopic (multiple kingdoms)
• Eukarya: eukaryotic, contain nucleus & organelles (protists, plantae, fungi, animalia)
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CHEMISTRY 1

biological elements

Living organisms are composed of matter; matter is composed of chemical elements

• Element: substance can’t be broken down to other substances
• 92 elements in nature, only a few in pure state
• Life requires 25 essential elements, some called trace elements
• The ordering of atoms into molecules represent lowest level of biological life

• Compound: Substance consisting of 2 or more different elements combined in fixed ration. Many compounds consist
  of only 2 elements (table salt, water)
• Many compounds in living organisms contain carbon, hydrogen, nitrogen, sulfur, phosphorous
• DNA: C, H, O, N, P
• Carbohydrates: C, H, O
• Lipids: C, H, O, P
• Proteins: C, H, O, N, S
• Different arrangements of elements provide unique properties for each compound

Atom is smallest unit of matter that still retains properties of element

• Proton: single + charge; mass of 1
• Electron: single – charge; no mass
• Neutron: no charge; mass of 1

Elements differ in number of protons, neutrons, electrons

• Number of protons determines properties of element
• Number of protons = atomic number
• Neutrons & protons packed in nucleus
• Protons + Neutrons = mass number

Isotopes

• All atoms of element have same atomic number (protons & electrons), but some differ in mass number (neutrons)
• Carbon 12 has 6 neutrons, Carbon 14 has 8 neutrons

Electrons

• Only electrons are involved in chemical activity
• Occur in energy levels: electron shells (info about distribution of electrons can be found in periodic table)
• 1st shell: Hydrogen & Helium; 2nd shell: Lithium, Beryllium, Boron, etc; 3rd shell: Sodium, Magnesium, etc.
• Atom may have 1, 2, or 3 electron shells
• Number of electrons in outermost shell determines chemical properties of atom
• First shell has 2 electrons, second and third will hold up to 8
• Atoms want to fill outer electron shells: can share, donate, receive electrons
• Chemical Bonds: attractions between atoms

• 2 or more elements combine to form new compound (A + B = AB; Reactants = products; 2H2 + O2 = 2H2O)
• Some reactions exchange parts between reactants (NaOH + HCI = NaCI + H2O
• Chemical reactions always involve electrons

Ion: atom/molecule with electrical charge resulting from gain/loss of electrons

• Electron lost: + charge | Electron gained: - charge
• 2 ions with opposite charge attract
• Ionic bond: when attraction holds ions together

• Covalent Bond: when atoms share outer-shell electrons
• Molecule is formed when atoms are held together by covalent bonds

• Compounds: substances with 2 or more elements
• Molecules: substances with 2 or more atoms

Atoms in covalently bonded molecule continually compete for shared electron

• Electronegativity: attraction/pull for shared electrons
• More electronegative atoms pull harder

Molecules of only one element, pull towards each atom is equal because each have same electronegativity

• Bonds formed are nonpolar covalent bonds (N-N)
• Water has atoms with different electronegativity’s
• Oxygen attracts shared electrons more strongly than hydrogen, so shared electron spends more
  time near oxygen
• This is a polar covalent bond

In water molecule…

• Area of oxygen atom has slight negative charge; are of hydrogen has slight positive charge
• Molecules with unequal distribution of charges (unequal sharing of electrons) are called
  polar molecules

• Hydrogen as part of polar covalent bond, attracts other atoms/molecules with a negative charge
• Water molecules are electrically attracted to oppositely charges regions on neighboring molecules
• Since positively charged region is always a hydrogen atom, it’s called hydrogen bond (hydrogen
  is + and attaches to oxygen which is - )

Hydrogen bonding is responsible for special properties of water

• Cohesion/adhesion
• Capacity to hold heat
• Density of ice
• Universal solvent

Water is solvent of life

• Solution is a liquid consisting of uniform mixture of 2 or more substances
• Solvent = dissolving agent | Solute = substance that is dissolved
• Water is versatile solvent that is fundamental to life processes
• It’s versatility results from its polarity
• Table sale is example of solute that will go into solution in water (sodium & chloride ions and water are attracted to each other because of their charges)

Water molecules can break apart into ions: hydrogen ions (H+) & hydroxide ions (OH-)

• Both are extremely reactive
• Balance between the two is critical for chemical processes to occur in living organism

Acids: chemicals that add H+ to solution

• Acidic solution has higher concentration of H+ (example: hydrochloric acid)

Bases: accept hydrogen ions and remove them from solution

• This reduces H+ concentration (example: sodium hydroxide provides OH- that combines with H+ to produce water)

PH scale (potential of hydrogen) is used to describe whether solution is acidic or basic

• Ranges from 0 (most acidic) to 14 (most basic)
• Neutral (neither acidic or basic) is 7
• Each step is 10x difference in concentration of H+

Solutions that resist a change in pH

• Can release or take up H+
• Helps maintain near constant pH
• Does not neutralize solution
• Very important in fluids in body/cells

Solute & Solvent

• Solutions with different concentrations of solute will set up a concentration gradient, which can lead to movement of substances between solutions

Process in which particles spread out evenly in available space

• Particles move from area of more concentration to less
• Particles diffuse down their concentration gradient
• Eventually, particles reach equilibrium where concentration is same throughout

Movement of water across semi-permeable membrane

• Moves from area of high water concentration to area of low
• Water will move into solution that has MORE solute
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CHEMISTRY 2

organic molecules

All biologically important molecules are based on carbon (carbon is structural backbone of all organic molecules)

• Carbon can make up to 4 chemical bonds
• Organic molecules contain at least C and H

 

Determines chemical properties of organic compounds

• Hydroxyl group (OH): hydrogen bonded to oxygen (alcohol)
• Carboxyl group (COOH): carbon double-bounded to both oxygen and a hydroxyl group (carboxylic acid)
• Amino group (NH2): nitrogen bonded to 2 hydrogen atoms and carbon skeleton (anime)
• Phosphate group (OPO32-): phosphorous atom bonded to 4 oxygen atoms (ATP)

4 classes: Carbohydrates, Proteins, Lipids, Nucleic Acids

• All 4 classes are macromolecules (large molecule made of smaller subunits)
• Polymers: large molecule made up of smaller subunits
• Monomer: subunit found in polymer
• Example: proteins are polymers of amino acids (monomer)
• Dehydration Synthesis: process in which polymers are built from monomers
• Hydrolysis: polymers are broken down

Range from small sugar molecules (monomers – monosaccharide) to large polysaccharides

• Contains C, H, O (formulas can be represented by CH2O)
• 1:2:1 ratio
• If it ends in “ose” it’s a carb
• Monosaccharide’s: glucose, fructose
• Polysaccharides: starch, cellulose
• Polysaccharides are hydrophilic (interact with water)
• Function: energy, energy storage, structure

Functions of polysaccharides

• Starch: storage polysaccharide composed of glucose monomers, found in plants
• Glycogen: storage polysaccharide composed of glucose which is hydrolyzed
  by animals when glucose is needed
• Cellulose: polymer of glucose that forms in plant cell walls
• Chitin: polysaccharide used by insects/crustaceans to build exoskeleton

Water insoluble (hydrophobic) compounds that are important in energy storage

• Contain twice as much energy as polysaccharide
• Fats, oils, phospholipids
• Contains C, H, O, P
• Major subunit: fatty acids
• Non-polar
• Function: energy, energy storage, structure

Fats & Oils

• Fatty acids linked to glycerol by dehydration reaction (fats/oils contain one glycerol linked to 3 fatty acids)
• Called triglyceride because of structure

Some fatty acids contain double bonds

• Unsaturated fatty acids (oils): double bonds between carbons, bent at double bonds
• Saturated fatty acids (fat): no double bonds, carbon completely filled with hydrogen

Phospholipids are structurally similar to fats and are important component of cells

• Major part of cell membranes, arranged into bilayer of phospholipids
• Hydrophilic phosphate heads are in contact with the water of the environment and internal part of cell
• Hydrophobic tails are in center of bilayer

Polymer built from various combinations of 20 amino acid monomers

• Have unique structures that are directly related to their functions
• Contains C, H, O, N, S
• Enzymes, cell structure, immunity, etc
• Most abundant biological molecule in cells

Amino acids (building blocks of proteins) have an amino group and a carboxyl group

• Both are covalently bonded to central carbon atom
• Also bonded to central carbon is hydrogen atom and other chemical group symbolized by R
• Each type of amino acid has specific R group which determines characteristics of amino acid
• Can be hydrophobic, hydrophilic, acidic, basic

Peptide bond: special name for covalent bond between amino acids in a protein

• Links carboxyl group of one amino acid to the amino group of next amino acid
• Polypeptide chain contains hundreds/thousands of amino acids links by peptide bonds
• Sequence of amino acids and their chemical characteristics causes the polypeptide to assume particular shape
• Shape of a protein determines its specific function

Protein can have 4 levels of structure: Primary, Secondary, Tertiary, Quaternary

• Primary structure: its unique amino acid sequence
• Determined by the cells genetic info
• Slightest change in sequence affects proteins ability to function
• Secondary structure: results from coiling/folding of polypeptide (which results from hydrogen bonding between certain areas of polypeptide chain)
• Tertiary structure: overall 3D shape of the protein
• Generally result from interactions between R groups
• Disulfide bridges (S=S) are covalent bonds that further strengthen protein’s shape
• Quaternary structure: 2 or more polypeptide chains (subunits) associate to form this
• Hemoglobin
• Many proteins have quaternary structure

Denaturation

• Causes polypeptide chains to unravel and lose their shape, and thus, their function (when protein shape is altered, it can’t function)
• Proteins can be denatured by changes in salt concentration and pH

DNA (deoxyribonucleic acid) & RNA (ribonucleic acid)

• Composed of monomers called nucleotides
• Nucleotides have 3 parts
• 5-carbon sugar: ribose (RNA) & deoxyribose (DNA)
• Phosphate group
• Nitrogenous base

DNA nucleotides contain nitrogenous bases

• A (adenine), T (thymine), C (cytosine), G (guanine)
• Sugar is deoxyribose

RNA nucleotides nitrogenous bases

• Also has A, C, G
• U (uracil) instead of T
• Sugar is ribose

DNA is double-stranded molecule

• 2 polynucleotide strands wrap around each other to form double helix
• 2 strands are associated because particular bases hydrogen bond to one another
• A with T, C with G

RNA is single stranded molecule

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TOUR OF THE CELL

cells

• Simplest collection of matter than can live
• Cell Theory: all living things are composed of cells & all cells come from other cells

• Surface area is important for carrying out cells’ functions (acquiring adequate nutrients & oxygen, etc.).
• Small cell has more surface area relative to its cell volume and is therefore more efficient.
• 2 types of cell structure: both have plasma membrane & 1 or more chromosomes & ribosomes
• Prokaryotic (bacteria & archaea): nucleoid and no true organelles
• Eukaryotic (all other forms of life): membrane-bound nucleus & organelles; life processes in eukaryotic cells depend on structure & organelles

4 life processes in eukaryotic cells that depend on structures/organelles

• Manufacturing: involves nucleus, ribosomes, endoplasmic reticulum, Golgi apparatus (manufacture of a protein, perhaps an enzyme, involves all of these)
• Breakdown of molecules: involves lysosomes, vacuoles, peroxisomes (breakdown of an internalized bacterium by a phagocytic cell would involve all of these)
• Energy processing: involves mitochondria in animal cells, and chloroplasts in plant cells (generation of energy-containing molecules, such as adenosine triphosphate, occurs in mitochondria and chloroplasts)
• Structural support, movement, communication: involve cytoskeleton, plasma membrane, cell walls (example of importance of these is the response and movement of phagocytic cells to an infected area)

Many similarities between animal & plant cells, but differences exist

• Plant cells don’t have lysosomes & centrioles
• Plant cells have rigid cell wall, chloroplasts, and a central vacuole not found in animal cells

Plasma membrane controls movement of molecules in/out of cell (selective permeability)

• Structure of membrane with its component molecules is responsible
  for this characteristic
• Membranes are made of lipids (mostly phospholipids), proteins,
  some carbohydrates
• Phospholipids form 2-layer sheet (phospholipid bilayer)
• Hydrophilic head faces outward (exposed to water)
• Hydrophobic tail points inward (shielded from water)
• Proteins are attached to the surface, some are embedded into phospholipid bilayer

Controls cell’s activities and is responsible for inheritance

• Chromatin: complex of proteins & DNA inside nucleus which makes up
  the cell’s chromosomes
• DNA is copied within nucleus prior to cell division
• Nuclear envelope is double membrane with pores that allow material to
  flow in/out of nucleus; it’s attached to network of cellular membranes
  called endoplasmic reticulum

Involved in cell’s protein synthesis

• Synthesized in nucleolus, which is found in nucleus
• Cells that must synthesize large amounts of protein have large number of ribosomes

Some ribosomes are free, others are bound

• Free ribosomes are suspended in cytoplasm
• Bound ribosomes are attached to endoplasmic reticulum associated with the nuclear envelope

Membranes within eukaryotic cell are physically connected and compose the endomembrane system

• Includes: nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuoles, plasma membrane
• Important function is synthesis, storage, export of molecules

Biosynthetic factories, 2 kinds of ER (differ in structure/function,
but are connected)

• Smooth ER (lacks attached ribosomes) is involved in diverse
  metabolic processes (ex. enzymes produced by smooth ER are
  involved in synthesis of lipids, oils, phospholipids, steroids)
• Rough ER (lines outer surface of membranes) makes proteins
  destined for secretion; once proteins are synthesized, they’re
  transported in vesicles to other parts of endomembrane system  

Functions in conjunction with the ER by modifying products of the ER

• Products travel in transport vesicles from ER to Golgi apparatus
• One side of GA functions as receiving dock for the product, other is shipping dock; products are modified as they go from
  one side of GA to the other and travel to vesicles to other sites

Membranous sac containing digestive enzymes

• Enzymes & membrane are produced by ER and transferred to the Golgi apparatus
  for processing
• The membrane serves to safely isolate these potent enzymes from rest of cell

One of several functions of lysosomes is to remove/recycle damaged parts of cell

• Damaged organelle is first enclosed in membrane vesicle
• Then a lysosome fuses with vesicle, dismantling its contents and breaking down damaged organelle

Membranous sacs that are found in variety of cells and possess assortment of functions

• Examples are central vacuole in plants with hydrolytic functions, pigment vacuoles in plants to provide
  color to flowers, contractile vacuoles in some protists to expel water from cell

Cellular respiration is accomplished in mitochondria of eukaryotic cells

• Conversion of chemical energy in foods to chemical energy in ATP

Mitochondria have 2 internal compartments separated by folded inner membrane (cristae)

• Intermembrane space & mitochondrial matrix (energy)

Photosynthesizing organelles of plants

• Photosynthesis: conversion of light energy to chemical energy in sugar molecules

Chloroplasts are partitioned into compartments

• Important parts: stroma, thylakoids, grana

Hypothesis of endosymbiosis proposes that mitochondria and chloroplasts were formerly small prokaryotes that began living within larger cells (symbiosis benefited both cell types)

• Mitochondria and chloroplasts have DNA and ribosomes
• Structure of DNA and ribosomes is very similar to that found in prokaryotic cells, and mitochondria and chloroplasts replicate much like prokaryotes

Network of protein fibers that functions in cell structural support and motility

• Scientists believe that motility and cellular regulation results when cytoskeleton
  interacts with proteins called motor proteins

Cytoskeleton is composed of 3 kinds of fibers

• Microfilaments (actin filaments) support the cell’s shape and are involved in motility
• Intermediate filaments reinforce cell shape and anchor organelles
• Microtubules (made of tubulin) shape the cell and act as tracks for motor protein

• Both are made of microtubules wrapped in an extension of plasma membrane
• Ring of 9 microtubule doublets surrounds central pair of microtubules
• Arrangement is called 9 + 2 pattern and is anchored in basal body with 9 microtubule triplets arranged in ring
• While some protists have flagella and cilia that are important in locomotion, some cells of multicellular organisms have them for different reasons
• Cells that sweep mucus out of lungs have cilia
• Animal sperm are flagellated

Cells synthesize and secrete the ECM that is essential to cell function

• ECM is composed of strong fibers of collagen, which holds cells
  together and protests plasma membrane
• ECM attaches through connecting proteins that bind to membrane
  proteins called integrins
• Integrins span plasma membrane and connect to microfilaments of the cytoskeleton

 

Adjacent cells communicate, interact, adhere through specialized junctions between them

• Tight junctions prevent leakage of extracellular fluid
  across layer of epithelial cells
• Anchoring junctions fasten cells together into sheets
• Gap junctions are channels that allow molecules to
  flow between cells

Plant cells have rigid cell wall

• It protects and provide skeletal support that helps keep plant upright against gravity
• Composed primarily of cellulose
• Plant cells have cell junctions called plasmodesmata that serve in communication between cells
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EUKARYOTIC CELL STRUCTURE & FUNCTIONS (SUMMARY)

Manufacturing

• Nucleus (central office): DNA/RNA synthesis; assembly of ribosomal subunits (in nucleoli)
• Ribosomes (assembly line): polypeptide (protein) synthesis
• Rough ER (conveyor belt): synthesis of membrane lipids & proteins, secretory proteins, hydrolytic enzymes; formation
  of transport vesicles
• Smooth ER (conveyor belt): lipid synthesis; detoxification in liver cells; calcium ion storage
• Golgi apparatus (packaging/shipping): modification/transport of macromolecules; formation of lysosomes & transport vesicles

• Lysosomes (animal cells/some protists) (collection center): digestion of ingested food/bacteria/cell’s damaged organelles/macromolecules for recycling
• Vacuoles (storage): digestion (like lysosomes); storage of chemicals; cell enlargement; water balance
• Peroxisomes (not part of endomembrane system): diverse metabolic processes, with breakdown of h2o2 by-product

• Mitochondria (generator): conversion of chemical energy of food to chemical energy of ATP
• Chloroplasts (plants/some protists): conversion of light energy to chemical energy of sugars

• Cytoskeleton (cilia, flagella, centrioles in animal cells) (bricks/steel): maintenance of cell shape; anchorage for organelles; movement of organelles within cells; cell movement; mechanical transmission of signals from exterior of cell to interior
• Extracellular matrix (animals): binding of cells in tissues; surface protection; regulation of cellular activities
• Cell junctions: communication between cells; binding of cells in tissues
• Cell walls (plants/fungi/some protists): maintenance of cell shape & skeletal support; surface protection; binding of cells in tissues
• Plasma membrane (door): controls movement of molecules in/out of cell (selective permeability)

 

 

 

 

 

 

 

 

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CELL MEMBRANE & TRANSPORT

vocabulary

• Semi-permeable: some molecules can move freely across while others can’t
• Kinetic energy: energy due to motion of an object
• Concentration Gradient: gradual difference in concentration of solutes in solution between two regions
• Active transport: molecules move against concentration gradient (from low to high concentration); requires energy (supplied through respiration using ATP); requires assistance of carrier protein
• Passive transport: molecules move along concentration gradient (from high to low concentration); no energy required; may/may not need assistance of membrane protein; driving force = kinetic energy (concentration gradient)
• Diffusion: movement of molecules/particles along concentration gradient (from high to low concentration); passive transport
• Simple diffusion: net movement of substance from area of high to low concentration (ex. upstairs begins to smell food being cooked downstairs)
• Facilitated diffusion: transport of substances across membrane (from area of high concentration to low) by means of carrier protein; no energy required; Example: charged molecules/ions dissolved in water can’t diffuse freely across membrane due to hydrophobic lipids, they require proteins forming transmembrane channels
• Osmosis: diffusion of water across semi-permeable membrane (from low to high concentration of dissolved substances)
• Solvent: liquid in which substances (solutes) are dissolved forming a solution
• Solute: substance dissolved in another substance
• Solution: homogenous mixture in which particles of one or more substances (solute) are distributed uniformly throughout another substance (solvent)
• Equilibrium: concentration of diffusing molecules are equal
• Tonicity: osmotic pressure/tension of a solution
• Hypotonic: solution has lower osmotic concentration than cell, so water will be drawn into the cell since water moves from low solute to high solute
• Hypertonic: solution has higher osmotic concentration than cell, water will be drawn out of cell 
• Isotonic: solution and cell have same osmotic concentration 
• Turgid (plant cells): cell no longer takes on water because of pressure of cell membrane against cell wall; occurs in hypotonic environment
• Flaccid (plant cells): limp; occurs is isotonic environment
• Plasmolysis (plant cells): cell membrane pulls away from cell wall: occurs in hypertonic environment
• Lysis (cells w/o cell walls): rupturing of cell membrane
• Crenation: loss of water from cell

Composed of phospholipids & proteins

• Described as fluid mosaic: surface appears mosaic because of the proteins embedded in the phospholipids & fluid because the proteins can drift about in the phospholipids
• Hydrophilic head of protein comes out top & bottom; Hydrophobic tail of protein embedded in phospholipid bilayer

Transport of substances

• Membrane is semi-permeable: some molecules can move freely across while others cant
• Substances move by diffusion, osmosis, facilitated diffusion, active transport

Process in which particles spread out evenly in an available space

• Particle move from area of high concentration to area of less concentration
• Particles diffuse down their concentration gradient
• Eventually they reach equilibrium, where concentration is same throughout

Movement of water across semi-permeable membrane

• Water moves from area of high water concentration to area of low water concentration
• Cytoplasm is a solution; Water is the solvent; Dissolved particles are the solute

Tonicity: ability of solution to cause a cell to gain/lose water, depends on concentration of solutes on both sides of the membrane

• Isotonic solution: concentration of a solutes is same on both sides; animal: normal; plant: flaccid
• Hypertonic solution: concentration of solutes is higher outside cell; water flows out of cell; animal: shriveled; plant: plasmolyzed
• Hypotonic solution: concentration of solutes higher inside cell; water flows into cell; animal: lysed; plant: turgid

 

Diffusion of molecule across membrane via a membrane protein

• Passive transport: does not require energy; substances move down concentration gradient
• Solute molecule uses transport protein to travel through membrane

Movement of substances against their concentration gradient

• Uses special membrane proteins
• Requires energy (uses ATP)
• Phosphorylation: A process involving the transfer of a phosphate group (catalyzed by enzymes) from a donor to a suitable acceptor
• Step 1: Solute binding (solute binds to transport protein)
• Step 2: Phosphorylation (ATP converts to ADP with phosphate attaching to transport protein)
• Step 3: Transport (protein changes shape)
• Step 4: Protein reversion (phosphate detaches)

Cell uses 2 mechanisms for moving large molecules across membranes, endocytosis & exocytosis

• In both cases, material to be transported is packaged within a vesicle that fuses with the membrane

Endocytosis: transport of solid matter or liquid into cell by means of coated vacuole or vesicle

• Phagocytosis: cellular eating; cell engulfs macromolecules/other cells/particles into its cytoplasm
• Pinocytosis: cellular drinking; cell takes fluid & dissolved solutes into small membranous vesicles
• Receptor-mediated phagocytosis: movement of specific molecules into cell by inward budding of membranous vesicles, which contain proteins with reception sites specific to the molecules being taken in.
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CELLULAR RESPIRATION & FERMENTATION 

vocabulary

• Metabolism: total of all chemical reactions in a cell
• Energy: ability to do work
• Catabolic reactions: breaks down complex molecules into smaller units, releasing energy
• ATP: Adenosine triphosphate; renewable source of energy that powers most forms of cellular work
• Substrate: particular molecule that an enzyme acts upon
• Metabolic pathway: series of chemical reactions that either break down or build up a complex molecule
• Aerobic respiration: requires O2; breakdown into CO2 & H2O; 36-38 ATP molecules; final electron acceptor = O2
• Anaerobic respiration: no O2 required; process of generation energy by oxidation of nutrients; final electron acceptor = nitrate, nitrite, sulfate, etc.
• Fermentation: partially degrades energy sources; pyruvate receives electrons from glucose (and is reduced) becoming waste, 2 ATP molecules per glucose molecule, waste depends on organism & fermentation enzymes
• Final electron acceptor: molecule that receives/accepts electrons from another molecule during redox reaction
• Redox reaction: chemical reaction involving both reduction & oxidation; results in changes in oxidation numbers of atoms included in the reaction
• Glycolysis: cellular degradation of glucose to yield ATP
• Krebs cycle: involves a cyclic series of enzymatic reactions by which pyruvate converted into Acetyl Coenzyme A is completely oxidized to CO2 and hydrogen is removed from the carbon molecules, transferring the hydrogen atoms and electrons to electron-carrier molecules (e.g. NADH and FADH2) as well as the metabolic energy to high energy bonds (e.g. ATP)
• Electron transfer phosphorylation: A metabolic pathway that generates ATP from ADP through phosphorylation that derives the energy from the oxidation of nutrients

Breathing & CR are closely related

• Breathing is necessary for exchange of CO2 produced during CR for atmospheric O2
• CR uses O2 to help harvest energy from glucose & produces CO2 in the process

Enzymes are necessary to oxidize glucose & other foods. NAD+…

• Is necessary coenzyme for respiration
• Carries electrons (e-) & protons (H+)
• Becomes reduced (NADH) when it accepts electrons,
  and oxidized when it gives them up
• FAD: same function as NAD+, just used in different places

Glucose is primary source of sugar for respiration/fermentation, though other biological molecules can be used to generate ATP

• Carbohydrates: disaccharides, polysaccharides
• Proteins: after conversion to amino acids
• Fats

Many metabolic pathways are involved in biosynthesis of biological molecules

• Cells must be able to biosynthesize molecules not present in foods to survive
• Often the cell will convert intermediate compounds of glycolysis & citric acid cycle to molecules not found in food
• Connection between catabolism & anabolism
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DNA REPLICATION & PROTEIN SYNTHESIS

Structure of DNA

The monomer unit of DNA/RNA is nucleotide containing…

• Nitrogenous base: A, G, T or C
• 2 types of bases: purines (A/G) are double ringed base structure; pyrimidines (T/C) are single ring structure
• Number of purines equals number of pyrimidines
• Chargaff’s rule: same number of A’s & T’s; same number of G’s & C’s
• 5-carbon sugar: deoxyribose
• Phosphate group (negatively charged)

Composed of 2 chains joined together by hydrogen bonding between bases, twisted into helical shape (double helix)

• Sugar-phosphate backbone on outside
• Nitrogenous bases are perpendicular to backbone in the interior
• Specific pairs of bases give helix uniform shape: A/T (2 hydrogen bonds), G/C (3 hydrogen bonds)

DNA

• Nucleotide structure: deoxyribose & A, G, T, C (Adenine & Guanine = Purines; Thymine & Cytosine = Pyrimidines)
• Molecule structure: double stranded
• Eukaryotes: in nucleus only

RNA

• Nucleotide structure: ribose & A, G, U, C
• Molecule structure: single stranded
• Eukaryotes: throughout cell

Replication follows a semi-conservative model

• Each new molecule has one old strand with one new strand
• Each strand of molecule is used as a pattern to produce a complementary strand, using rules of specific base pairing
• DNA can be faithfully copied because new DNA is built using existing DNA as template

Central dogma

• Genetic information flows from: DNA > RNA > Protein

Genotype

• Genetic makeup of organism
• Gene is a sequence of DNA that directs synthesis of specific protein
• DNA is transcribed into RNA (rewrite info from DNA to RNA)
• RNA is translated into protein (convert info from one type of molecule to another type)

Phenotype

• Characteristics of an organism
• Presence and action of proteins determine phenotype of organism

Connections between genes & proteins

• One gene-one enzyme hypothesis was based on studies of inherited metabolic diseases
• One gene-one protein hypothesis expands the relationship to proteins & other enzymes
• One gene-one polypeptide hypothesis recognizes that some proteins are composed of multiple polypeptides
• Inside nucleus { DNA (nucleic acid) > Transcription > RNA (nucleic acid) } Inside cytoplasm { Translation > Protein (amino acid)

Sequence of nucleotides in DNA provides a code for constructing a protein

• Code is made up of 3 letter words (codons), using letters A, T, C, G
• 64 codons are possible, but only 20 amino acids
• Some amino acids have more than one codon
• DNA strand > Transcription > RNA (3 letter codons) > Translation > Polypeptide (each codon = amino acid)

Characteristics of the genetic code

• Some amino acids have multiple codons, but each codon has only one amino acid
• Redundant: more than one codon for some amino acids
• Unambiguous: any codon for one amino acid does not code for any other amino acids
• Codons are adjacent to each other (no gaps) & nearly universal

Characteristics of codons

• 61 codons correspond to amino acids
• AUG codes for methionine and also signals START
• 3 STOP codons (do not code for amino acids): UAA, UAG, UGA

Role of RNA

• Messenger (mRNA) – carries genetic code to ribosomes
• Ribosomal (rRNA) – component of ribosomes
• Transfer (tRNA) – carries amino acids to ribosomes

Gene expression

• Transcription – make a mRNA copy of DNA
• Translation – make polypeptides based on codon sequence of mRNA

Process of transcription

• 2 DNA strands separate
• 1 strand used as pattern to produce RNA chain using specific base pairings (A in DNA = U is RNA)
• RNA polymerase builds mRNA from DNA template

Transfer RNA molecules math an amino acid to its corresponding mRNA codon

• Anticodon allows tRNA to bind to a specific mRNA codon (A with U, G with C)
• Structure allows it to convert one language to the other – working with rRNA responsible for translation

Translation occurs on surface of ribosomes

• Ribosomes have 2 subunits: small & large
• Each subunit composed of ribosomal RNAs & proteins
• Subunits come together during translation
• Ribosomes have binding sites for mRNA and tRNAs

Translation: initiation occurs in 2 steps

• mRNA binds to small ribosomal subunit, and the first tRNA binds to mRNA at start codon AUG
• Large ribosomal subunit joins small subunit, allowing ribosome to function

Elongation is the addition of amino acids to the polypeptide chain

• Codon recognition - next tRNA binds to the mRNA at the A site
• Peptide bond formation - joining of the new amino acid to the chain
• Translocation - tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site
• Elongation continues until the ribosome reaches a stop codon

Termination

• The completed polypeptide is released
• The ribosomal subunits separate
• mRNA is released and can be translated again

A change in the nucleotide sequence of DNA; ultimate source of genetic variations; mutations can be…

• Spontaneous: due to errors in DNA replication or recombination
• Induced by mutagens: high-energy radiation, chemicals

Types of mutations

• Base substitutions - replacement of one nucleotide with another
• Effect depends on whether there is an amino acid change that alters the function of the protein
• Deletions or insertions
• Alter the reading frame of the mRNA, so that nucleotides are grouped into different codons
• Lead to significant changes in amino acid sequence downstream of mutation
• Cause a nonfunctional polypeptide to be produced

Effects of substitution mutations

• Silent mutation: DNA mutation has NO effect on protein
• Missense mutation: single amino acid in mutant protein is altered
• Nonsense mutation: one codon changed to stop codon – non-functional protein produced
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CELL CYCLE, MITOSIS, MEIOSIS

cell cycle & chromosomes

• Interphase (duplicate cell contents):G1: growth, increase cytoplasm; S: chromosome duplication; G2: growth, prepare for division
• Mitotic phase (division): mitosis – nucleus division; cytokinesis – cytoplasm division
• Chromosomes: composed of chromatin (DNA + protein)
• S stage (DNA/chromosomes replicate): chromosome appears as 2 sister chromatids (joined at centromere), w/ identical DNA molecules
• Somatic cells have pairs of homologous chromosomes (1 from each parent); matched in length, centromere position, gene location

• Mitosis functions: asexual reproduction, growth, repair/replace cells
• Interphase: chromosome duplicate (S phase); nucleoli (site of ribosome assembly) visible
• Prophase: chromosome coil/compact; nucleoli disappear
• Prometaphase: spindle grows; nuclear envelope disappear
• Metaphase: spindle formed; chromosomes align cell equator
• Anaphase: sisters separate at centromeres;
  daughters towards opposite poles; cell elongates
• Telophase: nuclear envelope around chromosomes
  at each pole (establishing daughter nuclei);
  chromatin uncoil; nucleoli back; spindle gone
• Cytokinesis: cytoplasm divides; cleavage in animals,
  cell plate in plants

• Converts diploid (2 homologous sets of chromosomes)
  to haploid (1 set of chromosomes); occurs in sex organs;
  produces gametes
• Fertilization: union of egg/sperm; zygote diploid
  chromosome # (1 set from each parent)
• Meiosis I: homologous chromosomes separate (chro-
  mosome # reduced by ½); final cells haploid (2 of them)
• Prophase I: chromosomes coil/compact; homologous
  chromosomes pair (synapsis); each pair w/ 4 chromatids
  (tetrads); nonsister chromatids exchange genetic material
  by crossing over
• Metaphase I: tetrads align at cell equator
• Anaphase I: homologous pairs separate & move towards opposite poles
• Telophase I: duplicated chromosomes at poles; nuclear envelope forms around chromosomes (in some species);
  each nucleus has haploid number of chromosomes
• Meiosis II: sister chromatids separate (chromosome # remains the same); final cells haploid (4 of them)
• Prophase II: chromosomes coil/compact
• Metaphase II: duplicated chromosomes align at cell equator
• Anaphase II: sisters separate & chromosomes move to opposite poles
• Telophase II: chromosomes @ poles; nuclear envelope forms around each set of chromosomes;
  w/ cytokinesis 4 haploid cells produced

• Both involve one duplication of chromosomes
• Unique to meiosis: 2 divisions; pairings of homologous chromosomes; crossing over (exchange of genetic material)
• Mitosis outcome: 2 genetically identical cells with same chromosome # as original
• Meiosis outcome: 4 genetically different cells with half chromosome # as original

• Crossing over (prophase I): exchange of genetic material between homologous chromosomes; results in new combo of genes
• Nonsister chromatids join at a chiasma (attachment/crossing over site); Corresponding amounts of genetic material exchanged between maternal and paternal (nonsister) chromatids
• Independent Assortment (metaphase I): independent orientation of homologous chromosomes
• Each pair of chromosomes independently aligns at the cell equator; equal probability maternal or paternal chromosome facing
  a given pole
• The number of combinations for chromosomes packaged into gametes is 2n where n = haploid number of chromosomes
• Random fertilization: Combination of each unique sperm with each unique egg increases genetic variability
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PATTERNS OF INHERITANCE

law of segregation

• Allele pairs separate from each other during the production of gametes so that a sperm or egg carries only one allele for each gene
• Monohybrid cross tests single gene: parents – purple x white; F1 – all purple; F2 – ¾ purple, ¼ white
• Genotype refers to the alleles (alternative versions of genes) an individual carries for a specific gene
• For each characteristic (gene), organism gets 1 allele from each parent (2 total); can be homozygous (same) or heterozygous (different)
• If alleles differ, dominant allele determines appearance
• Phenotype: appearance/expression of trait; same phenotype may be determined by more than one genotype

• Homologous chromosomes: alleles of gene reside at same locus
• Homozygous individuals: same allele on both homologues; heterozygous: different allele on each homologue

• Each pair of alleles separates independently of the other pairs of alleles during gamete formation
• For genotype RrYy 4 gametes are possible: RY, Ry, rY, ry
• Dihybrid cross (9:3:3:1 ratio): parents – round yellow x wrinkled green; F1 – all round yellow; F2 – 9/16 round yellow, 3/16 round green. 3/16 wrinkled yellow, 1/16 wrinkled green

• Mating of unknown genotype x homozygous recessive; will show whether unknown genotype includes recessive allele; used to confirm true-breeding genotypes
• Genotype unknown because dominant phenotype can be either homozygous dominant or heterozygous recessive
• Dog example: Black (B_) x Chocolate (bb); black can be BB (leading to all black pups) or Bb (leading to 1 black & 1 chocolate pup)

• # of ways that event can occur out of the total possible outcomes
• Rule of multiplication (independent events): multiply probability of events that must occur together (rolling dice)
• If A & B are events: P (A & B) = P(A) x P(B)
• Rule of addition (mutually exclusive events): add probabilities of events that can happen in alternate ways
• If A & B are events: P(A or B) = P(A) + P(B)

• Shows inheritance of train in family through multiple generations
• Demonstrates dominant or recessive inheritance
• Can be used to deduce genotype of family members

• Dominant: freckles, widows peak, free earlobe; Recessive: no freckles, straight hairline,
  attached earlobe genetic disorders
• Recessive inheritance: 2 recessive alleles needed to show disease; heterozygous
  parents are carriers of disease allele; probability of inheritance increases w/ inbreeding;
  sickle cell = recessive
• Dominant inheritance: 1 allele needed to show disease; dominant lethal alleles usually eliminated in population

• Incomplete dominance: neither allele is dominant; expression of both alleles observed as intermediate phenotype in heterozygous person
• Multiple alleles: more than 2 alleles found in population; diploid individual can carry any 2 of them; ABO blood group has 3 alleles leading to 4 phenotypes (type A, B, AB, and O blood)
• Codominance: neither allele is dominant; expression of both observed as distinct phenotype in heterozygous person; type AB blood
• Pleiotropy: 1 gene influencing many characteristics; sickle-cell affects type of hemoglobin, shape of red blood cells, causes anemia & organ damage, related to getting malaria
• Polygenic inheritance: many genes influence 1 trait; skin color (at least 2 genes); height
• Phenotypic variations are influence by environment; skin color & sunlight exposure; disease susceptibility - hereditary/environmental

• Mendel’s Laws correlate with chromosome separation in meiosis; law of segregation depends on separation of homologous chromosomes in anaphase I; independent assortment depends on alternative orientations of chromosomes in metaphase I
• Linked genes: located close together on same chromosome; tend to be inherited together
• Bateson & Punnett example: parents – purple/long x red/round; F2 didn’t show 9:3:3:1 ratio, most
  had purple/long or red/round
• Linked alleles can be separated by crossing over; recombinant chromosomes are formed; geneticists
  measure genetic distance by recombination frequency

• X-linked: passed from mother to son or daughter & from father to daughter
• Y-linked: passed from father to son
• Reciprocal crosses show different results: white-eye female x red-eye male = red-eye females
  & white-eye males; red-eye female x white-eye male = red-eye female & red-eye males
• Males express X-linked disorders (hemophilia, color-blind) when recessive alleles are
  present in one copy
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