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UNIT I: CHEMISTRY OF LIFE

A. Elements

• All life forms made up of matter

• All matter made up of elements

• Elements

• Substances that cannot be broken down into smaller substances by chemical means

B. Essential Elements of Life

• 96% of the mass of all living things made up of 4 elements:

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

• Other elements (collectively 4% of biomass)

• Calcium (Ca)

• Phosphorus (P)

• Potassium (K)

• Sulfur (S)

• Sodium (Na)

• Chlorine (Cl)

• Magnesium (Mg)

• Trace elements

• IRon (Fe)

• Iodine (I)

• Copper (Cu)

C. Subatomic Particles

• Atom

• Smallest unit of an element

• Building blocks of physical world

• Subatomic PArticles

• Protons

• Packed with neutrons in nucleus

• Positively charged

• Most atoms have same amount of protons as electrons, making them electrically neutral

• Neutrons

• Packed with protons in nucleus

• No charge

• Isotopes

• Same element with different amount of neutrons in nucleus

• Vary in mass

• Radioactive isotopes decay spontaneously, giving off particles and energy

• Electrons

• Negatively charged

• Spin around nucleus

• Very small; effectively massless

• Electrons on an atom differ in their amounts of potential energy

• Electron’s state of potential energy is called its energy level, or electron shell

• Valence electrons are those in the outermost shell, or valence shell

• Chemical behavior of an atom is mostly determined by the distribution of electrons in electron shells

• Valence shell most important

• Elements with full valence shells are chemically inert 

• Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

• Atoms of different various elements differ in number of subatomic particles

• Atomic number=#protons in nucleus

• Mass Number= protons+neutrons

• Average of all isotopes

• Atomic mass+atom’s weighted average total mass

D. Compounds

• Compound occurs as result of 2 or more individual elements combining in a fixed ratio

• Different properties of individual elements

• Formed by chemical reaction        

• Bonds that hold compounds together

• Ionic bonds

• nonmetal+metal

• One or more electrons is transferred from one atom to another

• One atom loses electrons (becomes positively charged) while the other gains electrons (becomes negatively charged)

• Results from attraction of two oppositely charged ions

• Cation has a positive charge

• Anion has a negative charge

• Cation and anion form to create ionic bond

• Covalent bonds

• nonmetal+nonmetal

• Molecule consists of 2 or more atoms held together by covalent bonds

• Formed when electrons are shared between atoms

• In nonpolar covalent bond, electrons are shared equally

• In polar covalent bond, electrons are shared unequally

• In a single covalent bond, one pair of electrons is shared

• Double covalent when 2 pairs are shared, etc.

• Structural formula used to represent atoms and bonding

• Ex. H-H

• Molecular formula abbreviates structural formula

• Ex. H₂

• Electronegativity is an atom’s attraction for the atoms in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

• Hydrogen bonds

• Hydrogen atom covalently bonds to one electronegative ato is also attracted to another electronegative atom

• In living cells, hydrogen bonds are usually oxygen or other nitrogen atoms

• Van der Waals Interactions

• Weakest

• If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge

• Attractions between molecules that are close together as a result of these charges

• How geckos climb

E. Water: The Versatile Molecule

• In water, electrons are not shared equally in the bonds between hydrogen and oxygen

• Hydrogen atoms have a partial positive charge while oxygen atoms has a partial negative charge

• Water is polar

• Hydrogen bonds

• Weak attractions that result of water’s polarity

• Positive end of another polar molecule attracted to oxygen negative charge, and vice versa with the hydrogen end

• Hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• Weak Individually, but strong on a larger scale

• Lends watermany special properties

• Cohesion

• Tendency for water to stick to water

• Important during transpiration

• Water evaporates, pulls other water molecules with it, pulling all the way down from leaves to roots

• Adhesion

• Tendency of water to stick to other substances

• Cohesion + Adhesion = capillary action

• Allows water to flow up roots/trunks/branches of trees in thin vessels

• Surface tension

• Results from cohesion of water molecules

• Ex. water striders can sit on top of water without sinking

• High heat capacity

• Heat CApacity=ability of a substance to resist temperature changes

• Keeps ocean temperatures stable

• Allows organisms to keep constant body temperature, since most life forms are mostly made up of water

• Heat is absorbed  when hydrogen bonds break, released when hydrogen bonds form

• High heat of vaporization

• Heat a liquid must absorb for 1g to be converted to gas

• Evaporative cooling

• As a liquid evaporates, its remaining surface cools

• How sweat works to cool body down

• Expansion on freezing

• Lattice structure of ice causes water to expand on freezing

• Allows ice to float on top of lakes in winter

• Animal life can live beneath ice

• Versatility as a solvent

• Solution is a liquid that is a homogenous mix of substances

• Solvent is the dissolving agent of a solution

• Solute is the substance that is dissolved

• Aqueous solution is one where water is the solvent

• Polarity of water allows it to be a versatile solvent

• Can form hydrogen bonds easily

• Hydrophobic substances do not dissolve in water, but hydrophilic ones will

F. Acids and Bases

• Solution is acidic if it contains a lot of H⁺ 

• Solution is alkaline if it contains a lot of OH^-

• Measured on pH scale

• Logarithmic

• Numbered 1-14

• Acids 1-7 pH

• Bases 7-14 pH

• Buffers maintain stable pH

G. Organic Molecules

•  Organic compound contains Carbon

• Inorganic compound does not contain carbon

• Carbon often surrounded by hydrogen

• Carbon is a versatile atom

• Can bind with many elements

• Many “slots” to bind with elements

• 4 valence electrons

• Can form 4 covalent bonds

• Makes large, complex molecules possible

• In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape

• When 2 carbons are formed by a double bond, the atoms joined to the carbons are one the same plane as the carbons

• Electron configuration gives it covalent compatibility with other elements

• Hydrocarbons consist of only carbon and hydrogen

• Can undergo reactions that release a large amount of energy

• isomers are compounds with the same molecular formula but different structures/properties

• Usually only one isomer is biologically active

• Functional groups are the components of organic molecules that are most commonly involved in chemical reactions

• Number and arrangement of functional groups give each molecule its unique properties

• Most macromolecules are chains of building blocks called polymers. The individual building blocks of a polymer are called monomers

• Carbohydrates

• Contain carbon,  hydrogen, and oxygen in a 1:2:1 ratio

• Monosaccharides

• Most common are glucose and fructose

• Glucose

• Most abundant

• Part of food humans eat

• Made by plants during photosynthesis

• Broken down to release energy

• Fructose

• Common sugar in fruits

• Can be depicted as either straight or rings

• 6 carbon-sugars

• Formula: C₆H₁₂O₆

• Disaccharides

• 1 monosaccharide+1 monosaccharide=1 Disaccharide

• Formed by dehydration synthesis

• Aka condensation

• Hydrogen (-H) from one sugar combines with hydroxyl group (-OH) of another sugar molecule to create water as byproduct

• Bond is called glycosidic linkage

• Broken apart by hydrolysis

• Reverse of dehydration

• Water is used to break apart glycosidic linkage

• Polysaccharides

• Repeated units of monosaccharides

• Most common

• Starch

• Stores sugar in plants

• Made up of alpha-glucose molecules

• Cellulose

• Made up of ß-glucose molecules

• Chitin

• Structural molecule in walls of fungi/arthropod exoskeletons

• Used as surgical thread since it breaks down in body

• Glycogen

• Stores sugar in animals

• Proteins

• Amino acids=monomer of proteins

• 20 kinds of naturally occurring amino acids

• Contain:

• Carbon

• Hydrogen

• Oxygen

• Nitrogen

• 4 parts of an amino acid centered around a central carbon

• Amino group (-NH₂)

• Carboxyl group (-COOH)

• Hydrogen

• R group

• Aka side chain

• Interchangeable

• Vary in composition, polarity, charge, shape depending on specific side chain

• Polar R groups point outward, hydrophobic R groups point inward

• Polypeptides

• Amino acid + amino acid= dipeptide

• Formed by dehydration synthesis

• Bond is called a peptide bond

• Multiple amino acids= polypeptide

• Once a polypeptide chain twists and folds on itself, it forms a 3D structure called a protein

• Higher protein structure (4 levels total)

• Primary structure

• Linear sequence of amino acids

• Covalent (peptide) bonds

• Secondary structure

• Protein beings to twist--2 options

• Forms a coil (alpha-helix)

• Zigzagging pattern (known as beta-pleated sheets)

• Shape depends on R-group

• Formed by amino acids that interact with other amino acids closeby in the primary structure

• Hydrogen bonds between carbonyl and amino group

• Interactions between amino and carboxyl groups of protein backbone

• After secondary structure forms, formerly distant amino acids are now closeby--tertiary structure can form

• Tertiary structure

• Can be both alpha and beta helix/sheets within structure

• Covalent disulfide bridge often stabilizes structure

• Bonds between R groups

• Hydrogen bonds

• Ionic bonds

• Disulfide bridges

• Hydrophobic interactions

• Quaternary structure

• Several different polypeptide chains sometimes interact with each other

• Same bonds as above, but between peptide chains rather than between R groups

• Mistakes in structure can denature a protein

• Change of shape=change of function

• Ex. pH or heat can denature protein

• Protein folding can involve chaperone proteins (chaperonins)

• Help protein fold properly

• Make process more efficient

• Lipids

• Like carbs, consist of carbon, hydrogen and oxygen, but not in a fixed ratio

• Do not form polymers

• Little-no affinity for water

• Hydrophobic due to nonpolar covalent bonds of hydrocarbon

• Common examples:

• Triglycerides

• Glycerol molecule+3 fatty acid chains attached

• Fatty acid chain is mostly a long chain of carbons where each carbon is covered in hydrogen; One end of the chain has a carboxyl group (-COOH)

• Vary in length and #/location(s) of double bonds

• Glycerol is a 3-carbon alcohol with a hydroxyl group attached to each carbon

• Fats separate from water because water forms hydrogen bonds with itself while excluding the fats

• In order to be made, each of the carboxyl groups of the 3 fatty acids must react with one of the 3 hydroxyl groups of the glycerol molecule via dehydration synthesis

• bond=ester linkage

• Saturated fatty acid

• No double bond

• Carbon chain completely filled (“saturated”) with hydrogen

• Usually solid at room temp.

• Unsaturated fatty acid

• Double bond along carbon chain, causing a bend

• Bend allows triglyceride to become LESS dense, making it liquid at room temperature

• Polyunsaturated fatty acid has multiple double bonds within the fatty acid, causing many bends

• Phospholipids

• 2 fatty acid “tails” + 1 negatively charged phosphate “head”

  

• Tails are hydrophobic, while head is hydrophilic (negative charge on head attracts polar water)

• Amphipathic molecule (molecule that is both polar and nonpolar)

• In water, phospholipids self-assemble into a “bilayer arrangement”

• Hydrophobic tails face towards interior

• Found in cell membranes

• Steroids

• Cholesterol

• 4-ringed molecule dispersed throughout membrane

• Maintains membrane stability

• Increases membrane fluidity at lower temperatures by disrupting close packing

• Decreases fluidity at high temperatures through its constant movement

• Nucleic Acids

• Contain carbon, hydrogen, oxygen, nitrogen, and phosphorous

• Structure

• Nitrogenous base

• Pentose sugar

• Phosphate group

• Portion of nucleotide w/o phosphate group is called nucleoside

• Store, transmit, and help expres hereditary information

• monomer=nucleotides

• Amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Made up of DNA

• Deoxyribonucleic acid (DNA)

• sugar=deoxyribose

• Contains genetic/hereditary information

• Provides directions for its own replication

• Directs synthesis of messenger RNA (mRNA), and through mRNA, controls protein synthesis

• Occurs on ribosomes

• Ribonucleic acid (RNA)

• sugar=ribose

• Essential for protein synthesis

• 2 families of nitrogenous bases

• Pyrimidines

• Single 6-membered ring

• Ex.        

• Cytosine

• Thymine (only DNA

• Uracil (only RNA)

• Purines

• 6-membered ring fused to a 5-membered ring

• Ex.        

• Adenine

• Guanine

• Nucleotide Polymers

• Nucleotide polymers linked together to build a polynucleotide

• Adjacent nucleotides are joined by covalent bonds that form between the -OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next

• Links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

• RNA molecules usually exist as single polypeptide chains

• DNA molecules have 2 polynucleotides spiraling around an imaginary axis, forming a double helix

• Two backbones run in opposite 5’→3’ directions from each other (antiparallel)

• One DNA molecule contains many genes

• Nitrogenous bases pair up and form hydrogen bonds

• Adenine-Thymine

• Guanine-Cytosine

• Complementary base pairing

• In RNA, thymine is replaced by uracil, so A and U pair

F. Origins of the Earth

• Alexander Oparin and J. B. S. Haldane proposed that the primitive atmosphere contained the following gases:

• Methane (CH₄)

• Ammonia (NH₃)

• Hydrogen (H₂)

• Water (H₂O)

• No free oxygen (O₂)

• No oxidation/reduction

• Rocks do not release oxygen through weathering

• Gases collided, producing chemical reactions that eventually led to the organic molecules we know today

• Substantial support until 1953

• 1953, Stanley Miller and Harold Urey simulated the conditions of primitive Earth in a lab,

• Put theoried gases into flask, struck them with electrical charges to simulate lightning, and organic compounds similar to amino acids appeared

• Current theory of the origin of life suggests 4 main stages

• 1. Formation of amino acids

• 2. Monomers form polymers

• 3. Enclosure of small organic molecules into larger ones

• 4. Self-replicating molecules that can direct synthesis of other organic substances

• Energy sources for early organic synthesis

• Lightning

• Volcanic eruptions

• RNA world hypothesis

• Original life-forms were simple molecules of RNA

• RNA not restricted to double helix

• RNA capable of replicating and passing genes

• Complex organic compounds must have formed via dehydration synthesis

• Organic compounds then used as food by cells

• Simple cells evolved into complex cells

• Heterotrophs

• living organisms that rely on organic molecules for food

• Aka consumers

• Autotrophs

• Organisms that make their own food

• Most commonly via photosynthesis

• Aka producers

UNIT II: Cells

A. Living Things

• All living things are composed of cells

• According to cell theory, the cell is life’s basic unit of structure and function

• Cell is the smallest unit of living material that can carry out all the activities necessary for life

• Why not be a GIANT CELL?

• Specialization

• Must maintain high surface area:volume ratio to allow cellular exchanges across the membrane!

B. Types of Cells and Organelles

• Invention of electron microscopes allowed scientists to figure out the exact functions of cells

• Prokaryotic cells

• Only in domains Bacteria and Archaea

• Smaller

• Simpler

• Circular DNA

• In nucleoid region

• NO NUCLEUS

• Cell wall

• Made up of peptidoglycans that surround a lipid layer called the plasma membrane

• Filled with semi-fluid cytosol

• Have ribosomes

• Can have flagella

• Long projections used for motility

• May have a thick capsule outside their cell wall to give them extra protection

• No membrane-bound organelles

• Eukaryotic cells

• More complex

• Organized into smaller structures called organelles

• DNA in nucleus bounded by a membranous nuclear envelope

• Cytoplasm between plasma membrane and nucleus

C. Organelles

• Each organelle has its own special task

• Plasma Membrane

• Outer envelope

• Complex

• Phospholipid bilayer

• Encloses vacuole

• Regulates movement in/out of cell

• Flexible due to weak bonds holding it together

• Higher fluidity when more phospholipids have double bonds (causing a bend in the tail) since the molecules aren’t as packed

• Semipermeable

• Only small hydrophobic molecules can pass through unaided

• Anything large/hydrophilic must pass through active/passive transport

• Water can’t move through easily due to its polarity

• Fluid-mosaic model

• Peripheral proteins are loosely associated with the lipid bilayer

• Located on inner/outer surface of membrane

• Integral proteins are firmly bound into the plasma membrane

• Amphipathic to allow anchoring

• Some extend all the way through the membrane

• Membrane peppered with different proteins/carb chains

• Adhesion proteins

• membrane proteins form junctions between adjacent cells

• Receptor proteins

• Serve as docking sites for arrivals at the cell

• Ex. hormones

• Transport proteins

• Form pumps that use ATP to actively transport solutes across the membrane

• Hydrophilic channel that certain molecules/ions can use as a tunnel

• Specific for substance it moves

• Carrier Proteins

• Bind to molecules and change shape to shuttle them across the membrane

• Channel proteins

• Selectively allow the passage of ions/molecules

• Cell surface marker

• Exposed on cellular surface

• Play a role in cell recognition/adhesion

• Ex. glycoproteins

• Carbohydrate side chains

• Attached to surface of some proteins

• Found only on outer surface

• Cholesterol

• Maintain fluidity (see pg. 11)

• Unsaturated fats also lend membrane fluidity by increasing space between phospholipids due to bend

• Nucleus

• Largest organelle of cell

• Directs what  goes on in cell

• Responsible for cell’s ability to reproduce

• Home of hereditary information (DNA)

• DN organized into large structures called chromosomes

• Most visible structure of nucleus id nucleolus, which is where rRNA is made and ribosomes are assembled

• Ribosomes

• Sites of protein synthesis

• Manufacture all proteins required/secreted by the cell

• Consists of RNA and other proteins

• Bind messenger RNA and transfer RNA to synthesize proteins

• Round structures consisting of 2 subunits:te large subunit and the small subunit

• Composed of RNA and proteins

• Can either be free floating or attached to the endoplasmic reticulum (ER)

• Endoplasmic Reticulum (ER)

• Continuous channel that extends into many regions of the cytoplasm

• Lipid proteins synthesis/transport

• Rough ER

• Attached to nucleus

• Studded with ribosomes

• Proteins generated here are trafficked to/across plasma membrane, or used to  build Golgi bodies, lysosomes, or the ER.

• Smooth ER

• Lacks ribosomes

• Makes:

• Lipids

• Hormones

• Steroids

• Breaks down toxic chemicals

• Golgi Bodies

• Process proteins

• Once the ribosomes on the rough ER have completed synthesizing proteins, the Golgi bodies modify, process, and sort the products

• packaging/distribution centers for materials destined to be sent out of cell

• Package final products into vesicles

• Carry products to plasma membrane

• Involved in production of lysosomes

• Mitochondria

• “PoWeRhOUsE oF ThE cElL”

• Responsible for converting the energy from organic molecules into useful energy for the cell

• Energy molecule in the cell is adenosine triphosphate (ATP)

• Unique oblong shape and characteristic double membrane consisting of an inner portion and an outer portion

• Inner membrane forms folds called cristae

• Separates innermost area (called the matrix) from the intermembrane space

• Outer membrane separates the intermembrane space from the cytoplasm

• Production of ATP done on the cristae

• Lysosomes

• Tiny sacs that carry digestive enzymes

• Break down old/worn out organelles/debris/large ingested particles

• Cells clean-up crew

• Keep cytoplasm clear of unnecessary flotsam

• Sometimes contain hydrolytic enzymes that function only at an acidic pH, which is enclosed inside the lumen of the lysosome

• Centrioles

• Small. Paired, cylindrical structured often found within microtubule organizing centers (MTOCs)

• Most active during cellular division

• When  cell is ready to divide, centrioles produce microtubules, which pull the replicated chromosomes apart and move them to opposite ends of the cell

• Common in animal cells but not in plants

• Vacuoles

• Latin for “empty cavity”

• Fluid-filled sacs that store water/food/wastes/salts/pigments for later use/removal

• Larger in plant cells

• Peroxisomes

• Breakdown of long fatty acids through beta-oxidation

• Cytoskeleton

• Network of fibers that maintain cell shape

• Most important:

• Microtubules

•  Made up of protein tubulin

• Participate in cellular division/movement

• Integral part of centrioles/cilia/flagella

• Microfilaments

• Important for movement

• Composed of protein actin

• Actin monomers joined together and broken apart as needed to allow microfilaments to grow and shrink

• Assist during cytokinesis/muscle contraction/formation of pseudopodia extension during cell movement

• Cilia and Flagella

• Allow motion in single-celled organisms

• In respiratory tract, cilia sweep constantly back and forth to keep out pathogens/dust

• Every sperm cell has flagellum, enabling it to swim through the female reproductive organs to fertilize the waiting ovum

• Extracellular matrix

• Molecules secreted by cell

• Mostly glycoproteins or other carb/containing molecules, esp. collagen

• Provides structure/biochemical support

• Plant Cells vs. Animal Cells

• Plant have plasmodesmata

• Connections between plant cells that allow communication amongst them

• Plant cells have cell wall

• Rigid layer of cellulose

• Outside of plasma membrane

• Provides support for cell

• Prevents lysis        

• Plant cells have chloroplasts

• Contain chlorophyll, making them green

• Involved in photosynthesis

• In plants, most of cytoplasm taken up by enlarged vacuole that crowds out other organelles

• Contains cell sap in mature plants

• Full vacuole means plant is not dehydrated

• Plants do not contain centrioles

D. Transport Across the Plasma Membrane

• Ability to travel across the plasma membrane depends on (1) semipermeability of the plasma membrane and (2) the size and charge of the molecules that want o get through

• Lipid-soluble substances can cross the membrane easily due to the phospholipid tails of the membrane

• “Like dissolves like”

• Facilitated transport

• Substances must pass through a specific channel protein instead of directly through the membrane due to its hydrophilic/charge/etc.

• Depends on a number of proteins that act as tunnels through the membrane

• Ex.:Aquaporins are water specific-channels

• Simple transport: Simple and facilitated diffusion

• Diffusion

• A substance will move down its concentration gradient

• Simple Diffusion

• If the diffusion molecule is hydrophobic, the nonpolar molecule can drift through the membrane unaided

• Facilitated Diffusion

• Diffusion of a substance requires the help of a channel protein

• Called passive transport when that substance is moving down its concentration gradient

• No energy required

• At Dynamic equilibrium, as many molecules cross the membrane in one direction as the other

• Osmosis

• Process where water is diffused

• Water always moves from areas where it is more concentrated to where it is less concentrate

• Water moves to dilute solid particles

• In both diffusion and osmosis, the final result is that the solute concentrations are the same on both sides of the membrane. The only difference is that in diffusion that membrane is usually permeable to the solute, and in osmosis it is not

• Tonicity describes osmotic gradients

• A Isotonic solution, the solute concentration is the same inside as outside

• No net water movement

• A hypertonic solution has more total dissolved solutes than the cell

• Cell loses water

• A hypotonic solution has less total dissolved solutes than the cell

• Cell gains water

• Cell walls help maintain water balance

• A plant cell in a hypotonic solution swells until the wall opposes uptake, becoming turgid/firm; while an animal cell in a hypotonic solution will lyse/burst since their membrane are not as string

• Plant cells experience lethal plasmolysis in a hypertonic environment

• Plant cells become flaccid in an isotonic environment

• Water potential(Ψ) is the measure of potential energy in water and describes the eagerness of water to flow from an area of high water potential to an area of low water potential

• Affected by pressure potential Ψ_p and solute potential Ψ_s

• Equations on AP sheet

• ACtive Transport

• Allows a substance to move against its concentration gradient by using energy to help it  along

• Performed by specific proteins along membrane

• Ion Pumps

• Membrane potential=voltage difference across a membrane

• Voltage created by difference in the distribution of positive/negative ions across a membrane

• 2 combined forces (electrochemical gradient) drive diffusion of ions across a membrane

• Electrogenic pump is a protein that generates voltage across a membrane

• Ex.: Sodium-potassium pump

• Pushes out 3 Na⁺ and brings in two K⁺

• Depends on ATP

• Cotransport occurs when active transport of a solute indirectly drives transport of other solutes

• PRimary active transport directly uses ATP to transport something

• Secondary active transport occurs when a substance is moved across its concentration gradient by using the energy captured from the movement of another substance passively moving along its concentration gradient

• Endocytosis

• When the particles that want to enter a cell are too large to be transported by a channel protein, the cell uses a portion of the membrane to engulf that substance

• Membrane forms a pocket, pinches in, and eventually forms a vacuole/vesicle

• 3 types

• Pinocytosis

• Ingests liquids

• PHagocytosis

• Ingests solids

• receptor -mediated endocytosis

• Cell surface receptors work with endocytic pits that are lined with a protein called clathrin

• When a ligand binds to one of these receptors, it is brought into the cell by invagination (“folding in”) of the cell membrane

• Vesicle forms around incoming ligand and carries it to cell’s interior

• Exocytosis

• Large particles transported out of cell ex. Waste, specific secretion products (like hormones)

• `fusion of a vesicle with plasma membrane

• Reverse endocytosis

• Bulk Flow

• One-way movement of fluids brought about by pressure

• Ex. movement of blood through a blood vessel

• Dialysis

• Diffusion of solutes across a selectively permeable membrane

• Cell Junctions

• Result of cells in close contact with each other

• Allow neighboring cells to form strong communication connections/nutrient flow

• Fastens cells to each other

• Provide contact between neighboring cells or cell and extracellular matrix

• 3 types

• Desmosomes

• Hold adjacent animal cells tightly together

• Pair of discs associated with the plasma membrane of adjacent cells+intermediate filaments within cells that are also attached to discs

• Gap junctions

• Protein complexes that form channels in membranes and allow communication between cytoplasm of adjacent animal cells for the transfer of small molecules/ions

• Tight junctions

• Tight connections between membranes of adjacent animal cells

• So tight that there is no space in between cells

• Seal off body cavities

• Prevent leaks

• Cell Communication

• Involves transduction of stimulatory/inhibitory signals from other cells/organisms/environment

• Quorum sensing is when unicellular organisms make their numbers known to other members of their species

• Taxis is the movement of an organism in response to a stimulus

• positive=movement towards stimulus

• negative=movement away from stimulus

• Chemotaxis is movement in response to a certain chemical

• Ex.:

• Bacterial can control flagella rotation to avoid repellents/find food

• Used by neutrophils to respond to an infection

• Signalling can be short range (nearby cells) or long range (throughout organism)

• Done by cell junctions/ligands

• Cell’s response to an extracellular signal sometimes called the “output signal”

• Signal transduction is the process by which an external signal is transmitted to the inside of a cell

• 1. RECEPTION

• A signalling molecule binding to a specific receptor

• Intracellular or extracellular

• Even the same signal can have different effects in cells with different proteins and pathways

• Pathway branching and “cross-talk” further help the cell coordinate incoming signals

• 2. TRANSDUCTION

• Activation of a signal transduction pathway

• AMPLIFICATION

• Phosphorylation cascade

• one enzyme (kinase) phosphorylates another, causing a chain reaction leading to the phosphorylation of thousands of proteins

• At each step, the number of activated products is much greater than in the preceding step

• Scaffolding proteins are large relay proteins to which other relay proteins are attached; increase signal transduction efficiency by grouping together different proteins involved in the same pathway

• RESPONSE

• Affect gene expression

• Change enzymatic activity

• Apoptosis

• Programmed cell suicide

• Components of cell chopped up and packaged into vesicles which are digested by scavenger cells

• Mostly done by caspases (main proteases (enzymes that cut up proteins) that carry out apoptosis)

• Can be triggered by extracellular ligand, DNA damage, or proteins misfolding in ER

• Apoptosis evolved early in animal evolution

• Essential for development and maintenance if all mammals

• 3 classes of membrane receptors

• Ligand-gated ion channels

• Ion channel is opened upon binding to a specific ligand

• Catalytic receptors

• Aka enzyme-linked receptors

• Enzymatic active site on the cytoplasmic side of the membrane

• Initiated by ligand binding on the extracellular surface

• G-protein coupled receptor

• Largest family of cell-surface receptors

• A GPCR is a plasma membrane receptor that works with the help of a G protein

• G protein acts as an on/off switch

• If GDP is bound to the G protein, the G protein is inactive        

• Signal stopped by hydrolyzing GTP

• Receptor Tyrosine Kinases

• Membrane receptors that attach phosphates to tyrosines

• Can trigger multiple signal transduction pathways at once

• Abnormal functions of RTKs associated with many types of cancer

• Intracellular receptors

• Small or hydrophobic messengers can readily cross the membrane and activate receptors in cytoplasm

• Ex. steroid/thyroid hormones of mammals

• Secondary messengers diffuse easily into cell

• Can activaate a phosphorylation cascade

• Can act as a transcription factor, turning on many genes

• Signal transduction in eukaryotic cells usually involves many cells and complex regulation

• Bacterial cells use a much simpler, 2-component regulatory system in transduction pathways

• In plants

• No nervous system, but can product several proteins found within them ex. Neurotransmitter receptors

• Can generate electrical signals in response to environmental stimuli

• Some plants can also use chemicals to communicate with nearby plants

UNIT III: CELLULAR ENERGETICS

A.Bioenergetics

• Glucose, starch, and fat all energy-rich, but the bonds must be broken in order for the energy to be released

• First Law of Thermodynamics: Energy cannot be created or destroyed. The sum of energy in the universe is constant.

• Second Law of Thermodynamics: Energy transfer leads to less and less organization. The universe tends towards entropy

• Types of Reactions

• Exergonic

• Products have less energy than the reactants

• Energy is given off during the reaction

• Ex. oxidation of molecules in mitochondria

• Endergonic

• Require an input of energy

• Products have more energy than reactants

• Ex. plants’ use of CO₂ and water to form sugars

B. Gibbs Free Energy

• ΔG=ΔH-TΔS

• T=temperature

• H=enthalpy (measure of energy in a thermodynamic system)

• S=entropy

• Change in the Gibbs free energy of a reaction determines whether the reaction in favorable (spontaneous, negative) or unfavorable (nonspontaneous, positive)

• Used to figure out if, without adding energy, the reactants will stay as they re or be converted to products

• Spontaneous Reactions

• Occur without a net addition of energy

• ΔG<0=exergonic

• ΔG>0=endergonic

• Only occur if energy is added

• Activation Energy

• Even though exergonic reactions release energy, the reaction still needs energy to start off with

• Reactants must first go into transition state before turning into products

• Activation energy is the energy needed to achieve the transition state

• Bonds must be broken before new bonds can form

C. Enzymes

• Biological catalysts that speed up reactions

• Accomplished by lowering activation energy and helping transition state form

• Lowers activation energy by:

• Orienting substrate correctly

• Straining substrate bonds

• Providing favorable microenvironment

• Bonding to substrate

• Do NOT change the energy of the starting point or the ending point of the reaction. Only lower activation energy

• Enzyme Specificity

• Each enzyme catalyzes only one kind of reactions

• Enzyme are usually named after the molecules they target

• Replace suffix of substrate with -ase

• Ex. maltose catalyzed by maltase

• Substrates are the targeted molecules (reactant)

• Enzyme-Substrate Complex

• Enzyme brings about transition state by helping the substrate(s) get into position

• Accomplished through active site

• Once the reaction has occurred, the enzyme is released from the complex and restored to its original state

• Now the enzyme is free react with other substrates again

• Induced fit

• Enzyme slightly changes shape to accommodate the shape of substrates

• Sometimes certain factors are necessary for this process

• Cofactors sometimes aid induced fit and also help catalyze reactions

• Nonprotein helpers of enzymes

• Ex. vitamins

• Factors affecting reaction rates

• Temperature

• Although the rate of reaction increases with temperature, it only does so up to a point, because too much heat can denature an enzyme

• Q₁₀

• Measure of sensitivity of a physiological process of enzymatic reaction rate

• Temp must be celsius or kelvin

• Same unit for T₁ and T₂

• Two reaction rates (k₁ and k₂) must have same unit

• Reaction rates with Q₁₀=1 are temperature independent

• pH

• Most enzyme’s ideal pH is 7

• Enzyme Regulation

• Cell can control enzymatic reactions by regulating the conditions that change the shape of the enzyme

• Can be turned off/on by things that bind to them

• Some bind at active site

• Some bin at allosteric sites (non-active sites)

• Competitive inhibition

• If a substance has the exact complementary shape to the active site, it can compete with the substrate and block it from getting into the active site

• If there is enough substrate available, it will out-compete the inhibitor and the reaction will occur

• As substrate is used up, inhibitor out-competes the substrate and less reaction will occur

• Allosteric inhibitors/Non Competitive inhibition

• Binds to an allosteric site

• Distorts shape of enzyme so it cannot function until the inhibitor is removed

• Substrate can still bind if active site is intact, but the enzyme will not be able to catalyze the reaction

• Activators can also be used to stabilize the enzyme’s active state

• Inhibitors stabilize the inactive state

• Enzymes can also be controlled by negative feedback mechanisms

• Product of reaction the enzyme is helping is also an allosteric inhibitor

• Prevents a cell from wasting resources by synthesizing more of a product than is needed

D. Reaction Coupling

• ATP consists of a molecule of adenosine bonded to 3 phosphates

• Carries enormous amount of energy within phosphate bonds

• When a cell needs energy, it splits off the 3rd phosphate, forming adenosine diphosphate (ADP) and one loose phosphate (P_i) in the process

• ATP→ADP + P_i  + energy

• ATP is relatively neat and easy to form

• Sources

• Cellular respiration

• Sugar turned into ATP

• In plants, sugar is made by photosynthesis

• In animals, sugar is taken from food consumed

E. Photosynthesis

• 6CO₂ + H₂O → C₆H₁₂O₆ + 6O₂

• Chloroplast structure

• Stroma=inner fluid-filled region

• grana=structures inside stroma that look like stacks of coins

• thylakoids=”coins” of grana

• Contain chlorophyll, a light-absorbing pigment that drives photosynthesis

• Chlorophyll a

• Chlorophyll b

• Carotenoids

• Pigments gather light, but are not able to excite electrons, only one molecule in the reaction center can

• Contains enzymes involved in photosynthesis

• 2 reaction centers:

• Photosystem I (PS I)

• p700

• Photosystem II (PS II)

• P680

• Both comprised of a Light harvesting complex, where a photon of light is passed like a wave between pigments and a Reaction center complex, which contains chlorophyll-a and uses light energy to “boost” and electrons and pass onto primary electron acceptor

• Absorption spectrum measures how well a certain pigment absorbs electromagnetic radiation

• Opposite of emission spectrum

• Chlorophyll a and b absorb blue and red light but reflect green (reason why plants are usually green)

• Carotenoids absorb light at blue-green end, and reflect red light

• Light reactions

• When a leaf captures sunlight, the energy is sent to p680 of photosystem II

• Sidenote: it may seem weird that the light reaction starts off in PSII and not PS I but its only called PS I because it was discovered first

• Activated electrons trapped by p680 and passed down to molecule called the primary acceptor, and then they are passed down to carriers in the electron transport chain

• Photolysis

• To replenish electrons in the thylakoid, water is split into O^-, 2H⁺, and electrons

• Water is split again into hydrogen ions (used for ETC) and Oxygen (released)

• As the energized electrons from PSII travel down the ETC, they pump H⁺ into the thylakoid lumen

• Proton gradient is created

• As hydrogen ions move back into the stroma through ATP synthase along their concentration gradient, ATP is created

• After the electrons leave PS II, they enter PSI, where they are passed through a second ETC  until they reach the final electron acceptor NADP⁺ to make NADPH

Dark cycle on sketch notes below

F. Cellular Respiration

• C₆H₁₂O₆ + 6O₂ ⟶ 6CO₂ + 6H₂O + ATP

• Aerobic respiration: ATP made in the presence of oxygen

• Anaerobic respiration: ATP made without presence of oxygen

• 1. GLYCOLYSIS

• Glucose is split

• Glucose 6-carbon; when it is split it makes 2 3-carbon pyruvates

• Creates 2 ATP (net)

• NADH created from the transfer of electrons to NAD⁺

• Occurs in cytoplasm

• Glucose + 2 ATP + 2 NADh ⟶ 2 Pyruvate + 4 ATP + 2ND

• 2. FORMATION OF ACETYL CoA

• 2Pyruvate + 2 Coenzyme A + 2 NAD⁺ ⟶ 2 Acetyl-CoA + 2CO² + 2 NADH

• Extra carbons leave cell as CO₂

• 3. CITRIC ACID CYCLE

• Aka Krebs cycle

• Each acetyl coa will enter Krebs cycle on at a time, and all carbons will be turned into CO₂ eventually

• Acetyl CoA combines with oxaloacetate (4-carbon) to create citric acid

• Active transport into mitochondria via cotransport with oxygen

• citric eventually gets turned back into oxaloacetate

• 3 types of energy produced:

• 1ATP

• 3 NADH

• 1 FADH₂

• Atthis point there are 4 ATP, 10 NADH, and 2 FADH₂ total

• 4. OXIDATIVE PHOSPHORYLATION

• As electrons are removed from a molecule of glucose, they carry with them as much of the energy that was originally stored within their bonds

• These electrons are then transferred to readied carrier molecules--NADH and FADH₂

• Electron carriers shuttle electrons down to electron transport chain, and the resulting NAD⁺ and FADH can be recycled to be used again

• Hydrogen atoms are split

• H₂ ⟶ 2H⁺ + 2e^-

• High-energy electrons are passed down a series of protein carrier molecules that are embedded in the cristae

• Some proteins include NADH dehydrogenase and cytochrome C

• The electrons travel down the electron transport chain until they reach the final acceptor, oxygen

• Oxygen pulls the electrons through the chain due to its electronegativity and then combines with them and hydrogen to create water

• Allows For a gradual release of energy rather than a sudden, explosive one

• Chemiosmosis

• The energy released from the ETC is used to pump hydrogen ions across the inner mitochondrial membrane from the matrix into the intermembrane space

• Creates pH/proton gradient

• Potential energy created from gradient is responsible for the production of ATP

• Flow back in through ATP synthase and this movement provides the energy necessary to produce ATP

• ADP + P_i ⟶ ATP

G, Fermentation

• In anaerobic environments, cellular respiration doesn’t work

• No ETC, so electron carriers are useless

• No Acetyl CoA or Citric Acid cycle

• Only glycolysis can occur

• Glycolysis produces 2 pyruvate and 2 NADH

• In order to recycle NADH, pyruvate takes its electrons, creating lactic acid in muscles or ethanol in yeast

• Both products are unfortunately toxic

• ATTP created through substrate-level phosphorylation

• Common in bacteria

• In some, an ETC may exist, but SO₄ is the electron acceptor instead of o₂, creating H₂SO₄ as a byproduct

UNIT IV: MOLECULAR BIOLOGY

A.Molecular Structure of DNA

• Made up of repeated units of nucleotides

• Each nucleotide has:

• 5-carbon sugar

• Pentagon shaped

• Called deoxyribose

• Linked to phosphate and nitrogenous base

• Phosphate

• Nitrogenous base

• Adenine

• Purine (double-ringed)

• Guanine

• Purine

• Cytosine

• Pyrimidine (single-ringed)

• Thymine

• Pyrimidine

• Purines always pair up with pyrimidines to keep DNA width consistent

• Nucleotides linked together by phosphodiester bonds that make up the sugar-phosphate backbone

• Double helix structure discovered by scientists Watson, Crick, and FRanklin

• Nobel prize earned for discovery

• Franklin used X-Ray crystallography in its discovery

• Base pairing (Chargaff’s Rules)

• Each base can only bond with a specific complementary base

• A-T

• C-G

• Specific rations of each nucleotides in the same species

• Complementary strands

• Strands are antiparallel

• Run in opposite directions

• 5’  and 3’ end named after carbons that end them

• 5’ has phosphate group

• 3’ has hydroxyl group

•  Strands linked by hydrogen bonds

B. GEnome Structure

• Genetic code is the sequence of the base pairs

• Gene codes for a specific protein

• Prokaryotes: single DNA molecule

• Eukaryotes: multiple DNA molecules

• An species entire DNA sequence is its genome

• Chromosome is each separate chunk of DNA

• Prokaryotes have one circular chromosome, and eukaryotes have linear chromosomes

• chromosomes wrapped around proteins called histones, and histones are bunched in groups called a nucleosome

• How Tightly DNA is packaged depend on the section of DNA and what is going on in the cell at the time

• Euchromatin is extremely loose genetic material

• Heterochromatic is extremely tight genetic material with inactive genes

C. DNA Replication

• First step is to unwind the double helix by breaking the hydrogen bonds

• Accomplished by an enzyme helicase

• Single stranded Binding PRotein hold the strands apart

• Origin of replication=place where replication process begins; short stretch of DNA with specific nucleotide sequence

• Exposed DNA now forms a y-shaped replication fork

• DNA replication begins at specific sites called origins of replication

• Topoisomerase cuts and rejoins the helix to prevent tangling and relieve tension

• DNA polymerase III adds nucleotides to freshly built strand

• Can only add nucleotides to the 3’ end

• RNA primase adds a short strand of RNA nucleotides called an RNA primer

• Primase synthesizes RNA primer

• After replication, the DNA Polymerase I removes the RNA primer and replaces it with DNA

• Leading strand

• Synthesized continuously

• 5’ to 3’

• Replicated towards fork

• Lagging strand 

• Made in pieces called Okazaki fragments

• 3’ to 5’

• Replicated Away from fork

• Must be made in pieces since nucleotides can only added to 3’ end

• Fragments linked together by DNA ligase to produce a continuous strand

• DNA proofreading and repair

• DNA polymerase in charge of repair synthesis

• Nuclease removes damage

• Ligase seals newly repaired strands

• Repair enzymes detect damage

• Replicates semiconservatively because each new molecule is comprised of ½ of the original strand

• Semiconservative model proved by Meselson and Stahl’s experiments

• Created “heavy” template DNA using N15, measured weights of replicated DNA by looking at the layers that formed, semiconservative model was the only one that fit

• A few bases at very end cannot be replicated because the DNA polymerase needs to bind

• Every time replication occurs the chromosome loses a few base pairs

• Genome has compensated for this over time by putting bits of unimportant/less important DNA at the ends of a molecules called telomeres

• Key history

• Protein originally thought to be the carrier of genetic material due to its higher variety and specific functions

• Griffiths want to find out what substance causes transformation

R bacteria had been transformed into pathogenic S bacteria by unknown substance

• Avery, MacLeod, and McCarty isolated various cellular components from a dead virulent strain of bacteria

• Followed up on a previous experiment by Griffiths and added each of these cellular components to a strain of living non-virulent bacteria

• Only the component of the deadly bacteria was able to change the second bacteria into a deadly strain capable of reproducing

• DNA must be responsible for passing traits and it is inheritable

• Hershey-CHase

• Used bacteriophages and labelled protein parts of some with radiolabeled sulfur and labelled the DNA parts of other viruses with radiolabeled phosphorus

• Bacteriophages inject genetic material into cell so more genetic material will be created

• When viruses infected bacteria, only the labelled DNA was inside, but they were still able to replicate and make progeny viruses

• E. coli were infected by the phage, and there was more and more P that entered. They concluded that DNA carried the genetic information to produce DNA and proteins

• Central Dogma

• DNA’s main role is directing the manufacture of molecules that actually do the work in the body

• DNA expression:

•  1. Turn into RNA

• 2. Send RNA out into the cell and often gets turned into a protein

• Transcription turns RNA into DNA

• Takes place in nucleus (except in prokaryotes)

• Translation turns RNA into a protein

• Takes place in cytoplasm

• RNA

• Single stranded

• 5-carbon sugar is ribose instead of deoxyribose

• Uses uracil instead of thymine

• major types of RNA

• Messenger RNA (mRNA)

• Temporary version of DNA that gets sent to ribosome

• Ribosomal RNA (rRNA)

• Produced in nucleolus

• Makes up part of ribosomes

• Transfer RNA (tRNA)

• Shuttles Amino acids to the ribosomes

• Responsible for bringing the appropriate amino acids into place at the appropriate time

• Done by reading message carried by mRNA

• Interfering RNA (RNAi)

• Small snippets of RNA that are naturally made in the body or intentionally created by humans

• siRNA and miRNA can bind to specific sequences of RNA and mark them for destruction

• Transcription

• RNA copy of DNA code

• pre-mRNA synthesis

• Only a specific section is copied into mRNA

• Occurs as-needed on a gene-by-gene basis

• Exception: prokaryotes will transcribe a recipe that can be used to make several proteins

• Called polycistronic transcript

• Eukaryotes tend to have one gene that gets transcribed to one mRNA and translated into one protein

• Monocistronic transcript

• 3 steps: initiation, elongation, termination

• initiation

• Unwind and unzip DNA strands using helicase

• Transcription initiation complex

• Transcription factor proteins+RNA polymerase

• Forms at promoter

• Transcription only occurs as-needed to conserve resources

• ELongation

• Begins at special sequences of the DNA strand called promoters

• Free RNA nucleotides inside the nucleus used to create mRNA

• RNA polymerase used to construct mRNA

• Strand that serves as the template is called antisense strand, the non-coding strand, or the template strand

• Strand that lies dormant is the sense strand, or the coding strand

• Rna polymerase build RNA only to 3’ side

• Doesn’t need primer

• Promoter region is “upstream” of the actual coding part of the gene

• Official starting point if start site

• RNA strand is complementary to template DNA strand

• TErmination

• Once termination sequence is reached, it separates from the DNA template, completing the process of transcription

• RNA processing

• In eukaryotes the RNA must be processed before it can leave the nucleus

• Freshly transcribed RNA is called hnRNA (heterogenous nuclear RNA) and it contains both coding regions and noncoding regions

• Regions that express the code will be turned into protein are exons

• Non-coding regions in the mRNA are introns

• Introns removed by spliceosome 

• Spliceosome made up of many snRNPs

• snRNPs made up of ribozyme+small nuclear RNA

• ribozyme=RNA catalyst that can copy RNA strands

• Spliceosome identifies ends of an intron

• Folds chromosome

• Spliceosome cuts out the intron and binds the two exons together

• Non i prokaryotic cells

• 3 properties of RNA that allow it to function as an enzyme

• Single stranded

• Functional groups that act as catalysts

• Hydrogen bonds with other nucleic acids

• Introns allow more genetic diversity

• More possibilities for crossover

• Alternate splicing can yield new protein varieties

• Methyl cap added to 5’ end

• Helps mRNA leave nucleus

• Allows attachment to ribosome

• Modified guanine

• poly-A tail added to 3’ end

• Protects mRNA from endonucleases in cytoplasm, which can only attach to 3’ end

• 50-250 adenine

• No cap or tail in prokaryotic cells since they have no nucleus

• mRNA leaves nucleus through nuclear pore

• TRanslation

• Process of turning mRNA into a protein

• mRNA nucleotides will be read in the ribosome in groups of three

• Group of three nucleotides=codon

• Each codon corresponds to a particular amino acid

• mRNA attaches to the ribosomes to initiate translation and “waits” for the amino acids to come to the ribosome

• 3 sites on ribosome

• E=exit site

• P=polypeptide storage/exit

• A= place where tRNA brings in amino acid

• 1.mRNA attaches to mRNA binding site on small subunit. tRNA attaches onto A site

• 2. Large subunit attaches via GTP

• 1st tRNA is in P site

• 2nd tRNA comes in A site

• 3. rRNA in large subunit catalyzes a peptide bond between amino acids

• 4. 1st rRNA moves to exit site

• 2nd tRNA moves to P site

• New tRNA comes in through A site

• Steps 1-4 repeats until stop codon is reached

• As mRNA moves through ribosome, other ribosomes can attach to it at the same time (as long as mRNA has not degraded, especially on 5’cap

• 5. Release factor adds water to end of polypeptide; polypeptide detaches and exits through P-site tunnel

• 6. small/large subunit/mRNA disassemble and disassociate; process of translation can start over again

• tRNA carries amino acid

• Attaches to RNA via anticodon (complementary base pair to codon)

• Wobble pairing on third nucleotide (flexible bonds)

• Each tRNA becomes charged and enzymatically attaches to an amino acid in the cell’s cytoplasm and “shuttle” it to the ribosome

• Charging enzymes require ATP

• 3 phases:

• Initiation

• 3 binding sites:

• A site

• P site

• E site

• Start codon is AUG (methionine)

• TATA box=specific promoter for initiation

• RNA polymerase binds to a specific location on promoter

• Transcription factors attach to promoter to help guide RNA polymerase

• Elongation        

• As each amino acid is brought to the mRNA, it is linked to its neighboring amino acid by a peptide bond and eventually forms a full protein

• Termination

• Synthesis of a polypeptide ended by stop codons

• Gene Regulation

• Pre-transcriptional regulation

• Transcription factors can either encourage or inhibit the unwinding of DNA and the binding of RNA polymerase

• Operons

• Bacteria only

• Structural genes

• Code for enzymes in a chemical reaction

• Genes will be transcribed at the same time to produce particular enzymes

• PRomoter gene

• Region where RNA polymerase binds to begin transcription

• Operator

• Controls whether transcription will occur

• Where repressor/inducer binds

• Regulatory gene

• Codes for a specific regulatory protein called to repressor

• Repressor capable of attaching to the operator and blocking transcription

• If repressor binds to the operator, transcription will not occur

• If repressor does not bind to the operator, RNA moves along operator and transcription occurs

• inducible=presence of molecule turns gene on

• repressible=presence of molecule turns gene off

• Chromatin Modification

• Histone acetylation

• Acetyl groups added to histones

• Looser Chromatin

• Access for transcription increased

• DNA methylation

• Methyl groups added to bases

• Silences gene

• Tightens chromatin

• Enhancers

• Upstream of promoter

• Bends DNA

• Post-transcriptional regulation

• Occurs when the cell creates an RNA but then decides that it should not be translated into a protein

• RNAi molecules bind to an RNA via complementary base pairing

• Creates double-stranded RNA, signalling that RNA should be destroyed, preventing it from being translated

• Post-translational regulation

• Protein has already been made, but doesn’t need it yet, so it is deactivated

• Mutations

• Mutation is an error in the genetic code

• Occur because DNA is damaged  in cannot be repaired or because DNA is repaired incorrectly

• Caused by chemicals or radiation

• Can also occur when a DNA polymerase or an RNA polymerase makes a mistake

• RNA polymerases have proofreading abilities, but RNA polymerases do not

• Error in DNA not a problem unless that gene is expressed AND the error causes a change in the gene product

• Base Substitution

• Point mutations result when a single nucleotide is replaced for another

• Nonsense mutation

• Cause original codon to become a stop codon, which results in early termination of protein synthesis

• Missense mutation

• Cause original codon to be altered and produce a different amino acid

• Silent mutations

• codon that codes for the same amino acid is created and therefore does not change the corresponding protein sequence

• Frameshift mutations

• insertions/deletions result in the gain or loss of DNA or a gene

• Can have devastating consequences during translation

•  results in a change in the sequence of codons used by the ribosome

• Duplications

• Extra copy of genes

• Caused by unequal crossing-over during by meiosis or chromosome rearrangements

• ,ay result in new traits as one copy may evolve a new function

• Inversions

• Changes occur in the orientation of chromosomal regions

• May cause harmful effects if the inversion involves a gene or an important regulatory sequence

• Translocation

• 2 different chromosomes break and rejoin in a way that causes the DNA sequence to be lost, repeated, or interrupted

D. Biotechnology

• Recombinant DNA generated by combining DNA from multiple sources to create a unique DNA molecule that is not found in nature

• Ex. introduction of a eukaryotic gene of interest into a bacterium for production

• Polymerase Chain Reaction (PCR)

• Enables the creation of billions of copies of genes within a few hours

• DNA polymerase, DNA, and lots of nucleotides added in a small PCR tube

• Thermocycler

• PCR machine that heats, cools, and warms PCR tubes many times

• Each time the machine is heated, the hydrogen bonds break, separating the double-stranded DNA (Denaturation)

• As it cools, primers bind to the sequence flanking the region of the DNA we want to copy, primers can form hydrogen bonds with ends of target sequence (Annealing)

• When it is warmed, polymerase binds to the primers on each strand and adds nucleotides on each template strands (extension)

• REPEAT exponentially

• Transformation

• Transformation: process of giving bacteria foreign DNA

• Genes of interest (vectors) placed into small circular DNA molecule called a plasmid

• Plasmid usually codes for antibiotic resistance

• Small ring of DNA found in bacteria that is replicated separately form the chromosomal DNA

• Not in all bacteria

• 1. Extract the plasmid

• 2. Add a restriction enzyme that will cut the ring open

• Restriction enzymes usually used to cut up foreign DNA, but are used by scientists for this purpose

• Cuts palindromes, leaving “sticky ends”

• Always cut at the same nucleotide sequence

• 3. Cut a piece of human DNA with same restriction enzyme

• Reverse transcriptase must be used to process DNA since prokaryotes do not have RNA processing to remove introns

• DNA transcribed and mRNA is processed, and then reverse transcriptase turns mRNA back into DNA

• Reverse transcriptase also used by retroviruses

• Problems: vector may be too big, and there is no direct way to force the plasmid to accept the vector

• 4. Mix the cut plasmids with the cut human DNA-some will align right due to their sticky ends

• Ligase used to glue ends back together

• 5. Allow bacteria to take plasmid back in

• Heat shock/electric shock used to change membrane so plasmid can re-enter easily

• 6. Allow to reproduce

• Not all bacteria will be transformed, can be tested by using antibiotic resistance

• Allows the safe mass-production of proteins used for medicine

• Important role in the study of gene expression

• Transfection: putting a plasmid into a eukaryotic cell, rather than a bacteria cell

• Gel Electrophoresis

• DNA fragments can be separated according to their molecular weight using gel electrophoresis

• DNA put into wells on negative end, and when a current is run through the gel, the DNA moves across gel according to their weight

• Because DNA and RNA are negatively charged, they migrate through the gel toward the positive pole of the electrical field

• Smaller fragments move faster and farther

• Restriction enzymes used to create a molecular fingerprint

• Places where enzymes cut and thus the sizes are unique for each person

• Stem cells also very important in biotechnology since they can turn into many different kinds of cells, but it is controversial due to harvesting methods

• Totipotent cell: capable of giving rise to any type of cell or a complete embryo

• Pluripotent cell:capable of giving rise to different cell types

UNIT V: CELL REPRODUCTION

• Cell division

• Mechanism to replace dying cells

• Small part of life cycle of a cell

• Some types of cells are nondividing

• Usually highly specialized cells derived from a less specialized type of cell

• Made as needed, but cannot replicate themselves

• Ex. red blood cells

• Multicellular organisms depend on cell division for:

• Development from a fertilized cell

• Growth

• Repair

• Binary Fission

• Used by prokaryotes

• Chromosome replicates at origin of replication and the two daughter chromosomes actively move apart

• Plasma membrane pinches inward, dividing cell into two

• Mitosis likely evolved from binary fission

• Certain protists exhibit cell division that seem intermediate between binary fission and mitosis

A. Interphase

• Time span from one cell division to another

• Cell carries out regular activities

• All the proteins/enzymes the cell needs to grow are produced in interphase

• 3 Phases:G₁, S, G₂

• G₁

• Cell produces all enzymes required for replication

• G=”Gap” or “growth”

• S

• Cell replicates genetic material

• Every chromosome in nucleus is duplicated

• Sister chromatids created, held together by centromere

• To be called a chromosome, they each need to have their own centromere; once chromatids separate, they will be “chromosomes”

• CEll cycle checkpoints

• Checkpoints highly regulated by cyclins and cyclin-dependent kinases (CDKs)        

• To induce cell cycle progression, CDK binds to a regulatory cyclin. Once together, the complex is activate

• Can affect many proteins in cell

• Causes cell cycle to continue

• To inhibit cell cycle progression, CDKs and cyclins are kept separate

• Separated via dephosphorylation

• MEtaphase Checkpoint

• Chromosome spindle attcachment

• G₁ Checkpoint

• Check for:

• Nutrients

• Growth factors

• DNA damage

• Can put cell into G₀ is it doesn’t need to divide

• G₂ checkpoint

• Check for:

• Cell size

• DNA replication

• Make sure cell division is happening properly in cells

• Stops progression if cell is not ready to progress to next stage

• In eukaryotes, checkpoint pathways mainly function ay phase boundaries

• When DNA damage is detected, cell will not progress until damage is fixed, or apoptosis is started

• CAncer can result from a mutation in a protein that normally controls progression, resulting in unregulated cell division

• Oncogenes are genes that cause cancer

• Normally required for proper growth and regulation of he cell cycle

• Mutated versions can cause cancer

• proto-oncogene=normal, healthy oncogene

• Tumor suppressor genes

• Produce proteins that prevent the conversion of normal cells into cancer cells

• Detect damage within cell and work with CDK/cyclin complexes to stop cell growth until damage can be repaired

• Can trigger apoptosis is damage is too severe to be repaired

• In order for a cell to become a cancer cell. It must simultaneously override checkpoints, grow in an unregulated way, and avoid cell death

• Stop cell division

• Density-dependent inhibition

• Anchorage dependency

B. Mitosis

• Prophase

• Disappearance of the nucleolus and nuclear envelope

• Chromosomes thicken and become visible

• Now called chromatin

• Centrioles in microtubules organizing centers (MTOCs) start to move away from each other towards opposite poles of the cell

• Centrioles spin out system of microtubules known as spindle fibers

• Spindle fibers attach to kinetochore located on centromere of each chromatid

• Metaphase

• Chromosomes begin to line up along equatorial metaphase plate

• Moved along by spindle fibers attach to kinetochores on each chromatid

• Anaphase

• Sister chromatids of each chromosome separate at the centromere and migrate to opposite poles

• Pulled apart by shortening microtubules

• Non-kinetochore tubules elongate cell

• Telophase

• Nuclear membrane forms around each set of chromosomes

• Nucleoli reappear

• Cytokinesis

• Cytoplasm splits in half

• Cell splits along cleavage furrow

• Cell membrane forms along each new cell, split into distinct daughter cells

• In plant cells, a cell plate forms down the middle instead of a cleavage furrow

• Interphase

• Cells re enter initial phase, and are ready to start the cycle over again

• Chromosomes become invisible again

• Genetic material goes back to being chromatin

• Purpose of mitosis

• Produce daughter cells that are identical copies of parent cell

• Maintain proper number of chromosomes from generation to generation

• Occurs in almost every cell except for sex cells

• Involved in growth, repair, and asexual reproduction

C. Haploid vs. Diploid

• Diploid cell has 2 sets of chromosomes

• Most eukaryotic cells have 2 full sets of chromosomes: one for each parent

• Shown by “2n”

• Haploid cell has only one set of chromosomes

• Shown by “n”

• Homologous chromosomes are duplicate versions of each chromosome

• Similar in size and shape

• Express same traits, but may have different alleles

• Gametes

• Sex cells

• Haploid

• Offspring will get one gamete from each parent, creating a diploid zygote/offspring

D. Meiosis

• Production of gametes

• Limited to sex cells in gonads        

• gonads=sex organs

• Testes in males and ovaries in females

• Made up of germ cells

• Produces haploid cells which then combine to restore the diploid (2n) number during fertilization

• 2 rounds of cell division: meiosis I and meiosis II

• Just like in mitosis, double-stranded chromosomes are formed during S phase of interphase

• Meiosis I

• Prophase I

• Nuclear membrane disappears

• Chromosomes becomes visible

• Centrioles move towards opposite ends of cell

• Synapsis

• Chromosomes line up side-by-side with their homologs (counterparts)

• 2 sets of chromosomes come together to form a tetrad (aka bivalent) consisting of 4 chromatids

• Crossing over

• Exchange of segments between homologous chromosomes

• Genetic variation

• Begins in Prophase I as homologous chromosomes line up gene by gene

• Produces recombinant chromosomes (DNA combined from each parent)

• Homologous portions of two nonsister chromatids trade placed

• Chromatids that are farther apart are more likely to cross over

• Metaphase I

• Tetrads line up along metaphase plate

• Random alignment--more genetic variation

• Offspring will be a combination of all 4 grandparents

• ANaphase I

• Each pair of chromatids within a tetrad separates and moves to opposite poles

• Chromatids DO NOT separate at centromere

• Telophase I

• Nuclear membrane forms around each set of chromosomes

• 2 daughter cells

• Nucleus contains haploid number of chromosomes, but each chromosome is a duplicated chromosome consisting of 2 chromatids

• Meiosis II

• Purpose is just to separate sister chromatids

• Prophase II is the same

• Metaphase II: chromosomes move toward metaphase plate lining up in a single file, not in pairs

• Anaphase II:chromatids split at the centromere and each chromatid  is pulled to opposite ends of cell

• TElophase II: nuclear membrane forms around each set of chromosomes and a total of 4 haploid cells are produced

• MEiosis I separates homologous chromosomes; Meiosis II separates sister chromatids

• Gametogenesis

• Spermatogenesis if sperm cells are produced

• Oogenesis if egg cell/ovum is produced

• Produces one ovum instead of 4

• Other 3 cells, called polar bodies get only a tiny amount of cytoplasm and eventually degenerate

• Allows female to conserve as much cytoplasm as possible for the surviving ovum

• Meiotic Errors

• Nondisjunction: chromosomes fail to separate properly

• Produces wrong number of chromones

• Usually results in miscarriage or significant genetic defects

• Ex. Down syndrome is a result of 3 copies of the 21st chromosome

• Translocation

• One or more segments of a chromosome break and are either lost or reattach to another chromosome

UNIT VI: HEREDITY

A. Mendelian Genetics

• Genetics=study of heredity

• Explains how certain characteristics are passed from parents to children

• Heredity=transmission of traits from one generation to the next

• Variation is demonstrated by the differences in appearance that offspring show from parents and siblings

• Physical traits are not inherited; genes are inherited

• Gregor Mendel=”father of genetics”

• Traits

• Expressed characteristics

• character=feature(ex. Eye color); trait =specific version of that feature (ex. blue eyes)

• Influenced by one or more genes

• Gene=chunk of DNA that codes for a particular “recipe”

• DNA is passed from generation to generation, and genes/traits go along with it

• Chromosome contains many genes, each controlling the inheritance of a particular trait

• Locus=position of a gene on a chromosome

• Children do not inherit physical traits; they inherit genes, which influence physical traits

• Genes passed along by gametes (sperm/egg)

• clone=group of genetically identical individuals from same parent

•  common in asexual reproduction

• Sexual reproduction creates genetic diversity

• Diploid organisms typically have 2 copies of a gene, one on each homologous chromosome

• Copies of chromosome may be different from each other, containing different alleles

• Homozygous=organism has 2 identical alleles for a given trait

• heterozygous=organisms has 2 different alleles for a given trait

• Phenotype=physical appearance

• Genotype=genetic makeup

• Dominant vs. recessive allele

• Dominant allele is determined by which allele is the phenotype of a heterozygous organism

• Dominant allele showed by capital letter; recessive allele showed by lowercase of same letter

• Crosses

• 1st generation in an experiment is always called the parent/P1 generation

• Offspring of P1 are called the filial/F1 generation 

• Offspring of F1 are called F2 generation, etc.

• true-breeder=genetically pure; consistently produces same traits

• Law of Dominance

• One dominant trait masks the effect of the other trait

• Law of Segregation

• Monohybrid Cross

• 2 heterozygous individuals are crossed

• Ratios for cross of two heterozygotes

• Phenotype ratio= 3 dom.:1 rec.

• Genotype ratio= 1 homo dom: 2 het: 1 homo rec

• Gametes only get one of the 2 copies of a gene

• Law of Independent Assortment

• Each allele of the two traits will get segregated into two gametes independently and randomly along Metaphase plate of meiosis I

• Each pair of chromosomes sorts maternal/paternal homologues independently of the other pairs

• For humans, (n=23), there are more than 8 million (2²³ possible combinations of chromosomes, not including crossing over, mutations, etc.

• Dihybrid cross

• 2 heterozygotes for two genes are crossed

• 9:3:3:1 ratio

• Easier to use probability rather than a punnett square

• Random Fertilization also creates genetic variability

• Any sperm can fuse with any ovum

• 70 trillion diploid combinations

• Rules of Probability

• Probability of 2 independent traits occurring together= probability of trait A*probability of trait B

• Test Cross

• How to tell if an organism displaying dominant phenotype is homo-dom or het: USE TESTCROSS

• Breed mystery organism with a homo-rec

• If all offspring display dom phenotype, the organism is homo-dom

• If any offspring display rec phenotype, the  organism is het

• Linked Genes: group of genes on same chromosome tend to stay together/inherited together

• Cannot segregate independently since they are on the same chromosome, violating the law of independent assortment

• Can only be separated by crossing-over

• recombinant=offspring formed from recombination events

• Percentage of recombination= 

• Can be used as a measure of how far apart genes are/order

• Distance on a chromosome is measured in map units aka centimorgans on a linkage map

• One map unit=1% recombination frequency

• Farther apart 2 linked alleles are on a chromosome the more often the chromosome will cross over between them

• Genes on different chromosomes have 50% recombination frequency

• Karyotype: ordered display of the pairs of chromosomes in a cell

• 2 chromosomes in a pair=homologous chromosomes

• PEdigrees: show family history of allele(S)

• Describes interrelationships of parents and children across generations

• Inheritance patterns of particular traits can be traced back and described using pedigrees

• Alterations of Chromosome Number/Structure

• Nondisjunction

• Pairs of homologous chromosomes don’t separate properly during meiosis

• One gamete receives 2 of the same type of chromosome (trisome) while the other receives none (monosome)

• Results in Aneuploidy

• Deletion

• Removes a chromosomal segment

• CDE➝CE

• Duplication

• Repeats a segment

• CDE➝CDCDE

• Inversion

• Reverses orientation of segment within a chromosome

• CDE➝EDC

• Translocation

• Moves a segment from one chromosome to another

• Genome imprinting

• Phenotype depends on which parent passed along alleles for trait

• Involves silencing of certain genes that are “stamped” with an imprint during gamete production

• Extranuclear genes are inherited maternally because the zygote’s cytoplasm comes from the egg

B. Sex-Linked Traits

• autosomes=non sex chromosomes

• Sex chromosomes determines sex of individual

• female=XX

• male=XY

• Some traits carried on sex chromosomes

• Ex. color blindness/hemophilia

• Most only found on X-chromosome (“X-linked traits”)

• Since males have one X and one Y chromosome, he’ll express the trait even if it is recessive since there is no second allele that would cover it up

• Female will only express sex-linked trait if trait is dominant or individual is homo rec

• carrier=female that carries trait but does not exhibit it

• Barr Bodies

• X chromosome that is condensed and visible

• Females only have one X chromosome activated; other X deactivated during embryonic development

• Deactivated chromosome chosen randomly by each cell

• Incomplete dominance

• Aka blending inheritance

• Traits blend

• Alleles equally expressed

• Ex. red white=pink offspring

• Non dominant trait

• Codominance

• Equal expression of multiple alleles

• 2 alleles affect phenotype differently

• Ex. blood type options: I^A, I^B, i

• Polygenic inheritance

• Trait results from the interaction of many genes

• Non-nuclear inheritance

• Affected by genetic material in mitochondria

• Mitochondria always provided by egg during sexual reproduction 

• Most genes have pleiotropy (have multiple phenotypic effects)

• Responsible for the multiple symptoms of hereditary diseases

• Epistasis: a gene at one locus alters the phenotypic expression of a gene at another locus

• Norm of Reaction: phenotypic range of a genotype influenced by environmental factors

• Multifactorial characters

UNIT VII: EVOLUTIONARY BIOLOGY

A. NAtural Selection

• Charles Darwin

• British naturalist who sailed the world

• Developed theory of evolution based on natural selection after studying animals on Galapagos Islands

• Observed that there were similar animals on isolated animals, but they each had slight variations (ex. Beak shape, neck length, etc.)

• There must have originally been a variety of beak lengths, but only the longest ones could survive. Since those with the longest beaks could reproduce better, they were more likely to contribute offspring with the same traits to the next generation

• The Origin of Species

• Variation exists in the population and some of this variation is heritable

• Populations tend to make lots of offspring

• Resources are limited, thus a struggle ensues

• Those with better traits (phenotypes) will do a better job getting those resources and reproduce more

• The genes that code for “better” traits in the current environment start increasing in the population

• The earth is always changing what what may be good now may not be in the future; evolution will always be occurring

• “Survival of the fittest”

• Jean-Baptiste Lamarck

• Widely accepted theory of evolution in Darwin’s

• Acquired traits inherited and passed onto offspring

• “Law of use and disuse”

• According to Lamarck, giraffes have long necks because they constantly use them

• WRONG

• Changes in somatic cells do not change gametes and thus cannot be passed onto offspring

• Evidence for Evolution

• Paleontology

• Study of fossils

• Revealed great variety of organisms and the major lines of evolution

• Tend to form in sedimentary rock

• Biogeography

• Study of the distribution of flora and fauna in the environment

• Related species found in widely separated regions of the world

• Suggests a common ancestor between species

• Ex: pangea

• Embryology

• Study of the development of an organism

• Early stages of vertebrate development all look alike

• All vertebrates show fishlike “gill slits”

• Comparative anatomy

• Study of anatomy of various animals

• Vestigial Strucutres

• Structures with little-no function

• Remannts of structures that served important functions in the organism’s ancestors

• Homologous structures

• Similar structures that serve different functions

• Analogous structures

• Same function different structure

• Molecular biology

• Most compelling proof of evolution

• Examining nucleotide/amino acid sequences of different organisms

• Common genes and proteins

• Ex: Hox Genes (body paint controller genes)

• Shared structures help us to understand not only how structures develop but also supports shared shared ancestry

• Artificial Selection

• Humans selecting which organisms reproduce and survive so the future generations have traits that humans have selected

• Ex. dog breeds

B. Common Ancestry

• Phylogenetic trees

• Aka cladogram

• Study the relationships between organisms

• Begin with common ancestor and then branch out

• Anytime there is a fork in the road, it is called a common ancestor node

• Common ancestors likely do not exist anymore, but they are the point at which evolution went in two directions

• Outgroup

• Related to ingroup but diverged before others

• Serves as reference group

• Always stems from foot of tree

• Monophyletic=ancestral species+all descendants

• PAraphyletic=ancestral species+some descendants

• Polyphyletic=ancestral species+descendants+distantly related organism

• Taxonomic categories

• DOMAIN

• KINGDOM

• CHORDATA

• PHYLUM

• CLASS

• ORDER

• FAMILY

• GENUS

• SPECIES

C. Genetic Variability

• Genetic variability: differences in each person/individual

• Only identical twins have exactly identical sets of alleles

• Survival of a species is dependent on genetic variation, allowing a species to survive in a changing environment

• NAtural selection only occurs if some individuals have more evolutionary fitness and can be selected

• Cause of genetic variability

• Random mutations

• DNA polymerase errors

• Changes to DNA by transposons, etc.

• Meiosis

• Crossing-over

• Independent assortment

• Bacteria

• Conjugation

• Transduction

• Viruses pass around chunks of the bacterial genome during infection

D. Causes of Evolution

• Natural selection works internally through random mutations and externally through environmental pressures

• As long as a mutation does not kill an organisms before it reproduces, it may be passed on to the next generation

• Advantages brought about by a mutation will only be apparent until environmental pressure occurs

• Adaptation: variation favored by natural selection

• Any trati that causes an individual to reproduce better gives that individual evolutionary fitness

• Sexual selection can also spur evolution

• Speciation occurs once 2 populations can no longer reproduce together

• Biological Species Theory

• Species is a group of populations whose members have the potential to interbreed in nature and produce fertile, viable offspring

• They do not breed successfully with other populations

• Catastrophic events speed up natural selection

• Genetic drift

• Something that causes a change in a population besides natural selection

• Caused by random events that drastically reduce the number of individuals in a population

• Bottleneck effect

• Sudden change in environment reduces size of population

• New gene pool is not reflective of original population

• Founder effect

• Few individuals become so isolated from larger population and establish a new popluation that may not be representative of original population

• Gene Flow

• Tends to make a population more similar

• When a poppulation gains/loses alles by genetic additions/subtractions from population

• Only a few individuals are left to mate and regrow a population, so their traits become overemphasized without necessarily having any reproductive advantage

• Types of SElection

• Directional selection favors one extreme of the normal distribution

• Stabilizing selection: extreme traits are selected against

• Disruptive selection favors both extremes,common traits selected against

E. Species

• Divergent evolution

• In order for a population to split into different species, they must be reproductively isolated

• Allows the two groups to undergo natural selection and evolve differently

• a population evolves into 2 separate species due to different variation/environmental pressures until the 2 groups can no longer mate together

• Prezygotic barriers prevent fertilization

• Habitat isolation

• 2 species don’t encounter each other

• Same geographic area, but different habitats

• Temporal Isolation

• Species breed during different times of da/season/etc.

• Behavioral Isolation

• Different courting rituals

• Species do not respond to mating signals

• MEchanical isolation

• Unsuccessful mating attempt

• Species are anatomically incompatible

• Gametic isolation

• Sperm unable to fertilize eggs

• Gametes are unable to fuse to forma zygote

• Post-zygotic barriers are related to the inability of the hybrid to survive/reproduce

• Reduced hybrid viability

• Genes impair hybrid development

• Reduced hybrid fertility

• sTerile hybrids

• Hybrid breakdown

• Weaker hybrids over generations

• Offspring of htbrids are weak/sterile

• Convergent evolution

• Process by which two unrelated and dissimilar species come to have analogous traits

• Often due to exposure to similar selective pressures

• 2 types of speciation

• Allopatric

• Population becomes separated from the rest of the species by a geographic barrier so the 2 population can interbreed

• Sympatric

• New species form without any geographic barrier

• Common in plants

• Through polyploidy, sexual selection, habitat differentiation, etc.

• Polyploidy

• Presence of extra sets of chromosomes due to accidents during cell division

• Common in plants

• Autopolyploidy

• Individual with more than two chromosome sets

• derived from same species

• Allopolyploid

• Species with multiple sets of chromosomes derived from different species (interbreeding)

F. Population Genetics

• Hardy-Weinberg Equilibrium

• Law states that even with all the shuffling of genes that goes on, the relative frequencies of genotypes in a population still prevail over time, creating a stable gene pool

• 5 Conditions

• Large population

• No mutations

• No immigration/emigration

• Random mating

• Natural selection

• All populations violate one of these five--populations are always evolving

• p + q = 1

UNIT VIII: ANIMAL STRUCTURE AND FUNCTION

• Homeostasis

• Set of conditions that living things can live successfully in

• Body is constantly trying to maintain this state by taking measurements and adjusting accordingly

• Controlled by feedback pathways

• Negative Feedback

• Aka feedback inhibition

• End product turns pathway off

• Conserves energy

• Positive feedback

• End product stimulates the pathway

• Less common

• Ex. fruit ripening

A. Development

• Embryonic development

• morphogenesis=cell changing shape many times by going through a succession of stages

• When an egg is fertilized by a sperm, the result is a diploid zygote

• Fertilization triggers zygote to go through a series of divisions, and embryo becomes increasingly differentiated

• Organizer cells release signals that let cells knowhow they should develop

• Once a change has been made, it can’t go back

• Certain genes turned on/off in differentiation

• Homeotic genes

• Genes that turn cells into other types of cells

• Timing essential for activation of genes

• Severely damaged embryos will stop development

• Apoptosis also used in embryonic development

• Some parts used as “scaffolding” in development and then those cells undergo apoptosis

• Ex. webbed fingers and toes that become digits

B. Body Systems

• tissue=group of cells that all perform the same function

• organ=several tissues come together to form specialized structures

• Body system=several united organs

• Immune system

• Nervous system

• Endocrine system

• Circulatory

• Blood vessels carry blood around body to transport chemical signals and to bring supplies to cells and carry waste way

• The blood flow is controlled by the heart, which pumps blood through the blood vessels

• Respiratory

• Lungs are responsible for gas exchange (O₂ and CO₂)

• Help maintain pH levels in blood

• Digestive

• Esophagus, stomach, small intestine, large intestine, pancreas, liver, and gallbladder work together to break down food and absorb nutrients

• stomach=mixing/breakdown

• Small intestine=absorption

• pancreatic=enzyme secretion/secretion

• Excretory

• Kidneys filter blood and reabsorb things the body wants to keep and gets rid of the rest in urine

• Reproductive

• Male and female systems largely controlled by hormones and allow the production of gametes and the ability to reproduce

• Muscular and Skeletal

• Skeletal and smooth muscles contract via an action potential signal from nervous system

• Skeletal system provides:

• Structure

• Protection

• Calcium storage

C. Immune System

• Body’s defense system

• pathogens=disease-causing biological agents that can generally be divided into:

• Bacteria

• Prokaryotes of many shapes and sizes

• Shapes

• Cocci (sphere)

• Bachi (rod)

• spiral

• Infect many things

• Have cell wall

• Maintain cell shape

• Protect cell

• Prevent bursting in hypotonic environment

• Made of peptidoglycan

• Archaea contain polysaccharides and proteins

• Gram-positive  bacteria have simpler walls with a large amount of peptidoglycan

• Gram-negative bacteria have less peptidoglycan and an outer membrane than can be toxic

• More likely to be antibiotic resistant

• CApsule: polysaccharide/protein layer covering many prokaryotes

• Some bacteria develop resistant cells called endospores when that lack an essential nutrient

• thick -coated resistant cell produced by some bacteria cells when exposed to harsh conditions

• Fimbriae help stick to substrate

• Contain circular DNA and Plasmids

• Reproduce by binary fission; short generation times (1-3 hours)

• May or may not cause harm

• Divide By fission--does not increase genetic diversity

• Can perform conjugation with other bacterial cells and swap some DNA

• F-factor=piece of DNA required for production of oil

• Cells containing F Plasmid (F⁺) serve as donors; F^- cells are receivers

• F-factor transferrable during conjugation

• Bacterial Transformation

• Transduction

• Genetic variety among bacteria is leading to increased antibiotic resistance

• Horizontal gene transfer: movement from one organism to another

• Viruses

• Non Living agents capable of infecting cells

• Nonliving bc require a host cell’s machinery to replicate (hijack DNA Polymerase); can’t reproduce on their own

• envelope:glycoproteins which the cells of animals receive to allow entrance into the virus

• Determines attachment to cell

• Host range=types of cells virus can infect

• 2 main components

• Protein capsid

• Protein shell enclosing viral genome

• Many shapes: rod, polyhedral, etc.

• Genetic material made up of DNA or RNA, depending upon specific virus

• Very specific to which cells they infect

• host=victim cell of viral infection

• GOal=replicate and spread

• To do so, virus must make more genome and capsid and then these components will self-assemble

• Viral genome carries genes for building capsid and anything else the virus needs that the host cell cannot provide

• Sometimes, two viruses will infect a cell and their genomes wil mix

• Bacteriophage

• 3 cellular defenses against phages

• Natural selection

• Restriction enzymes

• lysogeny

• Virus that infects bacteria

• 2 types of replication cycles

• Lytic

• Virulent phages

• Virus immediately starts using host cell’s machinery to replicate genetic material and create more protein capsids

• Spontaneously assemble into new viruses and cause cell the lyse, releasing new viruses into the environment

• Lysogenic

• Temperate phages

• Prophage: viral DNA integrated into bacterial chromosome via lysogenic cycle

• Virus incorporates itself into host genome and remains dormant until it is triggered to switch into the lytic cycle by an environmental signal

• During the dormant phase, acell may replicate many times, replicating the viral genome along with it

• Transduction

• When a virus exercises (becomes unintegrated) from host genome, it sometimes accidentally takes some host NA with it

• New DNA is replicated and packaged into new viral particles, becoming part of other cells

• DNA may have carried a trait such as antibiotic resistance

• Enveloped viruses

• In animal cells, viruses don’t have to lyse the cell; they can just just exit via exocytosis

• Virus  becomes enveloped by a hunk of cell membrane that it takes with it

• Thus these viruses have a lipid envelope

• Retroviruses

• Eex. HIV

• RNA viruses that use reverse transcriptase to convert their RNA genomes into DNA so they can be inserted into a host genome

• Extremely high rates of mutation