Enriched Biology Notes pay back daddy lunch money

Levels of Knowledge

Fact – An observation that is repeatedly confirmed. Hypothesis – A testable statement about the natural world. Law – A generalization about how something works in the natural world (describes behaviors). Theory (in science) – A well substantiated explanation of an aspect of the natural world (the

best possible explanation).

Scientific Method

Purpose or Problem statement Hypothesis

o If…then…because… Methods and Materials Results Conclusions

o Mention hypothesis (accepted or rejected), errors that have occurred in the lab (scientific errors), analyze results (this is what we got, this is why I think we got this).

Lab write-up

Analyze:o The quality of your experimental design.o The quality of your write-up.

Make notes or comments in a different colored writing utensil. Don’t panic. You will have the opportunity to re-do. What are the elements of a good Purpose?

o Detailed yet brief.o Includes variables (What are you changing? What are you measuring?)

Independent variable: The variable that doesn’t depend on other variables and the one that you change during the experiment.

Dependent variable: What you’re measuring. It’s dependent on the independent variable.

What are the elements of a good Hypothesis?o Independent and dependent variables.o Prediction of results.o Justification for prediction (background information)o “If…then…because…” format for hypothesis.

What are the elements of a good methods section?o Detailed!

Step by step instructions

List all materials needed for the experiment to succeedo Multiple trialso Controlo Single variable being testedo Constants

What is a control group?o The absence of the independent variable.

What is an experimental group?o The group with the independent variable.

What is a constant?o All the details that should stay the same throughout the entire experiment in both the

experimental and the control group. Example: amount of soil, amount of water, etc.

What makes a good conclusion?o Was your hypothesis supported or rejected?

Don’t use the word “prove”o Explain your data.o Sources of Error vs. “Whoopsies”

Unit 1: Biochemistry

Chemistry Review

Matter – anything that takes up spaceo Atoms:

Most common atoms in living things are: C, H, O, N… and P, S Nucleus contains:

Protons (positive charge) Neutrons (no charge) Electrons (negative charge)

o Energy levels: Energy of electrons, based on distance from nucleus.

Octet Rule: Atoms “want” to fill outer energy level Share, donate, or accept electrons

Example: Carbon 6 total electrons 4 valence electrons:

o Electrons in outermost energy levelo Involved in chemical bonds

Molecule: 2+ atoms bonded togethero Examples: H2O, C6H12O6 (Glucose), DNA

Chemical Bonds

Strong Bonds:o Covalent Bonds – share electrons

Polar Bonds – share electrons unevenly Example: H2O

Non-Polar Bonds – Share electrons evenly. Example: Methane (CH4)

o Ionic Bonds – attraction between opposite ions Example: Sodium Ion, Chloride Ion, Positive Sodium Ion, Negative Sodium Ion.

Weak Bond:o Hydrogen Bonds – strong attraction, but a weak bond!

Hydrogen Bonds are the strongest kindergartners.

Properties of Water

Cohesion – water is attracted to itself. Adhesion – water is attracted to other substances. Temperature moderation – takes a lot of energy to heat up. Solvent – Used to dissolve many substances.

Biochemistry

Biochemistry is a discipline which focuses on the chemicals of living organisms.o “Bio-” means life.

All biological molecules are organic. All organic molecules have carbon in them. The Carbon atom: 4 valence electrons means it has a lot of bonding possibilities. Most biological molecules are Polymers (chains) of smaller Monomers (subunits).

Macromolecules

Polymers: Train-like (or chain-like) molecule made of repeating monomers.o “Poly-” means many.

Monomers: The “building blocks” or subunits of polymers.o “Mono-” means one.

Polymers are made through a process called Condensation Reactions.

Condensation Reactions

Similar to linking box cars together, these reactions:o Link monomers together.o Form relatively strong bonds where energy is stored.o Form water as a by-product (hence the name condensation reactions).

OH + OH = H2Oo If Condensation reaction builds a polymer, what breaks it down?

Hydrolysis

Polymers are “broken down” through a process called Hydrolysis.o Think of this like dismantling the train.o The bonds holding monomers together are broken, releasing energy.

Hydrolysis Reactions – Use water to help break polymers apart into their smaller monomers.o “Hydro-” means water.o “–lys” means to break.

All Biological molecules are synthesized and hydrolyzed in the same way.

4 Main Macromolecules

Carbohydrates: The main “fuel” which run most living organisms.o Structure:

Ring-shaped molecules. Three main types of carbohydrates:

o Monosaccharides (Simple Carbohydrates) Primary monomer of carbohydrate polymers.

General formula for all monosaccharides is C6H12O6. All monosaccharides have the same chemical formula. Examples: Glucose (C6H12O6), Galactose, Fructose.

o Disaccharides 2 monosaccharide monomers bonded/linked together. General formula for all disaccharides is C12H22O11. When 2 monosaccharides are bonded together, water is created as a by-

product; therefore, the formula will be missing 2 H and 1 O molecule. Examples: Maltose, Sucrose, Lactose.

o Polysaccharides (Complex Carbohydrates) Complex carbohydrates.

Long chains of monosaccharides bonded together. No general formula because there are so many different forms of

monosaccharides. Examples:

o Glycogen (stores energy in animals).o Cellulose (found in plant cell walls).

High fiber carbohydrate. Human body cannot break down cellulose; therefore, it

is not digested.o Starch (stores energy in plants).

Lipids:o Fats, oils, waxes, phospholipids, etc. o Structure:

All lipids have fatty acid tails. Saturated fats:

Long, straight chains of Hydro-carbon atoms. Saturated with Hydrogen atoms.

o Solid at room temperature.o Animal products

Unsaturated fats: Long, kinked chains of carbons due to one or more double bonds.

o Unsaturated with Hydrogen atoms.o Liquid at room temperature.o Plant products

o Functions: Long term energy storage molecule. Insulation (blubber) Cell membranes (Phospholipids) Protective coating Steroids (Cholesterol)

o Extra information about lipids: Low Density Lipoproteins (LDL):

Bad kind of lipid. Causes blockages in blood vessels. High Density Lipoproteins (HDL):

Good kind of lipid. Removes cholesterol from blood. Trans Fats

Use a chemical catalyst to add hydrogen atoms to an unsaturated fat to make it a Saturated Fat.

By hydrogenating, you make them more attractive for cooking and extend shelf life.

Problems with Trans Fat:o Body cannot metabolize or remove Trans fats, so they stay in

the blood stream longer.o Contribute to coronary heart disease by raising levels of (LDL)

and lowering levels of HDLo Suspected as contributing to other conditions such as certain

types of cancer, diabetes, and obesity. Nucleic Acids

o DNA (Deoxyribonucleic Acid), RNAo Structure:

Large Polymer

Monomers are called nucleotides. Each nucleotide contains:

o One 5 Carbon sugar Called Deoxyribose in DNA

o One phosphate groupo One nitrogen base

Adenine Thymine Cytosine Guanine Uracil

Phosphate Pentose Sugar Nitrogenous Base

o The order of the nucleotides determines how people/animals look.

o Functions: DNA stores genetic information. RNA used as codes or templates for making proteins.

Proteinso Grouped according to their function.o Skin, hair, muscle, blood, enzymes are made of proteins.

Structure:o Tons of different types and shapes of proteins.o Monomers are called amino acids.

Amino group – NH2

Every single amino acid has NH2

All amino acids also have a Carboxylic acid group – (C(O)OH) The ‘R’ group (side group) changes depending on what amino acid it is. There are 20 types of amino acids.

Arranging these in different combinations allows for a huge diversity of proteins.

Analogy: Our 26 letter alphabet can be used to create millions of different words.

o Peptide bonds : Formed between 2 amino acids following a condensation reaction (rxn)

between the acidic group and the amino group. Amino acids form H-bonds with each other to produce different 3D shapes.

Proteins: Energy and Enzymeso Energy – The ability to do work or cause change.

Potential Energy – Energy of position. Kinetic Energy – Energy of movement.

Exothermic Energy Diagram (Energy that is released from the reaction)

Endothermic Energy Diagram (Energy is needed/gained)

Enzymes o Proteins that speed up chemical reactions (AKA organic catalysts).

o Enzyme Structure Very specific 3-D shape. Active Site – Pocket of the enzyme that binds to the substrate (reactant).

Each enzyme can only work with certain reactants because of the specific shape.

o Enzyme Function 1. Substrate binds to active site of the enzyme. 2. Enzyme lowers activation energy and reaction occurs faster. 3. Products are released.

Activation Energy o The energy needed to start a chemical reaction.

o Example Salivary amylase

Enzyme in spit that breaks polysaccharide (starch) down to the monosaccharide (glucose).

o If it ends with “-ase”, it’s most likely an enzyme.o Coenzymes

(AKA Cofactor) assist in enzyme action by being part of the active site. Example:

o Vitaminso Competitive Inhibitors

Bind to the active site but don’t react; slow the reaction by getting in the way. Factors Affecting Enzymatic Speed

o Enzyme Concentration Increase enzymes, increase enzyme activity.

Due to more collisions between substrate molecules and the enzymes. Will eventually “level out”.

o Substrate Concentration Increase substrates, increase enzyme activity.

Due to more collisions between substrate molecules and the enzymes. Will eventually level out when the number of enzymes and substrates

even out.o Temperature

Increase in temperature increases enzyme activity. (Up to a certain point) If the temperature is too high, enzyme activity levels out and then declines

rapidly because the enzyme gets denatured. Denatured: A change in the shape of the enzyme where it’s no longer

functional. The same thing happens if the temperature gets too cold.

o pH Each enzyme has an optimal pH at which the rate of reaction is highest. Too drastic of a change in pH will also lead to denatured enzymes.

Unit 2: Cells

Types of Microscopes

Compound Microscopeo Allows humans to see things so small that it cannot be seen with the naked eye.o Allows us to see individual cells.

Stereomicroscope

o Sees things in greater detail.o Sometimes called a ‘Dissecting scope’.

Microscope Terms

Magnification: How much large an object appears. For our ‘scopes:

o Eyepiece 10x magnification

o Objective lenses Scanning: 4x magnification Low: 10x magnification High: 40x magnification

o Total magnification Scanning: 40x magnification Low: 100x magnification High: 400x magnification

Resolution: The ability of a microscope to distinguish two objects as separate. Field of View: Everything that can be seen through a microscope. Depth of Field: Portion of field that appears sharp.

o Determined by adjusting the fine adjustment knob.

Microscope Lab Skills

Carrying: 2 hands, 1 hand on arm, and 1 hand on base. Preparing a wet mount:

o Obtain a clean slide.o Put a drop of water on the slide and put your object on top of it.o Obtain a clean cover slip and put it over your object at a 45o angle and slowly push it

down into place. Focusing:

o Always begin with the scanning objective lens.o Use the course adjustment knob to adjust focus only when the scanning objective lens is

in use.o Never use the course adjustment knob when using the high power objective lens.o Use the fine adjustment knob when using high and low power lenses.

Cells

Discovery of the cello Robert Hooke (1635 – 1703): First identified cells using a microscope.o Anton von Leeuwenhoek (1632 – 1723): First person to identify living cells.o Cell Theory: (Schleiden, Schwann & Virchow, 1839)

All living things are made up of cells. Cells are the basic unit of structure and function in all living things. Cells come only from the reproduction of living cells.

Cells are limited in size. The only cell that is visible to the naked eye is a human egg cell. Why are they limited in size?

o Specific cells for specific functions.o They could fall apart if they’re too big.

Cell size: Small cells are more efficient because of the high surface area to volume ratio.

Eukaryotic Cells (plants, animals, fungi, protists)

Eukaryotic Cells

Eukaryotic Cells: Have a nucleus and other organelles.

Animal Cells

Have all the following structures/organelles:o Cell (plasma) membrane :

Regulates what enters/exits the cell.o Cytoplasm :

Cell’s interior; water with “stuff” dissolved in it.o Cytoskeleton :

Provide internal structure within the cell. Microtubules – Tracks for transporting vesicles. Microfilaments – Support, muscle contractions. Intermediate Filaments – Holds things in place.

o Ribosomes : Help build proteins.

Organelles

Organelles – Membrane bound structures.o Nucleus :

Contains DNA, controls the cell. Nucleolus :

Makes ribosomes.o Endoplasmic Reticulum (ER) :

Rough ER : Contains ribosomes; transports proteins. Smooth ER : Makes fats; breaks down toxins.

o Golgi Apparatus : Modifies proteins from Rough ER.

o Vesicles :

Transports materials through cell; rides on “tracks” of cytoskeleton.o Lysosomes :

Digests materials not needed by the cell.o Mitochondria :

Produce energy for the cell (“powerhouse” of the cell).

Plant Cells

Plant cells have all of the above (animal cells) PLUS…o Vacuoles :

Store material (water). Plant cells and some protists.

o Cell Wall : Protective barrier; supports cell shape.

o Chloroplasts : Produce energy by photosynthesis.

Animal Cell

DNA inside nucleus

Plant Cell

Prokaryotic Cells

Prokaryotic Cellso Ex: Bacteriao Smaller than eukaryotic cells.o Contain no membrane bound organelles, only:

Cell membrane Cytoplasm Ribosomes

Ribosomes are pieces of RNA. RNA are pieces of rewritten DNA. Nuclear Material

DNA RNA

Cell Wall

Other Cell Structures

Modes of Locomotion (movement):o Flagella : Long, whip-like tails.o Cilia : Short hair-like projections.

Cell Transport

Cells regulate movement of materials across their membrane.o This maintains internal balance (we call this homeostasis) despite changes in their

environment. Cell (plasma) membrane : regulates what can enter or exit a cell

o Selectively permeable : Only certain substances may pass through. “Fluid-Mosaic Model” – Name scientists use to describe the structure of the cell membrane.

o Membrane acts more fluid than solid. Components:

o Phospholipids “Head”: Hydrophilic (polar) (loves water) Two fatty acid tails(long Hydrocarbon chains): Hydrophobic (non-polar) (hates

water) Lipid Bilayer : Two layers of phospholipids, move laterally. If you added phospholipids to a mixture of oil and water, where will they align?

Heads facing the water, tails facing the oil.o Proteins : Perform various jobs within the membrane

Peripheral Proteins : Act as enzymes; NOT embedded in bilayer, on the surface.

Integral Proteins : Regulate transport across membrane, serve as markers; extend across entire membrane. Fully embedded in membrane.

Polar ends, non-polar mid section.

Membrane Transport

Equilibrium : Molecules move until the concentration is the same throughout a space. Concentration gradient : A difference in concentration of a substance across a space. Passive Transport : When molecules move from a high concentration area to a low concentration

area.o The movement of molecules, across the membrane, that does NOT use energy.o Substance moves “down” the concentration gradient (from high to low concentration).o 3 main types:

Diffusion NET movement of molecules from high to low concentration.

o Ex: food coloring, perfume, sugar cube Osmosis

The diffusion of water. Solvent molecules can diffuse across a membrane. Set up Eggs

o Types of Solutions Hypotonic : Solution with less dissolved particles than

the inside of the cell. Hypertonic : Solution with more dissolved particles than

inside of the cell. Isotonic : Solution with the same amount of dissolved

particles as the inside of the cell. Turgor Pressure : The pressure that water exerts against

the cell wall. Plasmolysis : Loss of pressure when cell shrinks away

from cell wall. Cytolysis : Animal cells bursting due to water diffusing

into the cell. Facilitated diffusion

Diffusion of molecules across a membrane using a channel or carrier proteins.

o Carrier proteins: Similar to enzymes, in that a specific shape allows a specific molecule to pass.

o Channel Protein: An open passage for molecules to pass through.

Active Transport o Transport of substance against the concentration gradient.

Molecules move from low concentration to high concentration. Uses energy and a membrane protein.

Vesicular Transport o Movement of large amounts of material using a vesicle.

Endocytosis : Moves substances into the cell. Exocytosis : Moves substances out of the cell.

Unit 3: Energy (Cellular Respiration and Photosynthesis)

Types of Energy

Kinetic Energy – Energy of motion. Potential Energy – Stored energy (energy of position).

Laws of Thermodynamics

First Law of Thermodynamics o Energy cannot be created or destroyed, it only changes forms.

Examples: Dropping a book. Dropping an object. Potential energy Kinetic energy Sound/heat energy. Converting food energy into usable (ATP) energy in our cells.

o Heat is given off in every energy transfer. Second Law of Thermodynamics

o Entropy of the universe always increases. The universe is always moving closer to chaos (entropy). Entropy – Measure of disorder (randomness/chaos).

o If entropy always increases, why can we clean our rooms? Room is a closed system. Use energy to clean. Put energy into a closed system. Using energy actually increases entropy.

By putting energy into something (like cleaning your room) you are increasing the entropy of the universe.

Living things work this way… we require an input of energy… therefore we increase the entropy of the universe.

o Heat is a highly disordered form of energy.

Overview of Photosynthesis

Where does all the energy that supports life come from?o The sun

Sunlight

o Photosynthesis converts solar energy into the chemical energy: 6CO2 + 6H2O + Sun C6H12O6 + 6O2

o Cellular Respiration C6H12O6 + 6O2 6CO2 + 6H2O + ATP

o Autotrophs : Organisms that can produce their own food. Example: Plants, algae, and certain bacteria.

Overview of Cellular Respiration

Converts food energy into usable energy, called ATP, for the cell (+heat) C6H12O6 + 6O2 6CO2 + 6H2O + ATP

Heterotrophs : Organisms that get their energy from another source.o Example: animals, fungi, bacteria, protists.

Overview of important molecules

ATP – Adenosine Triphosphateo Structure

Adenine (nitrogen base) Sugar THREE phosphates

o Energy in bonds between phosphates.o Function

Provides energy to cell for cellular processes and chemical reactions. Entire pool of ATP is recycled once per minute.

o ATP + H2O ADP + Inorganic Phosphate + Energy ATP Cycle

o ATP breaks down into ADP + phosphate Use energy!

Movement Active Transport Making molecules

o Transport energy from food to replenish the missing phosphate group Make ATP!

Breakdown of food. Food molecules: (carbohydrates, lipids, proteins)

o Food contains potential energy.o By breaking the chemical bonds in the good, we can release energy and transfer it to

other forms. Food

Release energy quickly producing heat and light Release energy slowly in the form of ATP

Wait… doesn’t food provide energy? Why do we need ATP?o We cannot utilize the energy that directly comes from food, so we need to convert it

into ATP so our body can use it. Electron Carriers : Temporary energy storing molecules.

o NADH and FADH2; NADPH NADH (Nicotinamine Adenine Dinucleotide) FADH2 (Flavin Adenine Dinucleotide)

Energy in Heterotrophs making ATP

Overview:o 3 Methods to make ATP.

Phosphocreatine Glycolysis and (Lactic Acid) Fermentation (Aerobic) Cellular Respiration

o Track two things: What energy transfers are occurring? Where are the carbon atoms?

Phosphocreatine : Enzyme that adds Pi (Phosphate) directly onto ADP to make more ATP.o Used for quick energy.o Anaerobic (doesn’t use oxygen)o Stored in muscles.o Only works for ~30 seconds!

1. Glycolysis: The partial breakdown of glucose.o Features:

Used for short term energy production. Anaerobic Occurs in the cytoplasm.

o Process: Priming: ATP is used to add phosphates to glucose. Cleavage: 6C unit split into 2 – 3C units. Energy Recovery: Production of ATP and NADH. Ends with 2 molecules of Pyruvate (AKA Pyruvic Acid).

Electron Carriers :o NADH is formed to temporarily hang on to energy before making ATP.

Nicotinamine Adenine Dinucleotide.o NAD+ and NADH are recycled over and over again!

Glycolysis Summary o Inputs

Glucose 2 NAD+

2 ATP

4 ADP + 2 Po Outputs

2 Pyruvate 2 NADH 2 ATP (NET gain)

After Glycolysis, the fate of Pyruvate depends…o Oxygen Absent

Fermentationo Oxygen Present

Cell Respiration

Energy in Heterotrophs Fermentation

If oxygen is NOT available, fermentation occurs.o Fermentation – Anaerobic process (does not require oxygen).o In animals – Lactic Acid Fermentation

Pyruvate is converted into Lactic Acid.o In plants and yeast – Alcoholic Fermentation

Pyruvate is converted into ethyl alcohol (ethanol) and CO2. Why go through Fermentation? Why not just stop and wait for Oxygen?

o To regenerate the NAD+.o Need Glycolysis to take place even when there’s no Oxygen.o Fermentation regenerates NAD+ from NADH so that Glycolysis can repeat.

Recall: NET of 2 ATP produced in Glycolysis! Why is Fermentation cool…

o Alcoholic Fermentation. If the plants are dead, what is alive that undergoes Glycolysis?

o Bacteria or yeast consumes the cells of the dead plant and it undergoes Glycolysis.

Energy in Heterotrophs

Fate of Pyruvateo Oxygen absent

Fermentation (in cytoplasm)o Oxygen present

Cellular Respiration (transition into mitochondria)

Energy in Heterotrophs Cellular Respiration

If oxygen IS available, cellular respiration continues in the mitochondria:o 4 main steps of Cellular Respiration:

1. Glycolysis 2. Transition reaction

3. Kreb’s Cycle 4. Electron Transport Chain

Features:o Used for long term energy production.o Aerobic (requires oxygen)o Occurs in mitochondrial matrixo Can use glucose, fats or proteins as fuel.

The Mitochondria:

2. Transition Reaction

Occurs between cytoplasm and the mitochondrial matrix.o Pyruvate combines with Coenzyme A (CoA) to produce Acetyl-CoA.o 2 CO2 releasedo 2 NAD+ is reduced to 2 NADH

End of Transition Reactiono So…

Where is the potential energy of glucose now being stored? Some of it is in the NADH, and some of it is in the Acetyl-CoA. In addition to ATP and NADH from Glycolysis.

Where are the 6 carbons we started with? 2 C exhaled as CO2

Other 4 C in Acetyl-CoA (2 each)

3. Kreb’s Cycle (Citric Acid Cycle)

Acetyl-CoA combines with a 4C molecule. The 6C molecule releases a CO2, and NAD+ is reduced to NADH. The 5C molecule releases another CO2, and NAD+ is reduced to NADH. ATP is generated. FAD+ and NAD+ are reduced to FADH2 and NADH. The 4C molecule is recycled.

Happens two times. NET Output of Kreb’s Cycle (per glucose molecule)

o 6 NADHo 2 FADH2

o 2 ATPo 4 CO2

End of Kreb’so So…

Where is the potential energy of glucose now being stored? NADH, FADH2, ATP In addition to ATP and NADH from Glycolysis and Transition.

Where are the 6 carbons we started with? All 6C exhaled as CO2

4. Electron Transport Chain (Electron Transport System)

What’s involved?o Electron carriers : NADH and FADH2 are temporarily storing energy.o Electron transport proteins : Membrane proteins (part of the mitochondrial

membranes). H + Pumps : Membrane protein to pump a proton against concentration gradient. ATP Synthase : Protein that uses energy released by movement of protons down

concentration gradient to make ATP. This process is called Chemiosmosis.

o Oxygen : An “input” and final electron acceptor of the process. “Catches” electrons and binds to H+ to form water.

Processo How many ATP does each NADH yield?

3 ATPo How many ATP does each FADH2 yield?

2 ATP

Aerobic Cellular Respiration

C6H12O6 + O2 H2O + CO2 + ATP C6H12O6 Glycolysis O2 ETC () +H+ + e-

H2O ETC CO2 Transition (2) Kreb’s (4) ATP

Energy in Heterotrophs Making ATP

End of electron transport chain:o Where is the potential energy of glucose now being stored?

ATPo Where are the 6 carbons we started with?

Exhaled as CO2

Energy in Autotrophs: Photosynthesis

Light Energy:o Light is a wave.

Wavelength (λ) – Distance between two peaks. Small wavelength = higher energy Large wavelength = lower energy Different wavelengths reflect different colors.

o Pigments: Molecules that absorb/reflect sunlight. Examples:

Chlorophyll (absorbs red, reflects green) Carotenoids (absorbs violet/blue, reflects yellow/orange)

How they work: Molecules absorb a photon of light. Electrons become energized and jump to a higher energy levels. Electrons typically fall back down, but in photosynthesis – they are

“caught” by electron carriers and are used to do work. Photosynthesis:

o Takes place in the Chloroplast: Thylakoid : Flattened disc; contains chlorophyll. Stroma : Fluid filled region. Grana : Stacks of Thylakoids.

o 2 Reactions 1. Light-dependent reactions

Occurs in Thylakoid membrane. 2. Light-independent Reactions (AKA Calvin Cycle)

Occurs in Stroma. Also known as Carbon fixation.

o Process Light-dependent Reactions:

1. Sunlight excites e- in chlorophyll of photosystem II and “caught” by an e- acceptor.

2. e- transferred along an electron transport chain (ETC). 3. Sunlight excites e- in photosystem I and again, it is “caught” by an e-

acceptor. 4. e- are transferred along the ETC and will eventually combine with

NADP+ to make NADPH. 5. Restoring Photosystem II:

o Enzyme in Thylakoid splits water into protons, electrons, and oxygen. (H2O e- + H+ + O2)

o Electrons replace photosystem II; protons are left inside Thylakoid; oxygen gas diffuses out.

6. Synthesis of ATP:o Chemiosmosis : Build up of a H+ concentration gradient (high in

Thylakoid space).o ATP Synthase : Located in the Thylakoid membrane, makes ATP

as H+ moves down the concentration gradient. Order of pigments is photosystem II, then photosystem I.

Light-independent Reactions (AKA Calvin Cycle): 1. CO2 enters and combines with RuBP to form PGA.

2. ATP and NADPH provide energy and H+ to convert PGA to PGAL. 3. Most PGAL is converted back to RuBP, but some is eventually used to

make GLUCOSE!

Cell Reproduction

Human (Eukaryotic) DNA

Storing DNAo Nucleus:

Nuclear Envelope : Double membrane surrounding the nucleus. Nuclear Pores : Small holes in the membrane.

o Packaging DNA Chromatin – Long, thin, uncoiled DNA. Histone Proteins – DNA wraps around to help coil. Chromosomes – DNA coiled, thick (stored this way for replication). Chromosome (cont.) Replicated Chromosomes

Chromatin replicates itself into 2 identical pieces of chromatin. Chromatin condenses and forms 2 identical chromosomes. Chromosomes connect together at a structure called centromere. When

they stick together at the centromere, it creates one big chromosome made up of two identical chromatids.

Sister Chromatids – Exact copies of DNA Centromere – Connects sister chromatids.

Karyotype : Photograph of all chromosomes in a cell.o Homologous Chromosomes – Two chromosomes that carry the same type of

information, but are not identical. Autosomes – Non-sex chromosomes (22 pairs). Sex Chromosomes – Usually XX or XY; determines sex (1 pair).

Quiz Time

How many chromosomes do human cells have?o 46

How many pairs of chromosomes do humans have?o 23

Autosomes?o 22

Sex chromosomes?o 1

Prokaryotic Cell Division

Binary Fission : o (Remember: no nucleus)o Single piece of DNA (circular)o Copies DNAo DNA moves to opposite sides.o Cell divides in half.o Happens very fast.

Eukaryotic Cells

Cell Cycle : Sequence of growth and division of a body cell.o Importance: Growth, healing, and repair.o 3 main parts:

Interphase Mitosis Cytokinesis

Structures involved:o Chromosomes : DNAo Spindle Fibers : Microtubules that attach to the centromere and move chromosomes.o Centrioles : Structures that anchor the spindles at opposite ends of the cells.

Cell Cycle: Interphase

Interphase is the cell carrying out its normal life activities and chromosomes become duplicated. G1 – “Gap” between cell division, cell grows. G0 – “Gap” phase. Cells are NOT undergoing any preparation for cell division – just “being”. S – “Synthesis”; DNA is copied.

o When the DNA is copied inside the nucleus. It’s preparing for the cell to divide. G2 – “Gap” cells prepare for division; Centrioles replicate, spindles form.

Cell Cycle: Mitosis

Prophase :o Chromatin coils to form visible chromosomes.o Nuclear membrane and nucleolus disappear.o Spindle fibers form between Centrioles, which move to opposite ends of cell.

Metaphase :o Chromosomes meet in the middle.o Each chromatid is attached to separate spindle fibers.

Anaphase :o Centromeres split and sister chromatids separate as they are pulled apart to opposite

sides of cell. Telophase :

o Nucleus and nucleolus reappear.o Cells form two new daughter nuclei.o Chromosomes begin to uncoilo Cell begins to divide.

Cell Cycle: Cytokinesis

Cytokinesis : Complete division of cytoplasm.o In plants, cell plate forms and eventually becomes the cell wall that separates the two

cells.o In animal cells, a protein ring encircles the plasma membrane.

Ring contracts producing a cleavage furrow.

Human Life Cycle

Haploid cells (n) : Only one copy of each chromosome.o Ex: Gametes – Egg and sperm cells.o n = 23 in humans.

(n) = Haploid. Diploid cells (2n): Two copies of each chromosome.

o Found everywhere except where the egg and sperm cells are produced.o Found in most body cells.o 2n = 46 in humans.

Eukaryotic Division – for sex cells

Meiosis: o Cell division that produces sex cells (sperm/egg).o This is DIFFERENT from mitosis/the cell cycle (which is used for growth and repair).

Meiosis

Two Divisions:o Meiosis I:

Separates homologous chromosomes (the pairs).

Diploid haploid. Total of 2 haploid cells at the end of division. 1 Diploid cell divides into 2 haploid cells.

o Meiosis II Separates sister chromatids (the “X”s). Haploid haploid

Total of 4 haploid cells at the end of division. 2 Haploid cells divide into 4 haploid cells.

Meiosis: The Process

DNA is replicated before Meiosis I occurs. Meiosis I: Separation of chromosomes.

o Prophase I Synapsis : Pairing of homologous chromosomes. Crossing Over : Process where regions of DNA are exchanged.

o Metaphase I Homologous pairs meet in the middle.

o Anaphase I Homologous pairs pulled apart to opposite poles.

o Telophase I DNA uncoils and one of each pair of homologous chromosomes is at each pole. Cytokinesis occurs. Haploid cells are formed.

Meiosis II: Separation of chromatids.o Prophase II

Chromosomes condense again. DNA does not replicate again.

o Metaphase II Chromosomes line up in the middle of the cell.

o Anaphase II Sister chromatids separate. Chromosomes are pulled to opposite poles.

o Telophase II Nuclei forms around the Chromosomes. Cytokinesis occurs.

o Haploid Cells Four gametes (animal)/spores (plant) are produced.

Pictures on next page.

Law of Independent Assortment

Each pair of chromosomes acts independently of the other pairs.o This leads to endless possibilities of gametes that we can produce!

Fertilization

Haploid Gamete (sperm) + Haploid Gamete (egg) = Diploid Zygote. 23 + 23 = 46

Errors in Meiosis

Changes in Chromosome Number:o Non-disjunction : Failure of homologous chromosomes or sister chromatids to separate

properly during meiosis.o Ex: Down’s Syndrome – Extra 21 chromosome.o Ex: Turner’s Syndrome – X_ (missing X chromosome)o Ex: Klinefelter’s Syndrome: XXY (extra X chromosome)

Changes in Chromosome Structure:o Mistakes occurs during crossing over.

Deletion – Part of chromosome gets lost during crossing over. Duplication – Part of chromosome gets copied during crossing over. Inversion – Part of chromosome gets flipped upside down during crossing over. Translocation – Part of chromosome switches places with another chromosome. Ex: Cri du Chat

Symptomso Small head (microcephaly)o Unusually round faceo Misshapen voice box “cat-like” cry as infants.

Sexual vs. Asexual Reproduction

Asexual Reproduction – A single parent passes copies of all its genes to each of its offspring (a.k.a. clone)

o Clones may be produced by: Binary fission Mitosis Fragmentation Budding

Sexual Reproduction – Two parents each form haploid gametes. o Gametes fuse together to form a diploid zygote.o Offspring have genetic variation due to the fusion of two different sets of chromosomes.o Occurs only in eukaryotes, including humans.

Effect on Genetic Diversity

Asexually reproducing organisms have very little genetic diversity.o Many offspring in a short period of time.

Sexually reproducing organisms have great genetic diversity.o Each generation has genetic variation.

Cancer

Cancer – Unregulated cell growth.o Cell cycle continues uncontrollably.o Keeps dividing and dividing… doesn’t stop.

Tumor: Cluster of cells from unregulated growth.o Benign

Not dangerous Not going to affect the body that much

o Malignant Dangerous Malicious

Metastasis – o Occurs in malignant tumorso Cancerous cells spread to different parts of the body the through bloodstream.

Risk factorso Sun exposure (UV rays)o Smokingo Family history (genetics)o Chemical exposureo Radono Radiationo Asbestos

Unit 5: Genetics

Gregor Mendel (1822-1884)

Austrian Monk Developed Laws of Inheritance Studied Pea plants (28,000) Called the “Father of Genetics” Mendel did not know that the physical traits inherited were actually chromosomes and DNA.

Genetic Terminology

Heredity – Passing of traits from parent to offspring. Genetics – Study of heredity. Traits – Any characteristic that can be passed from parent to offspring.

o Ex: Plant height, seed texture, seed color

Experiments with Pea Plants

Pollinationo Pollen is male plant sperm.o Plants have both male and female reproductive structures.o Self-pollination:

Flowers are fertilized by own pollen.o Cross-pollination:

Flowers fertilized by different flowers. Mendel produced pure strains by allowing the plants to self-pollinate for several generations. Parental (P) generation: Purple x White F1 Generation: All Purple F1 Purple x F1 Purple F2 Generation: 3:1 Ratio purple vs. white

Generations: P, F1, F2

More Terminology

Genotype – Gene combination for a trait (e.g. RR, Rr, rr)o TT, Tt, tt

Phenotype – The physical feature resulting from a genotype (e.g. red, white)o TT = Tastero Tt = Tastero tt = Non-taster

Alleles – Two forms of a gene (dominant and recessive) represented by letters.o T = Dominant alleleo t = Recessive allele.

Dominant – Stronger of two genes.o Expressed in the hybrid; represented by a capital letter (R).

Recessive – Gene that gets covered up by the dominant trait.o Represented by a lowercase letter (r).

Homozygous Genotype – Gene combination involving 2 dominant or 2 recessive genes (alleles). TT, tt, or RR, rr; also called true- or pure-bred.

Heterozygous Genotype – Gene combination of one dominant and recessive allele (Tt or Rr) also called hybrid.

Law of Segregation – A pair of “factors” is segregated, or separated, during reproduction.

Mendel’s Laws and Punnett Squares

Law of Independent Assortment :o Recall: One pair of chromosomes acts independently of other chromosome pairs.o New meaning: Alleles for different traits are distributed to gametes independently of

one another. Ex: Use “Rr” to represent one pair of chromosomes and “Yy” to represent

another pair. Dihybrid Cross : Cross involving two different traits.

o Ex: Tall (T) pea plants are dominant over short (t). Round seeds (R) are dominant over wrinkled (r).

TT – Tall Tt – Tall tt – Short -------------- RR – Round Rr – Round rr – Wrinkled

o Cross a plant that is heterozygous for both traits with another plant that is heterozygous for both traits.

Parent 1 genotype: Tt, Rr Parent 2 genotype: Tt, Rr

Keep traits together. In the trait pairs, put the capital letter first.o Another Dihybrid cross –

Cross a Black, short haired guinea pig (BBSS) with a brown, long haired guinea pig (bbss).

Exceptions to Mendel’s Laws

Incomplete Dominance : Neither allele is completely dominant; rather they combine to create a new mixed trait.

o RR’ = Heterozygouso RR = Redo RR’ = Pinko R’R’ = Whiteo Ex: Cross a Pink x Pink

Codominance : Both alleles are expressed equally; both phenotypes are produced.o Ex: Human blood type A, B, AB, O Groups

IA, IB, i IAIA = Homozygous dominant A genotype IAi = Heterozygous dominant A genotype IBIB = Homozygous dominant B genotype IBi = Heterozygous dominant B genotype IAIB = Heterozygous codominant AB genotype ii = Homozygous recessive O genotype IA and IB dominant alleles i recessive allele IAIB codominant allele

Rh factor – Another type of marker on your cellso If you have it, you’re “positive”o If you lack it, you’re “negative”o Positive is (dominant) over negative (recessive)o RR = Rh+

o Rr = Rh+

o rr = Rh-

Sex-linked traits – Genes that reside on the X chromosome; more commonly found in males.o Sex chromosomes

Recall: Females – XX, Males – XYo Examples:

Colorblindness

Polygenic Traits – Traits determined by multiple genes; gives a range of phenotypes.o Ex: Skin color, eye color, hair color, height, etc…

Simple Probability

Product Rule (AKA “AND” rule) – The probability that two events will both happen; probability = product of their individual probabilities.

Sum Rule (AKA “OR” rule) – Probability of an event that can happen in multiple ways; probability = sum of their individual probabilities.

Pedigrees

Family tree that traces inheritance of a certain trait.o May be autosomal or sex-linked.

Keyo Males = Squareso Female = Circleso Shaded = Affectedo Blank = Unaffectedo Half-shaded = Carrier

Not all pedigrees show carriers!

Unit 6: DNA and Protein Synthesis

DNA ( D eoxyribo n ucleic A cid)

Rosalind Franklin and Maurice Wilkins X-ray diffraction James Watson and Francis Crick Created 3D model of DNA

DNA

DNA is composed of strings of chemicals called nucleotides. Long sequences of these nucleotides are called genes. Genes are uniquely organized in each individual. Entire set of DNA are genome. Full spectrum of genomes is the gene pool.

DNA structure

Double Helix : Nucleotides are arranged like a twisted ladder.o Sides of ladder: Alternate sugar-phosphate

Held together by covalent bonds.o Steps: Pairs of nitrogen bases.

Held together by hydrogen bonds. Nucleotides:

o Sugaro Phosphateo Nitrogen Bases

Purines: Adenine Guanine

Pyrimidines Cytosine Thymine

Guanine will always pair with Cytosine Adenine will always pair with Thymine ‘T’ will always pair with ‘A’ ‘C’ will always pair with ‘G’

DNA Replication

What do we mean by replication?o Make copies of DNA

Why does DNA need to make copies of itself?o So every single one of new cells have the exact same amount of DNA.

Same as the ‘S’ phase of the cell cycle. Occurs in the nucleus Enzymes involved:

o Helicase – “Unzips” DNA (unwinding DNA)o DNA Polymerase – Adds complementary nucleotides, forming two new strands of DNA.

DNA Polymerase I – Adds complementary nucleotides. DNA Polymerase II – Proofreads new DNA strands.

Ex: Imagine you need to replicate your DNA. Use the following template strand of DNA to show this process.

o Write the complimentary base sequence of the new strand: A G C C T A A C T C G G G A T T C G G A T T G A G C C C T A

A with T, G with C What happens if DNA polymerase makes a mistake and adds the wrong nucleotide? Mutations : Changes in the nucleotide sequence.

o Occurs when DNA polymerase adds the wrong nucleotide.o Happens in ~1/10,000 nucleotides

Good news?... … DNA polymerase can proofread and repair mistakes!

**DNA to Protein Synthesis

Quick reviewo Describe the structure of proteins

Amino Acidso What cell structures build proteins

Ribosomeso What do proteins do

Enzymes Transport

o Amino Acids 20 types of Amino Acids

Arranging these in different combinations HUGE diversity of proteins. DNA “controls” the cell by determining what proteins are made! So… how does it do that?

o In a 2 step process: Transcription and Translation. Transcription

o Taking the information of DNA and transcribing (rewriting) it to RNA. Translation

o RNA leaves the nucleus and is translated into a protein. The process

o Transcription : Genetic information is copied from DNA to RNA (Ribonucleic Acid). Re-writing of DNAs instructions in the form of RNA. RNA structure

Single stranded Ribose sugar Uracil mRNA, tRNA, rRNA

Occurs in the nucleus.

DNA Vs RNA

DNAo Sugar

Deoxyriboseo Nitrogen Base

[A, T,] [C, G]o Function

Contains heredity information 2 strands

RNA (3 kinds)

o Sugar Ribose

o Nitrogen Base [A, U,] [C, G]

o Function mRNA: Provides instruction (messenger RNA) tRNA: Delivers amino acids (transfer RNA) rRNA: Combines with proteins to form ribosomes (ribosomal RNA) 1 strand

DNA to Protein Synthesis (transcription)

What’s involved?o DNA (the gene)

Promoter – Region where polymerase binds. Termination signal – Causes release of mRNA.

o RNA Polymerase : Forms complimentary base pairs between DNA strand and RNA nucleotides.

o mRNA – (messenger RNA) Molecules that will later be ‘read’ to make the protein.

DNA to Protein Synthesis: Transcription

Example: Transcribe the DNA base sequence written belowo Hint: Use complimentary base pairing to make a strand of mRNA.

DNA: G G C T T C G A A A T A C T G G T A A mRNA: CC G A A G C U U U A U G A C C A U U DNA (transcription) mRNA (translation) Protein

Translation:

Processo Translation : Assembling proteins from information encoded in the mRNA.o Occurs with the ribosomes, located in the cytoplasm/Rough ER.

What’s involvedo mRNA (messenger RNA):

Codons – 3 bases of mRNAo rRNA (ribosomal RNA): Ribosomes – Creates the protein by “reading” the mRNA.o tRNA (transfer RNA): Matches mRNA with correct amino acid

Anticodons – 3 bases on tRNA, complementary to mRNA.

Mutations

Mutation : A change in the base sequence of DNA. Four types of mutations:

o Silent mutationso Missense mutationso Nonsense mutationso Frameshift mutations

Types of Mutations

Silent mutation : The change in the base sequence does not change the amino acids. Missense mutation : The change in the base sequence causes a different amino acid to be

inserted into the protein. Nonsense mutation : The change in the base sequence results in a STOP Codon, which causes the

ribosome to stop adding amino acids. Protein synthesis stops. Frameshift mutation : A nucleotide is inserted or deleted. All the amino acids following the

mutation are incorrect.