AP Bio Notes

Unit 1: Chemical Foundation of Life

Chemistry Review:

Chemical bonding: Atoms share electrons by bonding with each other.

Ion: An atom with a charge, any atom with an uneven amount of electrons and protons.

Cation: Ion with a positive charge by losing electrons

Anion: Negatively charged ion by gaining ions

Electronegativity: (Determined by how many electrons are in the valence shell) Measurement of how much they will pull electrons toward themselves and the closer an electron is to eight electrons the more electronegative that element is.

  • Most Electronegative element is Fluorine

  • 2nd most electronegative element is Oxygen

  • 3rd most electronegative element is Nitrogen

Electropositivity: Ability of elements to donate electrons and form positive ions

Polar Molecules: Occur when there is an unequal sharing of electrons across a covalent bond meaning that electropositive elements who donate and electronegative elements who take are bonded and that electron is shared more with the electronegative element which is selfish.

Types of Bonds:

  • Ionic Bond: Formed between ions with opposite charges

  • Covalent Bonds: Stronger bonds than ionic bonds made with sharing electrons between atoms.

    • Non-Polar Covalent Bonds: Bonds with an electronegativity difference of less than 0.4

    • Polar Covalent Bonds: Bonds with an electronegativity difference of more than 0.4

  • Hydrogen Bond: individually weak bonds created by the attraction of an electronegative element in a molecule with a electropositive element in another molecule

Properties of Water:

Water & Hydrogen Bonding: Water is polar, therefore has uneven amount of charges, and this allows the electropositive end to attract to the electronegative end of water molecules forming hydrogen bonds. Hydrogen bonds are the reason for the properties of water.

Properties:

  • Cohesion: Water molecules attraction towards each other

    • Results in Surface Tension by which the cohesion of water makes the surface resistant to rupture by light objects

  • Adhesion: Water molecules attraction towards other polar molecules

    • Results in Capillary Action, by which water sticks to side of tubes, or plant roots, and goes up the sides.

  • High Heat Capacity: Waters resistance to temperature change.

    • Used by organisms to maintain homeostasis in the body

    • Takes a lot of energy to break the many hydrogen bonds in water

  • Density as a Solid: Water is less dense as a solid than liquid.

    • Creates ice sheets as a insulating barrier to protect life under the sheets from freezing

  • Solvency: What is a excellent solvent; dissolves other chemicals.

    • Very good at pulling ionic compunds like salt apart into ions

Biomolecules:

Biomolecule: Large or small molecule used by living organisms; an umbrella term

Macromolecule: Large molecules used by living organisms such as:

  • Carbohydrate

  • Lipid

  • Protein

  • Nucleic Acid

Elements of Macromolecules:

  • Carbon

  • Hydrogen

  • Oxygen

  • Nitrogen

  • Phosphorous

  • Sulfur

Biomolecule Metabolism

Metabolism: The combination of chemical reactions that synthesize and hydrolyze biomolecules for energy storage and release in an organism.

  • Catabolism: Creates energy

    • Breaks down biological polymers into monomers to help generate ATP

  • Anabolism: Synthesizer for storage of energy

    • Build up monomers into polymers

Dehydration Synthesis: monomers are covalently bonded together into polymers.

  • Anabolic process

  • Removes water to build larger molecule

  • Water is formed as a byproduct outside

  • Requires the assistance of enzymes to occur

Hydrolysis: Polymers are broken down into monnomers.

  • Catabolic

  • Add water to break down molecule

  • Requires the assistance of enzymes to occur

4 Types of Biomolecules

Carbohydrates: known as sugars

  • Monomers are monosaccharides

    • Such as Glucose

  • Polymers are polysaccharides

    • Such as Starch

  • Function:

    • Short term energy source

    • Energy storage

    • Provide structure in organisms

      • Such as cellulose in plants

  • Structure is hexamer rings

    • Always in a ratio of 1Carbon:2Hydrogen:1Oxygen

  • Types of Carbs:

    • Branched Structure used to break multiple monomers at once to allow for faster ATP generation -

    • Stacked structure giving organisms structural support -

Lipids: known as fats or oils

  • Monomers are fatty acids

  • Polymers are lipids

  • They are hydrophobic, water avoidant

  • Function:

    • Long term energy storage

    • Insulation and protection of organs

  • Structure is long hydrocarbon chains -

    • Ratio of 1Carbon:2Hydrogen: Low oxygen

  • Types of Lipids:

    • Saturated fats with no double bonds in their structure like the example above

      • These fats are linear and can stack to creat dolids at room temp which leads to build up in blood vessels

    • Unsaturated fats with double bonds

      • Stays liquid at room temp

Proteins: found in meats and muscles

  • Monomers are amino acids

  • Polymers are polypeptides

  • Function:

    • Wounds and tissue repair

    • Enzymes

    • Cell Signaling

  • Structure is very complex with four levels

  • Elemental Composition:

    • Carbon, Hydrogen, Oxygen, Nitrogen and Sulfur

    • Known as CHONS for short

  • There are many different types of proteins form proteins embeed into cell membrane to enzymes thtat help catalyze chemical reactions

Nucleic Acid: known as genetic material

  • Monomers are nucleotides with 3 parts

    • 5-carbon sugar (ribose or deoxyribose

    • Phosphate

    • Nitrogenous Base with pairings of A T G C or U

    • All linked by covalent bonds

  • Polymers are nucleic acids

  • Function:

    • Storage of genetic material

  • Elemental Composition:

    • Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorous

    • CHONP for short

  • Types of Nucleic Acids:

    • DNA which is deoxyribonucleic acid

      • Double helix

      • Stores genetic code

      • 4 nitrogen bases: ATGC

      • More stable than RNA

      • Found in Nucleus

    • RNA which is ribonucleic acid

      • Single Stranded

      • 3 types

        • Messanger mRNA

        • Transfer tRNA

        • Riobosomal rRNA

      • Used for protein synthesis

      • Instead of Thymine as a nitrogen base it is Uracil

      • Less stable than DNA

      • Made in nucleus and transported to cytoplasm

Protein Structure

Amino Acid Structure: Bonded to one carbon

  • Amine group

    • Indicated by bonded elements of NH2 or NH3

  • Carboxyl Group

    • Indicated by bonded elemnts of COOH or COO-

  • R Side Chain

    • Varies between the 20 amino acids

    • Determines if amino acid is hydrophobic, hydrophilic, acidic, or basic

  • One hydrogen bond to complete 4 covalent bonds of carbon

Primary Protein Structure

Peptide Bond: Bond created between two amino acids

  • Uses dehyration synthesis

  • Connects the amine group of one amino acid and the carboxyl group of another amino acid

A sequence of connected amino acids creates the primary structue of proteins:

Secondary Protein Structure

Hydrogen bonds between amino acids create two types of secondary structures

  • Will be broken if protein is outside of normal pH or temp

Alpha Helice:

Beta Pleated Sheets:

These shapes form because of the hydrogen bond attract certain sections to fold the protein into these forms.

Tertiary Structure

Hydrophobic Collapse: Occurs as the hydrophobic Amino Acids collapse away from the water and into the interior of hte tertiary structure of the protein. Driving factor in the formation of tertiary structure.

  • R side chains are either hydrophobic or hydrophilic

  • Hydrophobic side chained amino acids go inside and away from water

  • Hydrophilic side chained amino acids go outside and face the water

  • This is called the folding of amino acids

  • Protein is function at this point

Charge attraction: Occurs between acidic and base charges in R groups of amino acids

  • Will be broken if protein is outside of normal pH or temp

Disulfied Bridges: Covalent bonds between the sulfur atoms in side chains of two cysteine amino acids

  • Very strong and will not break outside of normal pH or temp

Quarternary Structure

A mix of tertiary protein molecules together

  • Not all proteins are inovlved in quarternary structures

Unit 2: The Cell

Eukaryotic vs Prokaryotic:

Eukaryotic:

  1. Nucleus

  2. Single or Multi Celled

  3. Membrane bound organelles

  4. Evolved from prokaryotic cells

  5. Cytoplasm region

Prokaryotic:

  1. No nucleus

  2. DNA is an unbound nucleoid region

  3. No membrane-bound organelles

  4. Cytoplasm bound by the plasma membrane

  5. Single celled only

3 Domains of Life:

  1. Archaea and Bacteria - prokaryotic

  2. Eukarya - eukaryotic

All Cells Possess:

  1. Plasma Membrane

  2. Cytosol

  3. Chromosomes

  4. Ribosomes

Organelles & Functions:

Ribosomes:

  • Make of protein and rRNA

  • Synthesizes proteins form mRNA

  • Free-floating or attached

Cytoplasm:

  • Liquid of water, salt and other nutrients

  • Helps maintain shape

  • Site of metabolic reactions

Cytoskeleton:

  • Helps maintain the shape of animal cells

  • Help vesicles get transported around the cell

  • 3 parts

    • Actin filaments, microtubules, intermediate filaments

Centriole:

  • Creates spindle fibers during mitosis and meiosis

  • Spindle fibers help pull chromosomes apart

Flagella and Cilia:

  • Help move cells around

  • Flagella are longer

  • Cilia are shorter

Nucleus:

  • Surrounded by double nuclear membrane which protects DNA from denaturation

  • Place where transcription (DNA to mRNA) happens

Nucleolus:

  • Site of ribosome synthesis

  • Makes rRNA

Smooth ER:

  • Synthesis lipid/steroid hormone/detoxification

  • Lipids and hormones get sent to the golgi apparatus

Rough ER:

  • Highly folded organelle

  • Contiguous with the nucleus

  • Has ribosomes attached

  • Packs and sends proteins to golgi

Golgi:

  • Fold And modify proteins

  • Packages proteins/lipids into vesicles

  • Sends vesicles to destinations

Peroxisome:

  • Lipid hydrolysis to break down lipids

  • Fatty acid from break down go to mitochondria for ATP

  • Uses catalase (enzyme) to break down hydrogen peroxide (toxic)

Lysosomes:

  • Apoptosis - Programmed cell death

  • Contains a lipid bubble of hydrolytic enzymes that break down cell waste and denatured proteins into their monomers

Vacuole:

  • Storing and releasing fluids/biomolecules

  • Stores waste products until they can be broken down

Mitochondria:

  • Two membranes which allows for compartmentalization of different chemical reactions

  • Folding of inner membrane increases surface area to allow for more ATP production 

Chloroplast:

  • Arranged in stacks of thylakoid membranes called grana

  • Multiple thylakoids increases surface area for more reactions

  • Also has two membranes allowing for compartmentalization of different reactions


Plasma Membrane:

Phospho-Lipids:

  • Phosphate head that is polar and hydrophilic

  • Lipid tail is hydrophobic and nonpolar

Cholesterol:

  • Controls fluidity of membrane

  • More or less fluid depending on temperature

Glycolipids:

  • Facilitated cell to cell adhesion and recognition

Glycoproteins:

  • Allows for cross linking of cells

Membrane Proteins:

  • Peripheral Proteins

    • Found on the inner membrane surface

  • Integral Proteins

    • Partially or completely (transmembrane) in the membrane

    • Amphipathic: Have both hydrophobic and hydrophilic regions

Endosymbiotic Theory:

Compartmentalization:

  • Mitochondria increases surface area through the inner membranes being folded

  • Chloroplasts have grana which increase surface area

Endosymbiosis: Ancestral eukaryotic cells engulfed an ancestral mitochondrion establishing a mutualistic relationship

  • Serves as the explanation for the origins of mitochondria and chloroplasts

  • Chloroplasts got engulfed after mitochondria

Mitochondria and Chloroplast Common Ancestry Evidence:

  • Contains circular DNA

  • Possess ribosomes

  • Have a double membrane

  • Are self-replicating

Cell Transport:

Concentration Gradient: Concentration of a particle (element or molecule) is higher in one area than in another.

  • Particle moving down the concentration gradient is moving from high to low (no resistance)

  • Particle moving up the concentration gradient is moving from low to high (resistance)

Passive Transport

Passive Transport: Movement of substances across the cell membrane without the input of energy

  • No energy required

  • Net movement of substance down their concentration gradient

Diffusion: Movement of substance down a concentration gradient

Dynamic Equilibrium: No concentration gradient as substances move in equal rates. There is no high and low concentration, it’s just constant. Substances STILL move back and forth across a membrane just in equal amounts.

Osmosis: Diffusion of water across a selectively permeable membrane

  • Moves from higher to lower water concentration across membrane

  • Moves from lower to higher SOLUTE concentration across membrane

    • More solute on a side means less water on that side as the solute takes up space for water

Aquaporins: Cells use aquaporins, which are transmembrane proteins, that allow the water to diffuse easily inside the cell.

Tonacity: measuring the solute levels inside and outside the cell with three types:

  • Hypotonic Solutions: Lower amount of solute outside the cell (lower inside)

    • Causes water to move INSIDE the cell as more water is outside

  • Hypertonic Solutions: Higher amount of solute outside the cell (higher inside)

    • Causes water to move OUTSIDE the cell as more water is inside

  • Isotonic Solutions: Equal amount of solute inside and outside

    • No NET movement of water but water still keeps moving in equal rates

Facilitated Transport

Facilitated Transport: uses membrane proteins to help substances pass the membrane. No energy is required still.

  • Channel Proteins: Allow specific substances to quickly go through hydrophilic passageways.

    • Aquaporins

    • Ion Channels

  • Carrier Proteins: solutes bind to protein which changes protein shape to let the protein out the other side of the membrane

    • Glucose carrier proteins

    • Amino acid carrier proteins

Active Transport

Active Transport: movement of substances against their concentration gradient, requiring an input of energy. (Movement from low to high)

Sodium-Potassium Pump: A protein that uses ATP to transport 3 NA+ ions out of the cell and 2 K+ into the cell.

  • Electrochemical gradient: A difference in chemical and charge concentrations across a membrane.

    • With a Sodium-Potassium Pump there is a higher concentration of potassium ions inside and higher concentration of sodium ions (Na+) outside

    • 3 positive charges pumped 2, 2 positive charges pumped in.

      • Leads to uneven amount of charges and a net negative charge inside from more positive charges being pumped out

Cotransport: protein actively pumps out a substance so it can diffuse back inside through passive transport through a cotransport protein and the substance that is having difficulty diffusing through the membrane takes a ride with the passively transported protein using the cotransport protein.

  • Technically the cotransport protein in itself is not using active transport but the pump protein that pumps out the substance for the cotransport protein to use DOES use active transport so the cotransport is using active transport INDIRECTLY.

Bulk Transport: Large molecules being transported across the membrane through vesicles.

  • Exocytosis: Intracellular vesicle often made by the golgi goes and fuses with the plasma membrane and the contents of the vesicle is excreted out.

  • Endocytosis: Vesicles form around big molecules entering the cell and a piece of the plasma membrane separates to form a vesicle inside the cell.

    • Phagocytosis (cell eating): Large, solid material is taken in by endocytosis.

Water Potential & Osmolarity

Osmoregulation: maintains water balance and solute concentrations to keep the cell in homeostasis

Water Potential

Water Potential: Measurement of the amount of free energy found in a mole of water. How likely water molecules are to move from their current position to somewhere else.

  • Mole: SI (International system of units) measure of amount of substance

  • Represented by greek letter psi ψ

  • Measured in bars

  • Free Energy: Movement

  • Low ψ means low movement and water molecules stay still

  • High ψ means high movement and water molecules move out when possible

  • Often for plant cells

Calculating Water Potential:

  • Formula: ψ = ψp + ψs

    • ψp = Pressure potential

      • Measures Turgidity of plant cells which is the pressure exerted by the cell wall on the water inside

    • ψs = Solute Potential

      • Formula: ψs = -iCRT

      • i = Ionization constant (how many elements result from dissolving one molecule)

        • Sodium Chloride: NaCl → 1Na+ + 1Cl- (i = 2)

        • Glucose: C6H12O6 → C6H12O6 (i = 1)

        • Calcium Chloride: CaCl2 0< 1Ca2+ + 2Cl- (i = 3)

      • C = Molar Concentration (M) (moles/liter)

      • R = Pressure constant (R = 0.0831 L-bar/Mol-K)

      • T = Temperature in Kelvin (K = C +273)

  • Pure water with an open container has a water potential of 0

    • High movement of water

  • Water potential goes down as solute is added to negatives

    • Low movement of water