Chapter 1: Evolution, the Themes of Biology, and Scientific Inquiry

1.1: The study of life reveals unifying themes

• Biology, the study of life, has enormous scope with five unifying themes: organization, information, energy/matter, interactions, and evolution.

• Organization: Hierarchy of biological organization

  • 1. Biosphere: All life on earth and all the places where life exists

  • 2. Ecosystems: Consists of all living things in a particular area, along with nonliving parts that life interacts with (ex. North American mountain meadow)

  • 3. Communities: Array of organisms inhabiting an ecosystem (ex. plants, animals, fungi, bacteria, etc. in meadow)

  • 4. Populations: All individuals of a species living within same area that interbreed with each other, set of populations that inhabit an area is community (ex. lupine flower in meadow)

    • Species: Can only reproduce with each other

  • 5. Organisms: Individual living things (ex. each plant in meadow)

  • 6. Organs: Body part made of multiple tissues with specific functions in the body (ex. lupine leaf)

  • 7. Tissues: Group of cells that work together to perform a specific function (ex. honeycombed tissue of lupine leaf)

  • 8. Cells: Life’s fundamental unit of structure and function

  • 9. Organelles: Various functional components present in cells (ex. chloroplasts)

  • 10. Molecules: Chemical structure consisting of 2+ atoms (ex. the atoms that make up chlorophyll)

• Emergent Properties: Properties emerge at each level that weren’t there on the last one, due to arrangement and interactions of parts as complexity increases

• Systems Biology: Analyze interactions among parts of system

• Cell Theory: All living organisms made of cells, and actions are based on cell activity

• Eukaryotic Cell: Membrane enclosed organelles and nucleus

• Prokaryotic Cell: No nucleus or membrane enclosed organelles, smaller than eukaryotic

• Chromosomes contain genetic material as DNA (deoxyribonucleic acid), which has hundreds or thousands of genes

• Gene Expression: The process which genetic information directs the production of a cellular product

• Genome: “Library” of genetic instructions that were inherited

• Genomics: Studying sets of genes in one or more species at once

• Proteomics: Studying of sets of proteins at once

  • Proteome: Entire set proteins

• Three research developments made these two approaches possible:

  • “High throughput” technology which analyzes many samples quickly

  • Bioinformatics: Use of computational tools to store, organize, and analyze data from this technology

  • Formation of interdisciplinary teams (groups of diverse specialists)

• Chemical energy goes from sun > producers > consumers

  • Energy flows in one direction

  • Chemicals go in a cycle, eventually returned to environment by decomposers

• At lower levels of organization, interactions are crucial for smooth operation

  • Feedback Regulation: Output of product regulates it

    • Negative Feedback: Most common, Response reduced initial stimulus

    • Positive Feedback: Product speeds up own production

1. A molecule consists of atoms bonded together

2. a. Life’s Processes Involve Expression and Transmission of Genetic Information ,b. New Properties Emerge at Successive Levels of Biological Organization, c. Life Requires the Transfer and Transformation of Energy and Matter

1.2: The core theme: Evolution accounts for the unity and diversity of life

• Evolution: As species’ adapt to different environments they become more and more different from their ancestors over time

• Three domains:

  • Bacteria & Archaea: Prokaryotic & Single Cell

  • Eukarya: Eukaryotes

    • Includes kingdom Plantae, kingdom Fungi, kingdom Animalia, & Protists

    • Distinguished (partly) by modes of nutrition

      • Plants produce use photosynthesis

      • Fungi absorb dissolved nutrients from surroundings

      • Animals eat and digest other organisms

      • Protists: Mostly single celled, most numerous & diverse group

• Natural Selection: Certain traits give organisms advantages over others

1. Nature selects traits which become advantageous, essentially letting it to select which traits to incorporate into the population.

2. The bird would be able to reach seeds that are further in and harder to reach

1.3: In studying nature, scientists form and test hypotheses

• Science: Our approach to understand the natural world

• Inquiry: Search for information and explanations of nature

• Data: Recorded observations

• Inductive Reasoning: Collecting and analyzing observations

• Hypothesis: Explanation based on observations and assumptions

• Experiment: Scientific test carried out under controlled conditions

• Deductive Reasoning: General > Specific

  • Opposite of inductive

  • If…then

• Theory: Broader scope than hypothesis, general enough to have sub-hypotheses, more evidence than hypothesis

1. Color is camouflaged > % camouflaged numbers

2. Inductive is specific to broad, deductive is broad to specific

3. In sandy areas, they’ll be a sandy color, in black rock areas, they’ll be dark. This is because of natural selection—the better camouflaged, the better chances to survive to reproduce and pass on the genes with the fur color alleles.

1.4: Science benefits from a cooperative approach and diverse viewpoints

• Model Organism: Species easy to grow in a lab and easy to investigate

Chapter 2: The Chemical Context of Life

2.1: Matter consists of chemical elements in pure form and in combinations (compounds)

• Matter: Takes up space and has mass

• Element: Substance that can’t be broken down into other elements

• Compound: A substance with 2+ elements combined in a fixed ratio

• 20-25% of the 92 elements are essential elements needed for an organism to survive and reproduce (varies between species)

• Trace Elements: Required by organism only in small quantities

1. When the two elements are combined to form a compound, it becomes edible. The edibility of table salt is an emergent property, since neither sodium or chlorine was previously edible.

2. A trace element is an essential element, since even thought it is only required in small quantities, it is still required to survive.

3. An iron deficiency might lead to decreased oxygen flow and prevent cellular respiration, as well as the production of ATP because of it

4. After a mutation, over time, the organism with the mutated gene might be able to survive and reproduce, eventually spreading its genes to the entire rest of the population.

2.2: An element’s properties depend on the structure of its atoms

• Atom: Smallest unit of matter that still has the properties of element

  • Composed of subatomic particles, including protons (+), neutrons, and electrons (-).

  • Atomic Nucleus: At center of the atom, a dense core of tightly packed neutrons and protons with a + charge because of the protons

  • Rapidly moving electrons form a “cloud” of - charge around the nucleus

  • Dalton: Atomic Mass Unit (AMU), protons and neutrons 1 each

• Mass Number: Total number of neutrons and protons (a)

• Atomic Number: Number of protons/electrons, which are the same (b)

• Atomic Mass: Exact mass

• Isotopes: Different atomic forms of elements

  • Behave the same way in reactions

  • Radioactive Isotope: Nucleus decays spontaneously, releasing particles and energy

  • Half Life: The time it takes for 50% of the parent isotope (original isotope) to decay into the daughter isotope (resulting isotope)

    • Radiometric Dating: Can use half lives to see how long ago an organism was fossilized or a rock was formed

• Energy: Capacity to cause change

  • Potential Energy: Energy matter possesses from its location to structure

    • The higher the distance of the electron shell to the nucleus, the greater its potential energy. (+ energy, one shell further, and vice versa)

• Valence Electrons: The electrons on the outermost (valence) shell

• Orbital: 3D space where electron is found 90% of time

1. 7

2. Super: 7, sub: 15, N

3. 7, 1

4. Number of shells, potential energy. Valence electrons, molecules that they can form covalent bonds with.

2.3: The formation and function of molecules and ionic compounds depend on chemical bonding between atoms

• Chemical Bonds: Hold attractions between atoms, which share and transfer electrons

  • Covalent Bond: Two atoms sharing a pair of valence electrons, usually nonmetals

    • Single Bond: Pair of shared electrons (ex. H—H)

    • Double Bond: Share 2 pairs of electrons (ex. O=O)

    • Valence: Bonding capacity of atom, # of atoms needed to complete the shell

  • Electronegativity: How much atom pulls shared electrons towards itself

    • Nonpolar covalent bond: Same electronegativity

    • Polar covalent bond: Electrons not shared equally

  • Ionic Bond: Cations & anions attract each other

    • Ions: Charged molecule, from when one atom is so electronegative it rips the electron from its partner

    • Cation: +

    • Anion: -

    • Ionic Compounds/Salts: Compounds formed by ionic bonds

• Hydrogen Bond: Noncovalent attraction between hydrogen and electronegative atom

• Dipole Dipole: Polar molecules attach to opposite ends like a magnet

• Van Der Waals: Adjacent molecules come together close enough that their electron clouds barely touch

• London Dispersion Forces: Temporary and very weak

• Covalent > Ionic > Hydrogen > Van Der Waals > Dipole Dipole > London Dispersion Forces

• Molecular shape is from the positions of an atom’s orbitals and affects function.

  • Similar shape means there are similar biological effects.

  • Biological molecules bind temporarily to each other through weak reactions only when their shapes are complimentary

1. In the diagram, carbon only has 6 valence electrons when it needs 8.

2. Ionic bonds

3. You can better understand the molecule’s function and which molecules do similar things

2.4: Chemical reactions make and break bonds

• Chemical Reactions: Making and breaking of chemical bonds

• Reactants in a chemical equation result in products

• Chemical Equilibrium: Number of reactants and products plateaus

• All atoms must be accounted for on both sides, and equations are reversible.

1. Neither, the reaction rate stabilizes and both are pretty much equal

2. Cellular respiration, used to make ATP from glucose. We inhale oxygen and expel carbon dioxide

Chapter 3: Water and Life

3.1: Polar covalent bonds in water molecules result in hydrogen bonding

• Water is polar, since the overall charge is unevenly distributed

• Oxygen, δ− Hydrogen δ+

• Very fragile hydrogen bonds, so it’s constantly shuffling and reforming

1. Electronegativity is how strongly an atom pulls electrons towards it, and since oxygen is partially negative, it has a higher electronegativity, which leads to water’s polarity.

2. Hydrogen bonds with oxygen and vice verse to result in complete valence rings

3. Hydrogen must bond with oxygen and vice versa

4. It would be nonpolar, altering the shape and properties

3.2: Four emergent properties of water contribute to Earth’s sustainability for life

• Cohesion of molecules

  • Cohesion: Attraction and sticking together of water molecules

    • Results in high surface tension (how hard to stretch or break the surface of a liquid)

  • Helps water and nutrients move upward against gravity in plants

    • Adhesion: Clinging of one substance to another, helps counter gravity’s downwards pull

• Temperature and heat

  • Kinetic Energy: Energy of motion

  • Thermal Energy: Total kinetic energy associated with atoms and molecules

  • Temperature: Average kinetic energy of molecules

    • Thermal is TOTAL, Temperature is AVERAGE. Not the same!

  • Heat: Thermal energy transferred from one body of matter to another

    • Calorie (cal): Amount of heat to raise the temperature of 1g of water by 1°C

    • Kilocalorie (kcal): Amount of heat to raise the temperature of 1 kilogram (kg) of water by 1°C

    • Joule (J): 0.239 cal (1 cal = 4.184 J)

  • Specific Heat: Amount of heat for 1g of the substance ± temperature by 1°C

    • Heat must be absorbed to break hydrogen bonds, and released when they form

  • Heat of Vaporization: Amount of heat to turn 1g liquid > gas

  • Evaporative Cooling: As water evaporates, the surface of the remaining liquid cools down

    • Contributes to the stability of water temperature in waters & lakes

    • Prevents organisms from overheating

• Floating of ice on liquid water

  • Water is less dense as a solid than a liquid

    • Hydrogen bonding makes a crystalline lattice

      • Holds molecules far apart, making it 10% less dense

      • Most dense at 4°C

• The solvent of life

  • Solution: Solute (dissolved) + solvent (dissolved in)

  • Aqueous Solution: Water is the solvent in a solution

  • Hydration Shell: Sphere of water around a dissolved ion

  • Hydrophilic: Affinity to water

  • Hydrophobic: Nonionic, nonpolar, repel water

  • Colloid: Stable suspension of fine particles in a liquid

  • Molecular mass: Sum of the mass of all atoms in a molecule

  • mol(e): Exact # of objects—6.02 x 10²³

  • Molarity: # moles per solute per Liter of solution

1. Water adheres to the tree and can “climb” using its high surface tension

2. The humidity

3. Idk lol

4. Its legs would not get wet even when submerged, but if hydrophilic it might absorb the water

3.3: Acidic and basic conditions affect living organisms

• Sometimes hydrogen atoms will shift from one molecule to the other, leaving its electron, the hydroxide (OH-) behind and only transferring the hydrogen (H+) ion. This makes a hydronium ion (H₃O+)

  • H+ and OH- are very reactive

• Acid: Higher hydrogen ion concentration

• Base: Lower hydrogen ion concentration

  • In an aqueous solution at 25°C, the product of H+ and OH- is always 10^-14.

  • pH = -log[H+]

    • H+ = 10^-pH

• Strong acids and bases completely dissociate in water

• Most living cells have a pH around 7

  • Human blood is at 7.4, can’t survive if ± 0.4

• Buffer: Substance that minimizes changes in pH

• Ocean Acidification: When CO₂ dissolves in seawater, reacting with water (making carbonic acid) and lowering ocean pH

  • Lowers pH and carbonate ion concentration, which is crucial in coral reef formation

1. 10⁵

Chapter 4: Carbon & Molecular Diversity

4.1: Organic chemistry is the key to the origin of life

• Organic Chemistry: Study of compounds containing carbon

• Major elements to life are C,H,O,N,S,P

• Abiotic: Nonliving

• Vitalism: There is a life force outside of natural laws

• Mechanism: Natural laws create all phenomena

1. The sparks created a source of energy

4.2: Carbon atoms can form diverse molecules by bonding to four other atoms

• Electron configuration determines bonds

• Carbon’s shape allows for 4 single bonds

• Valence: Number of covalent bonds an atom can form

• Hydrocarbons: Organic molecules consisting of only carbon and hydrogen

  • All of the above in the pictures

• Isomers: Same number of atoms of the same elements but different structures (so different properties)

  • Structural Isomers: Different covalent arrangements of their atoms

  • Cis-Trans Isomers/Geometric Isomers: Carbons have covalent bonds to the same atoms, but they differ in spatial arrangements

  • Encantiomers: Isomers that are mirror images of each other

1. Can’t

2. Butane and 2-Mehtopropane

3. Lots of hydrocarbon chains

4.3: A few chemical groups are key to molecular function

• Properties also depend on molecular components

• Functional group: Chemical group that is directly involved in chemical reactions

  • Hydroxyl Group: —OH, polar and forms h bonds with water, ends in -ol

  • Carbonyl Group: C=O, Ketone (sugars with these are ketoses) or aldehyde (sugars with these are aldoses)

  • Carboxyl Group: —COOH, acts as acid, can donate H+ because covalent bond between oxygen and hydrogen is so polar

  • Amino Group: —NH₂, acts as base, can pick up H+ from surrounding solution

  • Sulfhydryl Group: —SH, two can react and form a “cross link” to stabilize protein structure

  • Phosphate Group: —OPO_3^2-, contributes negative charge of -1 when in a chain of phosphates, -2 at the end

  • Menthyl Group: —CH₃, affects expression of genes when bonded to DNA or proteins that bind to DNA

• Adenosine Triphosphate (ATP): 3 phosphate string + adenosine, when it loses a P it becomes ADP

  • Stores potential to react with water or other molecules

1. Not sure

2. It releases a phosphate group

3. Can’t draw

Chapter 5: Structure & Function of Large Biological Molecules

5.1: Macromolecules are polymers, built from monomers

• Macromolecules: Large carbohydrates, proteins, and nucleic acids

  • Polymers: Long chain like molecule consisting of many similar building blocks linked by covalent bonds (picture a chain of boxcars)

    • Monomers: The building blocks of polymers

• Enzyme: Specialized macromolecules which speed up chemical reactions

• Condensation Reaction: The reaction that connects a monomer to a monomeror polymer, where two molecules are covalently bonded with the loss of a small molecule

  • Dehydration Reaction: Water molecule as byproduct, two molecules covalently bonded by its loss

• Hydrolysis: The reverse of dehydration synthesis, bond between monomers is broken by addition of a water molecule

1. Carbohydrates, lipids, proteins, nucleic acids. Lipids aren’t polymers since they don’t have a monomer unit

2. 9

3. Hydrolysis breaks the food down, dehydration fuses it with you

5.2: Carbohydrates serve as fuel and building material

• Carbohydrates: Sugars and polymers of sugars

• Monosaccharides: Simple sugars, monomers of more complex sugars

  • Molecular formula is a multiple of CH₂O

  • Either an aldose or ketose. Also count number of carbons, 3-7

    • Triose, pentoses, and hexoses are most common

• Disaccharide: 2 monosaccharides joined by gylcoside linkage

  • Glycoside Linkage: Covalent bond formed between two monosaccharides by a dehydration reaction

  • Must be broken down into monosaccharides to be used for energy by organisms

• Polysaccharide: Macromolcules formed by monosaccharides, used as storage material and structural building material

• Starch: Polymer of glucose monomers, stored as plastids

  • Plastids: Granules within cellular structures (including chloroplasts)

  • Extra sugar can be withdrawn by hydrolysis

  • Most of glucose monomers in syarch joined by 1-4 linkages. Simplest form (amylose) is unbranched, more complex is branched

• Glycogen: Polymer of glucose, more extensively branched than amylopectin

• Cellulose: Polysaccharide, major component of cell walls

• Two slightly different ring structures for glucose, alpha (a) and beta (b)

  • In starch, all a, so helical, efficiently stores glucose units

  • In cellulose all b, so it is straight and never branched. The h bonding between parallel cell walls hold them together

• Microfibrils: Units in which parallel cellulose molecules are held together and grouped

• Chitin: Carbohydrate used by arthropods to build their exoskeletons

  • First leathery and flexible, but is hardened when the proteins are chemically linked to each other or encrusted with calcium carbonate. b linkages

1. C₃H₆O₃

2. C₁₂H₂₂O₁₁

3. Adds helpful gut bacteria back in

5.3: Lipids are a diverse group of hydrophobic macromolecules

• Lipids: Hypdrophobic, the one class of large biological molecules that does not include true polymers, not macromolecules

• Fat: A glycerol (alcohol) joined to three fatty acids

  • Fatty Acid: Long carbon skeleton, 16-18 carbon atoms in length. Carbon at the end is part of a carboxyl group

    • (Relatively) nonpolar C—H bonds in hydrocarbon chains of the fatty acids are why the fats are hydrophobic

• Fatty acid is joined to glycerol by dehydration synthesis, resulting in an ester linkage

  • Ester Linkage: Bond between hydroxyl and carboxyl group

• Saturdated Fatty Acid: No double bonds beyween carbon atoms composing a chain, meaning lots of hydrogen and it is solid at room temperature

• Unsaturated Fatty Acid: 1+ Double bonds, one fewer hydrogen atom on each double bonded carbon

  • Hydrogenated: Added hydrogen to unsaturated fatty acid to make it solid at room temperature

  • Trans Fats: Unsaturated fats with trans double bonds

• Fats are used for energy storage, since 2 gram has >2x the amount of energy as a gram of a polysaccharide (such as starch)

  • Also cushions vital organs and insulates the body

• Phospholipid: Make up cell membranes, 2 fatty acids + glycerol, 3rd joined to a phosphate group, - charge

  • Hydrophobic tail, hydrophillic head

• Steroids: 4 fused rings, different steroids alter different chemical groups

  • Cholesterol: Animal cell membrane component, precursor of many other steroids

1. 3 lipid tails, and glycerol base, in phospholipids there are two tails and glycerol base + phosphat group

2. Because sex hormones are steroids which are lipids

3. Like a circle of single layered phospholipids around the oil droplet, with the tails facing the oil side

5.4: Proteins include a diversity of structures, resulting in a wide range of functions

• Enzyme proteins act as catalysts to regulate metabolsim, which speed reactions without being consumed

• Proteins are all connected by the same set of 20 amino acids

• Peptide Bond: Bond between amino acids

• Polypeptide: Polymer of amino acids

• Polypeptide Backbone: Repeating sequence of atoms (in purple in diagram)

• Protein: Biologically functional molecule with 1+ polypeptides, folded and coiled into a 3D structure

• Amino Acid: Organic molecule with amino and carboxyl group

• Proteins are 50%+ of dry mass of most cells

• Primary Structure: Unique sequence of amino acids

• Secondary Structure: Coils (a helix) or folds (b pleated sheet)

• Tertiary Structure: Overall shape of polypeptide from interactions resulting from side chains (R Groups)

  • Hydrophobic Interaction: Exclusion of nonpolar substances by water molecules which lead to

• Primary has peptide bonds

• Secondary has hydrogen bonds

• Tertiary has mainly disulfide bonds with some hydrogen bonds

• Quartenary has electrostatic bonds with some hydrogen bonds

  • Electrostatic Bond: One atom loses an electron, one gains one

1. Hydrogen Bonding

5.5: Nucleic acids store, transmit, and help express hereditary information

• Gene: Programs amino acid sequences of polypeptides

  • Nucleic Acid: Polymer made of monomers called nucleotides. DNA and RNA

• Deoxyribonucleic Acid (DNA): Provides directions for own replication, directs RNA synthesis, and RNA controls protein synthesis (gene expression)

  • Ribonucleic Acid (RNA): A nucleic acid that carries instructions from DNA to control synthesis of proteins, directs production of polypeptides

• Polynucleitides: Nucleic acids, consist of monomer nucleotides

  • Nucleotide: Three parts, a 5 carbon sugar (pentose), nitrogenous base, and 1-3 phosphate groups

• Two types of nitrogenous bases

  • Pyrimidine: One 6 membered ring of carbon and nitrogen atoms

    • CUT

  • Purines: Larger than pyrimidines, six membered ring fused to a 5 member ring

    • AG (Pure as gold)

• In DNA, the sugar is deoxyribose, in RNA, it’s ribose

• Sugar atoms have a prime symbol (‘) after a number

• Double Helix: Shape of DNA molecule

• Antiparallel: The sugar phosphate backbones in DNA go from 5’ → 3’

5.6: Genomics and proteomics have transformed biological inquiry and applications

• Bioinformatics: Use of computers and tools to analyze large datasets

• Genomics: Analyzing large sets of genes and sometimes comparing genomes to other species

• Proteomics: Protein sequences are determined using either biological techniques or translating DNA sequences