Chapter 1: An Introduction to Life on Earth

1. Explain the characteristics that define life.

- Acquire and use materials and energy
- Actively maintain organized complexity (homeostasis)
- Sense and respond to stimuli
- Grow
- Reproduce
- Collectively evolve

2. Explain why these characteristics are necessary to sustain life.

- Acquire and use materials and energy: any organism needs energy to survive. Most
energy can be directly linked to the sun through the process of photosynthesis.
- Actively maintain organized complexity (homeostasis): with different environments, it's
important for our bodies to maintain the optimal conditions that we perform well in.
- Sense and respond to stimuli: allows for organisms to sense when they need food and to
respond accordingly.
- Grow- growing matures organisms both physically and mentally which can help
organisms survive.
- Reproduce- Keeps the organism alive past its own generation also passes down DNA to
next generation.
- Collectively evolve- Allows organisms to change and become better (or worse)

3. Describe how reproduction allows evolution to occur.

- When an organism reproduces, the parent DNA is passed down to the new generation.
This process can lead to unexpected mutations. This mutation can also be past down to
the next generation. This mutation can be either harmful or beneficial to the organism
which leads to the natural selection of that specific organism.

4. Explain what mutations are, how they occur, what allows them to be inherited, and what
general types of changes mutations can produce.
- Mutations​- a change in the base sequence of DNA in a gene; often used to refer to a
genetic change that is significant enough to alter the appearance or function of the
organism.
- They can occur randomly, by copying error, or by damage by the sun.
- Mutations can be harmful (hemophilia, sickle-cell anemia, and cystic fibrosis all past
down through the parent), beneficial (which can lead to natural selection), or neutral (eye
color, hair color, etc.).

5. Explain how natural processes lead inevitably to evolution.

- Differences between members of a population- Mutations can occur during the
duplication of DNA.
- Inheritances of these differences by offspring. The mutations are passed down from
parent to their offspring.
 - Natural selection​- If the mutation is beneficial, those specific organisms will adapt better.
Depending on the environment that organism is in, they will adapt the certain
characteristics that make them better for that environment. Those with favorable traits
will continue to survive and reproduce compared to those who don’t.

6. Describe how a new species can be produced by natural selection.

- Charles Darwin’s finches can be used as an example. Due to the nature of their diet,
each finch has a different beak. Those with big but short beaks ate seeds which required
a greater amount of force to break its hard shell. Smaller and sharper beaks were used
to puncture through cacti and/or insects.

7. Describe the levels of biological organization.

(From largest to smallest)
- Biosphere​- all life on Earth and all the nonliving portions of it.
- Ecosystem​- all the living organisms and their nonliving environment in a defined area.
- Community​- population of different species living and interacting with one another in the
same area.
- Species​- organisms similar enough that they are able to interbreed.
- Population​- all the members of a species living in the same area.
- Multicellular organism​- an individual living thing composed of many cells.
- Organ system​- two or more organs working together in the execution of a specific bodily
function.
- Organ​- a structure composed of two or more distinct tissue types that function together.
- Tissue​- A group of similar cells that perform a specific function.
- Cell​- The smallest unit of life
- Molecule​- a particle composed of one or more atoms held together by chemical bonds,
the smallest particle of a compound that displays all the properties of that compound.
- Atom​- The smallest particle of an element that retains the properties of that element.

8. Explain how scientists name and categorize diverse forms of life.

- Classified into three groups called domains: Bacteria, Archaea, and Eukarya.
- Utilize a binomial system with the genus and species (Ex. ​Homo sapiens​).
9. Describe the fundamental differences between prokaryotic and eukaryotic cells.
Prokaryotic Both Eukaryotic

- DNA is not confined - Have a plasma - Has a nucleus that

within a nucleus. membrane contains the cells’
- Nucleoid - Contain hereditary DNA.
material DNA - Organelles
- Ribosomes

10. Describe the principles of underlying science.

- All events can be traced to natural causes.
- Natural laws do not change over time or distance.
- Scientific findings are “value neutral”

11. Outline the scientific method.

- Observation
- Question
- Hypothesis
- Prediction
- Experiment
- Conclusion

12. Explain why controls are crucial in biological studies

- Control​- a baseline; all variables are held constant to determine whether the experiment
is valid.
- Positive control​- know the outcome, it will do something.
- Negative control​- don’t know the outcome, it won’t do something.
- Positive and negative controls make sure that there won’t be any false negatives or
positives.

13. Explain why fundamental scientific principles are called theories.

- Scientific theories can be disproved or falsified.
- All diseases were thought to reproduce based on instructions from their genetic material.
Stanley Prusiner proved this wrong when he discovered that scrapie was triggered and
transmitted by a protein and has no genetic material. Prions are now responsible for
passing on mad cow disease and two fata human brain disorders.

Chapter 2: Atoms, Molecules, and Life

1. Define element and atom
- Element​- a substance that cannot be broken down or converted to a simpler substance
by ordinary chemical reactions
- Atom​- the smallest unit of an element that retains the properties of the element.
2. Name and describe the subatomic particles that make up the atom.
- Protons-​ positive charge; 1 amu
- Identifies the atom.
- Neutrons​- neutral charge; 1 amu
- Isotope​- one of several forms of a single element, the nuclei of which contain the
same number of protons but different numbers of neutrons.
- Electrons​- negative charge; 0 amu

3. Explain atomic number and mass number.

- Atomic number​- the number of protons in the nuclei of all atoms of a particular element.
- Mass number​- to total number of protons and neutrons in the nucleus of an atom.
- Atomic Weight​- the total weighted average of an element’s isotope’s mass

4. Explain radioactivity and its dangers and benefits.

- Radioactive​- an atom with an unstable nucleus that spontaneously breaks apart or
decays, with the emission of radiation.
- Pros: Can treat cancer cells. PET scans and X-rays. Experiments with radioactively
labeled DNA and protein allowed scientists to conclude that DNA is the genetic material
of cells.
- Cons: Can damage DNA and biological molecules rapidly. Skin cells are destroyed. The
cells lining the stomach and intestine break down, causing nausea and vomiting. Bone
marrow is destroyed. The lack of white blood cells increases the risk of infections and
loss of platelets crucial for blood clotting leads to internal bleeding.

5. Describe electron shells.

- Electron shells​- a region in an atom within which electrons orbit; each shell corresponds
to a fixed energy level at a given distance from the nucleus.
- Farther away from the nucleus, the greater amount of energy stored in the electrons
occupying the shell.
- The first shell holds two electrons; the next three hold eight.
- When electrons moves from a lower energy shell to a higher energy shell (usually
induced by heat energy) and back to its original place, both heat and light is released.

6. Explain what makes an atom reactive.

- An atom whose outermost electron shell is only partially full will react readily with other
atoms.
- Free radical​- a molecule containing an atom with an unpaired electron, which makes it
highly unstable and reactive with nearby molecules. By removing an electron from the
molecule it attacks, it creates a new free radical and begins a chain reaction that can
lead to the destruction of biological molecules crucial to life.
7. Define molecules and chemical bonds.
- Molecules​- a particle composed of one or more atoms held together by chemical bonds;
the smallest particle of a compound that displays all the properties of that compound.
- Chemical bond​- an attraction between two atoms or molecules that tends to hold them
together. Types of bonds include covalent, ionic, and hydrogen.

8. Describe and provide examples of ionic, covalent, and hydrogen bonds.

- Ionic​- formed by the electrical attraction between positively and negatively charged ions.

- Covalent​- a chemical bond between atoms in which electrons are shared.

- Nonpolar​- electrons are shared equally between atoms.
- Polar​- electrons are shared unequally between atoms.

- Hydrogen​- the weak attraction between a hydrogen atom that bears a partial positive
charge (due to polar covalent bonding with another atom) and another atom (oxygen,
nitrogen, or fluorine) that bears a partial negative charge; hydrogen bonds may form
between atoms of a single molecule or different molecules.

9. Describe the unique properties of water and the importance of these properties of life.
- Cohesion​- the tendency of molecules of a substance to stick together. (Ex. Water is
being continuously pulled through a plants leaf as it evaporates.
- Surface tension​- the property of a liquid to resist penetration by objects at its
interface with the air, due to cohesion between molecules of the liquid. (Ex. a bug
on top of the water without it sinking)
- Adhesion​- the tendency of polar molecules to adhere to polar substances.
- Capillary action​- the movement of water within narrow spaces resulting from its
properties of adhesion and cohesion. (Ex. water going up the stem of a plant)
10. Explain how polar covalent and hydrogen bonds contribute to the unique properties of water.
- Solvent​- a substance that completely surrounds and disperses the individual atoms or
molecules of another substance.
- Water is a universal solvent due to its polarity, it causes ions such as Na​+ ​and Cl​-
to be attracted and surrounded by the H​2​O molecules.
- Specific heat​- the amount of energy required to raise the temperature of 1 gram of a
substance by 1​o​C.
- Water has a high specific heat because it requires energy for the hydrogen bonds
to be broken and an additional amount of energy to raise its temperature.
- Heat of vaporization​- the energy that must be supplied to a compound to transform it
from a liquid into a gas at its boiling temperature.
- Water has a high heat of vaporization because it requires the water to absorb
enough energy so that it can break the hydrogen bonds.
- When forming ice, water molecules form hydrogen bonds with four other molecules,
developing a hexagonal arrangement that keeps the distance between water molecules
greater than if it were in liquid form, therefore making it less dense in solid form.

11. Explain the concept of pH and how acids, bases, and buffers affect solutions.
- Acid-​ a substance that releases hydrogen ions (H+) into solution; a pH less than 7.
- Greater H+ concentration
- Base​- a substance capable of combining with and neutralizing H+ ions in a solution; a
solution with a pH greater than 7.
- Greater OH- concentration.
- pH scale​- has values from 0-14 and is used for measuring the relative acidity of a
solution, at a pH of 7, a solution is neutral, pH 0-7 is acidic, and pH 7-14 is basic; each
unit on the scale represents a tenfold change in H+ concentration.
- Buffer​- a compound that minimizes changes in pH by reversibly taking up or releasing
H+ ions.

Chapter 3: Biological Molecules

1. Define organic molecules and explain why carbon is so important to life.
- Organic molecules​- contains both carbon and hydrogen.
- Carbon is so important because nearly all of the biological molecules are based on the
carbon atom.
- Carbon is versatile in its bonding properties; making single or double bonds with itself or
2-4 other atoms, in addition to making single, double, or triple covalent bonds.

2. Explain why functional groups are important in biological molecules.

- Functional group​- one of several groups of atoms commonly found in an organic
molecule all of which determine the characteristics and chemical reactivity of the
molecule. They are less stable than the carbon backbone and more likely to participate
in chemical reactions
3. Names and describe the properties of seven functional groups.
- Hydroxyl​- polar; involved in dehydration and hydrolysis reactions; forms hydrogen bonds.

- Carbonyl​- polar makes parts of molecules hydrophilic

- Carboxyl​- polar and acidic; the negatively charged oxygen may bond H+ forming
carboxylic acid (-COOH); involved with peptide bonds.

- Amino​- polar and basic; may become ionized by binding a third H+; involved in peptide
bonds.

- Sulfhydryl​- nonpolar; forms disulfide bonds in proteins.

- Phosphate​- polar and acidic; links nucleotides in nucleic acids; forms high-energy bonds
in ATP.

- Methyl​- nonpolar; may be attached to nucleotides in DNA (methylation), changing gene

expression.

4. Name and describe the reactions that create and break apart biological polymers.’
- Dehydration synthesis​- a chemical reaction in which two molecules are joined by a
covalent bond with the simultaneous removal of a hydrogen from one molecule and a
hydroxyl group from the other, forming water; the reverse of hydrolysis.
 - Hydrolysis​- the chemical reaction that breaks a covalent bond by means of addition of
hydrogen to the atom on one side to the atom on the other side; the reverse of
dehydration synthesis.

5. Describe the major types of carbohydrates.

- Carbohydrates are composed of C, H, and O with the chemical formula of (CH​2​O)​n​.
- Monosaccharides​- singular unit of carbs composed of a chain of carbon atoms bonded
to hydrogen and hydroxyl groups.
- Disaccharide​- a carbohydrate formed by the covalent bonding of two monosaccharides.
- Polysaccharides​- composed of branched or unbranched chains of repeating
monosaccharide subunits, normally glucose or modified glucose molecules.

6. Provide examples of each type of carbohydrate and explain how organisms use them.
- Glucose​-most common monosaccharide. C​6​H​12​O​6​; used for energy. Other
monosaccharides include fructose and galactose.
- Common disaccharides include sucrose (glucose & galactose), maltose (glucose x2),
and lactose (glucose & galactose); often used for short-term energy storage in plants.
- Starch​- a polysaccharide composed of branched or unbranched chains of glucose
molecules; used by plants as a carbohydrate-storage molecule (long term).
- Glycogen​- highly branched polymer of glucose that is stored by animals in the muscles
and liver and metabolized as a source of energy.
- Cellulose​- an insoluble carbohydrate composed of glucose subunits; forms the cell wall
of plants. No vertebrates synthesize an enzyme that can attack the bonds between
glucose molecules in cellulose except for cows and termites.
- Chitin​- a compound found in the cell walls of fungi and the exoskeletons of insects and
some other arthropods; composed of chains of nitrogen containing, modified glucose
molecules.

7. Describe protein subunits and how proteins are synthesized.

- Amino acids​- the individual subunit of which proteins are made, composed of a central
carbon atom bonded to an amino group (-NH​2​), a carboxyl group (-COOH), a hydrogen
atom, and a variable group of atoms denoted by the letter R.
 - Synthesized by dehydration synthesis which results in a peptide bond.
- Peptide bond​- covalent bond between the nitrogen of the amino group of one
amino acid and the carbon of the carboxyl group of a second amino acid, joining
the two amino acids together in a peptide or protein.

8. Explain the four levels of protein structure and why a protein’s three-dimensional structure is
Important.
- Primary​- the amino acid sequence of a protein specified by the DNA. Involves peptide
bonds.
- Secondary​- hydrogen bonds allow the primary structure to become helical or a pleated
sheet.
- Tertiary​- the disulfide bonds between the cysteine amino acid folds the secondary
structure onto each other. Based on the primary and secondary structure and
environment, the hydrophobic parts of the protein is folded more inwards whereas
hydrophilic parts are exposed.
- Quaternary​- polypeptides are linked together by hydrogen bonds or disulfide bridges.
- The three dimensional structure is important because its function is dependant on it.

9. List several functions of proteins and provide examples of proteins that perform each
function.
- Structural- keratin; silk
- Movement- actin and myosin in muscles for contraction
- Defense- antibodies to fight disease; venoms to deter predators and disable prey.
- Storage- albumin provides nutrition for embryo
- Signaling- insulin promotes glucose uptake into cells
- Catalyzing reactions- amylase digests carbohydrates

10. Describe the properties of intrinsically disordered proteins.

- Intrinsically disordered proteins​- proteins or segments of proteins with no stable
secondary or tertiary structure.
- Has a primary structure with mostly hydrophilic amino acids that float freely in their
watery surroundings hence lacking a secondary or tertiary structure, allowing them to be
flexible and versatile.

11. Describe the general structure of nucleotides

- Nucleotide​- a subunit of which nucleic acids are composed; a phosphate group bonded
to a sugar (deoxyribose in DNA), which in turn bonded to a nitrogen-containing base
(adenine, guanine, cytosine or thymine in DNA). Nucleotides are linked together, forming
a strand of nucleic acid, by bonds between the phosphate of one nucleotide and the
sugar of the next nucleotide.
12. List three different functions of nucleotides.
- Adenosine triphosphate (ATP)​- a molecule composed of the sugar ribose, the base
adenine, and three phosphate groups; the major energy carrier in cells. The last two
phosphate groups are attached by “high-energy” bonds.
- Cyclic adenosine monophosphate (cAMP) acts as a messenger molecule in cells; NAD​+​,
and FAD are electron carriers transporting energy in the form of electrons.
- Subunits of nucleic acids DNA and RNA.

13. Explain how nucleic acids are synthesized.

- DNA is double stranded helix of deoxyribose nucleotides that run antiparallel to each
other linked by hydrogen bonds between the bases of the nucleotides on adjacent sides.
- RNA is a single strand of ribose nucleotides.

14. Give two examples of nucleic acids and their functions.

- DNA- contains the genetic information of all living cells
- RNA- involved in converting the information in DNA into protein, also the genetic material
in some viruses.

15. Compare and contrast the structure and synthesis of fats and oils.
- Lipids​- contains a large nonpolar regions composed of solely of carbon and hydrogen,
which make lipids hydrophobic and insoluble in water; includes oils, fats, waxes,
phospholipids, and steroids.
- Fatty acids​- an organic molecule composed of a long chain of carbon atoms, with a
carboxylic acid (-COOH) group at one end; may be saturated (all single bonds between
the carbon atoms) or unsaturated (one or more double bonds between carbon atoms).
- Three fatty acids and a glycerol make a triglyceride, a subunit of a lipid.
- Fats are saturated therefore are solid at room temperature; oils are unsaturated and
therefore a liquid at room temperature.
- Saturated​- a fatty acid with as many hydrogen atoms as possible bonded to the
carbon backbone; no double bonds.
- Unsaturated​- a fatty acid with fewer than the maximum number of hydrogen
atoms bonded to its carbon backbone; one or more double bonds in its carbon
backbone.
16. Describe the function of fats, oils, and waxes.
- Fat can be used for both insulation and energy.
- Oils like that of in avocado were used to attract enormous seed-dispersing mammals like
the extinct giant ground sloth.
- Waxes​- a lipid composed of fatty acids covalently bonded to long-chain alcohols; highly
saturated and solid at outdoor temperatures.
- Used as a water repellent on plants and on the feathers of birds.

17. Provide two reasons why cholesterol is important in the body

- Steroid​- a lipid consisting of four fused carbon rings, with various functional groups
attached; soluble in the phospholipid cell membrane and can cross them to act inside
the cell.
- Makes up 2% of the human brain that insulates nerve cells.
- Used to synthesize other steroids such as the female and male sex hormones estrogen
and testosterone