Jireh Huang 1

Biology Study Guide

> Enzymes~
Enzymes are proteins that act as biological catalysts.
A catalyst is a substance that speeds up the rate of a chemical reaction.
Enzymes speed up chemical reactions that take place in cells.
Enzymes provide a site where reactants can be brought together to react. The reactants of enzyme-
catalyzed reactions are known as substrates.
Substrates (reactants) bind to the active site of an enzyme -> Chemical reaction occurs; substrates are
converted into products -> Products are released~
Enzymes can be affected by any variable that influences a chemical reaction. Factors that affect enzyme
speed or can potentially denature (cause to lose conformation) an enzyme:
Temperature, pH value, and proteins (most cells contain proteins that help to turn key enzymes “on”
or “off”).
A competitive inhibitor BLOCKS the active site.
A non-competitive inhibitor CHANGES the shape of the active site, so the substrates can’t bind into the
active site.

> Exothermic vs. Endothermic Reactions~

An exothermic reaction is a chemical reaction that releases energy in the form of heat.
An endothermic reaction is a chemical reaction that requires heat (heat is a reactant) to occur.

> Macromolecules and their Monomers~

Macromolecules are “giant molecules” that are made from 1,000’s or even 100,000’s of smaller molecules
and are formed by a process known as polymerization.
Polymerization – in which large compounds are built by joining smaller ones together. Monomers join
together to form polymers. The monomers in a polymer may be identical or different.
Four groups of organic compounds found in living things are carbohydrates, lipids, nucleic acids, and
proteins; ([all] sometimes referred to as biomolecules).
Living things use carbohydrates as their main source of energy. Plants and some animals use
carbohydrates for structural purposes. Carbohydrates are made of monosaccharide (single sugar
molecules).
Lipids can be used to store energy. Some lipids are important parts of biological membranes and
waterproof coverings. Lipids are made of glycerol and fatty acids.
Nucleic acids store and transmit hereditary, or genetic, information. Types: ribonucleic acid (RNA)
(ribose) and deoxyribonucleic acid (DNA) (deoxyribose). Nucleic acid is made of nucleotides.
Some proteins control the rate of reactions and regulate cell processes. Some are used to form bones
and muscles. Others transport substances into or out of cells or help to fight disease. Proteins are made
of amino acids.

> Osmosis, Diffusion, Solutions~

Osmosis is the diffusion of water through a selectively permeable membrane.
Diffusion – The process in which particles tend to move from an area where they are more concentrated
to an area where they are less concentrated, until the concentration of the solute is the same throughout
a system AKA has achieved “equilibrium”.
Isotonic solution – equally concentrated solution; “same strength”
The concentration of solutes is the same inside and outside of the cell.
Hypertonic solution – more concentrated solution; “above strength”
Solution has a higher solute concentration than the cell, so the cell shrinks.
Hypotonic solution – less concentrated solution; “below strength”
Solution has a lower concentration that the cell, so the cell swells/expands.

> Eukaryotes and Prokaryotes~

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Eukaryotes contain nuclei; prokaryotes do not contain nuclei.
Prokaryotic cells have genetic material that is not contained in a nucleus; generally smaller and
simpler than eukaryotic cells.
Eukaryotic cells contain a nucleus in which their genetic material is separated from the rest of
the cell; can be unicellular or form large, multicellular organisms. Plants, animals, fungi, and protists
are eukaryotes.

> Functions of Cell Parts~

The nucleus contains nearly all the cell’s DNA and with it the coded instructions for making proteins and
other important molecules.
Chromatic consists of DNA bound to protein.
When a cell divides, chromatin condenses to form chromosomes.
Most nuclei also contain a small, dense region known as the nucleolus, where the assembly of
ribosomes begins.
Proteins are assembled on ribosomes – small particles of RNA and protein found throughout the
cytoplasm. They produce proteins by following coded instructions that come from the nucleus (protein
synthesis).
The endoplasmic reticulum is the site where lipid components of the cell membrane are assembled,
along with proteins and other materials that are exported from the cell.
The function of the Golgi apparatus is to modify, sort, and package proteins and other materials from the
endoplasmic reticulum for storage in the cell or secretion outside the cell.
Lysosomes are small organelles filled with enzymes. One function of lysosomes is the digestion, or
breakdown, of lipids, carbohydrates, and proteins into small molecules that can be used by the rest of the
cell.
Vacuoles are saclike structures in some cells that store materials such as water, salts, proteins, and
carbohydrates.
Mitochondria are organelles that convert the chemical energy stored in food into compounds that are
more convenient for the cell to use.
Chloroplasts are organelles that capture the energy from sunlight and convert it into chemical energy in
a process called photosynthesis.
The cytoskeleton is a network of protein filaments that helps a eukaryotic cell to maintain its shape;
also involved in movement. Microfilaments (threadlike structures made of protein called akin) and
microtubules (hollow structures made up of proteins known as tubulins) are two of the principal protein
filaments that make up the cytoskeleton.
All cells are surrounded by a thin, flexible barrier known as the cell membrane, which regulates what
enters and leaves the cell and also provides protection and support; mostly composed of a double-layered
sheet called a lipid bilayer.
Many cells also produce a strong supporting layer around the membrane known as a cell wall, whose
main function is to provide support and protection for the cell.
Active transport requires energy to transport small molecules or ions across a cell membrane; generally
carried out by transport proteins or “pumps” that are found in the membrane itself.
Passive transport is basically diffusion and does not require the use of the cell’s energy.

> Photosynthesis~
Electron Carriers:
NADP+ (nicotinamide adenine dinucleotide phosphate) – accepts and holds 2 high-energy electrons along
with a hydrogen ion (H+), converting it into NADPH.
Light-dependent reactions produce oxygen gas and convert ADP and NADP+ into the energy carriers
ATP and NADPH.
A. Pigments in photosystem II (first photosystem because it was discovered after photosystem I)
absorb light -> light energy is absorbed by electrons which become high-energy electrons and are passed
on to the electron transport chain; thylakoid membrane replenishes lost electrons from water
molecules (H2O).
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B. High-energy electrons move through the electron transport chain from photosystem II to
photosystem I, and their energy is used by the molecules in the electron transport chain to transport H+
ions from the stroma into the inner thylakoid space.
C. Pigments in photosystem I use energy from light to reenergize the electrons. NADP+ then picks
up these high-energy electrons, along with H+ ions, at the outer surface of the thylakoid membrane, plus
and H+ ion, and becomes NADPH.
D. As electrons are passed from chlorophyll to NADP+, more hydrogen ions are pumped across the
membrane, and the inside of the membrane soon fills up with positively charged hydrogen ions, making
the outside of the thylakoid membrane negatively charged while the inside is positively charged. The
difference in charges across the membrane provides the energy to make ATP (E), which is why
H+ ions are so important.
E. H+ ions cannot cross the membrane directly. However, the cell membrane contains a protein called
ATP synthase that spans the membrane and allows H+ ions to pass through it.
As H+ ions pass through ATP synthase, the protein rotates like a turbine, binding ADP and a phosphate
group together to produce ATP. Because of this system, light-dependent electron transport
produces not only high-energy electrons, but ATP as well.
Light-dependent reactions use water, ADP, and NADP+, and they produce oxygen and two
high-energy compounds: ATP and NADPH.

The Calvin Cycle uses ATP and NADPH from the light-dependent reactions to produce high-energy
sugars.
A. Six CO2 + six 5-carbon molecules = twelve 3-carbon molecules
B. ATP and NADPH are used to convert the twelve 3-carbon molecules into higher energy forms (ATP
-> ADP, NADPH -> NADP+).
C. Two of the twelve 3-carbon molecules are removed from the cycle to produce sugars, lipids,
amino acids, and other compounds.
D. The ten remaining 3-carbon molecules are converted back into six 5-carbon molecules, which are
used in the next cycle.

Photosynthesis Equation:
6CO2 + 6H2O –light-> C6H12O6 + 6O2
Carbon dioxide + water –light-> sugars + oxygen
Photosynthesis uses the energy of sunlight to convert water and carbon dioxide into high-energy
sugars and oxygen.

Factors Affecting Photosynthesis:

Water: Since water is one of the raw materials of photosynthesis, a shortage of water can slow or even
stop photosynthesis.
Temperature: Photosynthesis depends on enzymes that function best between 0 and 35 degrees
Celsius. Temperatures above or below this range may damage the enzymes, slowing down the rate of
photosynthesis or even stopping it entirely.
Intensity of Light: Increasing light intensity increases the rate of photosynthesis, but after the light
intensity reaches a certain level, the plant reaches its maximum rate of photosynthesis, and light intensity
above that would no longer affect its photosynthesis.

> Cellular Respiration~

Cellular respiration is the process that releases energy by breaking down glucose and other food
molecules in the presence of oxygen (aerobic).
6O2 + C6H12O6 -> 6CO2 + 6H2O + Energy
Oxygen + glucose -> carbon dioxide + water + energy

Glycolysis (the first set of reactions in cellular respiration) is the process in which one molecule of glucose
is broken in half, producing two molecules of pyruvic acid, a 3-carbon compound. Glycolysis occurs in the
cytoplasm.
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In glycolysis, 2 ATP is used (transformed to 2 ADP) and 4 ATP is gained (energized from 4 ADP), resulting
in a net gain of 2 ATP molecules for the cell. Also, 2 electron carriers (NAD+) are energized (into
NADH) and 2 pyruvic acids are produced.

During the Krebs cycle, pyruvic acid is broken down into carbon dioxide in a series of energy-extracting
reactions.
A. Pyruvic acid, a carbon is released (CO2), electrons are used to energize a NAD+ to NADH,
coenzyme A joins the resulting 2-carbon molecule, forming acetyl-CoA. 2-carbon acetyl group (from
acetyl-CoA) is added to a 4-carbon compound, forming citric acid.
B. Citric acid is broken down into a 5-carbon compound, then a 4-carbon compound; two
molecules of CO2 are released in the process, and electrons join NAD+ and FAD, forming NADH and
FADH2. In addition, one ATP is generated.
SUMMARY: Pyruvic acid -> 4 NADH + 1 FADH2 + 1 ATP

Fermentation releases energy from food molecules by producing ATP in the absence of oxygen. The
two main types of fermentation are alcoholic fermentation and lactic acid fermentation.
Alcoholic Fermentation:
Pyruvic acid + NADH -> alcohol + CO2 + NAD+
Yeasts and a few other microorganisms use alcoholic fermentation, forming ethyl alcohol and carbon
dioxide as wastes.
Lactic Acid Fermentation:
Pyruvic acid + NADH -> lactic acid + NAD+
Lactic acid is produced in your muscles during rapid exercise when the body cannot supply enough oxygen
to the tissues.

> Ecosystems~
Levels of Organization in an Ecosystem
Simplest to most complex:
Individual -> Species -> Populations -> Communities -> Ecosystem -> Biome -> Biosphere
Individual – … do I really need to explain this?
Species – a group of organisms so similar to one another that they can breed and produce fertile
offspring.
Populations – groups of individuals that belong to the same species and live in the same area.
Communities – assemblages of different populations that live together in a defined area.
Ecosystem – a collection of all the organisms that live in a particular place, together with their nonliving,
or physical, environment.
Biome – a group of ecosystems that have the same climate and similar dominant communities.
Biosphere – the highest level of organization that ecologists study.

Unequal Heating
As a result of differences in latitude and thus the angle of heating, Earth has three main climate zones:
polar, temperate, and tropical.
Unequal heating of the Earth results in the weather (day-to-day condition), climate (average year-
after-year condition), and climate zones.

A niche is the full range of physical and biological conditions in which an organism lives and the
way in which the organism uses the conditions.

The competitive exclusion principle states that no two species can occupy the same niche in the
same habitat at the same time.

Symbiotic Relationships
Any relationship in which two species live closely together is called symbiosis, which means “living
together”. The three main classes of symbiotic relationships in nature are: mutualism, commensalisms,
and parasitism.
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Mutualism – both species benefit from the relationship.
Commensalism – one member benefits and the other is neither helped nor harmed.
Parasitism – one organism lives on or inside another organism and harms it. The parasite obtains all or
part of its nutritional needs from the other organism, called the host. Parasites generally weaken but do
not kill their host.

> Cycles of Matter~

Nitrogen Fixation – in which bacteria, which live in the soil and on the roots of plants called legumes,
convert nitrogen gas into ammonia.
Limiting Nutrient – a single nutrient that is scarce or cycles very slowly and limits an ecosystem.
When an aquatic ecosystem receives a large input of limiting nutrient, the result is often an immediate
increase in the amount of algae and other producers, AKA an algal bloom.

> Energy Flow~

Food Pyramid – only about 10% of the energy available within one trophic level is transferred to
organisms at the next trophic level. The rest is lost as heat.
Food Web – a chart that links all the food chains in an ecosystem together, showing the feeding
relationships among the various organisms in an ecosystem.
Trophic Levels – each step in a food chain or food web. Producers make up the first trophic level.
Consumers make up all higher trophic levels. Each consumer depends on the trophic level below it for
energy.
Energy flows in ONE DIRECTION while matter is RECYCLED within and between ecosystems.

> Populations~
Three important characteristics of a population are its geographical distribution, density, and
growth rate.
Population density is the number of individuals per unit area.
Three factors can affect population size: the number of births, the number of deaths, and the number
of individuals that enter or leave the population.
Immigration – the movement of individuals INTO an area.
Emigration – the movement of individuals OUT of an area.

Exponential growth (J-shaped curve) occurs when the individuals in a population reproduce at a
constant rate. Under the ideal conditions with unlimited resources, a population will grow
exponentially.
Logistic growth (S-shaped curve) occurs when a population’s growth slows or stops following a period of
exponential growth. As resources become less available, the growth of a population slows or stops.
Carrying capacity – the largest number of individuals that a given environment can support. After a
period of exponential growth, a population experiences logistic growth when the population reaches a
certain environment’s carrying capacity.

Limits to Growth
A limiting factor is a factor that causes population growth to decrease.
A limiting factor that depends on population size is called a density-dependent limiting factor.
Density-dependent limiting factors include competition, predation, parasitism, and disease.
The regulation of a population by predation takes place within a predator-prey relationship, one of the
best-known mechanisms of population control.
In a nutshell: When predators become over-populated, prey becomes scarce and competition
increases, resulting in higher death rates for predators and/or an increase in emigration. When prey
becomes over-populated, competition decreases, resulting in higher survival rates for predators
and/or an increase in immigration.
Density-independent limiting factors affect all populations in similar ways, regardless of the
population size. Unusual weather, natural disasters, seasonal cycles, and certain human activities
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– such as damming rivers and clear-cutting forests – are all examples of density-independent limiting
factors.

Human Population Growth

Like the populations of many other living organisms, the size of the human population tends to increase
over time.
The world population in 2010 was approximately 7 billion. The projected world population in 2050 is
expected to be about 9 billion.

Demographic transition – a dramatic change in birth and death rates.

The demographic transition is complete when the birthrate falls to meet the death rate.
The United States experienced such a transition from 1790 to 1910. Japan and Europe also
experienced such a trend. Many parts of South America, Africa, and Asia are still in this phase. The
worldwide human population is still growing exponentially. Much of the population growth today is
contributed by only 10 countries, with India and China in the lead, where birthrates remain high.

> Protein Synthesis~

There are three main types of RNA: messenger RNA, ribosomal RNA, and transfer RNA.
Messenger RNA (mRNA) carries copious of instructions for assembling amino acids into proteins.
Ribosomal RNA (rRNA) and several dozen proteins make up ribosomes, on which proteins are
assembled.
Transfer RNA (tRNA) transfers each amino acid to the ribosome as it is specified by coded messages in
mRNA.

Transcription
RNA molecules are produced by copying part of the nucleotide sequence of DNA into a complementary
sequence in RNA, a process called transcription. Transcription requires an enzyme known as RNA
polymerase that is similar to DNA polymerase.
During transcription, RNA polymerase binds to DNA and separates the DNA strands. RNA polymerase
then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA.
RNA polymerase will bind only to regions of DNA known as promoters, which have specific base
sequences.

Forming Final mRNA

Introns are not involved in coding for proteins, so they are cut out of DNA to form pre-mRNA, and the
remaining exons are then spliced together to form final mRNA.

Translation
The decoding of an mRNA message into a polypeptide chain (protein) is known as translation. Translation
takes place on ribosomes. During translation, the cell uses information from messenger RNA to produce
proteins.
tRNA molecules come in carrying amino acids along with anticodons which are complementary to
mRNA codons. The ribosome then forms a peptide bond between the amino acids and breaks the bond
between the tRNA and the amino acids.

> Cancer~
Cancer is a disorder in which some of the body’s own cells lose the ability to control growth and is caused
by a defect in the genes. not just one but many mutations in combination are necessary for the
development of cancer.
Cancer cells do not respond to the signals that regulate the growth of most cells. They divide
uncontrollably and form masses of cells called tumors.
Tumors can damage surrounding tissue. Not all tumors are cancerous – benign tumors lack the invasive
properties of a cancer and are often harmless. Malignant tumors, however, divide constantly and are
extremely harmful.
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Causes of cancer (carcinogens) include tobacco, radiation, exposure, diet, weight, viral infections,
chemicals, heredity, sun exposure, and AGE.
Pro onco cells are cells that maintain regular reproduction.
Onco cells keep reproducing without stopping.

> Meiosis~
Interphase I -> Prophase I -> Metaphase I -> Anaphase I -> Telophase I and Cytokinesis ->
Prophase II -> Metaphase II -> Anaphase II -> Telophase II and Cytokinesis
Interphase – Cell (diploid) undergoes DNA replication, forming duplicate chromosomes.
Prophase I – Corresponding homologous chromosomes form tetrads.
Metaphase I – Spindle fibers attach to the chromosomes.
Anaphase I – Spindle fibers pull homologous chromosomes toward opposite ends of the cell.
Telophase I – Nuclear membranes form.
Cytokinesis – The cell separates into two cells.
Prophase II – Meiosis I results in two haploid daughter cells, each with half the chromosomes as the
original cell.
Metaphase II – Chromosomes line up across the center of the cell.
Anaphase II – Sister chromatids separate and move toward opposite ends of the cell.
Telophase II & Cytokinesis – The two haploid cells separate; Meiosis II results in four haploid cells.