Virginia SOL: Biology Review
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Scientific Investigation:
Scientific Method:
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Observation: the act of gathering information about a system or environment using one or
more of your five senses.
Hypothesis: an educated guess or prediction about the answer to the question, or solution to
the problem.
 Identify Variables: factors that change and can be measured in experiments.
 Independent Variable (A): a variable that the scientist changes.
 Dependent Variable (B): a variable that changes due to the independent
variable.
 If (A) then (B)
Gather Data: graphing and arithmetic calculations are used as tools in data analysis.
Controlled Experiment:
 Contains both a Control (standard against which experimental results can be
measured) & Experimental group (group in which the variable is applied)
Conclusion: formed based on recorded quantitative and qualitative data.
Life at a Molecular Level:
Water:
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Occurs naturally in 3 phases: solid, liquid, gas
Chemical formula: H2O
 2 hydrogen atoms covalently bonded to one oxygen atom
Water is polar (slightly negative charge): Unequal sharing of electrons between the oxygen
atom and the hydrogen atoms.
 Oxygen is slightly negative
 Hydrogen is slightly positive
 Attraction forms between the negative end of one
molecule and the positive end of another
 Hydrogen Bonding
Unique Properties of Water:
 Water has a high specific heat (takes a lot of energy to increase its
temperature)
 Universal solvent
 Cohesion: water has a strong tendency to stick together
 Adhesion: water likes to stick to other substances
 Causes capillary action in plants
Four Macromolecules:
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All living things are made up of the same four basic organic kinds of substances called
Macromolecules.
1. Carbohydrates:
 Composed of carbon, hydrogen, and oxygen atoms
 Chemical formula: (CH2O)n : n is equal to the number of carbon
atoms in the carbohydrate molecule
 High energy molecule
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Broken into 3 different categories:
1) Monosaccharides (“Mono”-means “one”): Simplest
carbohydrates (glucose)
2) Disaccharides (“Di”- means “two”): formed through
dehydration synthesis (lactose, sucrose, maltose)
3) Polysaccharides (“Poly”- means “many”): storage
forms of carbohydrates (starch, glycogen), and structural
material (cellulose in plants)
 Plants use Starch to store glucose
 Animals use Glycogen to store glucose
2.
Lipids
 Large organic molecules that are insoluble (fats, oils, steroids, and
waxes)
 Contain 3 fatty acids and one glycerol molecule
 Types of fats:
1) Saturated Fats: Contains only single bonds between
carbons (Big Mac fat- BAD!)
2) Unsaturated Fats: Contains at least one double bond
(corn oil, olive oil)
3.
Proteins
 Most abundant macromolecule found in living things
 Key structural element in all living things
 Made up of repeating subunits called Amino acids.
 20 different types of amino acids (building blocks of life)
 Joining 2 amino acids forms a dipeptide
 Joining 3 or more amino acids forms a
polypeptide
 Proteins are composed of one
or more polypeptides.
 Enzymes are special proteins that assist chemical reactions that take
place inside the cells of organisms.
 Act as Catalysts (molecules that, when added to a
chemical reaction, will speed up the rate at which
products are formed by lowering Activation Energy
required for the reaction to start)
 Lock-and-Key Theory
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Factors controlling enzyme activity and reaction rate:
 Concentration
 Temperature
 Cell acidity
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4.
Nucleic Acids
 Made up of repeating subunits called Nucleotides
 Nucleotides are composed of a simple sugar, phosphate
group, and a nitrogenous base.
 Two types of Nucleic Acid:
1) DNA (Deoxyribonucleic Acid): stores genetic
information
2) RNA (Ribonucleic Acid): essential for protein synthesis
Photosynthesis & Cellular Respiration:
Photosynthesis:
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Occurs in Autotrophs (organisms that are able to make their own food)
 Example: plants and algae
Photosynthesis is a series of biochemical reactions during which the reactants- sunlight
(photons), carbon dioxide (CO2), and water (H2O)- are used to generate glucose (C6H12O6),
water (H2O), and oxygen (O2)
 Chemical Formula: CO2 + H2O + Sunlight  C6H12O6 + O2 + H2O
Initial stages take place in the chloroplasts
 Inside chloroplasts are stacks of coinlike structures called Grana.
 Grana membranes contain specialized pigments called Chlorophyll
 Chlorophyll gives plants their characteristic green color
There are 2 stages of photosynthesis
1) The Light Reaction (Production of ATP and NADPH):
 Starts when photons of sunlight strike a leaf, activating chlorophyll and
exciting electrons.
 Solar energy is absorbed by the photosynthetic pigments and used to split a
water molecule into its components (hydrogen and oxygen).
 Freed oxygen atoms bond to one another to form atmospheric
oxygen (O2)
 Hydrogen atoms then bond to NADPH to get them into the dark
reaction.
 The splitting of water molecules also produces electrons that get
the energy ball rolling along the Electron Transport Chain.
 Energy carried by these electrons are used to power the
formation of ATP (adenosine triphosphate)
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2) The Dark Reaction or Calvin Cycle (Production of Glucose):
 Doesn’t require the presence of sunlight
 ATP and NADPH created during the light reaction combine with carbon
dioxide and from Glucose and other organic molecules.
 Glucose then becomes the starting reactants used to
power the processes involved in cellular respiration
Variables affecting the rate of photosynthesis:
 Light intensity
 Carbon dioxide concentration
 Temperature
Cellular Respiration:
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Occurs in Heterotrophs (organisms that are unable to produce their own food)
Both plants and animals carry out cellular respiration
Cellular Respiration is a series of biochemical reactions during which the reactants produced
during photosynthesis (carbohydrates and molecular oxygen) react to form carbon dioxide,
water and cellular energy molecules (ATP).
Chemical formula: C6H12O6 + O2  CO2 + H2O + 36 ATP
Occurs in 2 different forms:
1) Aerobic Respiration (oxygen present)
2) Anaerobic Respiration (oxygen not present)
 Stage One: Glycolysis (doesn’t require oxygen, occurs in the cytoplasm)
 Glucose produced during photosynthesis is broken down to create 2
Pyruvic Acid and a total of 2 ATP
 Stage Two: Oxidation of Glucose (Require Oxygen , occurs in the mitochondria)
 Pyruvate (pyruvic acid) is converted into acetyl-CoA and enters the Kreb’s
Cycle
 Acetyl-CoA is converted into other carbon compounds
that result in the production of carbon dioxide and water
molecules in addition to ATP
 The next largest gain of ATP occurs during the final steps of the aerobic
respiration process that takes place in the electron transport chain in the
inner membrane of mitochondria.
 The process of aerobic cellular respiration results in
the production of 36 ATP molecules, which become
the energy source that fuels all other cellular activities.
When there is no oxygen present cellular respiration processes must take place along a
different path that results in a much less energetic outcome.
 Under Anaerobic conditions pyruvate molecules produced during glycolysis remain
in the cytoplasm and undergo Fermentation reactions.
 There are 2 types of Fermentation reactions:
1) Alcoholic Fermentation:
 Takes place in bacteria and yeast. Ethyl alcohol and
carbon dioxide are produced along with 2 ATP
2) Lactic Acid Fermentation:
 Takes place in muscles. Lactic acid is produced in
addition to 2 ATP
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Factors affecting the rate of cellular respiration:
 Regulated by the amount of ATP available in the cell through feedback inhibition.
 When there are high levels of ATP within the cell, ATP molecules bind to
specific key enzymes that are directly involved in the production of ATP
molecules.
 By binding to an enzyme, ATP shuts down the enzyme’s ability to
make additional ATP molecules.
 As ATP concentrations drop within the cell, the bond between
ATP and the key enzyme is broken, thereby releasing the ATP
molecule and allowing the enzyme to again engage in the
production of ATP molecules
The Cell:
The Scientists:
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Cell Theory:
1) Cells can only come from other cells
2) All living things are made up of cells
3) Cells are the unit of function in all living things.
Robert Hooke: first person to observe a cell; coined the term “cell”
Anton van Leeuwenhoek: constructed a simple microscope that could magnify 270 times.
 Discovered bacteria, protozoa, sperm cells, red blood cell, and yeast cells.
Matthias Schleiden: concluded that plants are composed of cells
Theodore Schwann: concluded that all animals are composed of cells.
Rudolf von Virchow: concluded that all cells were derived from preexisting cells
Prokaryotes:
 Prokaryotes are small, single-celled organisms that lack internal membrane-bound
organelles. No nuclei!
 Molecules surrounded by a cell membrane and a cell wall
 Cytoplasm contains necessary proteins, fats, enzymes, and carbohydrates.
 Reproduce using binary fission (cell simply divides in half)
 Examples: bacteria and cyanobacteria
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Eukaryotes:
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Eukaryotic organisms come in all shapes and sizes, ranging form the tiny paramecium to the
largest animal on Earth today.
 The cells of eukaryotic organisms all share the same general structural
characteristics:
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Nucleus: command center of the cell. Specialized compartment
that houses the genetic information of the cell.
 DNA is located here.
Nucleolus: a small organelle located inside the nucleus that aids in
the synthesis of ribosomes.
Ribosomes: small, spherical, membrane-bound organelles located
in the cytoplasm. Site of protein synthesis.
Endoplasmic Reticulum (ER): network of membrane-bound
canals that transport lipids and protein products to other locations
within the cell.
 When ER is bumpy or studded with ribosomes, it’s called
Rough ER. Proteins are marked to be transported out of
the cell in this organelle.
 When ER lacks ribosomes it’s called Smooth ER
Golgi Apparatus (Golgi Vessicle): modifies proteins; packaging a
distribution center for materials destined to be sent out of the cell.
Lysosomes: contain digestive enzymes that break down
carbohydrates, lipids, proteins, and nucleic acids.
Vacuoles: Store macromolecules, wasters, or products that will be
transported out of the cell. Also help to maintain plants rigid and
upright shape.
Mitochondria: powerhouse of the cell; converts the potential
energy locked in organic molecules into a form of energy that the
cell can use. Mainly ATP
Chloroplasts: play a key role in photosynthesis in green plants and
algae.
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Centrioles: cylinder-shaped organelles tha are found near the
nucleus. Assist in cellular division. Spindle fibers are produced
here.
Cytoplasm: medium inside the cell in which organelles are
suspended. Contains protein fibers that assist in cell division and
help maintain the cell’s shape.
Plasma Membrane: Phospholipid bilayer that surrounds a cell to
separate its contents from the surrounding environment.
Cell Wall: rigid structure found in some eukaryotic organisms,
such as plants, fungi, and algae. Protective function
Plant cells vs. Animal cells:
Structure
Cell Wall
Plasma membrane
Organelles
Nucleus
Centrioles
Examples
Prokaryotes
YES
YES
NO
NO
NO
Bacteria
Plant Cells
YES
YES
YES
YES
NO
Cactus
Animal Cells
NO
YES
YES
YES
YES
Human
Viruses:
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Do not contain the full array of organelles that prokaryotes and eukaryotes have.
Contains short segment of nucleic acids, surrounded by a protein coat called a Capsid.
Cannot replicate on their own
 Infect cells and then harness and utilize the DNA replication machinery of the
infected cell to reproduce their own nucleic acid strands.
Modeling the Cell Membrane:
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The cell membrane is made up of two layers of phospholipids.
 Proteins float in the double-lipid layer
 “heads” of the lipids face out
 “tails” of the lipids face in
 this arrangement is known as the Fluid Mosaic.
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Transport:
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There a different methods in which different substances can move across the cell membrane:
 Simple Diffusion:
 When substances move from a high concentration to a low concentration
inside the cell.
 Moving from high to low concentration is known as passive
transport because it requires no energy.
 Facilitative diffusion: a type of passive transport
 Special proteins called carrier proteins can help
lipid-insoluble substances get across the cell
membrane
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Active Transport:
 Substances move from a region of low concentration to a region of high
concentration.
 Requires energy
 Moves substances across the cell membrane against the
concentration gradient
 Types of active transport:
 Pinocytosis (Endocytosis): (“cell drinking”) vacuoles form at the
surface of the cell membrane, then suck in substances on the cell
surface and transport them into the cell to be digested.
 Phagocytosis (Exocytosis): (“cell eating”) large food particles are
engulfed by the cell and brought into the cell for intracellular
digestion.
Cell Communication
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Neurotransmitters: bind to specific receptor proteins on a cell’s surface, causing physical,
chemical, or electrical changes in the cell membrane and cytoplasm.
 Nervous and endocrine systems are responsible for moving messages from cell to
cell using these transmitters.
Hormones: endocrine cells secrete this special chemical messenger molecule
 Bind with specific receptors to bring about change in the cell.
Life at the Systems and Organisms Level:
Important Scientists:
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Jean Baptiste de Lamarck: proposed that organisms change in response to their needs in a
given environment.
 Organisms adapt to their environment and then pass these acquired characteristics to
their offspring.
Thomas Robert Malthus: said that populations increase faster than their environment’s
ability to suppor them, creating a “struggle for existence.”
Charles Darwin: developed the theory of natural selection by adapting Malthus’s theory.
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Archaebacteria
and Eubacteria
Complexity
Divided into 2
kingdoms:
Archaebacteria and
Eubacteria.
Protists
Gas Exchange
Plants
Animal
Unicellular and
multicellular. First
motile species.
Multicellular and cell
specialized. Cell
wall contains chitin.
Contain hyphae
(collection of
hyphae- mycelium)
which are long,
slender filaments
made of strings of
cells that are not
completely separated
from one another
(leads to the
formation of septapermits the flow of
cytoplasm and
cellular organells
between cells)
Multicellular and
autotrophic.
No cell wall, with
specialized cells
organized into tissues
and organ systems.
Bacteria divided into
3 groups:
Autotrophs,
Chemotrophs, and
Heterotrophs
Autotrophs harness
energy from the
sun’s light.
Heterotrophs are
active hunters.
Paramecium use cilia
to move food into its
oral groove and
excretes waste
through its anal
pore. Amoeba use
pseudopodia that
close around chunks
of food forming food
vacuoles.
Heterotrophicsecrete enzymes that
breakdown decaying
matter and then
absorb it.
Autotrophicphotosynthetic.
Absorb trace
elements through
specialized root
structures called
rhizoids
Proper digestive
tract- food is digested
through extracellular
digestion (food is
digested in
specialized cavities,
then transported to
the cells)
Happens directly
through the cell
membrane
Simple diffusion
Stomata regulate the
amount of oxygen,
carbon dioxide, and
water that enters and
leaves a leaf.
Organized cells form
tissues that carry out
gas exchange
functions. Simple
invertebrates
(earthworms) diffuse
oxygen and carbon
dioxide directly
across their outer
covering. Larger
organisms have
evolved gills and/or
lungs.
No membrane-bound
organelles.
Unicellular
Metabolism
Fungi
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Monera
Protists
Fungi
Plants
Animal
Active and passive
transport to move
things across cell
membrane.
Active and passive
transport to move
things across cell
membrane.
Active and passive
transport to move
things across cell
membrane.
Vascular tissue:
specialized tissues
that carry materials
upward toward the
leaves (xylem) and
down toward the
roots (phloem).
Active and passive
transport in simple
organisms. Open
Circulatory Systems
(grasshopperspumped into large
spaces called
sinuses)
Closed Circulatory
Systems (humanscontained in the
vessels)
Flagella and cilia
Amoebapseudopodia
Euglena-flagella
Paramecium- cilia
N/A
N/A
Move in search of
food, shelter, and
mates. Accomplished
through organization
of cells into tissues
and structures that
propel organisms in a
desired direction.
Reproduction
Asexual
reproduction: binary
fission. Each new
cell produced in
identical to the parent
cell.
Amoeba: asexual
reproduction through
mitosis.
Some protists switch
between asexual and
sexual modes of
reproduction.
Asexual
reproduction: spores
form in the
reproductive tips of
hyphae, and wind
carries spores to
different locations
forming new fungal
hyphae.
Sexual
reproduction:
nuclear mitosis and
shared nuclei.
The stamen is
composed of an
anther (contains
pollen) and the
filament.
The pistil contains
the style, stigma, and
ovary.
Double fertilization:
pollen grain enters
pistil, and divides
into 2 sperm cells. 1
sperm cell eventually
forms the new plant,
the other fuses with
polar bodies and
becomes food for the
plant embryo.
Most animals
participate in 1 of 2
types of sexual
reproduction:
External
fertilization: egg and
sperm come together
outside of the body.
Internal
fertilization: egg and
sperm come together
inside the body.
Environment
Form Endospores
(protective thickwalled structures
around DNA) in
extreme conditions
Environmental stress
can force organisms
to switch from
autotrophic to
heterotrophic modes,
and asexual to sexual
modes of
reproduction.
Spores remain
dormant until
environmental
conditions are
favorable.
Hormones respond to
environmental changes.
Tropism (a plant
growth response either
toward or away form an
external stimulus)
Photoperiodism
(response to changing
ratios between light and
dark periods.
Dormancy
When under
environmental stress
animals move to a
more hospitable
environment.
Transport
Locomotion
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Cell Reproduction & Genetics:
The Cell Cycle:
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All living things grow and multiply through a cycle made up of 4 phases:
 First 3 phases (G1, S, and G2 of Interphase), the cell is growing and metabolically
active.
 Forth phase is cellular division
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Mitosis is the process of making identical copies of somatic (body) cells
through asexual reproduction.
 2 things occur during this process:
1) cell duplicates its genetic material
2) cell splits in half, forming 2 identical daughter cells
 Mitosis begins when DNA replication happens during interphase.
 Chromosomes in the nucleus duplicate themselves
Mitosis:
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When identical chromosomes are linked together they are called
sister chromatids.
 Sister chromatids are held together by a centromere
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4 Stages of Mitosis:
1) Prophase: nuclear envelope disappears, centrioles start to
move to opposite poles, spindle fibers begin to appear, and
chromosomes condense and become visible.
2) Metaphase: spindle fibers neatly line up chromosomes
along the equator of the cell.
3) Anaphase: sister chromatids pulled apart at the centromere by
the spindle fibers, and moved to the opposite end of the cell.
 Once the sister chromatids are separated, they
are called chromatin
4) Telophase: Nuclear envelope begins to reform, spindle fibers
disappear, and cytokinesis takes place. Formation of 2 identical
daughter cells.
 Cytokinesis is the process of evenly dividing
cytoplasm in the cell
Binary Fission:
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Binary fission is a form asexual reproduction that prokaryotic cells undergo.
 Just like mitosis:
 Bacteria replicate their chromosomes and divide into 2 identical daughter
cells
 Most common in Paramecium and Ameoba
Budding:
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Budding is a process in which little buds sprout form the parent and eventually develop into a
fully formed offspring.
 Most common in Yeast and Hydra
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Sporulation:
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A form of asexual reproduction that involved spores.
 Fungi produce spores (airborne cells) that are release from the parent organisms into
the air.
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Meiosis is the process by which sexually reproducing organisms maintain the same number of
chromosomes from generation to generation.
 Chromosomes exist in pairs called homologous chromosomes.
 Homologs are similar in shape and function.
 Humans have 23 pairs of homologous chromosomes.
 Humans have 46 chromosomes in each somatic (body) cell.
 The total number of chromosomes in each cell of an organism is referred to
as the Diploid Number (2n)
 Humans have half the number of chromosomes in each Gamete (sex) cell; 23
 The number of chromosomes found in gametes are referred to as Haploid
Number (n)
Meiosis:
Stages of Meiosis: 2 Stages; Meiosis I and Meiosis II
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Meiosis I
1) Prophase I: nuclear membrane disappears, centrioles move to opposite ends of the cell, and
homologous chromosomes pair up during a process called Synapsis to form Tetrads.
 A tretrad consists of 4 chromatids.
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Synapsis is followed by crossing-over
 Crossing-over is the exchange of
segments of homologous chromosomes.
2) Metaphase I: tetrads are aligned at the equator of the cell
by the spindle fibers.
3) Anaphase I: Tetrads (homologous chromosomes) separate, and the
Chromosomes move to opposite ends of the cell.
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4) Telophase I: nuclear membrane reforms around each
set of chromosomes, and the cell undergoes cytokinesis.
 2 identical daughter cells with half the number
of chromosomes as the mother cell are formed.
 Meiosis II:
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Results in four haploid gametes.
5) Prophase II: chromosomes condense, nuclear envelope
disappears, centrioles move to opposite ends of the cell,
and spindle fibers appear
6) Metaphase II: chromosomes move towards the equator
of the cell
7) Anaphase II: chromatids of each chromosome split at the
centromere and move to opposite ends of the cell.
8) Telophase II: new nuclear membrane begins to form
around each set of chromosomes, and four new daughter
cells are produced.
Gametogenesis:
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Gemetogenesis is the process of producing sperm cells or egg cells through meiosis.
 Spermatogenesis: when meiosis takes place in male gonads (testes).
 Produces four identical sperm cells that are all haploid in nature
 Oogenesis: when meiosis takes place in female gonads (ovaries).
 Produces 1 large egg cell (ovum) and 3 smaller polar bodies
 The difference in size is due to an unequal distribution of
cytoplasm during cytokinesis
 3 polar bodies are simple act as receptacles for the excess
chromosomes.
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The Human Reproductive System:
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The goal of the reproductive system is to produce haploid (n) gametes, better known as eggs
and sperm cells.
 Gametes are produced during meiosis.
 Fertilization takes place when an egg and sperm fuse, forming a diploid
cell
Male Reproductive System:
 Manufactures sperm (semen) in a process called spermatogenesis
 Stored in the testes
 Testes are also the site of testosterone production
 Semen exits the body through the urethra
Female Reproductive System:
 Main role of the ovaries are:
 To manufacture ova
 To secrete estrogen and progesterone, the principal female sex hormones
 Follicle stimulating hormone (FSH): stimulates an egg to mature within
the ovary
 Luteinizing hormone (LH): stimulates the production the corpus luteum
(structure formed from the ovarian follicle)
 Progesterone: prepares the uterine environment for implantation of a
fertilized egg.
The Laws of Heredity:
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Heredity: a study of how certain characteristics are passed on from parents to children.
Genetics is the study of heredity
Gregor Mendel: the “Father of Genetics”
Genes: a segment of a chromosome that produces a particular trait.
 The position of a gene on a chromosome is called it locus
Alleles: a pair of hereditary factors. Two alleles make up a gene.
 Dominant Allele: produce observable characteristics. Represented by a capital letter
 Recessive Allele: unexpressed traits. Represented by a lowercase letter
Phenotype: The physical appearance of an organism
Genotype: The genetic makeup of an organism
Homozygous: two identical alleles for a single trait (TT) or (tt)
Heterozygous: two different alleles for a single trait (Tt)
Parent Generation (P1): The first generation
Filial Generation (F1): The offspring of the first generation
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Mendelian Genetics:
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Monohybrid Cross: the crossing on one trait. “Mono” means “one”
o Example: Mendel conducted monohybrid crosses with garden peas. He focused on one
trait:
 Height: short (tt) or tall (TT)
 Flower color: white or purple
 Seed shape: round or wrinkled
o How to perform a cross: Let us consider a cross between a true breeding tall plant (TT)
and a true breeding short plant (tt).
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Punnet Squares are good for showing all the possible combinations of gametes and
the likelihood that each will occur
o Used to predict the Probability of getting an organisms with specific
characteristics
Mendelian Laws:
1) Rule of Unit Factors: there are units in the cell that were responsible for traits, and that these
units came in pairs
 We now know that these units factors are Genes that are located on chromosomes
 Different gene forms are called Alleles
 One allele is inherited from the female parent and one is inherited from the male parent.
2) Rule of Dominance: Pertains to observable traits and disappearing traits
 Observable traits are Dominant Traits. Dominant traits are represented by uppercase
letters
 Unexpressed traits are known as Recessive Traits. Recessive traits are represented by
lowercase letters.
3) Law of Segregation: During gamete formation gene pairs (alleles) separate.
 A parent passes on at random only one allele for each trait to each offspring
4) Law of independent Assortment: genes from different traits are inherited independently of each
other.
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This can be seen in a Dihybrid Cross; this type of cross is used to determine the
genotype and phenotype of offspring when two types of traits are considered.
Beyond Mendelian Genetics:
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Only a few traits can be analyzed with punnett squares because there are more complex patterns of
heredity.
o Incomplete Dominance: The phenotype of the heterozygote is intermediate between
those of the 2 homozygotes.
 Example: if you cross a white snapdragon plant (dominant) and a red
snapdragon plant (recessive), the result will be a pink snapdragon plant.
o Codominance: An equal expression of both alleles
o Example: and individual can have an AB blood type. In this case both alleles are equally
expressed.
The only remaining factors to affect inheritance patterns is mutation.
The Structure of DNA:

Deoxyribonucleic Acid is the molecule of heredity
o Watson and Crick (1953): first determined that double helix structure of DNA
o It is a double stranded molecule that consists of subunits called Nucleotides
 Nucleotides are composed of 3 parts
1) Simple sugar (deoxyribose)
2) Phosphate Group
3) Nitrogen Base
 Purines: double ring nitrogen bases
1. Adenine (A)
2. Guanine (G)
 Pyrimidines: single ring nitrogen bases
1. Thymine (T)

2. Cytosine (C)
Base Pairing: Chargaff’s Rule states that there is a
1:1 ration between Adenine and thymine and a 1:1
ratio between Guanine and Cytosine.
1. Adenine-Thymine
2. Guanine-Cytosine
17
DNA Replication:

DNA Replication is the process of coping DNA that takes place during Interphase. Results in the
formation of 2 DNA molecules, each identical to the original DNA molecule.
o Steps of DNA Replication:
1) Separation of DNA strands
 Enzymes break the weak hydrogen bonds between the nitrogen
bases that hold the 2 DNA strands together.
2) Base Pairing
 Free nucleotides that are floating around the unwinding DNA,
bond to the single strands of DNA with the help of the enzyme
DNA Polymerase
o Free guanine will bond with cytosine
o Free adenine will bond with thymine
3) Bonding of Bases
 The sugar and phosphate parts of the once free nucleotides now
bond together to form the sugar-phosphate backbone of the new
strand of DNA
Differences between DNA and RNA:
Differences between DNA and RNA
DNA (double-stranded)
Sugar
Deoxyribose
Adenine
Bases
RNA (single-stranded)
Ribose
Adenine
Thymine
Uracil
Guanine
Cytosine
Guanine
Cytosine
Types of RNA: RNA are the key players in the synthesis of protein synthesis
1) Messenger RNA (mRNA): brings in the information from the DNA in the nucleus to the ell’s
cytoplasm.
2) Ribosomal RNA (rRNA): clamp onto the mRNA and use its information to assemble the amino
acids in the correct order.
18
3) Transfer RNA (tRNA): transport amino acids to the ribosome to b assembled into a protein.
Proteins and the Genetic Code:
1) DNA Replication: the process of making DNA from DNA
2) Transcription: the process of making mRNA from DNA
3) Translation: the process of making amino acids (subunits of proteins) from RNA
Transcription:


Transcription is the process within the cell nucleus where enzymes make an mRNA
copy of a DNA strand.
Steps of Transcription:
1) Separation of Strands
 Enzymes break the hydrogen bonds between the nitrogen bases
that hold the 2 DNA strands together
2) Base Pairing
 Free RNA nucleotides pair with complementary DNA nucleotides
on one of the DNA strands. This is done with the enzyme RNA
Polymerase.
3) Reforming of DNA Molecule
 The mRNA molecule breaks away as the DNA strand rejoins
4) Exiting the Nucleus
 The mRNA leaves the nucleus and enters the cytoplasm
Translation:

Translation is the process of converting the information in a
sequence of nitrogen bases in mRNA into a sequence of amino
acids that make up a protein.
19
o
Steps of Translation:
1) mRNA attaches to the ribosome
 The mRNA start codon attaches to the ribosome
2) A-U-G (start codon) signals the start of protein synthesis
 Once the start codon codes for the amino acid methionine,
the ribosome slides along the mRNA to the next codon
3) New tRNA molecule
 After the ribosome slides to the next codon, a new tRNA
molecule carrying an amino aid pairs with the 2 nd mRNA
codon
4) Bonding of the Amino Acids

The 1st and 2nd amino acids are joined together
by an enzyme
 The enzyme forms a Peptide Bond between the 2 amino
acids
5) Stop Codon
 This process continues, and a chain of amino acids is
continually formed until the ribosome reaches one of the
3 possible stop codons on the mRNA strand.
Once the stop codon is reached, translation ends and the
amino acid strand is released from the ribosome;
becoming a protein.
Taxonomy and Ecology:
Taxonomy:
 Taxonomy is a branch of biology that groups and names organisms based on studies of their
different characteristics
 Classification is the grouping of objects or information based on similarities
 Modern day classification is based on a system developed by Carolus Linnaeus.
 Linnaeus developed Binomial Nomenclature (two-word naming system)
 Two-word naming system involves a Genus and species

Taxonomic Ranking System:
 Kingdom
 Phylum
 Class


Order
 Family
 Genus
 Species
Kings
Play
Chess
On
Fridays
Generally
Speaking
Remember…
 Similar genera are united into a family
 Similar families are combined into an order
 Similar orders are collected into a class
 Similar classes are united into a phylum
 Similar phyla are collected into a kingdom

The evolutionary history of a species is known as Phylogeny
 Phylogenetic classification shows the evolutionary history of species.

Cladistics is a biological system of classification that is based on phylogeny.
 This method of classification assumes that groups of organisms diverge and evolve
from a common ancestral group.
20



Cladograms are models of phylogeny of species.
 When two branches of the diagram meet at a certain point, this
represents the shared characteristics between the two groups.
Taxonomy and Technology: technological advances have enabled biologists to study the
genes that produce that traits used to classify organisms.
 DNA nucleotide sequences of different organisms are compared.
 Mutations (changes in DNA) are looked at.
 As time passes, more mutations tend to accumulate in the DNA of
a particular species.
 DNA acts as a molecular clock.
 The more similar the DNA sequences of the two
species, the more recently their common ancestor
must have lived, and the more closely they are
related.
In Convergent Evolution, organisms evolve similar features independently, often because
they live in similar habitats.
 Similar features that evolve through convergent evolution are known as Analogous
Structures. Do not share common ancestry.

Wings of birds and those of bats, the arms of a human, the leg of a dog, and the
flippers of a whale are all Homologous Structures. Suggest common ancestry
21
Classification:

Organisms are classified into one of 6 Kingdoms.
1)
2)
3)
4)
5)
6)
Eubacteria
Archaebacteria
Protista
Fungi
Plantae
Animalia
Modern Classification:

Closely related organisms pass through similar stages during their embryologic development.
 The embryologic development of all vertebrates (animals characterized by
backbones), from fish to humans, are characterized by gill pouches, a tail, and limb
buds.
 These common structures develop into distinctive features for each
organisms.
 The similarities between these embryonic structures unify different
classes of fish, amphibians, reptiles, birds, and mammals into the
same phylum: Chordata
Fish
Turtle
Chick
Human
Agents of Disease:

The primary goal of all living things is to find and secure suitable resources such as food,
shelter, and mates. These goals all serve the purpose of increasing the probability that their
genes will be passed on to the next generation.
 Some species have developed strategies whereby their greatest success for securing
resources comes through reliance on other organisms.
 Unfortunately, the reliance of certain microorganisms on plant and animal
hosts, including humans. Often causes disease.
22



Bacteria:
 Many common and formerly common human diseases (bubonic plague, cholera, and
typhoid fever) are the result of infections by parasitic bacteria that attach cells and
secrete toxins.
 Alexander Flemming first discovered penicillin in 1928 that led to the
development of antibiotics in the 1940’s.
 Antibiotics are effective treatments for such bacterial infections as
tuberculosis, pneumonia, and middle ear infections.
 The overuse of antibiotics can lead to drug-resistant
strains of bacteria
Viruses:
 The cause of smallpox, polio, influenza, and acquired immune deficiency syndrome
(AIDs).
 Viruses defy standard medical treatments like antibiotics.
 Certain viral infections can be avoided through the use of Vaccines
(A weakened form of the viral strain)
Protists:


While not all protists are parasites ( organisms that inhabit other organisms and are
harmful to the host in which they live), some are can cause serious diseases in plants
and animals.
 Taxoplasmosis: a disease caused by protists that lead to severe health
implications for unborn children
 Entamoeba: parasitic protist that infects humans directly through
contaminated food and water supplies and causes amoebic dysentery.
 Plasmodium: parasitic protist that infects mosquitoes that then become the
agent of infectious disease, spreading malaria-causing protist from one
human host to the next.
Fungi:
 Certain fungi cause disease in humans.
 Examples: thrush (athlete’s foot), and ringworm
23


Fungal infections like those caused by powdery mildews, rusts, and smut
cost farmers millions of dollars each year in decrease crop yields and
fungicide sprays.
Worms:
 Flatworms represent the largest group of parasitic macroorganisms, with more than
6,000 species in all.
 Similar to parasitic protists, flukes and tapeworms also utilize a human host
intermediate.
 Other plant and animal parasites include over 50 species of roundworms.
 Infection by Trichinella causes trichinosis in humans who
consume undercooked or poorly cooked pork.
 Other common parasitic roundworms include the intestinal
roundworm Ascaris and hookworm, such as Necator.
The Fossil Records:

Fossils (preserved or mineralized remains, such as the bones, shells, teeth, or footprints of
organisms that live in the distant past) provide the most direct evidence that evolution has
occurred.
 Fossils are formed at the same time as the sedimentary rocks in which they are found

Sedimentation, Fossil Formation, and the Rock Record

Weathered rock fragments, called sediments, are carried by rivers or streams to a
standing body of water.




As the running water leaves the river and moves into an ocean, the sediment
that it carried is deposited on the bottom of the ocean, forming a horizontal
layers of sediment.
Layers of sediment pile up as more and more sediment is deposited.
The remains of dead marine organisms are eventually buried as more
sediment continues to be piled on.
Over time, the increasing weight of the top layer increase pressure on the
lowest rock layers, creating sedimentary rock and fossils.

The Principle of Superposition states that in undisturbed rock
layers, the oldest layer is at the bottom, and the youngest layer is
found at the top.


Fossils found in undisturbed rock layers are oldest at the
bottom of the column and youngest at the top.
Fossil organisms are simplest at the bottom and increase
in complexity toward the top of the column.

These two factors together provide scientists
with a handy tool called the fossil record, which
assists them as they track changes in life forms
through geologic time.
24
***Layer A is older than Layer B, Layer B is older
than Layer C

Rate of Evolution: Gradualism vs. Punctuated Equilibrium

Gradualism (Darwin’s Model of Evolution): fossil evidence suggests that
evolution is a slow, gradual, and continuous process in which species change over
long periods of time.

Punctuated Equilibrium (Stephen Jay Gould and Niles Eldridge): characterized
by long periods of stasis (little or no physical changes) followed by short periods
punctuated by abrupt physiological change in species.
 Scientists theorize that these abrupt changes result as a function of changing
environmental pressures.
 During these periods of change, new species appeared in the fossil
record while other species disappeared or became extinct.
25

Population Change Through Time:

Fossil records indicate that many groups of organisms, including horses, have
undergone significant physiological changes throughout the course of geologic time.


Fossil records are tools that can be used for tracking trends (directional
changes in the characteristic features of patterns of diversity in a group of
organisms) in the evolution of groups of organisms.
Emergence of New Species:

Speciation: the process by which genetically distinct species arise.
 Results from the accumulation of adaptations over time

Species: a population of organisms that can and does interbreed under natural
environmental conditions producing fertile offspring.
 Hybrids: offspring produced form cross-species mating.
 Cross-species mating most often results in sterile offspring

Isolating mechanisms that lead to speciation are:
1) Geographic Isolation: the physical separation of species
populations by geographic barriers.
 Example: ocean, mountains, or canyons
 Geographic isolation of a small population results in
changes in gene frequency as well as selection for
adaptations that make the species well suited for the new
environment.
 Over time, different environmental conditions
and different selective pressures result in the
production of two genetically distinct
populations.
26
2) Reproductive Isolation: Species that are reproductively isolated
from each other are those in which:
 Their reproductive organs are incompatible
 They are genetically incompatible due to differences in
chromosome number or genetic composition
 Gamete production takes place at different times of the
day, month, or year.
 Species do not recognize courtship behavior of other
species.
Ecology:



Ecology is the study of the interactions of living organisms with one another and with their
physical environment.
Population: a group of organisms that belong to the same species and inhabit a given
geographic location at a given time.
 All of the populations of different species living together in a given location at a
given time form an ecological Community.
 An Ecosystem is how an ecological community interacts with the nonliving
environment in which it is found.
 Earth’s Biosphere is the portion of the earth in which living things
exist.
Dynamic Equilibrium:

Each population is a system that has its own dynamics and interrelationships.

Dynamic Equilibrium is achieved when the number of births in a
population are equal to the number of deaths and when the number of
individuals moving into a population (immigrating) is equal to the number
of individuals leaving a population (emigration)

If populations increased unchecked, the population would grow
Exponentially.

Most environments cannot support exponential growth.

A logistical growth curve shows a more common pattern
of population growth.


Populations may begin to grow exponentially,
but growth rate soon slows as population density
approaches the Carrying Capacity (maximum
number of individuals of a species that a given
geographic region can support) of the
environment.
As a population approaches carrying capacity,
death rate equals birth rate, achieving dynamic
equilibrium.
27

2 types of Limiting Factors help to keep population size in check:
1) Abiotic limiting factors are nonliving environmental factors that
affect a population regardless of its size.
 Examples: oxygen concentration, moisture
availability, and weather conditions.
2) Biotic limiting factors are environmental factors that result from
population interactions within the population (intraspecific) or
with other populations (interspecific) within the ecosystem.
 Examples: food, water, mineral, or light,
predation, and parasitism.

Symbiosis is the interrelationship between organisms that share an ecosystem. The three types
of symbiosis are:
1) Commensalism: one organism benefits from the relationship with an
member of a different species. The second organism neither benefits nor is
harmed.
 Example: remora-shark relationship remora benefits
from the food scraps produced by the shark as the shark
feeds.
2) Mutualism: results in benefits for both interacting organisms.
 Example: A lichen is a mutualistic relationship between a
fungus and an alga in which the fungus provides the alga
with protection, and the alga provide the fungus with food
from photosynthesis.
3) Parasitism: relationship in which one organism benefits at the expense of
another.
 Example: Mosquitoes, fleas, and ticks are external
parasites that feed on living organisms and may introduce
disease as they feed.
28

Nutrient Cycling and Energy Flow Through Ecosystems:

The cycling of carbon, hydrogen, and oxygen as a result of the complementary
processes of photosynthesis and cellular respiration.

Nitrogen Cycle: decomposers are essential to converting nitrogen-containing
compounds to forms that are accessible to plants. Animals incorporate nitrogen
absorbed from plants during consumption into their own tissues through digestion.
29

Water Cycle: Water functions as a reactant, product, and solvent and is critical to
homeostasis in most living organisms. Both abiotic and biotic factors interact as
water is transformed from one phase to another.

Energy Cycle: Energy enters as solar energy, which is absorbed by autotrophic
organisms (producers-plants, and algae). Producers then convert the energy into
accessible forms for heterotrophic organisms (consumers- protists, fungi, and
animals). Decomposers such as fungi and bacteria obtain energy from both
producers and consumers after these organisms die.


A Food Chain is used to show a linear transfer of energy
through the ecosystem from a producer to a final consumer.
 The food chain always begins with energy from
the sun
 A Food Web is a complex interaction of a
number of food chains within an ecosystem.
Energy flow, biomass (the total mass of all the organisms in an area), and population
size within an ecosystem can be represented in a pyramid.

Organisms that are higher up on the pyramid are less numerous and have
less biomass.
30





Producers that make their own food
Primary consumers (herbivores) that eat producers
Secondary consumers (heterotrophs and carnivores) that
eat primary consumers
Tertiary consumers (heterotrophs and omnivores) that
eat all of the above.
Succession Patterns in Ecosystems:


Ecological Succession is the sequential replacement of one ecological community
by another.
 Ecological succession is complete with the establishment of the Climax
Community (a stable, self-perpetuating community)
Steps of Succession:
1) Bare rock (succession can also begin after a environmental event; volcanic
eruptions, forest fires, or tornadoes)
2) Pioneering Species establishes itself on the rock (Example: Lichen)
3) Rock is broken down by enzymes secreted by the pioneering species
4) Newly liberated minerals mixed with organic matter form the first very
immature soil
5) Newly formed soil supports seeds from grasses and other herbaceous plants
6) Animals lured into the delicate environment by grasses and other plants
7) Animals contribute organic matter to the developing soil
8) Soil continues to develop through the physical and chemical weathering
action of larger plants and the addition of more organic matter
9) New species of both plants and animals move into and dominate the area
until a climax community becomes established
31