NMAT Review 2018 Module - Biology

U.P.
Pre-Medical Honor Society
BIOLOGY
MODULE
U.P. Pre-Medical Honor Society Biology module 2018
BIOLOGY
GENERAL CONCEPTS
Biology: From Greek βίος, bios, "life" – the  Response to environment
study of life  Evolutionary adaptation: All
organisms living today are modified
Unifying Principles of Life: descendants of common ancestors
 Biological organization and order  Structure/function relationship
Classifying Organisms
Emergent properties: properties at

each larger level that aren’t found in
the previous level Mnemonic: Dear King Philip Came Over For
Good Spaghetti
 Reproduction
 Homeostasis: Regulatory Scientific names:
mechanisms maintain an organism’s
 Always italicized
internal environment
 Growth and development:  The first letter of the genus name is
CAPITALIZED, everything else is in
according to heritable information
lowercase
 Energy processing: The
 Example: Homo sapiens
transformation of one type of energy
into another
BOTANY
1. Parenchyma
Botany - the scientific study of plants.
- Have thin primary walls.
Basic Types of Plant Cells and Tissues - Most common type and
Tissue constitutes all soft parts of a
plant.
 a group of cells organized - They are metabolically active
into structural and - Alive at maturity.
functional unit.
- Has numerous functions
 masses of cells that are
within the plant.
alike in origin, structure,
and function.
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2. Collenchyma
Plant Organs
- Have unevenly thickened
primary walls. Organ
- Alive at maturity - Consists of several types of tissues
- Mainly functions to provide that altogether carry out particular
plastic support functions.
- Present in elongating shoot
tips that must be long and The Root
flexible. - Anchors a vascular plant in the soil.
- Absorbs minerals and water.
Two main systems of roots:

a.) Taproot system
 Consists of a main vertical root

and gives rise to lateral roots.
 Developed from an embryonic
origin.
 Typical in eudicots (plants with
seeds that have two cotyledons)
and gymnosperms (plants with
naked seeds)
3. Sclerenchyma
b.) Fibrous
- Have primary walls and system
secondary walls.
- Dead at maturity  Consists
- Primarily provides elastic of small
support and some (tracheary roots
elements) are involved in that
water transport. emerge
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from the stem (adventitious: a parts: a flattened blade and a stalk,

term that describes a plant organ called a petiole, that connects the
that grows in an unusual location, leaf to the node of the stem
such as roots arising from stems
or leaves)
Arrangement of veins:
 This system is composed of thin
roots forming a mat that spreads a) Parallel
out below the soil surface.
- Most monocots
 Typical in most monocots, such
- Veins run through the length of
as grasses.
the blade.
b) Branched
The Stem
- Most eudicots
- Raises
or separates
leaves to
expose them Spatial arrangement of leaves:
to sunlight
a) Simple
- Raises
reproductive - Has a single
structures undivided
such as fruits blade.
and flowers. b) Compound
- Node - points in the stem wherein
- Blade
leaves are attached.
consists of
- Internodes - stem segments
multiple
between nodes
leaflet.
- Axillary bud - structures in the upper
- A leaflet has no axillary bud at
angle (axil) formed by each leaf and
its base.
the stem. It grows into a lateral shoot
or more commonly called a branch.
The Leaf
- Main
photosynthetic
organ in most
vascular plants
(sometimes a
photosynthetic
stem is present).
- Composed of
two general
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Plant Hormones
Hormone Site of Major Functions

Production/Location
Auxin (AA) - Shoot apical meristems - Stimulates stem elongation (low

- root apical meristems concentrations only)
(depends on shoot for - Promotes formation of lateral and
auxin) and young adventitious roots.
leaves. - Regulates fruit development
- Developing seeds and - Enhances apical dominances
fruits. - Promotes vascular differentiation
- Retards, leaf abscission
- Functions in phototropism and
gravitropism
Cytokinin - Roots - Regulates cell division in shoot

and root
- Promotes lateral bud growth
- Promote movement of nutrients
into sink tissues
- Stimulate seed germination
- Delay leaf senescence.
Gibberellins - Meristems of apical - Regulate sex detemination and

buds and roots transition from juvenile to adult
- Young leaves phases
- Developing seeds - Stimulate the following:
- Stem elongation
- Pollen development
- Pollen tube growth
- Fruit growth
- Seed development germination
Brassinosteroids - Present in all plant - Promote cell expansion and cell

tissues division in shoots.
- Promote root growth (low
concentrations).
- Inhibit root growth (high
concentrations)
- Promote xylem differentiation
- Inhibit phloem differentiation
- Promote seed germination
- Promote pollen tube elongation
Abscisic acid - Present in all plant cells - Inhibits growth

(ABA) - Promotes stomatal closure during
drought stress.
- Promotes seed dormancy
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- Inhibits early germination

- Promotes leaf senescence
- Promotes desiccation tolerance
Ethylene - Present in most parts of - Promotes fruit ripening

plant (GASEOUS) - Promotes leaf abscission
- Promotes triple response in
seedlings (inhibition of stem
elongation, promotion of lateral
expansion, and horizontal growth)
- Enhances rate of senescence
- Promotes root and root hair
formation
CELL BIOLOGY
No membrane-bound w/ membrane-bound
Cell Biology organelles organelles
Cell: Basic unit of structure and function
Circular DNA Linear DNA
Cell Theory
Matthias Schleiden (1838): All
Smaller ribosomes Larger Ribosomes
plants are composed of cells
Theodore Schwann (1839): All Domains Bacteria Domain Eukarya
animals are composed of cells and Archaea
Rudolf Virchow (1855): Cells only
come from other cells
Cell Parts
1. All living things are composed of one
The Nucleus: contains genetic material
or more cells
2. Cells are the organism’s basic unit of - Nuclear envelope: Double
structure and function membrane enclosing the nucleus,
3. Cells only come from existing cells perforated with pores, continuous
Prokaryotic vs Eukaryotic Cells with endoplasmic reticulum
- Nucleolus: nonmembranous,
Prokaryotes Eukaryotes involved in production of ribosomes
- Chromatin: material consisting of
DNA and proteins, which condense
Small Generally larger
into chromosomes in dividing cells
No nucleus (may w/ nucleus

have nucleoid)
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The Plasma Membrane: encloses the cell substance down

concentration
Phospholipid bilayer: composed of
gradient
phospholipids with a hydrophobic tail and a
hydrophilic head ■ Facilitated diffusion:
Transport protein aids
in moving a
substance across a
membrane
■ Ion channels & carrier
proteins
○ Active transport: expends
energy (usually ATP) in
 Fluid mosaic model: The plasma moving substances against
membrane is not static/rigid, most of the concentration gradient,
the lipids and some of the proteins usually considers the
can shift about laterally electrochemical gradient
○ Factors affecting membrane ■ Cotransport:
fluidity: Movement of one
■ Unsaturated vs substance across a
saturated membrane facilitates
hydrocarbons: Double the movement of
bonds in unsaturated another substance in
hydrocarbons cause the opposite direction
“kinks,” increasing ○ Bulk
fluidity. ■ Exocytosis: Transport
■ Presence of vesicles migrate to
cholesterol: Reduces plasma membrane,
fluidity by reducing fuse, then release
movement, but ■ Endocytosis:
prevents solidification Molecules enter cells
■ Temperature: within vesicles that
increase membrane pinch off from plasma
fluidity membrane
 Protein types
○ Integral: Embedded in
plasma membrane The Mitochondria: functions in cell
respiration where ATP is produced
○ Peripheral: Loosely bound to
surface of membrane Endoplasmic Reticulum: A network of
 Transport across the plasma membranous sacs and tubes
membrane
- Rough ER: Contain many
○ Passive
membrane-bound vesicles called
■ Diffusion:
ribosomes, responsible for protein
Spontaneous
synthesis, folding, and dispatch
movement of
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- Smooth ER: Does not have - Composed primarily of cellulose (in

ribosomes, responsible for synthesis plants) or chitin (in fungi)
of lipids and some steroid hormones - Not present in animal cells
Ribosome: As stated above, they function Chloroplasts: Photosynthetic organelles in
in protein synthesis; may be free-floating or plants and some algae
embedded in endoplasmic reticulum
- Not present in animal cells
Golgi apparatus: Involved in synthesis, Vacuole: For storage, breakdown of waste,
sorting, modification, and secretion of cell hydrolysis of macromolecules in plants
products
- Not present in animal cells
Lysosome: Secretes digestive enzymes Plasmodesmata: Channels in cell walls
that connect the cytoplasms of adjacent
Peroxisome: Produces hydrogen peroxide
cells; function in cell communication
as a byproduct of other metabolic reactions
and converts it to water - Not present in animal cells
Cytoskeleton: Reinforces cell shape and
functions in cell movement Photosynthesis :“Synthesis using light”
6CO2 + 6H2O à C6H12O6 + 6O2
- Microfilaments
- Intermediate filaments Chloroplasts: contain specialized light-
- Microtubules absorbing pigments (chlorophylls)
- Centrosome: Region where - Thylakoid: location of thylakoid
the cell’s microtubules are reaction
initiated - Light --> chemical energy
- Cilia and flagella: motile Photosynthetic pigments: Absorption of
appendages containing energy of sunlight
microtubules as well as the
protein dynein - Chlorophyll a and b: abundant in
Cell Wall: Maintains cell shape, protects green plants; differ in side chain (-
cell from damage, functions in cell CH3 in a, -CHO in b)
communication - Carotenoids: considered accessory
pigments because light energy from
them is transferred to chlorophylls
ORGANIZATION OF PHOTOSYNTHETIC APPARATUS
- Stroma: contains enzymes for carbon fixation

- Thylakoid membranes: photosynthesis; PSI and ATP synthase are found in the regions that
protrude into the stroma; PSII is in the grana lamellae
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Photosystem: consists of:

Light-harvesting complex: Consist of various
pigment molecules bound to proteins
Reaction center complex
Two photosystems: PSI (P700) and PSII (P680)
Linear/Noncyclic Electron Flow: Involve PSI and PSII
1. Photon strikes pigment molecule in LHC, electron is excited, “passes on” energy to a
nearby pigment molecule until it reaches the P680 pair of chlorophyll a molecules,
exciting e- there to higher state.
2. Electron is transferred to primary acceptor
3. Enzyme catalyzes splitting of water molecule, supplying electrons to P680+, and H+ into
the thylakoid lumen. O2 is formed.
4. Electron transfer chain: passing of photoexcited electrons from primary electron acceptor
of PSII à PSI via ETC. ETC is made up of plastoquinone, a cytochrome complex, and
plastocyanin.
5. Exergonic fall provides energy for ATP synthesis. H+ is pumped into thylakoid lumen.
6. Transfer of light energy via LHC to PSI, exciting 2 of the P700 CHl molecules (like
earlier)
7. Photoexcited electrons passed in redox reactions in ETC via ferredoxin. No proton
gradient is formed.
8. NADP+ reductase catalyzes transfer of e- from Fd to NADP+. 2e- required to form
NADPH.
Cyclic Electron Flow
When ATP is low, primary electron acceptor in

PSI can cycle e- back to ferredoxin to produce
more ATP (but no NADPH). In some groups,
CLE is the only way to generate ATP.
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ATP Synthesis
Hydrogen ions pumped out during ETC create chemiosmotic
gradient in the thylakoid space. Protons diffuse across the
membrane via ATP synthase, forming ATP.
Carbon Fixation: Conversion of carbon into a form usable by the
plant
The Calvin Cycle:
1) Carboxylation of ribulose-1,5-bisphosphate, forming 2
molecules of 3-phosphoglycerate
2) Reduction of 3PG, forming glyceraldehyde-3-
phosphate
3) Regeneration of 1,5RBP from G3P
Alternative Methods of Carbon Fixation

● Photorespiration/Oxidative photosynthesis:
Result of oxygen buildup
○ RuBisCo can catalyze both carboxylation
and oxygenation of ribulose bisphosphate
○ RuBisCo adds O2 to Calvin Cycle instead
of CO2, forming 2-carbon intermediate
○ This process releases CO2 without producing ATP or sugar
○ Possibly a metabolic relic from when atmosphere had less oxygen and more
carbon dioxide
○ Can drain as much as 50% of carbon fixed by carbon cycle
● C4: Sugarcane, corn, some grasses
○ Minimizes photorespiration by incorporating CO2 into 4-carbon compounds in
mesophyll cells (SPATIAL modification of C3)
○ Export carbon to bundle sheath cells: release CO2 for photosynthesis
○ CO2 concentration is maintained
● Crassulean Acid Metabolism (CAM)
○ Stomata open at night, incorporating CO2 into organic acids
○ Stomata close during the day, during which CO2 is released from organic acid,
conserving water
○ PEP fixes CO2 to oxaloacetate, forming MALIC ACID for transport to vacuole
○ TEMPORAL modification of C3
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Cell Respiration
Photosynthesis: Turning energy from light into energy-rich molecules
Respiration: extraction of stored energy from glucose to form ATP (oxidation of glucose)
Substrate-level phosphorylation: enzymatic transfer of phosphate group from an intermediate
to ADP
Oxidative phosphorylation (from which 90% of ATP is formed): chemiosmosis couples
electron transport to ATP synthesis; NADH and FADH2 act as electron carriers
Stages of Cell Respiration:

1. Glycolysis: breakdown of 6C glucose molecule to two 3-C molecules of pyruvic acid or
pyruvate
2. Krebs cycle/Citric acid cycle: further breakdown of remnants of glucose molecule to CO2
and H2O, formation of electrons
3. Electron transport chain: passage of resulting electrons from stage 2
4. Oxidative phosphorylation: energy from electrons move through ETC, used to form ATP
from ADP and phosphate
Glycolysis/Embden-Meyerhoff Pathway:
- Formation of pyruvate from glucose
- Two phases:
1. Energy Investment: Glucose → glyceraldehyde-3-phosphate (G3P)
2. Payoff: G3P → Pyruvate
- Net products: 2 ATP + 2 NADH
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Fate of electron acceptors: Dependent on organism and availability of oxygen
Anaerobic pathways:
1. Ethanol fermentation: pyruvate → ethanol
2. Lactate fermentation: pyruvate → lactate
Pyruvate Acetaldehyde O2
Abundant when Abundant when Usually abundant

needed needed when needed
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Expensive Expensive Cheap
Toxic product Toxic product Nontoxic product
Citric Acid Cycle/Tricarboxylic Acid Cycle/Krebs Cycle

- Takes place in the mitochondrial matrix
- Aka tricarboxylic acid cycle because most intermediates are TCA
- Preliminary step: transfer of pyruvate from cytosol into mitochondrial matrix
- Oxidation and carboxylation of pyruvic acid, forming acetyl-CoA
- NADH formation (1/pyruvate, 2/glucose)
Electron Transport Chain

- Transfer of electrons from NADH and FADH2 to oxygen along increasingly stronger
oxidizing agents, eventually creating ATP
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- ATP produced is also dependent also on shuttle used

- In summary:
-
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The Cell Cycle

Cell division:
Mitosis: Results in 2 genetically identical daughter cells
1. Prophase: Nucleoli disappear, chromatin fibers condense into chromosomes

2. Prometaphase: Nuclear envelope fragments, chromatids now each have a kinetochore
3. Metaphase: Chromosomes convene at metaphase plate; for each chromosome
kinetochores of sister chromatids are attached to kinetochores at opposite poles
4. Anaphase: Sister chromatids separate, becoming full-fledged chromosomes, and being
moving towards opposite ends of the cell
5. Telophase: Two daughter nuclei form, nuclear envelope reforms, nucleoli reappear,
chromosomes decondense
- Cytokinesis: Division of cytoplasm in animal mitosis, usually coincides with
telophase
- Cell plate formation: The formation of a future cell wall dividing the daughter cells
in plant mitosis
- Mitosis (M) alternates with interphase

- G1 (Gap 1): First stage of growth of a dividing cell
- S(Synthesis): DNA is duplicated, preparing the cell
for mitosis
- G2 (Gap 2): Second growth stage, preparing the
cell for mitosis
Cell cycle control:
- Cyclins activating cyclin-dependent kinases to
form cyclin-CDK complexes allow the cell to
proceed to the next stage of the cell cycle
- Checkpoints also exist where the cell cycle stops until a “go-signal” is received
- Density-dependent inhibition
- Anchorage dependence
GENETICS
Genetics: the scientific study of heredity and hereditary variation
Definition of terms:
 DNA: Deoxyribonucleic acid, the hereditary material in all organisms
 Character: A heritable feature that varies among individuals (eg. eye color)
 Trait: A variant of a character (eg. blue eyes or brown eyes).
 Gene: A unit of heredity transferred from a parent to an offspring that determines a certain
character. It is a set sequence of nucleotides in an organism’s DNA.
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 Allele: An alternative form of a gene

 Gamete: A reproductive cell that transmit genes from one generation to the next (sperm
and egg)
 Somatic cell: All other cells that comprise the body
 Chromosomes: A structure found in the nucleus of an organism that is comprised of
packaged and organized DNA
○ Homologous chromosomes: Paired chromosomes (1 maternal, 1 paternal)
joined at a centromere; they contain genes coding for the same traits
○ Sex chromosomes: Chromosomes which determine an organism’s biological sex
(eg. X and Y in humans)
○ Autosomes: The non-sex chromosomes in an organism
 Diploid cell: Any cell with 2 sets of chromosomes (2n)
 Haploid cell: Any cell with only 1 set of chromosomes (n), such as gametes
 Asexual reproduction: Type of reproduction in which offspring is genetically identical to
the sole parent
 Sexual reproduction: Type of reproduction in which the offspring has a unique
combination of genetic material from both parents
 Meiosis: A type of cell division that reduces chromosome number (from diploid → haploid)
○ Cell divides twice
 Meiosis I: separates homologous chromosomes

○ Prophase I: Chromosomes begin to condense and sister chromatids pair up
(synapsis)
■ Crossing over: A genetic rearrangement between non-sister chromatids
■ Chiasmata (sin. chiasma): locations at which synapsis occurs
○ Metaphase I: Homologous chromosomes are arranged at the metaphase plate.
Sister chromatids are attached to kinetochores from opposite poles.
○ Anaphase I: Homologous chromosomes are pulled to opposite poles of the cells
○ Telophase I and Cytokinesis: Two haploid cells are formed. No duplication of
chromosomes occurs.
 Meiosis II: separates sister chromatids, is more or less identical to mitosis
○ Four daughter cells are formed which are all genetically distinct from each other
and from the parent cell
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MITOSIS MEIOSIS
DNA replication During interphase, During interphase,

before prophase before prophase I
# of divisions 1 2
Synapsis Does not occur Occurs during

prophase I
# and genetic 2, identical to 4, genetically

composition of parent cell distinct
daughter cells
Role Growth and Produces gametes,

development, introduces genetic
asexual variability due to
reproduction (in crossing over
some species)
Mendelian Genetics
 Homozygous: When an organism has two of the same allele for a certain trait
 Heterozygous: When an organism has different alleles for a certain trait
 Dominant: An allele that manifests itself in a heterozygote, referred to by a capital letter
(eg. A)
 Recessive: An allele whose effect is “masked” in a heterozygote, referred to by a small
letter (eg. a)
 Hybridization: The mating of two true-breeding/homozygous varieties
 P generation: “Parental generation,” the generation that is hybridized
 F1 generation: The offspring of the P generation
 F2 generation: The offspring of the F1 generation, obtained via self- or cross-fertilization
 Phenotype: An organism’s external appearance
 Genotype: An organism’s genetic makeup
Gregor Mendel: Austrian monk who came up with the “gene idea” after experimenting with
garden peas; considered the “father of modern genetics”
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 Mendel’s experiment: after crossing true-breeding purple and white flowers, he observed
that the F1 generation was all purple. However, after these plants were allowed to
reproduce with each other, around ¼ of the offspring were white, indicating that the white
trait was not diluted but instead masked
Mendelian model:
1. Alternative versions of genes (alleles) account for
variability in traits
2. For each character, an organism inherits two copies
of a gene -- one from each parent
3. If two alleles at a locus differ, the dominant allele
determines appearance while the recessive allele’s effect
is masked
4. Law of segregation: Two alleles separate during
meiosis and end up in different gametes
Punnett square: Used to determine combinations of offspring

obtained from a cross
Other terms:
 Testcross: To determine the genotype of an organism
manifesting the dominant characteristic (eg. PP or Pp), it is
crossed with a homozygous recessive organism (eg.
pp) and the parent’s genotype is deduced from the
offspring’s phenotypic ratio
 Monohybrid cross: A cross observing organisms
heterozygous for a single trait being observed (eg. Aa
x Aa)
 Dihybrid cross: A cross observing organisms
heterozygous for two traits (eg. AaBb x AaBb)
 Law of independent assortment: Each pair of

alleles separate independently from other alleles
during gamete formation
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Probability laws:
 Addition rule: The probability that any one of two or more mutually exclusive events will
occur is calculated by adding their individual probabilities
 Multiplication rule: The probability that two or more independent events will occur
together in some combination is calculated by multiplying the probability of each event
Non-Mendelian Genetics
Mode of Description Example

inheritance
Incomplete The heterozygote phenotype In snapdragons, truebreeding flowers are

dominance is intermediate between the either red (CR) or white (CW). The
two homozygous heterozygous varieties are pink.
phenotypes
Codominance Both homozygous In the MN blood typing system in humans,

phenotypes are manifested individuals with only M alleles (MM)
in the heterozygote reproducing with individuals with only N
alleles (NN) will result in heterozygous
offspring containing both alleles (MN)
Multiple alleles More than two alleles exist In humans, there are three alleles that
for a certain trait determine ABO blood type: IA, IB, and i. IA
and IB are codominant to each other (hence
the blood type AB), and both are dominant
over i.
Pleiotropy A single gene affects more A mutation in the gene that codes for
than one trait phenylalanine hydroxylase has several
phenotypic effects, such as mental
retardation and reduced hair and skin
pigmentation. (This disease is called
phenylketonuria.)
Epistasis The phenotypic expression Labrador coat color is inherited in a simple

of a gene at one locus alters dominant manner, but if they are
the expression of another homozygous recessive for pigment
gene at another locus deposition, then the labrador will be golden
regardless of what their genotype for coat
color is. Hence, the gene for pigment
deposition is epistatic to the gene for coat
color.
Polygenic Several genes influence a Height in humans is controlled by at least

single trait, such as those three separate genes; a dominant allele will
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inheritance that exist in a continuum. contribute a certain amount of “height.”
Sex-linked The gene for a certain Elaborated on below.

inheritance characteristic is located on
the sex chromosomes.
Sex-linked inheritance
- Found on X chromosome
- X-linked recessive: more common in males as they only need one allele to
manifest the phenotype compared to 2 in females
- E.g. Red/green colorblindness, hemophilia, Duchenne muscular
dystrophy
- X-linked dominant: Only one allele is needed to manifest the phenotype in both
males and females
- E.g. X-linked hypophosphatemia, Rett syndrome
- Found on Y chromosome (Y-linked): Passed from father to son, only males can
manifest
Genetic disorders: result from changes in chromosome structure or chromosome number

Based on chromosome number:
 Nondisjunction: chromosomes fail to separate during meiosis I or meiosis II, resulting in
gametes that have n-1 or n+1 chromosomes
 Aneuploidy: When an aberrant chromosome is united with a normal one (n) during
fertilization
○ Monosomy: 2n-1, missing a copy of one chromosome
○ Trisomy: 2n+1, extra copy of one chromosome
○ Aneuploidy in sex chromosomes: may be caused by Barr bodies
 Polyploidy: more than two complete chromosome sets in somatic cells (eg. 3n or 4n)
Based on chromosome structure:

 Deletion: Chromosome fragment is lost
 Duplication: Chromosome fragment is repeated, might arise from a deleted segment
becoming attached to a sister chromatid
 Inversion: A segment within a chromosome is reversed
 Translocation: A segment from a chromosome is transferred to a nonhomologous
chromosome; may be reciprocal or nonreciprocal
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Common genetic disorders:
Disease Chromosomal Description

aberration
Down syndrome Trisomy 21, may Characteristic facial features,

also be caused by short stature, heart defects,
translocation developmental delays
Klinefelter 47XXY Phenotypically male but with

syndrome small sex organs, sterile, some
female characteristics such as
enlarged breasts
Triple X Syndrome 47XXX Slightly taller than average, at

risk for learning disabilities, but
are fertile
Turner syndrome 45X Phenotypically female but sex

organs do not mature, sterile
Cri-du-chat Deletion in Intellectually disabled, unusual

syndrome chromosome 5 facial features, has a cry that
sounds like a mewling cat
Cystic fibrosis Deletion in Production of abnormally thick

chromosome 7 mucus, resulting in blockage of
respiratory tract
The Molecular Basis of Inheritance

The genetic material
DNA: deoxyribonucleic acid; structure was discovered by James Watson
and Francis Crick in 1953
 Made of molecules called nucleotides, which consist of:
○ Phosphate group
○ Deoxyribose (a pentose sugar)
○ A nitrogenous base
■ Purines: Adenine (A) and Guanine (G): two-ringed
■ Pyrimidines:Cytosine (C) and Thymine (T): single-
ringed
■ Chargaff’s rules:
1. Base composition varies between species
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2. # of A = # of T, # of G = # of C
 Double helix: nitrogen bases are paired with their complementary base (A and T, G and
C)
 Antiparallel
Central Dogma of Molecular Genetics
Replication
 Semiconservative: The parental strands separate and each one acts as a template for
the new strands through Chargaff’s rule of base pairing
 Origin of replication
 Leading strand: 5’ → 3’
 Lagging strand: 3’ → 5’
 Summary of steps:
1. Helicase unwinds the parental double helix
2. Single-strand binding proteins stabilize the unwound strands
3. DNA polymerase III continuously adds nucleotides to the leading strand.
4. Meanwhile, primase synthesizes a primer for the lagging strand’s DNA, which is
replicated in short fragments called Okazaki fragments. DNA polymerase III and
DNA polymerase I are responsible for adding nucleotides to the fragments.
5. DNA ligase joins completed Okazaki fragments together.
Transcription: DNA directs the synthesis of a complementary strand of mRNA (messenger RNA)
 Stages:
1. Initiation
a. Determined by presence of promoter (certain sequence of nucleotides,
eg. TATA box)
b. Transcription factors: Help RNA polymerase recognize promoters and
form transcription initiation complex
2. Elongation: RNA polymerase adds
complementary nucleotides to growing RNA
strand while unwinding double helix
3. Termination
Translation: RNA to protein

● t-RNAs are used with A, P, and E sites
● Codons in mRNA (nucleotide triplets) are translated
via the universal genetic code into either amino
acids or stop signals
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ECOLOGY
Ecology – from the Greek root oikos (“household”); study of distribution and abundance of
organisms, their interactions with other organisms, and their interactions with their physical
environment
Population – group of individuals of the same species living in the same area
Community – group of populations living in the same area
Biosphere – composed of all regions of the earth that contains living things
Habitat – type of place where an organism usually lives
Niche – describes all the biotic (living) and abiotic (nonliving) resources in the environment
used by an organism; occupational or functional slot within an ecosystem that is generally
filled by a particular species
Note: Niche is not the same as habitat. Habitat is a place. Niche is a pattern of living.
Niche rule – no two species can occupy the same niche very long because of competition
Ecosystem – ecological unit; group of diverse interacting populations found within the
regional limits of a habitat; describes interrelationships between organisms in a community
and their physical environment
Ecological pyramids – show relationship between trophic levels; horizontal bars
represent relative sizes of trophic levels, each represented in terms of energy
(productivity), biomass, or numbers of organisms; tiers are stacked upon one another in
the order in which energy is transferred between levels
Image taken from Pack (2007)

Ecological efficiency – proportion of energy represented at one trophic level that is transferred
to the next level; relative sizes of tiers in an energy pyramid (or pyramid of productivity) indicate
ecological efficiency of ecosystem
Two kinds of flowcharts often sued to show flow of energy between specific organisms:
Food chain – linear flow chart of who eats whom
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Food web – an expanded, ore complex version of a food chain

Features of an ecosystem:
1. Energy flow
Plants and animals are organized into trophic levels

that reflect their main energy source. Energy moves
through the community of an ecosystem in a single
direction by means of a food chain (web) which is
composed of:
Image taken from Magloire (2009)
Producers: first group in a food chain; usually consists of green plants which
convert some of the energy of the sun through photosynthesis into organic
molecules they use and store in their tissues
Consumers: animals that feed on green plants and each other

Primary consumers: herbivores; eat producers
Secondary consumers: primary carnivores; eat primary consumers
Tertiary consumers: or secondary carnivores; eat secondary consumers
Detritivores: eat dead plants and animals (detritus)
Decomposers: smallest detritivores; bacteria, fungi, plants, or
animals that feed on dead organisms and release the bound
organic material of the organisms to the food chain
2. Nutrient cycling - As energy in a food chain is passed along from one link to another, its
useful capacity for work is diminished in accordance with the second law of
thermodynamics. Heat is given off with every transformation. At the end of the food chain
little or no free energy is left, so that recycling is not possible. On the other hand, matter
is not lost as it passes from one component of the food chain to another—the passage of
organic molecules and their elemental units along the food chain may be described in
terms of a cycle.
Reservoirs Assimilation Release

Hydrologic Oceans, air (as water Plants absorb water Plants transpire;
(water) cycle vapour), groundwater, from soil; animals animals and plants
glaciers drink water or eat decompose
other organisms
(which are mostly
water)
Carbon cycle Atmosphere (as CO2), Plants use CO2 in Plants and animals
fossil fuels (coal, oil), photosynthesis; release CO2 through
peat, durable organic animals consume respiration and
material (e.g. plants or other decomposition; CO2
cellulose) animals is released when
organic material
24
(such as wood and

fossil fuels) is
burned
Nitrogen cycle Atmosphere (N2); soil Plants absorb Denitryifying
(NH4+ or ammonium, nitrogen either as bacteria convert
NH3 or ammonia, NO2- NO3- or as NH4+; NO3- back to N2
or nitrate, NO3- or animals obtain (denitrification);
nitrate) nitrogen by eating detrivorous bacteria
plants or other convert organic
animals. Stages in compounds back to
assimilation of NH4+
nitrogen are: (ammonification);
Nitrogen fixation – animals excrete
N2 to NH4+ by NH4+ (or NH3), urea,
nitrogen-fixating or uric acid
prokaryotes (in soil
and root nodules);
N2 to NO3- by
lightning and UV
radiation
Nitrification – NH4+
to NO2- and NO2- to
NO3- to organic
compounds by
plant metabolism
Phosphorus Rocks and ocean Plants absorb Plants and animals
cycle sediments (erosion inorganic PO43- release phosphorus
transfers phosphorus (phosphate) from when they
to water and soil; soils; animals decompose; animals
sediments and rocks obtain organic excrete phosphorus
accumulate on ocean phosphorous when in their waste
floors return to surface they eat plants or products
as a result of uplifting other animals
by geological
processes)
3. Regulation of population size (number of individuals)
Population ecology – study of the growth, abundance, and distribution of populations
Size (N) – total number of individuals in the population

Density – total number of individuals per area or volume occupied
Dispersion – describes how individuals are distributed
25
3 broad distribution patterns (Eugene P. Odum):

1. Random distribution – individuals are
scattered without pattern throughout the
habitat
2. Uniform distribution – regular patterns of
dispersal occur
3. Clumping – irregular groupings are
discerned
Image taken from Raven & Johnson
(2002)
Population distribution in bacterial
colonies.
Patterns of dispersal are influenced by:
- Degrees of socialization in a population
- Nature of terrain and arrangement of its plant life
- Interactions with other species
- Availability of resources
Dispersive factors tend to scatter members of a population. Cohesive factors tend to

bring individuals together.
Age structure – description of abundance of individuals of each age; often graphically
expressed in an age structure diagram:
Image taken from Raven & Johnson (2002)

Population pyramids are graphed according to a population’s age distribution. Kenya’s
has a broad base because of great number of individuals below child-bearing age. U.S.’s
demonstrates increase in births between 1945 and 1964.
Pyramid-shaped: rapidly growing populations; large portion of population is young
Equal width: stable populations, with little or no population growth (zero population
growth)
26
Survivorship curves – describes how mortality of individuals in a species varies during

their lifetimes
Type I – most individuals survive to middle age;
mortality is high at middle age (e.g. humans)
Type II – length of survivorship is random; likelihood
of death is same at any age (e.g. many rodents and
certain invertebrates such as Hydra)
Type III – most individuals die young, with only a
relative few surviving to reproductive age and
beyond (e.g. oysters, other species that produce
free-living larvae that make up a component of
marine plankton)
Image taken from

Pack (2007)
Terms that describe population growth:
Biotic potential – maximum growth rate of a population under ideal conditions, with
unlimited resources and without any growth restrictions. The following factors contribute
to biotic potential:
 Age at reproductive maturity

 Clutch size (number of offspring produced at each reproductive event)
 Frequency of reproduction
 Reproductive lifetime
 Survivorship of offspring to reproductive maturity
Carrying capacity – maximum number of individuals of a population that can be

sustained by a particular habitat
Mechanisms of maintaining uniform population size (or limiting factors – elements that
prevent a population from attaining its biotic potential):
1. Density-dependent mechanisms – sensitive to the size of the population and increase
in effectiveness as population size increases
2. Density-independent mechanisms – operate independently of population size and
exert similar destructive effects on crowded or sparse populations
∆𝑁
Reproductive rate or growth rate (r) - = 𝑟𝑁 = 𝑏𝑖𝑟𝑡ℎ𝑠 − 𝑑𝑒𝑎𝑡ℎ𝑠 (where N is the
∆𝑡
population size at the beginning of the interval for which the births and deaths are counted;
numerator is net increase of individuals)
27
Intrinsic rate for growth – when r is maximum; when deaths exceed births, r will be
negative and population size will decrease; when births and deaths are equal, growth rate
is zero and population size remains constant (zero population growth)
Two general patterns of population growth:
1. Exponential growth – reproductive rate is greater than zero; population versus time graph
forms J-shaped curve
2. Logistic growth – limiting factors restrict population size to carrying capacity of habitat;
∆𝑁 𝐾−𝑁
equation for reproductive rate is modified as: = 𝑟𝑁 ( ) (where K is the carrying
∆𝑡 𝐾
capacity); when population size increases, reproductive rate decreases until at carrying
capacity (N = K) where the reproductive rate is zero and the population size stabilizes;
plot forms S-shaped or sigmoid curve

Population cycles – fluctuations in population size in response to varying effects of limiting
factors
Exponential and logistic growth patterns are associated with two kinds of life-history strategies:
28
1. r-selected species - exhibit rapid growth (J-shaped curve); opportunistic species; quickly
invade habitat; quickly reproduce, and then die; produce many offsprings that are small;
mature quickly; require little, if any, parental care (e.g. grasses, many insects)
2. K-selected species – population size remains relatively constant (at carrying capacity,
K); produce small number of relatively large offspring that require extensive parental care
until they mature; reproduction occurs repeatedly during their lifetimes (e.g. humans)
Factors that made exponential growth in human population possible:

1. Increase in food supply
2. Reduction in disease – due to advances in medicine
3. Reduction in human wastes – by developing water purification and sewage systems
4. Expansion of habitat – by having better housing, warmer clothing and easy to access
energy
Types of ecosystems:
Land regions have been more intensively probed than marine or fresh aquatic habitats.
Biome – any of several unique terrestrial ecosystem types; constitute the largest community units
classified by ecologists
Tropical rain forest Dense forest tracts

Warm temperatures
Very heavy rainfalls
Trees are abundant – tall, branch only at their tops, forming a
spreading canopy that allows little light to reach forest floor;
epiphytes (plants that live commensally on other plants) and
vines commonly grow on trees; little grow on forest floor
Soils are of poor quality
Desert Extremely scanty rainfall
Modest plant life – annual plants’ growth limited to short periods
following rains; other plants adapted to hostile conditions with
leathery leaves, deciduous leaves, or leaves with reduced spines
(cacti)
Many animals have thick skin, produce no or very concentrated
urine to conserve water; restrict activity to nights
Chaparral Prolonged, hot, dry summers and temperate rainy winters
Temperate rainy winters
Dominant vegetation forms are small trees and shrubs
Animals are usually small with bland coloration
Savannas Grasslands with scattered trees
Tropical – subject to high temperatures
Light and seasonal rain
Temperate grasslands (ex. Large tracts of land in temperate zones
North American prairie) Limited water availability during much of the year – less water
and subject to lower temperatures than savannas
Clumps of scrub grass, shrubs, and some annual plants
predominate
29
Small rodents coexist with large carnivores, which are

dependent on the smaller mammals
Taiga Northern forests thick with massive cone-bearing evergreen
trees
Animal life includes smaller animals, such as hares, mice,
shrews, and lynxes, an larger ones, such as bears, elks, deer,
and moose
Snow is present most of the year
Tundra Modified grassland region of upper northern areas
So cold that a permanent layer of frozen undersoil (permafrost)
exists
A short growing season during the northern summer provides
sustenance for shrubs and rushes and for animal life (fauna)
Temperate deciduous forest Rich stands of trees that shed their leaves during the cold
season, bushes and shrubs, and grasses interspersed with
cryptogamic plants (mosses and liverworts)
Cold winters alternate with warm summers of adequate rainfall
Abundant animal life (mice, chipmunks, raccoons, wolves,
mountain lions)
Deciduous trees shed leaves during winter – an adaptation to
poor growing conditions (short days and cold temperatures)
Freshwater biomes Ponds, lakes, streams, rivers
Marine biomes Estuaries (where oceans meet rivers), intertidal zones (where
oceans meet land), continental shelves (relatively shallow
oceans that border continents), coral reefs (masses ofcorals that
reach the ocean surface), and the pelagic ocean (deep oceans)
The marine (saltwater) environment makes up about 70% of the surface of the Earth. The oceans
can be divided into:
a. neritic – region above continental shelf
littoral zone – portion of the neritic region just offshore; rich in plant and animal life
because of its currents and complete penetration by the sun due to its shallowness
intertidal zone – shoreward of littoral zone; periodically covered with water at high
tide and exposed at low tide
b. oceanic depths – beyond relatively shallow shelf
i. pelagic zone – rich in plankton
ii. abyssal zone
30
Image taken from Fried & Hademenos (2009)

Although ecosystems demonstrate some flexibility and tend to maintain their integrity, they may
be irreplaceably harmed by
1. Sudden shifts in the environment that destroyed a significant portion of the community
2. Uncontrolled increase in numbers of particular populations due to failure of the
mechanisms for population control
3. Loss of key minerals or other nutrients in the ecosystem
4. Human interference, which may lead to destruction of habitats, an overkilling of specific
species, or pollution with toxic materials that cannot be handled within the ecosystem
Community Ecology – concerned with interactions of populations

Interactions among competing species shape ecological niches:
1. Competitive exclusion principle or Gause’s principle – stressed role of competition in
determining species survival within the ecosystem
2. Resource partitioning – by pursuing slightly different resources or securing their

resources in slightly different ways, individuals minimize competition and maximize
success
3. Character displacement (niche shift) – as a result of resource partitioning, certain
characteristics may enable individuals to obtain resources in their partitions more
successfully. Selection of these characteristics reduces competition with individuals in
other partitions and leads to a divergence of features, or character displacement.
4. Realized niche – actual niche a species occupies; may be considerably smaller than
fundamental niche because of interspecific interactions
31
Interspecific competition – two species attempt to utilize the same resources

when there is not enough of the resources to satisfy both
Interference competition – fighting over resources
Exploitative competition – consuming shared resources
Fundamental niche – entire niche a species is capable of using, based on its
physiological requirements and resource needs
Predation – another form of community interaction; predator is any animal that totally or partly
consumes a plant or another animal
Different categories of predators:
1. True predator – kills and eats another animal
2. Parasite – spends most or all of its life living on another organism (the host), obtaining
nourishment from the host by feeding on its tissues
3. Parasitoid – insect that lays egg on host (usually an insect or spider)
4. Herbivore – animal that eats plants; some, especially seed eaters (granivores) act like
predators in that they totally consume the organism; others such as those that eat grasses
(grazers) or leaves of other plants (browsers) may eat only part but may weaken plant in
the process
Symbiosis – two species that live together in close contact during a portion (or all) of their lives
Symbiotic relationship Relationship Example

Mutualism Both benefit Lichens are symbiotic
associations of fungi and
algae. The algae supply
sugars produced from
photosynthesis, and the fungi
provide minerals, water, a
place to attach, and protection
from herbivores and
ultraviolet radiation.
Note: Some researchers

consider lichen symbiosis
closer to parasitism because
in some cases, fungal hyphae
invade and kill some of their
symbiotic algae cells.
Commensalism One species benefits, while Birds build their nests in trees.
the second species is neither Trees are generally neither
helped or harmed helped nor harmed by the
presence of the nests.
Parasitism Parasite benefits from the Tapeworms live in the
living arrangement while the digestive tract of animals and
host is harmed steal nutrients from their
hosts.
32
Coevolution – evolution of one species in response to new adaptations that appear in another
species
Examples of coevolution:
1. Secondary compounds – toxic chemicals produced in plants that discourage would-be
herbivores e.g. tannins in oaks and nicotine in tobacco are toxic to herbivores
2. Camouflage (or cryptic coloration) – any color, pattern, shape, or behaviour that
enables an animal to blend in with its surroundings e.g. snowshoe hare has white fur in
winter and brown fur in summer
3. Aposematic coloration (or warning coloration) – conspicuous pattern or coloration of
animals that warns predators that they sting, bite, taste bad, or are otherwise to be avoided
4. Mimicry – when two or more species resemble one another in appearance
Two kinds of mimicry:
a. Müllerian mimicry – when several animals, all with some special defense
mechanism, share the same coloration e.g. bees, yellow jackets and wasps all have
yellow and black markings
b. Batesian mimicry – an animal without any special defense mechanism mimics the
coloration of an animal that does possess a defense e.g. some defenceless flies have
yellow and black markings
5. Pollination of many kinds of flowers occurs as a result of coevolution of finely-tuned traits

between the flowers and their pollinators e.g. red, odourless, tubular flowers coevolved
with hummingbirds who are attracted to red and have long beaks and little sense of smell;
flowers provide copious amount of nectar in exchange for transfer of pollen to other flowers
Ecological succession – slow change in the makeup of the community within a habitat;
continues until a climax community is formed
Over time, succession may occur because species that make up communities alter the habitat by
their presence and so the conditions that made the habitat initially attractive to the resident
species may no longer exist, making the habitat more favourable to new species. Some of the
changes induced by resident species are:
1. Substrate texture (change from solid rock to sand to fertile soil as rock erodes and
decomposition of plants and animals occur)
2. Decrease in soil pH due to decomposition of certain organic matter
3. Soil water potential – ability of soil to retain water; changes as soil texture changes
4. Light availability (change from full sunlight to partly shady, to near darkness as trees
become established)
5. Crowding – increases with population growth; may be unsuitable to certain species
Pioneer species – plants and animals that are first to colonize a newly exposed habitat; typically
opportunistic, r-selected species; have good dispersal capabilities; fast-growing; produce many
progeny rapidly
33
Two kinds of succession:

1. Primary succession – occurs on substrates that never previously supported living things
2. Secondary succession – begins in habitats where communities were entirely or partially
destroyed by some kind of damaging event
Biomass – weight of living organisms within an ecosystem; often applied to particular trophic
levels
Food (energy) pyramid – a broad producer base is topped by ever-diminishing populations of
consumers; terminal consumer forms the apex of the pyramid
Upsetting the Stability of an Ecosystem: Younger communities, which are far more active and
productive than more mature systems, are less able to resist environmental insult.
Pollution – introduction of harmful materials to an ecosystem
Note: Pollutants become more concentrated as they move along a food chain.
Eutrophication – overabundance of nutrients in waters of a river or lake, stimulatin overgrowth
of phytoplankton or algae
Sources:
Pack, P. E. (2007). Cliffs AP biology (3rd ed.). Hoboken, NJ: Wiley.
Magloire, K. (2009). Cracking the AP Biology Exam. New York, NY: Random House.
Fried, G., & Hademenos, G. J. (2009). Schaum's Outline of Biology. New York: McGraw-Hill.
Raven, P. H., & Johnson, G. B. (2002). Biology (6th ed.). Boston, MA: McGraw-Hill.
34

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U.P.

Pre-Medical Honor Society

Emergent properties: properties at

Two main systems of roots:

 Consists of a main vertical root

from the stem (adventitious: a parts: a flattened blade and a stalk,

Hormone Site of Major Functions

Auxin (AA) - Shoot apical meristems - Stimulates stem elongation (low

Cytokinin - Roots - Regulates cell division in shoot

Gibberellins - Meristems of apical - Regulate sex detemination and

Brassinosteroids - Present in all plant - Promote cell expansion and cell

Abscisic acid - Present in all plant cells - Inhibits growth

- Inhibits early germination

Ethylene - Present in most parts of - Promotes fruit ripening

No nucleus (may w/ nucleus

The Plasma Membrane: encloses the cell substance down

- Smooth ER: Does not have - Composed primarily of cellulose (in

ORGANIZATION OF PHOTOSYNTHETIC APPARATUS

- Stroma: contains enzymes for carbon fixation

Photosystem: consists of:

Cyclic Electron Flow

When ATP is low, primary electron acceptor in

Alternative Methods of Carbon Fixation

Stages of Cell Respiration:

Fate of electron acceptors: Dependent on organism and availability of oxygen

Abundant when Abundant when Usually abundant

Expensive Expensive Cheap

Toxic product Toxic product Nontoxic product

Citric Acid Cycle/Tricarboxylic Acid Cycle/Krebs Cycle

Electron Transport Chain

- ATP produced is also dependent also on shuttle used

The Cell Cycle

1. Prophase: Nucleoli disappear, chromatin fibers condense into chromosomes

- Mitosis (M) alternates with interphase

 Allele: An alternative form of a gene

 Meiosis I: separates homologous chromosomes

DNA replication During interphase, During interphase,

Synapsis Does not occur Occurs during

# and genetic 2, identical to 4, genetically

Role Growth and Produces gametes,

Punnett square: Used to determine combinations of offspring

 Law of independent assortment: Each pair of

Mode of Description Example

Incomplete The heterozygote phenotype In snapdragons, truebreeding flowers are

Codominance Both homozygous In the MN blood typing system in humans,

Epistasis The phenotypic expression Labrador coat color is inherited in a simple

Polygenic Several genes influence a Height in humans is controlled by at least

inheritance that exist in a continuum. contribute a certain amount of “height.”

Sex-linked The gene for a certain Elaborated on below.

Genetic disorders: result from changes in chromosome structure or chromosome number

Based on chromosome structure:

Common genetic disorders:

Disease Chromosomal Description

Down syndrome Trisomy 21, may Characteristic facial features,

Klinefelter 47XXY Phenotypically male but with

Triple X Syndrome 47XXX Slightly taller than average, at

Turner syndrome 45X Phenotypically female but sex

Cri-du-chat Deletion in Intellectually disabled, unusual

Cystic fibrosis Deletion in Production of abnormally thick

The Molecular Basis of Inheritance

Central Dogma of Molecular Genetics

Translation: RNA to protein

Image taken from Pack (2007)

Food web – an expanded, ore complex version of a food chain