BELLARMINE COLLEGE PREP

Biology Honors Semester Two

All-inclusive Study Guide
Evan W. Noronha
5/23/2010

The contents of this study guide include absolutely everything needed to earn an A on Mark Riese’s
Biology Honors Semester Two final. All data was collected from BSCS Biology: A Molecular Approach and
compiled into outline format by Evan Noronha ‘13. Roughly 20% of the diagrams used were created by
Kevin Korb ’13. All rights reserved.
©Evan Noronha and Kevin Korb 2010.
Evan Noronha
Mr. Riese
Bio Honors
Semester Two Study Guide

I. Chapter 8- The Cell Cycle

A. 8.2 The Phases of the Cell Cycle (ref. to figure 1 on following page)
1. Single Cell -> Cell cycle -> 2 daughter cells
2. When Eukaryotic cell breaks down, nuclear membrane breaks down
a) Individual chromosomes separate and are sorted into daughter cells
3. Mitosis: Process of sorting and distributing of chromosomes
4. Interphase: period between divisions
a) Chromosomes not visible during this stage
b) Divided into 3 parts
i. G1, S, G2
5. Cell is ALWAYS in one of 5 stages of cell cycle
a) G1- Gap one (AKA prereplication)
b) S- DNA Synthesis
c) G2-Gap 2 (AKA premitosis)
d) M- Mitosis
e) G0- Gap 0 (Non-dividing cell)
6. Gap Stages
a) Cells grow and synthesize RNA, proteins, and other macromolecules
i. Preparing for either next S or M phase
b) Sequence same for all cells
i. Different cells spend diff. amounts of time in various stages
7. When a cell in G0 or G1 receives signal to divide, it passes the restriction point
a) “Point-of-no-return”
b) Commits the cell to a full
8. Different cells vary in ability to pass restriction point
a) Ex. Stem Cells- constantly dividing
b) Liver cells almost always in G0
9. After passing restriction point, cell enters S Phase
a) DNA of each chromosome replicate
i. Exact copying ensure that each daughter cell gets a complete
copy of genetic information
10. After S phase, cell enters G2
a) Prepares for mitosis by synthesizing specific types of RNA and proteins
i. Required by mitosis in upcoming M Phase
11. M phase easiest to recognize because chromosomes are condensed and in the
center
a) Visible through a light microscope
b) Sometimes called nuclear division because nucleus divides into two
nuclei w/ identical sets of nuclei
12. After Mitosis, who cell divides in cytokinesis then enters G1

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Semester Two Study Guide

Figure 1: The Cell Cycle

B. 8.3 DNA Structure (ref. to figure 2)

1. Process of DNA replication depends on the molecular shape of DNA and its
nucleotide bases
2. Base pairing depends on how many hydrogen bonds Figure 2 DNA Structure
ea. nitrogen base can form w/ its counterpart
a) Adenine(A) pairs Thymine(T)
i. 2 hydrogen bonds
b) Guanine(G) pairs Cytosine(C)
i. 3 hydrogen bonds
c) Sugar-phosphate backbones have opposite
orientations
i. Strands are parallel but run in
opposite directions- known as
antiparallel structure
 Important to DNA replication
C. 8.4 DNA Synthesis (ref to figure 3 on following page)
1. Synthesis of DNA is a multi-step process
a) Divided into 3 major partd
i. Binding of enzymes to existing DNA

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ii. Unwinding of the double helix

iii. Synthesis of a new matching strand
for each existing strand
2. Process:
a) Enzymes and other proteins bind to regions of
chromosomes called replicator origins
i. Chromosomes have more than one replication origin
 But Prokaryotes only have one
ii. Proteins includes an unwinding enzyme, and RNA synthesizing
enzyme, and DNA polymerase which catalyzes the formation of
new DNA strands
iii. Combination of DNA and proteins is a replisome
b) DNA splits at the origin and enzyme (RNA primer) prepares ea.
individual strand for synthesis of a matching strand
i. Synthesis is continuous on leading strand
 DNA Polymerase adds nucleotides to the end of the
RNA primer
ii. On lagging strand, DNA synthesis occurs in short unconnected
bursts due to antiparallel structure
c) Replisomes move away from replication origin in both directions
d) End result is to replace the original double helix strand with two new
ones
i. Each is half old strand half new strand- known as semi-
conservative
ii. Once replication is complete, there are two new chromosomes
Figure 3 Replication Forks in place of the original one

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Semester Two Study Guide

D. 8.6 The Stages of Cell Division (ref. to figure 4)

1. Cell goes to G2 phase after S
2. Copies of chromosomes made in S phase are called sister chromatids
a) Now rady to be separated and delived to the new nuclei
b) Still attached by centromere at the center of the chromosomes
3. Separation of sister chromatids called chromosome segregation
a) Mistakes result in daughter cells w/ abnormal number of chromosomes
i. AKA aneuploid cells
4. Mitosis is continuous but usually divided into 4 steps
a) Prophase
i. Membrane breaks down into small vesicles
ii. Chromosomes condense; become visible under a light
microscope
iii. Microtubules form around the nucleus and join forming a
mitotic spindle
iv. If cell has centrioles, they are pushed to the opposite ends by
microtubules
 Microtubules at the end of spindle are anchored to
protein structures that surround the centrioles- these
sites known as spindle poles
v. Each centriole contains a protein complex called a kinetochore
 Microtubules in the spindle bind to the kinitochores
b) Metaphase
i. By this time, motor proteins in kinetochores have pulled
chromosomes into a ring between the two poles
 Forms metaphase plate- perpendicular to the spindle
c) Anaphase
i. Enzymes break down protein holding sister chromatids together
 Separate and kinetochores pull them along the spindle
microtubules to opposite spindle poles
 Each segregated chromatid is now a chromosome
d) Telophase
i. Chromosomes expand and nuclear envelope forms around
them- produces two nuclei
ii. Cytokinesis divides the cell in two new daughter cells
 Both enter G1
 May enter G0 or start another cycle

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Semester Two Study Guide

Figure 4 Stages of the Cell Cycle

E. 8.8 and 8.9- Regulation of the cell cycle (ref to figure 5)

Figure 5 Control of the Cell
Cycle

II. Chapter 9- Expressing Genetic Information

A. 9.1 Genetic Material (ref to figure 6)
1. Consists of two biomolecules
a) DNA
b) RNA
2. Living cells store genetic information in Dan

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a) Indirectly direct protein function

3. When a gene becomes active, an enzyme makes a temporary RNA copy of the
gene in process called transcription
a) Messenger RNA- provides the pattern that is used to assemble proteins
4. Synthesis takes place on ribosomes
a) Ribosomes are made of proteins and ribosomal RNA
5. Each amino acid that is used in making a protein is attached to transfer RNA
Figure 6 Types of RNA

Figure 7 Codons and Anticodons
6. Eukaryotic cells also have a variety of small nuclear RNA that can interact with
proteins during RNA processing
7. Genetic code describes how a sequence of bases in DNA and RNA translates
into amino acids then proteins
a) Similar to a Language- needs at least 20 different code words, one for
each amino acid
i. 4 Nucleotides are letters (A,T,G,C)
ii. 3 nucleotides in a row is a “word” that codes for a particular
amino acid
iii. Different “words” or codons, can mean the same thing
 Ex. UAA, UAG, and GUA are all “stop” codons
 GGU, GGA, GGC, GGG all code for glycine
 UUU and UUC code for phenylanine
iv. In translation, a codon pairs with a tRNA molecule with the
correct amino acid
 Pairs according to which tRNA has the correct
anticodon(ref to figure 7)
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v. Studies indicate that this genetic code is nearly universal

B. 9.2 Importance of Proteins

1. Proteins serve as material that makes op cells or tissues
a) Keratin- main structural material in skin, hair, and feathers
b) Colagen- major component of connective tissues
c) Myosin- molecular motor that makes your muscles contract
2. Serve as enzymes
a) Makes chemical reactions of a living system fast enough to be useful
3. Bind to specific molecules
a) Ex. Hemoglobin in red blood cells binds to oxygen
4. Help with internal communication
a) Ex. Insulin is a protein hormone that helps maintain homeostasis
i. Hormones- chemical signals given off by cells in one part of an
organism that regulate behavior of cells in another part
C. 9.3 RNA Synthesis (ref. to figure 8 on following page)
1. Transcription enzyme- RNA Polymerase joins RNA nucleotides according to
base sequence in DNA
2. Transcription is more complex in Eukaryotes, but general process is the same
3. In eukaryotes, protein synthesis occurs outsife the nucleus using mRNA, rRNA
and tRNA made in the nucleus
a) RNA molecules then modified, moved out of the nucleus into the
cytoplasm
b) rRNA transcriptions takes place in nucleolus- specialized region of the
nucleus
i. Also where as many as 70 proteins are assembled into
ribosomal subunits
ii. 2 ribosomal subunits and an mRNA come together during
protein synthesis to form a functional, intact ribosome
4. Only one strand of DNA directs RNA synthesis
5. Transcription has three stages
a) Initiation
i. RNA polymerase attaches to a specific region of DNA called the
promoter site
 Site promotes transcription
 Located right before the segment of the DNA coding
strand that will be transcribed
 Proteins called initation factors must be presen for the
RNA to attach to the promoter site
b) Elongation

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i. RNA polymerase partially unwinds the DNA, exposing the coding

strand
ii. Enzyme moves along the DNA away from the promoter site
 Sequence of DNA determines sequence of RNA
transcript
c) Termination
i. RNA polymerase reaches terminator reigon
Figure 8 Transcription ii. Enzyme and primary transcript are released from the DNA

D. 9.4 RNA Processing (ref. to figure 9 on following page)

1. In prokaryotes, new mRNA is translated and broken down rapidly
2. Life span depends on how the primary transcript is processed
3. Primary mRNA transcript can contain up to 200,000 nucleotides
a) Average for humans is 5000)
4. mRNA in the cytoplasm averages only 1000
a) In processing of the primary transcript, enzymes modify, add, and
remove additional nucleotides
5. Processing Steps
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a) Enzymes add a cap of modified guanine nucleotides(methyl-guanine)

i. AKA mG cap
ii. Helps the mRNA attach to a ribosome and begin translation
b) Other enzymes replace part of the opposite end with a tail of 100-200
adenine nucleotides
i. AKA poly-A tail
ii. Helps transport mRNA out of the nucleus
iii. Cap and tail help protect the mRNA from enzymes that break
down nucleic acids
c) Splicing of introns
i. Introns- segments of the RNA that don’t code for proteins
ii. Remaining pieces of code are called exons
iii. Process recognizes the sequence GU at the end of an intron and
AG at the other end
Figure 9 RNA Processing

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E. 9.5 Translation
1. Protein synthesis translates the codon sequence of mRNA into amino-acid
sequence of proteins
a) Happens on the ribosome where tRNA acts as a molecular adapter
i. One end carries specific amino acid while other end has
anticodon that pairs with the mRNA codon (see figure 10) that
Figure 10 Structure of a codes for the corresponding amino acid
tRNA molecule
2. Attachment of the amino acid to tRNA molecule is called tRNA charging
a) Carried out by 20 different enzymes
b) Each enzyme forms a bond between a specific amino acid and its
matching tRNA
i. A molecule of ATP provides energy to form bond
c) Charged tRNA, mRNA and the growing poly-peptide chain meet at
ribosomal binding sites where anticodons base-pair with codons
i. This is how the codon sequence dictates the amino-acid
sequence
3. Binding Sites (ref to figure 11)
a) P site
i. Holds the tRNA carrying the growing polypeptide chain
b) A site
i. Holds the tRNA carrying the next amino acid to be added
c) E site
i. Exit Site where uncharged RNA leaves the E site
Figure 11 Protein Synthesis

4. Stages of translation- same stages as transcription

a) Initiation
i. Ribosome attaches at a specific site on the mRNA

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 This site is the start codon- AUG

b) Elongation
i. Peptide bonds join each amino acid with the next in sequence
ii. Charged tRNA w/ an anticodon matching the next codon enters
at the A site
 Positions the attached amino acid to be added to the
growing chain w/ a peptide bond
iii. Once bond is formed, the polypeptide chain transfers to the
tRNA at the A site
 Entire ribosome moves down to the next codon
iv. Uncharged tRNA exits at the E site
c) Termination
i. Translation ends when stop codon reaches the A site
 3 possible stop codons- UAA, UAG, UGA
ii. tRNA releases the polypeptide; ribosome lets go of the mRNA
and tRNA and ribosomal subunits separate
F. 9.7 Translation Errors (ref. to figure 12)
1. Most errors in translation are caught and corrected
2. Most common errors result from misreading nucleotide sequence
3. Initiation determines where the translation will begin
a) From this point onward, grouping of bases into codons is the reading
frame
b) If start begins one or two nucleotides in either direction, there will be a
frame shift
Figure 12 Frame Shifts

4. Some errors caused by splicing mistakes or changes in DNA

a) Ex. If one nucleotide is lost, a frame shift results

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b) Ex. If one nucleotide changes so that a stop codon is produced,

translation will terminate early
i. Results in partial polypeptide
III. Chapter 10- Animal Growth and Development
A. 10.1 Beginnings of an Embryo
1. Development of animals begins with fertilization
a) Union of male and female parent’s cells
i. Sperm and Egg (known as gametes)
ii. Animal Sperm usually very small and have flagellum they use to
swim towards an egg
iii. Eggs are much larger and their cytoplasm contains a yolk
 Energy rich collection of lipids and proteins and a
variety of RNA molecules
iv. Each parent cell has half the chromosome set found in each of
the parents cells
2. Begin fertilization- sperm cell touches the surface of the egg cell and fuses with
it
Figure 13 a) Sperm nucleus and egg nucleus fuse
The Process of Cellular Differentiation i. Reestablishes the full chromosome set
3. Fertilized cell- zygote, is the earliest stage of the human embryo
4. Before fertilization, eggs are metabolically inactive
a) Use little energy and make almost no proteins and RNA
b) Fertilization turns on the eggs metabolism
i. This is known as activation
ii. Cell respiration increases and new proteins are made using
mRNA already in the cytoplasm
iii. Results in rapid change in the plasma membrane which blocks
fertilization by a second sperm
iv. Rearrangement of the zygote cytoplasm by movements in the
cytoskeleton
 Helps to produce differences among cells when they
divide
c) When zygote begins to divide, it is as metabolically active as mature
cells
B. 10.2 Growth, Differentiation, and Form
1. Animal development consists of growth, cell specialization, and formation of
tissues and organs
2. Embryo becomes multicellular through cell division
a) Increased number of cells causes it to grow larger
b) As it continues to divide, some cells become different from others
i. Process called differentiation (ref. to figure 13)
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3. Cell is completely differentiated when it possesses all features of a specific cell

type
a) Ex. Muscle cell
b) Ex. Skin Cell
4. As cells differentiate, they form tissues and organs
a) Period of development is called morphogenesis
5. Cells that differentiate have special structure
a) Ex. Skin Cells
i. Tough, thin, and flat; designed to protect the body
b) Ex. Muscle Cells
i. Filled with protein fiber that help them contract
6. Each cell type has a specific location and each performs a specialized role
7. Proteins are key to differentiation in animals
a) Cell movements in morphogenesis involves proteins on each cells
surface
b) Specific genes are expressed in each cell
i. Leads to production of specific proteins
c) Differences between cells in protein synthesis lead to differences in cells
C. 10.5 Human Development (ref to figure 14)
1. Development of humans and most mammals is unique- Develop within the
mother
a) Mother provides a warm protected environment
b) Blood circulation provides nutrition and oxygen to the embryo and tkes
away wastes and CO2
2. Human egg is roughly 0.1mm; contains little yolk
3. Zygote cleaves as it moves into the uterus
4. After about 5 days, the embryo, called a blastocyst, resembles the hollow
blastula of other animals

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a) Sinks into the wall of the uterus to develop and grow

Figure 14 A Developing Fetus

5. Part of a thick mass of cells inside the blastocyst forms the disk that becomes
the embryo
a) Rest of the blastocyst becomes membranes that surround, nourish, and
protect the embryo.
i. Amnion immediately surrounds the embryo
ii. Chorion encloses all the other membranes; forms thin outer wall
 Extends fingerlike projections (villi) into the lining of the
uterus
 Villi and uterine lining form the placenta-
exchanges nutrients, wastes, oxygen and
carbon dioxide with the mother

6. Human takes about 40 weeks to develop in the uterus
a) After 8th week, the embryo is a fetus
b) After 3 months(first trimester) most organ have begun to form; skeleton
can be seen through ultrasound
c) Last 3 months (last trimester) is a period of rapid growth and
maturation of organ systems
IV. Chapter 11 Plant Growth and Development (ref. to figure 15)
A. Put a plant in the ground, give it water, it grows
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Mr. Riese
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1. Whoopdy-Doo…
2.
Figure 15 A Tree...

V. Chapter 12- Reproduction Figure 16 Binary Fission

A. 12.1 Asexual Reproduction
1. Requires a single parent
2. Results in a genetically identical clone
3. Prokaryotes reproduce by dividing in two
a) Process called binary fission(ref to figure 16)
B. 12.2 Chromosome number (ref to figure 17)
1. Each species has characteristic number of chromosomes
a) Prokaryotes typically have 1
i. Single circle of DNA
b) Number varies among eukaryotes
i. Ex. Humans and fish called Black Mollies have 46
ii. Ex. Turkeys have 82
iii. Ex. Giant Redwoods have 22
2. Cells of organism that reproduce sexually have pairs of similar chromosomes
a) Each parent provides one member of each pair
b) Cells that have a double set of chromosomes are diploid
i. Represented by 2n
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c) Cells with only one set are haploid

i. Represented by n
3. In diploid organisms, two chromosomes in a pair are
called homologous
a) These chromosomes, homologues, are
similar in structure
b) Carry the same genes; DNA
sequence may be slightly
different
i. Differences produce the
variety among members of
the same species
4. In sexual reproduction, each parent
contributes half the normal number of Figure 17
chromosomes (haploid number) Changes in chromosome Number
a) Otherwise, if parents each contributed diploid number, chromosome
number would double with every generation
b) Parent gametes are all haploid
i. Haploid sperm and Haploid egg join to form a diploid zygote
5. Meiosis produces haploid gametes
a) Complementary to Fertilization; Meiosis produces haploid gametes and
fertilization reunites them as diploid cells

C. 12.3 Meiosis and the Production of Gametes (ref. to figure 18 on following page)
1. Different from mitosis in 3 important ways
a) Cells divide twice in meiosis, but are only duplicated after first division
b) Meiosis distributes random mixture of maternal and paternal
chromosomes to each gamete
i. Results in new genetic combinations
c) Homologous chromosomes pair up during the first meiotic cell division
where they exchange corresponding pieces of DNA
i. Process known as crossing-over; adds to genetic variety of the
gametes
2. Meiosis has 2 nuclear divisions- Meiosis I and Meiosis II
a) Produces four haploid cells
b) Both divisions have same four steps as mitosis, but small differences
i. Meiosis I vs. Mitosis
 In prophase I, homologues cross-over
 Sister chromatids don’t separate in anaphase I
 Migrate [together] to opposite poles

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 Results in a pair of cells, each with a single pair

of chromosomes; each chromosome consists of
a pair of sister chromatids
ii. Meiosis II
 Chromatids separate
iii. Overall it’s a complex process for three reasons
 Reduces chromosomes to the haploid number
 Provides genetic variation
 Ensures correct distribution of chromosomes
3. Doesn’t always divide cytoplasm equally
a) In most males, meiosis produces four equal sized sperm
b) In females, most cytoplasm remains in one cell
i. Largest cell becomes the ovum
ii. 2 small cells-polar bodies, usually break down and disintegrate
D. 12.6 Sexual Reproduction in Animals [as relevant to humans]
1. Animals that reproduce sexually have organs called gonads that produce
gametes
a) Ovaries that produce ova
b) Testes that produces sperm
2. Land animals and a few aquatic animals like whales use internal fertilization
a) Male releases sperm into a female reproductive organ
b) Fertilization occurs within the body of the female
c) Protects gametes and requires fewer gametes than external fertilization
d) Most efficient
i. Fewer eggs are required
3. Internal fertilization is an evolutionary trend among larger, more complex
organisms
a) Mammals are the most extreme examples of this trend
4. Sperm are usually much smaller than eggs

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a) Egg is adapted as a storehouse for nutrients and organelles that support

the embryo’s development

Figure 18
Stages of Meiosis for a cell with 2n=4

b) Sperm just the nucleus and the flagellum and a few mitochondria to
sustain itself for a short time
i. Most still die before reaching the egg

E. Egg production and the Menstrual Cycle

1. In human females, ovaries are contained within body cavities
a) Usually release eggs one at a time

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i. Egg travels through one of two oviducts to the uterus where

embryo develops(if fertilized)
 During birth, baby is pushed out from the uterus
through the vagina
 This route also functions as passageway for
male to deposit sperm
2. Egg releasing cycle-menstrual cycle, usually lasts 28 days
a) Inner lining of the uterus builds up in prep for receiving a fertilized egg
i. If not fertilized, the lining and rich blood is sloughed out
through the vagina
b) First day of menstrual flow marks the first day of the cycle
3. Regulated by nervous system and several other glands and organs;
Hypothalamus acts like a thermostat (fluctuates to adjust hormone levels)
a) Start of menstrual flow, estrogen and progesterone released into the
bloodstream by the ovaries are at low levels
i. Low levels cause hypothalamus to secrete gonadotropin-
releasing hormone (GnRH) that is received by the pituitary gland
ii. GnRH stimulates the pituitary to release follicle –stimulating
hormone (FSH) and luteinizing hormone (LH)
 FSH causes the egg to start maturing
 Both stimulate the follicle to release more estrogen-
signals the lining of the uterus to thicken
b) 14-day of the cycle
i. Sudden increase of LH makes the follicle burst and release the
egg
 Process called ovulation
ii. Ruptured follicle becomes corpus luteum and continues to
release estrogen and progesterone
iii. Hypothalamus detects high levels of estrogen and slows release
of FSH and LH
c) If egg not fertilized, corpus luteum degenerates and levels of
progesterone and estrogen decline
i. Signals lining of uterus to break down and menstruation begins,
marking a new cycle
d) If egg is fertilized, undergoes mitosis and becomes an embryo,
implanting itself in the uterus upon entry; forms a placenta
i. Releases the human chorionic gonadotropin
 Signals the corpus luteum to continue releasing high
levels of progesterone and estrogen which support the
uterine lining and indirectly prevent menstruation

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ii. Corpus Luteum functions for first three months of gestation

(development of embryo within the uterus)
iii. After first trimester, placenta stops releasing HCG and replaces
the corpus luteum as the main source of estrogen and
progesterone
e) At birth, small peptide known as oxytocin is released that makes the
muscles of the uterus contract
i. After birth, it causes the uterus to contract and stimulates milk
release
ii. Placenta separates from the uterine wall shortly after and is
expelled as the afterbirth
F. 12.8 Sperm Production
1. In human males, the testes are located within the scrotum
a) Outer pocket of the body wall
b) Keeps them cooler than body temperature
2. Sperm are produced by meiotic cell division in highly coiled tubes called
seminiferous tubules in the testes then stores in the epididymis, a coiled part
of the sperm duct
3. Prostate glands and seminal vesicles produce seminal fluid which transports
sperm
a) Seminal fluid also contains fructose
i. Provides energy for sperm
b) Released during ejaculation with sperm in a mixture called semen
i. If not ejaculated, sperm are eventually reabsorbed by the
tissues in the male reproductive tract
4. Males have same regulatory hormones as females
a) GnRH stimulates the pituitary gland to release FSH and LH
b) LH stimulates cells between tubules to secrete androgens, group of
male hormones
i. Major androgen is testosterone
c) FSH stimulates other cells in testes to produce sperm
d) No evidence that males have a reproductive cycle like females
VI. Chapter 13- Patterns of Inheritance
A. 13.2 Mendel and the Idea of Alleles
1. 1860’s, Gregor Mendel studied pea plants to study heredity and genetics
a) Choice of peas was important
i. Easy to grow
ii. Self-fertilizing
b) Only studied traits found in the either-or form
i. Found Seven of those traits (ref. to figure 19)
Figure 19 Pea Plant Traits studied by Mendel
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c) Worked to make sure he had true-breeding plants

i. Produce identical offspring generation after generation
d) Crossbred his plants ant classified the offspring; looked for patterns of
inheritance
i. Ex. Crossed green pods and yellow pods
 First gen. offspring were all green
 First generation self-fertilized and some produced
offspring with green pods
ii. Blending theory couldn’t explain these results
iii. Demonstrated that both parent pass on genetic factors that
remain separate
 Ex. Yellow pod factor remained hidden in the first
generation offspring, but appeared in the second
generation

2. Genes have now replaced Mendel’s idea of factors

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a) Gene- a segment of DNA whose sequence of nucleotides codes for a

specific functional product
b) Most exist in more than one form or allele
i. Each allele has a different base sequence
3. Change in gene for a protein can result in a different sequence, thereby
producing a different protein
4. All organism have alleles
a) Ex. Widow’s Peak
b) Ex. Male-pattern baldness
c) Many traits controlled by multiple alleles
B. 3.3 Genes and Chromosomes
1. Arrangement of genes on Eukaryotic chromosomes
a) Eukaryotic Chromosomes are long DNA molecules w/ some non-coding
regions
i. Only about 1% of eukaryotic DNA is expressed
2. Prokaryotic Chromosomes
a) Have a single circular chromosome
b) Don’t have introns
i. About 90% is translated
c) May also contain plasmids
i. Circles of DNA that contain genes
ii. Can be moved from one bacterium to another
 Used in genetic engineering
3. Karyotypes (ref. to figure 20)
a) A display of all the chromosomes in a person’s genome
i. Sorted by size, and homologous chromosomes are placed side-
by-side
Figure 20 A Karyotype of a Human Cell

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C. 13.4 Probability and Genetics

1. Distribution of alleles in diploid organisms is up to chance
a) Probability is used to predict the chance of particular alleles being
passed on
i. Probability- branch of math that predicts chance of a particular
event
 Ex. Flip a coin- ½ heads, ½ tails
 Ex. Draw a card from a deck - 1/13 chance it’s an ace
 Each event is Independent
 Ex. If you flip a coin 3 times, the 4th flip isn’t
influenced by the other 3
 Chance of two or more independent events both
happening is their probability multiplied together
 Ex. Flipping heads twice= ½*½= ¼ chance
 Ex. Pulling 2 aces out of a deck =1/13*1/13=1/169
2. Geneticists use probability to predict the alleles of offspring
a) Predictions can be compared with results of breeding experiments
b) Mathematical tests show whether the prediction and observations are
significantly different
3. Genetic ratios are estimations; not absolute numbers; the larger the sample
size, the closer the numbers will be to the prediction
D. 13.5 Inheritance of Alleles (ref. to figure 21)
Figure 21 A monohybrid cross
1. Mendel crossed plants that differed in only one trait
a) Known as a monohybrid cross- diagramed with a Punnett square as in
figure 21
b) Crossed plants with true-breeding, green-podded peas with true-
breeding yellow-podded peas
i. Plants involved in the first cross(first generation) are called the
parental (P) generation
ii. Offspring from P generation are called first filial, or F1
Generation
 Absolutely all were green-podded
 Allowed these to self fertilize
iii. Offspring from the F1 Generation are the second filial, or F2
generation
 428 were green-podded and 152 were yellow-podded
 3:1 ratio
2. Of all traits that Mendel studied, only one of the two would appear in the F 1
offspring
a) He called this trait the dominant trait

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b) He called the other trait (that was hidden in the F1 generation but
showed up in the F2)the recessive gene

3. Mendel used his observations to form the principle of segregation

a) Says that through meiosis and gamete formation, each parent passes on
only one factor (today called allele) to its offspring
b) Alleles segregate during gamete formation and meiosis
4. Today, allele for dominant genes is represented by a capital letter and
recessive allele is represented by the lowercase letter
a) Ex. G for green pods and g for yellow pods
b) Ex. T for tall stem and t for short stem
c) Since most multicellular organisms are diploid, their genotype consists
of two alleles
i. Genotype- genetic makeup, of true-breeding green-podded
plants would be GG
 Two dominant alleles is homozygous dominant
ii. Genotype of true-breeding yellow plants would be gg
 Two recessive alleles is homozygous recessive
iii. If the two alleles are different (Gg), then the plant is
heterozygous
d) Phenotype- physical appearance, is dictated by the genotype
i. Ex. GG and Gg (homozygous dominant and heterozygous) both
have the dominant allele so they will be green-podded while gg
(heterozygous) will be yellow-podded because there is no
dominant allele to “hide” the recessive one
5. F2 Genotype Explained (ref to figure 21 on previous page)
a) Half of the gametes produced by F1 Generation had g allele and half had
the G allele
i. Chance that a plant would receive a g allele from one parent is ½
ii. Chance that a plant would receive the G allele from one parent is
½
 Therefore, chance of receiving g allele from both parents
(and thereby being homozygous recessive) is 25%
 Would be a true-breeding yellow-podded plant
 Chance of receiving G allele from both parents (and
thereby being homozygous dominant) is 25%
 Would be true-breeding green-podded pea
 50% chance of receiving one of each (Gg or gG have
same result)
 Would be green-podded pea plant carrying the
recessive allele
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Figure 22 Dihybrid Cross

6. Following inheritance of two characteristics is done with a dihybrid cross (ref.

to figure 22)
a) Cross of organisms with two differing traits
b) Organisms that are heterozygous for both traits will return a ratio of
9:3:3:1
i. Ratio is characteristic of the F2 generation in a dihybrid cross
ii. This led Mendel to the principle of independent assortment
 Alleles for one characteristic divide up among gametes
independently of alleles of other characteristics
E. 13.6 Sex Determination (ref to figure 23 on following page)
1. All chromosomes come in matching pairs except for the sex chromosomes
a) Labeled X and Y
b) Females have 2 X chromosomes while males have 1 X and 1 Y
2. All eggs have 1 X chromosome while 50% of sperm have an X and 50% have a Y
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a) Therefore, the sperm determine the sex of offspring

Figure 23
Distribution of X and Y chromosomes

F. 13.7 Multiple Alleles and alleles without Dominance(ref to figure 24)

1. Some genes don’t follow the dominant-recessive pattern
a) Ex. Red-flowered snapdragons cross with White-Flowered snapdragons
to produce pink-flowered snapdragons
i. Known as incomplete dominance
b) Ex. Human blood type depends on the presence of A or B carbohydrates
on the surface of red blood cells
i. Possible alleles: IA and IB code for different forms of an enzyme
that add different sugars to the carbohydrate bound to the
blood cell’s membrane
 IA and IB are codominant alleles while i codes for no
active enzybe
 Possible genotypes:
 IAIA and IAi =type A
 IBIB and IBi =type B
 IAIB- type AB
 Ii- type O
 While there are three alleles, any individual can only
possess two at a time
G. 13.8 Linked Genes (ref. to figure 24 on following page)
1. Genes on the same chromosome are said to be linked
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a) Often inherited together

b) Somewhat goes against the principle of
independent assortment
2. Alleles of linked genes sometimes separate
a) Could be exchanged with other chromosomes
during crossing-over
b) The farther apart they are, the more likely they
are to separate
3. Frequency of separation of linked traits indicated where
they are in relation to each other on a chromosome
a) Enables people to identify-disease related genes
i. Ex. Huntington’s disease

H. 13.9 X-Linked Traits

1. Researchers found that when a white-eyed male fly
mated with a normal red-eyed female, all offspring had
red eyes
a) Confirmed that white eyes were recessive trait
b) Only males had white eyes
c) Crossed white-eyed females and red-eyed males
i. F1 offspring included only red-eyed
females and white-eyed males
ii. Explanation was that the gene for eye
color in a fly is passed on the X
chromosome Figure 24
 No eye-color gene on the Y Crossing over and Separation
of Linked genes
chromosome
 Whatever allele the male receives will be exhibited in its
phenotype
 Females will display the dominant eye-color because
they have 2 X chromosomes and therefore two alleles
2. Mary Lyon suggested that one X chromosome becomes deactivated early in
female development
a) Occurs at random
b) In some cells, the maternal X-linked genes are expressed while in
others, the paternal ones are
c) Explained that this deactivation could explain the dark stain in a nucleus
called a Barr Body
i. Errors in meiosis could give a female an extra X chromosome
 Cells of these females have two Barr Bodies, indicating
that one X chromosome remains active
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 Embryos with extra chromosomes typically don’t

survive, but females with more than 2 X chromosomes
do
VII. Chapter 14- Other forms of inheritance
A. 14.1 Understanding Gene function (ref. to figure 25)
1. Genetics builds on previous research
a) Ex. Mendel’s observations formed basis of modern genetics 50 yrs later
2. Modern scientific explanations are in keeping with evidence and well-reasoned
thinking
3. We learn a lot from mutations
a) Provide important clues about how the gene is supposed to work
4. Particular mutations could have different results in different people
a) Ex. One abnormal allele can produce stomach ulcers in one family
member, but cause kidney stones in another
5. Expression of genes depends on binding or RNA polymerase on nearby site
called promoter; RNA polymerase must bind to promoter and pass the
operator sequence before a gene is transcribed
6. Entire set of genes and its control sequence is called an operon
Figure 25 Bacterial Operon

7. Repressor can bind to the operator, blocking RNA polymerase from

transcribing mRNA, thereby stopping expression of that gene
a) Environmental factors can make the repressor protein change shape,
allowing the RNA polymerase to transcribe the mRNA, expressing the
gene
8. Eukaryotic gene regulation
a) Variety of factors can influence which gene is expressed, at what level,
at what time
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i. Ex. Steroids hormones influence gene transcription

 Hormone enters cell and binds to a receptor protein
 Combination of Hormone and receptor protein
enters nucleus and acts as a transcription
factor; binds to regulatory DNA sequence
known as response element
 Response element responds to outside stimulus
 Binding transcription factor at response
element activates the nearby gene
b) Other hormones regulate through a “domino effect” of biochemical
reactions
B. 14.2 Cytoplasmic Inheritance
1. Mitochondria and Chloroplasts have their own DNA
a) Because they are found in the cytoplasm, their DNA is the sourse of
Cytoplasmic inheritance
b) Eukaryotic cells have 100’s~1000’s of mitochondria, and each had
several copies of mitochondrial DNA (mtDNA)
i. Double-stranded, circular molecule
Figure 26 Mitochondrial Inheritance ii. Codes for 13 polypeptides, 2 rRNAs, 2 tRNAs
 Not sufficient for all mitochondrial activities; rest is
controlled by DNA molecules in the nucleus
iii. mtDNA is copied independently; new mitochondria are made
through fission like prokaryotes
 Do not sort evenly between daughter cells during
meiosis and mitosis
c) Mitochondria (and mtDNA) is always passed on through the mother(ref.
to figure 26)
i. Ovum is a large cell with lots of mitochondria to sustain its
growth
ii. Sperm have few mitochondria in its tail
 At fertilization, the sperm loses its tail and at that point,
the zygote that will develop into a new organism only
has maternal mitochondria
C. 14.5 Genetic anticipation(ref to fig 27 on following page)
1. Doctors observed that with certain inherited diseases, symptoms would develop at
younger ages as generations progressed
a) Shift toward earlier symptoms is called genetic anticipation
i. Best known ex. Huntington’s Disease
 In certain genes, number of copies of a repeated sequence
of three bases can increase or decrease within a normal
range
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 If there are too many copies, the gene becomes unstable;

then number of bases will always increase with each
generation
 Situation is called trinucleotide repeat expansion

Figure 27 Huntington's disease pedigree

VIII. Chapter 15- Advances in molecular Genetics

A. 15.6 Mutations and DNA Repair
1. Mutations are changes in the DNA sequence
a) Many different causes
i. Chemical exposure
ii. Radiation
iii. Etc.

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2. Most common cause of mutation is errors in copying DNA

a) Can affect protein structure directly, or occur in regulatory regions of
the genome
b) Most common type of mutation is point mutation- one base pair
changes into a different one
i. If it changes an important amino acid, it is a missense mutation
ii. If it changes to a stop codon, it is called a nonsense mutation
 Results in an abnormally short protein
c) Frameshift Mutations delete one or two base pairs (see section 9.7)
i. Change every subsequent codon
ii. Usually produces a new stop codon
iii. Results in a shortened, nonfunctional protein
3. Different mutations in same gene can cause same phenotype
a) Ex. Different mutations found in phenylalanine hydroxylase
i. Normally converts phenylalanine to tyrosine
ii. Any mutation that reduces the activity of this enzyme results in
a physical disorder called phenylketonuria (PKU)
4. Some genetic disorders are caused by one specific point mutation
a) Ex. Sickle-cell anemia
b) Ex. Form of dwarfism called achondroplasia
i. 98% of cases are caused by the same point mutation in the gene
that encodes the receptor for a growth hormone
c) Detection tends to be easy
5. When many mutations lead to the same disease, detection is more difficult
a) Ex. PKU, cystic fibrosis, breast cancer
b) Testing is more difficult if the gene is large
6. Large regions of chromosomes can also be mutated by deletion or mutation of
genetic material
a) Common in cancer cells
b) Clue to how chromosomal rearrangements leads to cancer was revealed
in leukemia study
i. 70% of patients had cancer cells with a mutation called the
Philadelphia chromosome
 Parts of 9 and 22 chromosome break off and are
translocated
 Result is a fused gene
 Consists of the promoter and beginning of one
gene from chromosome 22 and the end of a
different gene from chromosome 9
 Promoter ensures that the mutant protein is
continuously expressed
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7. Mutations can occur in somatic cells of multicellular organisms

a) Some not so bad- worst case is that mutant cell dies
b) Others cause uncontrolled cell growth that leads to cancer
c) Gene Amplification- normal part of development in many animal
species (but not humans)
i. Creates extra copies of specific genes
ii. Specialized cells produce large quantities of particular proteins
 Ex. Glandular cells in the pancreas produce insulin
IX. Chapter 17
A. 17.1 The Big Bang
1. Life on Earth can’t be older than earth itself
2. Measurements of light coming from deep space indicates that the universe
used to be smaller
a) Hubble telescope consistently detects redshifts, indicating things it is
viewing are moving away from it
3. By calculating the rate of expansion, scientists think that 15 billion years ago,
the universe was one super dense mass that exploded
a) Following this hypothesis, Earth was formed 4.6 Billion years ago
b) Analysis of moon rocks indicate that the moon is also this age
i. Could have formed when a meteor hit Earth and blew a chunk
of it into orbit

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c) Geologists have worked out a history of Earth from evidence in its rocks
(ref. to figure 28)

Figure 28 Geologic Timescale

B. 17.2 Early Earth

1. Evidence indicates that Earth’s interior is hot
a) Miners experience higher temps deep underground
b) Volcanoes and hot springs

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2. Decay of radioactive elements (Uranium, Thorium, and some isotopes of

potassium) is primary source of heat
3. Entire planet was probably hot when it first formed
a) As it cooled, gasses were released from the crust, forming the primitive
atmosphere
i. Nitrogen, Carbon Dioxide, Water Vapor, Hydrogen and small
amounts of Carbon Monoxide
ii. Probably didn’t have much oxygen
 Only became present after photosynthetic organisms
produced it 3-3.5 billion years ago
 Would have been bound in compounds like iron oxide
 Earliest rocks we have found have very little
oxygen containing compounds
C. 17.3 The beginnings of Life
1. Surface of early earth probably wouldn’t sustain modern life
a) Organic compounds don’t form easily in an atmosphere rich in nitrogen
and carbon dioxide
b) UV radiation from the sun zapped everything
i. Is harmful to DNA
ii. Today, we are protected by the ozone layer
 Made of ozone (O3) gas
2. Three popular explanations for the origin of life
a) Life originated on some other planet and traveled to Earth
i. Doesn’t explain origin of life
b) Life originated by unknown means
i. Earliest life could have been very different from today’s
organisms
ii. Very difficult to investigate
c) Life evolved from nonliving substances through interactions with the
environment
i. Can be tested in nature and labs
ii. Most suited to scientific investigation
iii. Can be stated in the form of a hypothesis
D. 17.4 Chemical Evolution (ref. to figure 29)
1. 1920’s Soviet- Alexander Oparin and British- J.B.S. Haldane both described the
hypothesis that life evolved on Earth from nonliving substances
a) Worked separately
b) Said that energy sources like radioactivity, lightning, etc., caused gasses
in the atmosphere to react and form organic compounds
i. Organic compounds accumulated in oceans

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ii. Hypothesized that life further evolved in the oceans trough

complex chemical reactions
Figure 29 The heterotroph hypothesis

2. Their ideas led to the heterotrophy hypothesis

a) Oparin-Haldane version requires three major steps
i. There had to be a supply of organic molecules, produced by
nonbiological processes
ii. Some processes had to assemble those small molecules into
polymers such as nucleic acids and proteins.
iii. Other processes had to organize the polymers into a system
that could replicate itself, using the organic molecules produced
in step 1.
b) Each step is a major change from nonliving to living
3. Explaining Step 1
a) Harold Urey and Stanley Miller (Urey and Miller)
i. Recreated conditions of early Earth in an airtight apparatus
 Methane, hydrogen, ammonia gas circulated through an
electric spark
 Boiling water added water vapor
 Cooled and formed “rain”
ii. Recorded two visible changes
 Small mass of tar appeared in the apparatus
 Water turned red
 Found many organic compounds including
amino acids in the water
iii. Repeated with only water vapor, hydrogen, carbon dioxide and
nitrogen
 Produced only simple amino acids
 Noted that a little methane is needed to produce
complex amino acids
iv. Their experiments produces 13 of 20 common amino acids
4. Explaining step 2
a) 1985, A.G. Cairns-Smith
i. Suggested clay could have formed the first organic polymers
 Consists of tiny layered crystals that can attract and
contain certain molecules
 Crystals could have catalyzed the bonding of these small
molecules concentrated on their surface

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5. Explaining step 3
a) Self replication of life presents a “chicken-and-egg problem”
i. Structure of proteins are coded by DNA
ii. Replication of DNA requires proteins
b) RNA has provided a possible solution
i. Components can be produced nonbiologically
ii. Can join spontaneously
iii. Some catalyze their own reactions
c) According to this RNA-world hypothesis, RNA was the information
molecule and catalyst and DNA showed up later
d) RNA can also undergo simulated Darwinian evolution
E. 17.7 Eukaryotes
1. Lynn Margulis hypothesized that mitochondria and plastids were once free-
living prokaryotes
a) Said that eukaryotes evolved from a symbiotic relationship between
large anaerobic prokaryotes and smaller photosynthetic prokaryotes
b) Large cells absorbed the small ones, and instead of being digested, the
smaller cells survived
i. Smaller cells produced sugars and ATP that benefitted the host
cells
ii. Eventually, the internal partners- endosymbionts -lost the
ability to exist separately
2. Now known as the endosymbiont hypothesis
a) Supported by large body of evidence:
i. Mitochondria have their own DNA and ribosomes
ii. Genes and ribosomes are similar to those of bacteria
iii. Both have double membranes
X. Chapter 20
A. I’m tired, and there’s only six questions on this chapter, so just use this:
B. Evolutionary Advancements
1. Opposable thumbs and big toes (fine manipulations)
2. Nails instead of claws
3. Binocular vision (depth perception
4. Omnivores (eat many things)
5. Color vision
6. Bipedalism (leaves hands free)
7. Single births
C. Early Homos
1. Australopithecines
a) -“Southern Apes”
b) -Lived 4 MYA to 2.5 MYA
c) -First hominids
d) -About 50 pounds and 1m tall
e) -cranial capacity=400

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f) -“Handyman”
g) -Used crude stone tools
h) -Lived 2.5 MYA to 1.5 MYA
i) -cranial capacity=600-700
j) -May have had fire
2. Homo Erectus
a) -“Traveling Man”
b) -Lived 1.5 MYA to 500,000 years ago in Africa
c) -Lived 1.5 MYA to 250,000 years ago in Europe
d) -About 5 feet tall and 100 pounds
e) -cranial capacity=900-1000
f) -Had crude wooden shelters and fire
g) -Lived in groups of 20-50
h) -Hunter Gatherers
3. Homo Sapien Neanderthalensis
a) -Big game hunters
b) -strong and robust
c) -Lived 250,000 years ago to 30,000 years ago
d) -cranial capacity=1750
e) -Buried dead with weapons, jewelry, food, etc.
4. Homo Sapien/Cro Magnon
a) -“Modern Man”
b) -Lived 30,000 years ago to present
c) -Cave dwellers (artistic)
d) -Taller and more slender
e) -cranial capacity=1350

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