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AP Biology Semester 1 Final Exam Review

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Kathryn McKibben

on 18 December 2013

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Transcript of AP Biology Semester 1 Final Exam Review

AP Biology Semester 1 Final Exam Review
Zahra Vasaya
Kathryn McKibben
2nd period

2. DNA, RNA, & Proteins
3. Animal Behavior and Evolution
4. Genetics
1. Machinery of Life
5. Cell Cycle

◦double stranded helix

◦contains genetic material

◦Purines are larger than pyrimidines

◾Purines (A & G)

◾Pyrimidines (C & T & U)

◾Purines bond with Pyrimidines (A-T, C-G, A-U in RNA)

DNA (Deoxyribose Nucleic Acid)

◦Ribose has an extra oxygen molecule compared to deoxyribose; this changes entire function


◦Nucleotides contain a phosphate group, pentose sugar, and nitrogenous base

◦5’ end of one side will always connect to 3’ end of other side of DNA

◾Antiparallel strands

◦Histones are proteins that help to package DNA into chromatin in the nucleus

◾positively charged in order to attract DNA

Griffith's Experiment

◦One of the first experiments about genetic material

◦Injected bacteria into mice; S cells kill the mice and R cells don’t. However, when dead S cells and living R cells were injected into mice, the mice die. The two different bacteria must have combined their genetic material

Hershey and Chase Experiment

◦experiment done to determine whether DNA or proteins was the main genetic material

◦used radioactive molecules to trace the DNA and proteins

◦determined that DNA is the genetic material, not proteins

Avery, MacLeod, McCarthy

◦Did an experiment in which transformation only occurred when DNA was left active and not RNA or proteins

DNA Replication

◦semi-conservative (one half of the new DNA comes from the original strand that was replicated)

◦DNA polymerase adds complementary base pairs to the template

◦DNA replication begins at the origin of replication

◾in eukaryotes, replication begins at many sites along the DNA molecule of each chromosome

◾in prokaryotes, there is one replication bubble because the shape of DNA is circular

◦Prokaryotes are able to copy their DNA at a faster rate because of less DNA

◦How it works:

◾Helicase unwinds the DNA, breaking the hydrogen bonds

◾Primase attaches RNA primers to the template strand of DNA

•RNA primers help add RNA onto the strand and allow polymerase to know where to begin replication

◾Single strand binding proteins stabilize the parental strands

◾DNA polymerase attaches complementary base pairs and their nucleotides to the template strand and engages in mismatch repair

◾Ligase fills in the gaps of the sugar phosphate backbone

◾There is a leading (continuous) strand and a lagging (split-up) strand

•Leading Strand

◦DNA Polymerase III is always responsible for producing the entire leading strand

•Lagging Strand

◦made up of Okazaki fragments

◦The DNA polymerase looks for RNA primers and replicates a fragment up until the next primer

•The new strand is always built in the 5’ to 3’ direction (so that the parent is in the 3’ to 5’ direction)

◦The DNA loses telomere and gets shorter after multiple replications

◾telomeres are in eukaryotes and contain noncoding DNA

◾telomeres help keep the rest of the DNA intact and semi-stable

◦Nucleotide Excision Repair

◾nuclease breaks off the DNA that is not attached properly

◾DNA polymerase adds the correct nucleotides

◾DNA ligase fills in the gaps and checks the reconstructed DNA to ensure they are matched properly

Transcription & Translation

◦Transcription (produces RNA)


•Start point is included in the promoter region (TAC)

•A eukaryotic promoter includes a TATA box

◦Several transcription factors must bind to the DNA before RNA polymerase II can do so

◦All the transcription factors and RNA polymerase II bound to the DNA forms the transcription initiation complex


•RNA transcript is produced


•caused by stop codon (UAA, UAG, UGA)

◦RNA Processing

◾A 5’ cap and a poly-A tail are added to the pre-mRNA

•they preserve and protect what’s inside (like telomeres)

•help RNA leave nucleus through nuclear pores

◾Introns (non-coding segments) are cut out and exons (coding segments) are spliced together

•introns are cut out by spliceosomes


◾mRNA travels to ribosome to be translated into a polypeptide chain

•Initiator tRNA (Met amino acid), mRNA binding site, small and large ribosomal subunits make up the translation initiation complex

•The sequence of nucleotides on the mRNA is read in triplets called codons

•Ribosome contains A, P, and E sites

◦In the A site, the anticodon of tRNA binds to the codon of mRNA

◾Aminoacyl-tRNA synthetase is an enzyme that allows amino acids to connect to tRNA

◦In the P site, the amino acid carried by the tRNA is added to the growing polypeptide

◦In the E site, the amino acid-less tRNA exits the ribosome

•When a stop codon is reached on the mRNA, a release factor binds to the A site which frees the polypeptide

◦Mutations (incorrect base pair substitutions, insertions, and deletions)

◾Silent (no effect on amino acid sequence)

◾Missense (changes the codon to code for a different amino acid)

◾Nonsense (changes a codon to a stop codon)


◦composed of different combinations of amino acids

◾amino acids are joined by peptide bonds to form polypeptides

◾amino acids are composed of an amino end and a carboxyl end

◾Polar amino acids are hydrophilic and nonpolar are hydrophobic

◦There are 4 structures in the process to fold polypeptide chains into a protein

◾Primary: unique sequence of amino acids

◾Secondary: coils and folds of polypeptide chain

•alpha helix & beta pleated sheets

◾Tertiary: overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids; polypeptide subunits

•hydrophobic interaction: as a polypeptide folds into its functional shape, amino acids with hydrophobic side chains usually end up in clusters at the core of the protein

•disulfide bridges also reinforce the shape of the protein

◦the sulfur of one cysteine bonds to the sulfur of the second on the side chains

◾Quaternary: overall protein structure that results from the aggregation of the polypeptide subunits

◾The structure of the protein should relate to its function

•chaperonin proteins help fold the polypeptides

◦Phenotypes are determined through protein activities


◦A regulatory gene is a sequence of DNA encoding a regulatory protein or RNA

◦Expression of a gene can be turned on by an inducer or turned off by a repressor

◦Behavior is an action carried out by muscles or glands in response to a stimulus

◦Animals use tactile, auditory, visual, olfactory, chemical sensory information

◦Fixed action pattern: instinctive behavior

◾Sticklebacks: attack any other red-stomached fish

◦Kinesis: change in behavior

◦Taxis: moving towards or away from a stimulus

◦Habituation: distinguishing between relevant and irrelevant stimuli

◦Sexual Selection: females choose their mates and the behavior/characteristic they like best.

◾desired behaviors/ traits would be passed on, affecting evolution

◾Sexual Dimorphism: heaving different phenotypic appearances for different genders

◦Kin selection: animals choose to help increase the fitness of their relatives

◦Hamilton’s Rule:

◾rB>C, then an organism will protect another organism

•r= coefficient of relatedness

•B= benefit

•C= cost

Animal Behavior
Hardy-Weinberg Principle

◦genes will remain constant during each generation and evolution will not take place if there is:

◾large population

◾random mating

◾no mutatations

◾no migration

◾no selection

◦Allelic frequency:

◾p + q = 1

•p= frequency of all dominant alleles

•q= frequency of all recessive alleles

◦Genotypic frequency:

◾p^2 + 2pq + q^2 = 1

•p^2 = frequency of homozygous dominant genotype

•2pq = frequency of heterozygous genotype

•q^2 = frequency of homozygous recessive genotype

Important Scientists


◾catastrophism; immigration of new populations instead of evolution


◾inheritance of acquired traits; use and disuse


◾classification of organisms


◾modern geology; uniformitarianism


◾descent with modification; natural selection through competition and sexual selection


◾overproduction of offspring takes place


◾natural selection through adaptations


◾theory of gradualism (over time, things will change)


◦Individuals that are well suited to their environment tend to leave more offspring than other individuals and over time, favorable traits accumulate in the population (NATURAL SELECTION)

◾Directional selection: mean population shifts in one direction

◾Disruptive (diversifying) selection: mean population shifts to extremes of a trait

◾Stabilizing selection: selection against both extremes

◾According to Darwin’s theory of natural selection, competition for limited resources results in differential survival

individuals with more favorable phenotypes are more likely to survive and reproduce

◦Sexual Selection: a type of natural selection where certain inherited characteristics are favored by individuals that are choosing a mate

◾Intersexual: chooses who you mate with (pick best genes)

◾Intrasexual: (fighting to get a mate)

◦Evidence for evolution:

◾fossil record (see species changing over time)

◾homologous structures (structures that are seen in different organisms and were shared by a common ancestor)

•vestigial structures (structures that are non-functioning that indicate a past evolutionary connection)

•development of structures controlled by hox genes

◦Divergent evolution (two species evolve and have a more recent common ancestor- homologous structures)

◦Convergent evolution (two distant species evolve independently but may share similar characteristics (analogous structures)

◦Geographic variation- caused by different genes of separate populations

◾Cline: graded change of allele frequencies along a geographic axis

◦Gene flow: movement of organisms

◦Genetic Variation

◾Mutation: change in DNA that can induce genetic variation over time and lead to greater gene diversity

•primary source of genetic variation

•can be caused by errors in DNA replication or repair mechanisms, and external factors like radiation and reactive chemicals

•changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected by environmental conditions (adaptations)

◾Darwinian fitness (differential reproductive success): contribution of an individual relative to other individuals within future offspring

◾Relative fitness: contribution of a genotype within a population that is passed through generations

◾Evolutionary fitness: measured by reproductive success

◾Heterozygous advantage: over time 2 or more alleles will be passed down if the heterozygote genotype is more favorable than the homozygous genotype

◾Reduction of genetic variation within a given population can increase the differences between populations of the same species

◾Population ability to respond to changes in the environment is affected by genetic diversity. Species and populations with little genetic diversity are at risk for extinction

•genetic diversity allows individuals in a population to respond differently to the same changes in environmental conditions

◦Genetic Drift (chance events that cause certain phenotypic variations to be present)

◾more significant in small populations

◾cause random allele frequency changes (tend to lean recessive)

◾loss of genetic variation can result

◾harmful alleles may become fixed

◾Can be caused by bottleneck effect (small portion that survives may be much different from the original representative population)

◾Can be caused by founder effect (smaller gene pool and higher likelihood of genetic disorders because of inbreeding)

Evolutionary Eras

◦Archean era is longest

◦Cambrian Explosion: explosion of species and diversity

◦Permian Extinction: large extinction during Permian era

◦Prokaryotes believed to be first living organisms

◾Earth formed 4.6 bya, and the earliest fossil evidence for life is 3.5 bya

◾Stromatolites: rocks formed by first prokaryotes

◾Prokaryotes developed eukaryotes through endosymbiosis

•The endosymbiotic theory describes how a large host cell and ingested bacteria could easily become dependent on one another for survival, resulting in a permanent relationship. Over millions of years of evolution, mitochondria and chloroplasts have become more specialized and today they cannot live outside the cell

◾Miller-Urey Experiment produced amino acids through simulated early earth conditions

•The atmosphere was recreated and organic (carbon) compounds were derived from inorganic (non-carbon) compounds

◦absence of significant quantity of oxygen (Oxygen content increased due to photosynthesis)

◾Protobiont: compounds that are believed to help make first life forms (abiotically produced molecules)

•Liposomes: lipids added to water that can help replicate

◦may have been first membranes

◦can carry out metabolism with the presence of enzymes

•Ribozymes: help produce RNA by acting as enzymes

◦Might be first nucleotide bases

◦RNA World hypothesis proposes that RNA could have been the first genetic material

•these molecules served as monomers, or building blocks for the formation of more complex molecules, including amino acids and nucleotides

◦joining of monomers produced polymers, with the ability to store, replicate, and transfer information

◦Evidence for evolution

◾All organisms on Earth share a common ancestral origin of life (UCA)

•molecular building blocks that are common to all forms of life

•common genetic code

◾Biochemical and genetic similarities between related organisms

•DNA nucleotide and protein sequences


•How fossils are dated

◦Radiometric dating: decay of radioactive isotopes

◾Measuring ratios of Carbon-14 to Carbon-12 gives the fossils’ age

◦relationships within phylogenetic trees

◾look at morphological homologies such as vestigial structures

◦mathematical calculations that take information from chemical properties and/or geographical data

◾Phylogenetic trees and cladograms

•Represent traits that are either derived or lost due to evolution

•illustrate that speciation has occurred, in that any relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor

Prokaryotes vs. Eukaryotes

◦Prokaryotic organisms have circular chromosomes; eukaryotic organisms have multiple linear chromosomes

◦Plasmids: small, extra-chromosomal, double-stranded circular DNA molecules

◦Transformation: uptake of naked DNA in prokaryotes

◦Conjugation: cell to cell transfer of DNA

◦Transposition: movement of DNA segments within and between DNA molecules

6. Viral Storm

•Transduction: viral transmission of genetic information

•genetic information is transmitted from one generation to the next through DNA or RNA

•Retroviruses: alternate flow of genetic information; from RNA to DNA, made possible from reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. The DNA then becomes part of the host’s genome where it can be transcribed and translated for the assembly of new viruses

•Lytic cycle: one virus produces many progeny

•Lysogenic cycle: viruses integrate their DNA into the host’s DNA and establish a latent infection. The latent viral genomes can result in new properties for the host

•Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes

◦RNA viruses lack replication error-checking mechanisms, and thus have higher mutation rates

◦Related viruses can combine/recombine information if they infect the same host cell, swapping genes and certain phenotypes



◾contains DNA

◾DNA is wrapped here

◾DNA unwound here by RNA polymerase


◦short, repetitive nucleotide sequences that do not contain genes

◦“cap” ends of chromosomes

◦50-100 bases are lost at these ends of chromosomes every time cell undergoes division

•homologous recombination: repairs breaks in DNA

◦Golgi Apparatus

◾process & sort different chemicals

◦Nuclear membrane

◾double layered, surrounds nucleus

◾allows RNA to leave through pores

◦Endoplasmic Reticulum (ER)

◾sort & arrange new proteins; packaging

◾rough ER: ribosmone-studded

◾smooth ER

◦Extracellular matrix

◾helps connect cells to each other

◾conduit for transmitting external stimuli into the cell

◾made of collagen


◦programmed cell death (cell suicide)

◦assisted by enzyme caspases (disassemble proteins)


◦help cells communicate by sending signals all over body


◾released in times of strong emotions (fear, excitement)

◾heart beats faster

Neurons, Synapses, and Signaling


◾functional unit of nervous system

◾composed of

•dendrites:receive incoming messages from other cells

•axons: transmit messages to other cells


◾junction between 2 neurons

◦Myelin sheath:

◾insulates axons

◾increases speed of transmission in nerves


◾chemical messengers released from vesicles


◾regulates electrical signals

help make more DNA, RNA, mRNA

DNA Photolyase
removes damaged nucleotides attached to healthy ones

Red blood cells:
produce hemoglobin (carries oxygen)
manufactured in bone marrow
albumin: most plentiful protein in blood serum; delivers fats & drugs
insulin & glucagon: hormones responsible for regulating blood sugar
bad cholesterol in blood: LDL
good cholesterol: HDL
blood clotting occurs when tissue factor is exposed
lipids: difficult to transport within blood serum

contains proteins actin (thin) & myosin (thick) filaments

polymers made of amino acids monomers
membrane proteins: transport, pass through Golgi & ER to get to membrane
actin: smallest & most plentiful protein in cells. Form filamentous network to help connect cells
proteasomes: protein shredders
ubiquitin: signals that a protein needs to be recycled
protein shape is crucial to protein shape; function is changed if protein not folded properly
chaperonins: protein molecules, assist in proper folding of proteins within cells
4 levels of protein structure:
Primary structure: unique sequence of amino acids
peptide bonds link amino acids
Secondary structure: result of hydrogen bonding
Alpha helix: coiled shape
Beta pleated sheet: accordion shape
Tertiary structure: overall globular shape of polypeptide, resulting from interactions between R-groups such as:
hydrophobic interactions
van der Waals interactions
hydrogen bonds
disulfide bridges
Quaternary structure: overall large protein structure that results from the aggregation of polypeptide subunits

energy storage
glycogen in animals
structural support
cellulose in plants
sugars, hydroxyl groups, glucose is packaged

make up cell membrane (selectively permeable)
regulate what enters cell membrane
blocks metal & water
porin proteins let nutrients in
arranged in a bilayer in forming the cell membrane

sugar phosphate backbone

hydrophilic heads
(glycerol backbone)
facing outside environment
negatively charged

hydrophobic tails-
sandwiched in between heads
do not dissolve in water

Extra oxygen molecule
less stable than DNA
disposable copy; leaves nucleus while DNA stays

UV rays
attack DNA nucleotides
results from mutation in DNA that caused by sunlight or chemical exposure
Stem Cells
can reproduce indefinitely
can produce other specialized cells
enormous potential for medical applications

first line of defense in blood plasma; immune proteins
having different DNA helps fight off invaders

complement system
helps antibodies clear pathogens

Law of Gravity doesn’t apply to molecules

6 essential elements of life: CHONPS

protective layer: lipid bilayer
help make Vitamin B12 & Vitamin K
build specialized enzymes
contains millions of base pairs
flagellum: allows bacteria to move & sense nutrients
flagellar motor: for movement in all directions
protected from our digestive enzymes & antibodies by their biofilm
switch genes with each other
transfer plasmid
become resistant to antibiotics

E. Coli
mutualistic relationship with humans
help us digest food, produce nutrients
flagellar motor for locomotion and sensing
use electrons to create gradient to make ATP
uses ¼ of its molecular resources to produce energy

cell cycle: complex set of stages highly regulated with checkpoints that determine the ultimate fate of the cell.

The cell cycle is directed by internal controls or checkpoints.

Internal and external signals provide stop-and-go signs at the checkpoints.

• Mitosis-promoting factor (MPF)

• Action of platelet-derived growth factor (PDGF)

Cyclins and cyclin-dependent kinases control the cell cycle

protein enzymes that control the cell cycle.
active only when connected to cyclin proteins: cyclin-dependent kinases (Cdk)
kinases give go-ahead signals at G1 and G2 checkpoints

human somatic cells
all body cells except gametes
46 chromosomes

human gametes
sperm & egg cells
23 chromosomes
result from meiosis

Mitosis alternates with interphase in the cell cycle.
Interphase consists of three phases:


S: synthesis of DNA
when chromosomes are replicated, each duplicated chromosome consists of 2 sister chromatids attached by a centromere
A lack of Shugoshin proteins leads to sister chromatids not staying attached to each other

G2: preparation for mitosis.


division of cell’s nucelus

passes a complete genome from the parent cell to daughter cells.

occurs after DNA replication.

followed by cytokinesis produces two genetically identical daughter cells.

plays a role in growth, repair, and asexual reproduction

(replication, alignment, separation).

Prophase, Metaphase (best for karyotyping), Anaphase, Telophase

cytoplasm of cell is divided
animal cells: cleavage furrow forms that eventually divides cytoplasm
plant cells: cell plate

Meiosis followed by fertilization ensures genetic diversity in sexually reproducing organisms.

each gamete receives one complete haploid (1n) set of chromosomes.

Homologous pairing
homologous chromosomes are paired
one homologue originating from the maternal parent
one from the paternal parent

Separation of the homologous chromosomes ensures that each gamete receives a haploid (1n) set of chromosomes composed of both maternal and paternal chromosomes.

Crossing over: homologous chromatids exchange genetic material; increases genetic variation in the resultant gametes.

fusion of two gametes ncreases genetic variation (new combinations of genetic information in the zygote)

restores the diploid number of chromosomes

Density-dependent inhibition
process by which crowded cells stop dividing

Cancer cells do not exhibit Density-dependent inhibition

mass of abnormal cels within otherwise normal tissue
benign tumor: abnormal cells remain at original site
malignant tumor: becomes invasive enough to impair functions of organs (cancer)
metastasis: spread of cancer cells; malignant tumors may have cells that separate from the original tumor and enter blood vessels or lymph vessels

the process by which new species arise
Speciation rates can vary, especially when adaptive radiation occurs when new habitats become available
Speciation results in diversity of life forms. Species can be physically separated by a geographic barrier
reproductive isolation prevents gene flow
New species arise from reproductive isolation over time


Species extinction rates are rapid at times of ecological stress.
Humans have an impact on ecosystems and species extinction rates

3 parts
promoter: where RNA polymerase attaches
operator: controls access of RNA polymerase to the genes
genes of operon

Chromosome Theory of Inheritance

genes have specific locations on chromosomes
chromosomes segregate & assort independently

proteins; DNA wrapped around them
condense DNA into smaller volume
histone acetylation
acetyl groups are added to amino acids of histone proteins
thus making chromatin less tightly packed-- encouraging transcription

Inheritance Patterns
complete dominance: heterozygote and homozygote for the dominant allele are indistinguishable
codominance: 2 alleles are dominant and affect the phenotype in 2 different but equal ways (ex: blood type)
incomplete dominance: F1 hybrids have an appearance that is in betweeen that of the two parents (ex: red + white flowers= pink)
epistasis: the interaction of genes to produce different phenotypes; the interaction between genes do not have to be on the same locus in this process

Segregation and independent assortment of chromosomes result in genetic variation
Segregation and independent assortment can be applied to genes that are on different chromosomes.
Genes that are adjacent and close to each other on the same chromosome tend to move as a unit
the probability that they will segregate as a unit is a function of the distance between them
Genetic Disorders
Certain human genetic disorders can be attributed to the inheritance of single gene trait or specific chromosomal changes, such as nondisjunction.

• Sickle cell anemia

• Tay-Sachs disease

• Huntington’s disease

• X-linked color blindness

• Trisomy 21/Down syndrome

• Klinefelter’s syndrome
Sex Chromosomes
Some traits are determined by genes on sex chromosomes.

• Sex-linked genes reside on sex chromosomes (X in humans).

• In mammals and flies, the Y chromosome is very small and carries few genes.

• In mammals and flies, females are XX and males are XY
X-linked recessive traits are always expressed in males.

• Some traits are sex limited, and expression depends on the sex of the individual, such as milk production in female mammals and pattern baldness in males.
Environmental factors influence many traits both directly and indirectly.

• Height and weight in humans

• Flower color based on soil pH

• Seasonal fur color in arctic animals

• Sex determination in reptiles

• Density of plant hairs as a function of herbivory

An organism’s adaptation to the local environment reflects a flexible response of its genome.

A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.









Blood Type
Antigens on red blood cells determine blood type (A, B, AB, or O)
antibodies to nonself blood antigens already exist in body
transfusion with incompatible blood leads to destruction of transfused cells-- life threatening
Understanding genes helps us understand:
1. evolution of pathogens (viruses,
2. similarities and differences in various
3. protein synthesis
4. protein synthesis & growth and
development of organisms
5. epigenetic changes
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