Enduring understanding 2.E: Many biological processes involved in growth, reproduction and dynamic homeostasis include temporal regulation and coordination

Essential knowledge 2.E.1: Timing and coordination of specific events are necessary for the normal development of an organism, and
these events are regulated by a variety of mechanisms.

a. Observable cell differentiation results from the expression of genes for tissue-specific proteins.

b. Induction of transcription factors during development results in sequential gene expression.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Homeotic genes are involved in developmental patterns and sequences.

2. Embryonic induction in development results in the correct timing of events.

3. Temperature and the availability of water determine seed germination in most plants.

4. Genetic mutations can result in abnormal development.

5. Genetic transplantation experiments support the link between gene expression and normal development.

6. Genetic regulation by microRNAs plays an important role in the development of organisms and the control of cellular functions.

c. Programmed cell death (apoptosis) plays a role in the normal development and differentiation.
Students should be able to demonstrate understanding of the above concept by using an illustrative example such as:
• Morphogenesis of fingers and toes
• Immune function
• C. elegans development
• Flower development
✘✘Names of the specific stages of embryonic development are beyond the scope of the course and the AP Exam.

Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information.

a. Genetic information is transmitted from one generation to the next through DNA or RNA.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.

2. Noneukaryotic organisms have circular chromosomes, while eukaryotic organisms have multiple linear chromosomes, although in
biology there are exceptions to this rule.

3. Prokaryotes, viruses and eukaryotes can contain plasmids, which are small extra-chromosomal, double-stranded circular DNA
molecules.

4. The proof that DNA is the carrier of genetic information involved a number of important historical experiments. These include:
i. Contributions of Watson, Crick, Wilkins, and Franklin on the structure of DNA
ii. Avery-MacLeod-McCarty experiments
iii. Hershey-Chase experiment

5. DNA replication ensures continuity of hereditary information.
i. Replication is a semiconservative process; that is, one strand serves as the template for a new, complementary strand.
ii. Replication requires DNA polymerase plus many other essential cellular enzymes, occurs bidirectionally, and differs in the
production of the leading and lagging strands.

6. Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by
reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and
becomes transcribed and translated for the assembly of new viral progeny. [See also 3.C.3]
✘✘ The names of the steps and particular enzymes involved, beyond DNA polymerase, ligase, RNA polymerase, helicase and
topoisomerase, are outside the scope of the course for the purposes of the AP Exam.

b. DNA and RNA molecules have structural similarities and differences that define function. [See also 4.A.1]
Evidence of student learning is a demonstrated understanding of each of the following:

1. Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are connected by covalent
bonds to form a linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.

2. The basic structural differences include:
i. DNA contains deoxyribose (RNA contains ribose).
ii. RNA contains uracil in lieu of thymine in DNA.
iii. DNA is usually double stranded, RNA is usually single stranded.
iv. The two DNA strands in double-stranded DNA are antiparallel in directionality.

3. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (
A-T or A-U) and cytosine pairs with guanine (C-G).
i. Purines (G and A) have a double ring structure.
ii. Pyrimidines (C, T and U) have a single ring structure.

4. The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.
i. mRNA carries information from the DNA to the ribosome.
ii. tRNA molecules bind specific amino acids and allow information in the mRNA to be translated to a linear peptide sequence.
iii. rRNA molecules are functional building blocks of ribosomes.
iv. The role of RNAi includes regulation of gene expression at the level of mRNA transcription.

c. Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein.
Evidence of student learning is a demonstrated understanding of each of the following:
1. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that
determine the order of amino acids in the polypeptide.

2. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Addition of a poly-A tail
• Addition of a GTP cap
• Excision of introns

3. Translation of the mRNA occurs in the cytoplasm on the ribosome.

4. In prokaryotic organisms, transcription is coupled to translation of the message. Translation involves energy and many steps, including
initiation, elongation and termination.
✘✘ The details and names of the enzymes and factors involved in each of these steps are beyond the scope of the course andthe AP®Exam.
The salient features include:
i. The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon.
ii. The sequence of nucleotides on the mRNA is read in triplets called codons.
iii. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more
than one codon.
✘✘ Memorization of the genetic code is beyond the scope of the course and the AP Exam.

iv. tRNA brings the correct amino acid to the correct place on the mRNA.
v. The amino acid is transferred to the growing peptide chain.
vi. The process continues along the mRNA until a "stop" codon is reached.
vii. The process terminates by release of the newly synthesized peptide/protein.
d. Phenotypes are determined through protein activities.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Enzymatic reactions
• Transport by proteins
• Synthesis
• Degradation

e. Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Electrophoresis
• Plasmid-based transformation
• Restriction enzyme analysis of DNA
• Polymerase Chain Reaction (PCR)

f. Illustrative examples of products of genetic engineering include:
• Genetically modified foods
• Transgenic animals
• Cloned animals
• Pharmaceuticals, such as human insulin or factor X

Essential knowledge 3.B.1: Gene regulation results in differential gene expression, leading to cell specialization.

a. Both DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Promoters
• Terminators
• Enhancers

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

b. Both positive and negative control mechanisms regulate gene expression in bacteria and viruses.
Evidence of student learning is a demonstrated understanding of each of the following:
1. The expression of specific genes can be turned on by the presence of an inducer.

2. The expression of specific genes can be inhibited by the presence of a repressor.

3. Inducers and repressors are small molecules that interact with regulatory proteins and/or regulatory sequences.

4. Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control).

5. Regulatory proteins stimulate gene expression by binding to DNA and stimulating transcription (positive control) or binding to repressors
to inactivate repressor function.

6. Certain genes are continuously expressed; that is, they are always turned "on," e.g., the ribosomal genes.

c. In eukaryotes, gene expression is complex and control involves regulatory genes, regulatory elements and transcription factors that
act in concert.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Transcription factors bind to specific DNA sequences and/or other regulatory proteins.

2. Some of these transcription factors are activators (increase expression), while others are repressors (decrease expression).

3. The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the
gene product will be produced.

d. Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.

Essential knowledge 3.B.2: A variety of intercellular and intracellular signal transmissions mediate gene expression.

a. Signal transmission within and between cells mediates gene expression.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Cytokines regulate gene expression to allow for cell replication and division.
• Mating pheromones in yeast trigger mating gene expression.
• Levels of cAMP regulate metabolic gene expression in bacteria.
• Expression of the SRY gene triggers the male sexual development pathway in animals.
• Ethylene levels cause changes in the production of different enzymes, allowing fruits to ripen.
• Seed germination and gibberellin.

b. Signal transmission within and between cells mediates cell function.
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Mating pheromones in yeast trigger mating genes expression and sexual reproduction.
• Morphogens stimulate cell differentiation and development.
• Changes in p53 activity can result in cancer.
• HOX genes and their role in development.

Essential knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation.  

a. The imperfect nature of DNA replication and repair increases variation.

b. The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer) and transposition (movement of DNA segments within and between DNA molecules) increase variation. [See also 1.B.3]

✘✘ Details and specifics about the various processes are beyond the scope of the course and the AP Exam.

c. Sexual reproduction in eukaryotes involving gamete formation, including crossing-over during meiosis and the random assortment of chromosomes during meiosis, and fertilization serve to increase variation. Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms. [See also 1.B.1, 3.A.2, 4.C.2, 4. C3]

✘✘ The details of sexual reproduction cycles in various plants and animals are beyond the scope of the course and the AP Exam. However, the similarities of the processes that provide for genetic variation are relevant and should be the focus of instruction.

Essential knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts.

a. Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms. [See also 1.B.3]
Evidence of student learning is a demonstrated understanding of each of the following:
1. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes.

2. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle.

3. Virus replication allows for mutations to occur through usual host pathways.

4. RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.

5. Related viruses can combine/recombine information if they infect the same host cell.

6. HIV is a well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection.

b. The reproductive cycles of viruses facilitate transfer of genetic information.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Viruses transmit DNA or RNA when they infect a host cell. [See also 1.B.3]
To foster student understanding of this concept, instructors can choose an illustrative example such as:
• Transduction in bacteria
• Transposons present in incoming DNA

2. Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. These latent viral
genomes can result in new properties for the host such as increased pathogenicity in bacteria.