6 Gene Expression and Regulation

Describe the structures involved in passing hereditary information from one generation to the next.

• Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.
  • i. Prokaryotic organisms typically have cir cular chromosomes.
  • ii. Eukaryotic organisms typically have multiple linear chr omosomes that are comprised of DNA. These chromosomes are condensed using histones and associated proteins.
• Prokaryotes and eukaryotes can contain plasmids, which are extra-chromosomal circular molecules of DNA.

Describe the characteristics of DNA that allow it to be used as hereditary material.

• Nucleic acids exhibit specific nucleotide base pairing that is conserved through evolution.
  • i. Purines (guanine and adenine) have a double ring structur e.
  • ii. Pyrimidines (cytosine, thymine, and uracil) ha ve a single ring structure.
  • iii. Purines pair with pyrimidines: adenine with thymine (or uracil in RNA) and guanine with cytosine.

Describe the mechanisms by which genetic information is copied for transmission between generations.

• DNA replication ensures continuity of hereditary information.
  • i. DNA is synthesized in the 5’ to 3’ direction.
  • ii. R eplication is a semiconservative proc ess, meaning one strand of DNA serves as the template for a new strand of complementary DNA.
  • iii. Helicase unwinds the DNA strands.
  • iv. T opoisomerase relaxes supercoiling in front of the r eplication fork.
  • v. DNA polymerase requires RNA primers to initiat e DNA synthesis.
  • vi. DNA polymerase synthesizes new strands of DNA c ontinuously on the leading strand and discontinuously on the lagging strand.
  • vii. Ligase joins the fragments on the lagging strand.
  • Exclusion: The names of the steps and particular enzymes involved, excluding DNA polymerase, ligase, RNA polymerase, helicase, and topoisomerase, are beyond the scope of the AP Exam.

Describe the mechanisms by which genetic information flows from DNA to RNA to protein.

• The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.
  • i. Messenger RNA (mRNA) molecules carry inf ormation from DNA in the nucleus to the ribosome in the cytoplasm.
  • ii. Distinct transfer RNA (tRNA) molecules bind specific amino acids and ha ve anticodon sequences that base pair with the codons of mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence.
  • iii. Ribosomal RNA (rRNA) molecules are functional building block s of ribosomes.
• RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. This process is known as transcription.
• The enzyme RNA polymerase synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction.
• In eukaryotic cells the mRNA transcript undergoes a series of enzyme-mediated modifications.
  • i. The addition of a poly-A tail makes mRNA more stable.
  • ii. The addition of a GTP cap helps with ribosomal recognition.
  • iii. The excision of introns, along with the splicing and retention of exons, generates different versions of the resulting mature mRNA molecule. This process is known as alternative splicing.

Explain how the phenotype of an organism is determined by its genotype.

• T ranslation of the mRNA to generate a polypeptide occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells, as well as the cytoplasmic surface of the rough ER of eukaryotic cells.
• In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed.
• T ranslation involves many sequential steps, including initiation, elongation, and termination. The salient features of translation include:
  • i. T ranslation is initiated when the rRNA in the ribosome int eracts with the mRNA at the start codon (AUG, coding for the amino acid methionine).
  • ii. The sequence of nucleotides on the mRNA is read in triplets, c alled codons.
  • iii. Each codon encodes a specific amino acid, which can be deduc ed by using a genetic code chart. Many amino acids are encoded by more than one codon.
  • iv. Nearly all living organisms use the same genetic code , which is evidence for the common ancestry of all living organisms.
  • Exclusion: The details and names of the enzymes and factors involved in each of these steps are beyond the scope of the AP Exam. Memorization of the genetic code, with the exception of the start codon AUG, is beyond the scope of the AP Exam.
• 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 is transcribed and translated for the assembly of new viral progeny.

Describe the types of interactions that regulate gene expression.

• Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription. Some genes are constitutively expressed, and others are inducible.
• Epigenetic changes can affect gene expression through reversible modifications of DNA or histones.
• The phenotype of a cell or an organism is determined by the combination of genes that are expressed and the levels at which they are expressed.
  • i. Observable cell differentiation results from the expression of genes for tissue-specific proteins.
  • ii. Induction of transcription factors during development results in sequential gene expression.
  • iii. The function and amount of gene products determine the phenotype of organisms.

Explain how the location of regulatory sequences relates to their function.

• Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated.
  • i. Prokaryotes regulate operons in an inducible or repressible system.
  • ii. In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression. 119 Gene Expression and Regulation UNIT 6

Explain how the binding of transcription factors to promoter regions affects gene expression and the phenotype of the organism.

• RNA polymerase and transcription factors bind to promoter or enhancer DNA sequences to initiate transcription. These sequences can be upstream or downstream of the transcription start site.
• Negative regulatory molecules inhibit gene expression by binding to DNA and blocking transcription.

Explain the connection between the regulation of gene expression and phenotypic differences in cells and organisms.

• Gene regulation results in differential gene expression and influences cell products and functions.
• Certain small RNA molecules have roles in regulating gene expression.

Describe the various types of mutation.

• Alterations in a DNA sequence are mutations that can cause changes in the type or amount of the protein produced and the consequent phenotype. DNA mutations can be beneficial, detrimental, or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.
  • i. Point mutations occur when one nucleotide has been substituted for a diff erent nucleotide.
  • ii. Frameshift mutations occur when one or more nucleotides are ins erted or deleted, causing the reading frame to be shifted.
  • iii. Nonsense mutations occur when there is a point mutation that causes a pr emature stop.
  • iv. Silent mutations occur when the change in the nucleotide sequence has no eff ect on the amino acid sequence.
  • Exclusion: Knowledge of specific mutations and their effects is beyond the scope of the AP Exam.

Explain how changes in genotype may result in changes in phenotype.

• Errors in DNA replication or DNA repair mechanisms as well as external factors, including radiation and reactive chemicals, can cause random mutations in the DNA.
  • i. Whether a mutation is beneficial, detrimental, or neutral depends on the environmental context.
  • ii. Mutations are a source of genetic variation.
• Errors in mitosis or meiosis can result in changes in phenotype.
  • i. Changes in chromosome number resulting from nondisjunction often result in new phenotypes caused by triploidy (aneuploidy).
  • ii. Changes in chromosome number often result in disorders with developmental limitations.
  • iii. Alterations in chromosome structure lead to genetic disorders.
  • Exclusion: Knowledge of specific disorders related to changes in chromosome number is beyond the scope of the AP Exam.

Explain how alterations in DNA sequences contribute to variation that can be subject to natural selection.

• Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected for by environmental conditions.
  • i. The horizontal acquisitions of genetic information in prokaryotes via transformation (uptake of DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer of DNA), and transposition (movement of DNA segments within and between DNA molecules) increase genetic variation.
  • ii. Related viruses can recombine genetic information if they infect the same host cell.
  • iii. Reproductive processes that increase genetic variation are evolutionarily conserved and are shared by various organisms.

Explain the use of genetic engineering techniques in analyzing or manipulating DNA.

• Genetic engineering techniques can be used to analyze and manipulate DNA and RNA.
  • i. Gel electrophoresis is a process that separat es DNA fragments by size and charge.
  • ii. During polymerase chain reaction (PCR), DNA fragments ar e amplified by denaturing DNA, annealing primers to the original strand, and extending the new DNA molecule.
  • iii. Bacterial transformation introduces foreign DNA int o bacterial cells.
  • iv. DNA sequencing technology determines the order of nucleotides in a DNA molecule. T ypically, these techniques result in a DNA fingerprint that allows for the comparison of DNA sequences from various samples.
  • Exclusion: Knowledge of the details of each of these genetic engineering techniques is beyond the scope of the AP Exam.