AP Biology Unit 6: Gene Expression and Regulation COMPLETED Topic Learning Objective(s) 6.1 DNA and RNA Structure IST-1.K Describe the structures in
AP Biology
Topic 6.1: DNA and RNA Structure
The primary source of heritable information is DNA (deoxyribonucleic acid), a molecule that carries the genetic instructions for the development, functioning, growth, and reproduction of all known living organisms.
Genetic information is transmitted from one generation to the next through the process of reproduction, where DNA is passed from parent organisms to their offspring. This can occur through sexual reproduction, where gametes (sperm and egg cells) fuse to form a zygote with a unique combination of DNA, or through asexual reproduction, where genetically identical offspring are produced from a single parent organism.
DNA is a double-stranded molecule composed of nucleotides, each containing a phosphate group, a sugar molecule (deoxyribose), and one of four nitrogenous bases: adenine (A), cytosine (C), guanine (G), and thymine (T).
DNA is stored in the nucleus of eukaryotic cells, where it is organized into linear chromosomes. In prokaryotic cells, DNA is stored in the nucleoid region, a concentrated area of the cytoplasm, and is typically circular in shape.
Prokaryotic DNA is typically circular and exists as a single, coiled chromosome located in the nucleoid region of the cell.
Eukaryotic DNA is linear and organized into multiple chromosomes housed within the nucleus. It is associated with histone proteins and packaged into chromatin, which undergoes further condensation to form visible chromosomes during cell division.
The amount of DNA differs between prokaryotes and eukaryotes, with prokaryotes typically having much less DNA than eukaryotes. Prokaryotic genomes are typically smaller and contain a single circular chromosome, while eukaryotic genomes are larger and contain multiple linear chromosomes.
A plasmid is a small, circular DNA molecule that can replicate independently of the chromosomal DNA. Plasmids are commonly found in bacteria and some other microorganisms.
Two functions of plasmids include:
Carrying accessory genes that provide bacteria with additional functions, such as antibiotic resistance or the ability to metabolize certain nutrients.
Serving as vectors for the transfer of genes between bacteria through horizontal gene transfer mechanisms like conjugation, transformation, and transduction.
Two biotechnical uses for plasmids include:
Gene cloning: Plasmids are commonly used as vectors to introduce foreign DNA into host cells for cloning purposes, such as the production of recombinant proteins or the creation of transgenic organisms.
Gene editing: Plasmids can also be used as vehicles for delivering gene-editing tools, such as CRISPR-Cas9, into cells for precise genome modifications, including gene knockout, knock-in, or gene regulation.
DNA is a better hereditary material than RNA due to its greater stability, fidelity in replication, and ability to store genetic information for longer periods. DNA's double-stranded structure provides protection against chemical and physical degradation, reducing the likelihood of errors during replication and transmission of genetic information.
The nucleotide base pairing rules dictate that adenine (A) pairs with thymine (T) in DNA or with uracil (U) in RNA, and guanine (G) pairs with cytosine (C). This complementary base pairing ensures the accurate replication and transmission of genetic information during DNA replication and transcription.
The structure of a purine consists of a heterocyclic aromatic ring fused to an imidazole ring. Purines have a two-ring structure, which includes adenine and guanine.
Adenine and guanine are the nitrogenous bases classified as purines.
The structure of a pyrimidine consists of a single heterocyclic aromatic ring. Pyrimidines have a single-ring structure, which includes thymine, cytosine, and uracil.
The nitrogenous bases classified as pyrimidines are cytosine, thymine (in DNA), and uracil (in RNA).
Purines always pair with pyrimidines due to their complementary base pairing in DNA and RNA. This pairing ensures that the width of the DNA double helix remains constant, as purines (larger double-ring structures) pair with pyrimidines (smaller single ring molecules) to form stable hydrogen bonds, maintaining the overall structure of the DNA molecule.
If there is 20% thymine in a DNA strand, the amount of cytosine would also be 20%. In DNA, the amount of adenine is equal to the amount of thymine, and the amount of guanine is equal to the amount of cytosine due to complementary base pairing. Therefore, if thymine constitutes 20% of the DNA, cytosine would also constitute 20%, as they pair with each other.
Topic 6.2: Replication
DNA is synthesized in the 5' to 3' direction.
DNA polymerase reads the DNA template in the 3' to 5' direction.
Helicase unwinds the double-stranded DNA molecule by breaking the hydrogen bonds between the complementary base pairs, allowing access to the DNA template strands during replication.
Topoisomerase relieves the tension ahead of the replication fork by cutting and rejoining the DNA strands, preventing the accumulation of supercoiling and allowing DNA replication to proceed smoothly.
DNA polymerase catalyzes the synthesis of new DNA strands by adding nucleotides in a complementary fashion to the template strand during DNA replication.
RNA primers and primase initiate DNA replication by synthesizing short RNA primers complementary to the DNA template, providing a starting point for DNA polymerase (DNA pol III) to begin synthesis.
RNA primers are required for DNA replication because DNA polymerase can only add nucleotides to an existing nucleic acid strand, not initiate synthesis de novo. Therefore, RNA primers provide the initial starting point for DNA polymerase to begin DNA synthesis.
The leading strand is synthesized continuously in the 5' to 3' direction toward the replication fork, while the lagging strand is synthesized discontinuously in short fragments called Okazaki fragments, which are later joined together.
DNA ligase joins the Okazaki fragments on the lagging strand by catalyzing the formation of phosphodiester bonds between adjacent nucleotides, sealing the nicks between the fragments and completing the synthesis of the new DNA strand.
During DNA replication, helicase unwinds the double-stranded DNA molecule at the replication fork, while topoisomerase relieves the tension ahead of the fork. Primase synthesizes short RNA primers on the template strand, which are then extended by DNA polymerase. The leading strand is synthesized continuously in the 5' to 3' direction, while the lagging strand is synthesized discontinuously in short fragments. DNA ligase then joins the Okazaki fragments on the lagging strand, completing the synthesis of the new DNA strands. This process ensures accurate and faithful replication of the entire DNA molecule.
Topic 6.3: Transcription and RNA Processing
What is transcription?
What is the central dogma?
What is the function of mRNA?
What is the function of tRNA?
What is the function of rRNA?
How does the mRNA, tRNA, and rRNA all interact?
How does the DNA sequence determine the RNA sequence?
What is the function of RNA polymerase?
Which strand is the template strand?
What are the other names of the template strand?
Which direction does transcription take place (which direction is the RNA synthesized)?
Which direction is the template strand READ?
Describe the process that takes place during transcription.
Identify three post-transcriptional modifications that alter the pre-mRNA prior to its release from the nucleus.
What is the function of the poly-A tail?
What is the function of the GTP cap?
What is the function of RNA splicing?
How can multiple proteins be synthesized from the same mRNA transcript?
Transcription is the process by which the genetic information encoded in DNA is copied into RNA. It involves the synthesis of an RNA molecule complementary to one strand of the DNA template.
The central dogma of molecular biology states that genetic information flows from DNA to RNA to protein. This principle describes the sequential steps involved in gene expression: transcription, where DNA is transcribed into RNA, and translation, where RNA is translated into protein.
The function of mRNA (messenger RNA) is to carry the genetic information from DNA to the ribosome during protein synthesis. It serves as a template for protein translation, specifying the amino acid sequence of the protein.
The function of tRNA (transfer RNA) is to deliver amino acids to the ribosome during protein synthesis. Each tRNA molecule carries a specific amino acid and has an anticodon that recognizes the complementary codon on the mRNA.
The function of rRNA (ribosomal RNA) is to serve as structural and functional components of ribosomes, the cellular machinery responsible for protein synthesis. Ribosomes consist of rRNA molecules and proteins and facilitate the assembly of amino acids into proteins based on the sequence of mRNA.
During protein synthesis, mRNA carries the genetic code from DNA to the ribosome, where it is read and translated into a specific sequence of amino acids by tRNA molecules. Ribosomal RNA provides the structural framework for the assembly of mRNA and tRNA during translation.
The DNA sequence determines the RNA sequence through complementary base pairing. During transcription, RNA polymerase synthesizes an RNA molecule using one strand of the DNA double helix as a template, with the RNA sequence determined by the complementary base pairing rules (A-U, C-G).
RNA polymerase is an enzyme responsible for catalyzing the synthesis of RNA from a DNA template during transcription. It binds to the promoter region of the DNA and unwinds the DNA double helix, allowing RNA synthesis to proceed.
The template strand, also known as the antisense strand or noncoding strand, is the DNA strand used as a template for RNA synthesis during transcription.
Transcription takes place in the 5' to 3' direction, with RNA synthesized in the 5' to 3' direction.
The template strand is read in the 3' to 5' direction during transcription.
During transcription, RNA polymerase binds to the promoter region of the DNA and initiates RNA synthesis by unwinding the DNA double helix. RNA polymerase synthesizes an RNA molecule complementary to the template strand of the DNA. The RNA transcript undergoes post-transcriptional modifications, including capping, splicing, and polyadenylation, before it is released from the nucleus as mature mRNA.
Three post-transcriptional modifications that alter pre-mRNA include:
Addition of a 5' cap: A modified guanine nucleotide is added to the 5' end of the mRNA, which protects the mRNA from degradation and facilitates mRNA transport out of the nucleus. RNA splicing: Introns (noncoding regions) are removed from the pre-mRNA transcript, and exons (coding regions) are joined together to form mature mRNA. Addition of a poly-A tail: A stretch of adenine nucleotides is added to the 3' end of the mRNA, which protects the mRNA from degradation and plays a role in mRNA stability and translation.
The poly-A tail protects the mRNA from degradation, enhances mRNA stability, and facilitates the export of mRNA from the nucleus to the cytoplasm.
The GTP cap is added to the 5' end of the mRNA and is important for mRNA stability, mRNA export from the nucleus, and initiation of translation.
RNA splicing is the process by which introns are removed from the pre-mRNA transcript, and exons are joined together to form mature mRNA. This process occurs in the nucleus and is mediated by the spliceosome, a complex of RNA and protein molecules.
Multiple proteins can be synthesized from the same mRNA transcript through alternative splicing, where different combinations of exons are joined together to produce different mRNA isoforms. This allows for the generation of protein diversity from a single gene.
Topic 6.4: Translation
Translation, the process of synthesizing proteins from mRNA, occurs in the cytoplasm of both prokaryotic and eukaryotic cells. However, there are differences in the specifics of where translation takes place and how it affects gene expression between these two types of cells.
In prokaryotes, such as bacteria, translation occurs in the cytoplasm since they lack membrane-bound organelles like the nucleus. In contrast, in eukaryotes, translation begins in the cytoplasm but can also occur in specialized organelles called ribosomes attached to the endoplasmic reticulum (ER) or within other membrane-bound organelles.
The location of translation affects gene expression in prokaryotes because it allows for rapid response to environmental changes. Since transcription and translation can occur simultaneously in the cytoplasm, prokaryotic cells can quickly synthesize proteins in response to environmental cues without the need for processing and transport of mRNA.
The three steps of translation are initiation, elongation, and termination.
The three sites found on a ribosome are the A site (aminoacyl site), P site (peptidyl site), and E site (exit site). Their functions are as follows: A site: This is where the incoming aminoacyl-tRNA binds, carrying the next amino acid to be added to the growing polypeptide chain. P site: This is where the peptidyl-tRNA is located, holding the growing polypeptide chain. E site: This is where the uncharged tRNA exits the ribosome after its amino acid has been transferred to the growing polypeptide chain.
In the initiation step of translation, the small ribosomal subunit binds to the mRNA molecule. Then, the initiator tRNA carrying methionine binds to the start codon (usually AUG) on the mRNA.
In the elongation step of translation, amino acids are added one by one to the growing polypeptide chain. This occurs as the ribosome moves along the mRNA molecule, matching tRNA anticodon sequences with mRNA codons and catalyzing the formation of peptide bonds between amino acids.
In the termination step of translation, a stop codon (UAA, UAG, or UGA) on the mRNA enters the A site of the ribosome. This signals the end of protein synthesis, and a release factor binds to the stop codon, causing the completed polypeptide to be released from the ribosome.
The chemical process that releases the growing polypeptide from the ribosome is called hydrolysis.
Translation starts with the binding of the small ribosomal subunit to the mRNA molecule near the 5' cap in eukaryotes, or to the Shine-Dalgarno sequence in prokaryotes.
A codon is a sequence of three nucleotides on mRNA that codes for a specific amino acid or serves as a start or stop signal for protein synthesis.
There are 64 possible codons, and each codon consists of three nucleotides.
Using a codon chart:
UAU codes for the amino acid tyrosine.
Codons that code for lysine include AAA and AAG.
Multiple codons can code for the same amino acid due to redundancy in the genetic code. This redundancy is due to the fact that there are 64 possible codons but only 20 amino acids.
False. One codon codes for only one amino acid. However, multiple codons can code for the same amino acid due to redundancy in the genetic code.
The genetic code demonstrates common ancestry because it is nearly universal across all organisms, suggesting that all life on Earth shares a common evolutionary origin.
The central dogma of molecular biology states that genetic information flows from DNA to RNA to proteins.
A retrovirus violates the central dogma because it uses reverse transcriptase to transcribe its RNA genome into DNA, which is then integrated into the host cell's genome. This process involves the reverse flow of genetic information, from RNA to DNA.
Examples of retroviruses include HIV (Human Immunodeficiency Virus) and HTLV (Human T-cell Lymphotropic Virus).
The function of reverse transcriptase is to catalyze the synthesis of DNA from an RNA template.
A virus incorporates its viral genome into a host genome by integrating its DNA (produced by reverse transcriptase) into the host cell's DNA, usually through the action of viral integrase enzymes.
A virus forms progeny viruses through the assembly of viral components within the host cell, followed by the release of new virions, which can infect other cells.
Topic 6.5: Regulation of Gene Expression
What are regulatory sequences?
What is the promoter region?
What is the TATA box?
What is the enhancer region?
What are epigenetic changes?
How is DNA modified to initiate transcription (to regulate gene expression)?
How is DNA modified to inhibit transcription (to regulate gene expression)?
How are histones modified to initiate transcription (to regulate gene expression)?
How are histone modified to inhibit transcription (to regulate gene expression)?
True or False: All somatic cells have the same DNA.
What is cell differentiation?
Why can different phenotypes result from different levels of gene expression?
What is the function of transcription factors?
Regulatory sequences are specific stretches of DNA that control the expression of genes. They can either enhance or repress gene expression by binding to regulatory proteins or transcription factors.
The promoter region is a regulatory sequence located upstream of a gene that serves as the binding site for RNA polymerase and transcription factors, initiating the transcription process.
The TATA box is a specific DNA sequence (TATAAA) within the promoter region of genes that plays a crucial role in the initiation of transcription by providing a binding site for transcription factors and helping to position the RNA polymerase.
The enhancer region is a regulatory sequence that can be located upstream, downstream, or within a gene, and it enhances the transcription of genes by interacting with transcription factors and other regulatory proteins.
Epigenetic changes refer to heritable modifications in gene expression that occur without changes to the underlying DNA sequence. These changes can include DNA methylation, histone modifications, and chromatin remodeling, which can influence gene expression by affecting the accessibility of DNA to transcription machinery.
DNA is modified to initiate transcription by the addition of activating epigenetic marks, such as histone acetylation and DNA demethylation, which promote an open chromatin structure and facilitate the binding of transcription factors and RNA polymerase to the promoter region.
DNA is modified to inhibit transcription by the addition of repressive epigenetic marks, such as DNA methylation and histone deacetylation, which promote a closed chromatin structure and hinder the binding of transcription factors and RNA polymerase to the promoter region.
Histones are modified to initiate transcription by the addition of activating marks, such as histone acetylation and methylation of specific lysine residues, which loosen the chromatin structure and make the DNA more accessible to transcription machinery.
Histones are modified to inhibit transcription by the addition of repressive marks, such as histone deacetylation and methylation of specific lysine residues, which tighten the chromatin structure and restrict access to the DNA by transcription machinery.
False. While all somatic cells in an organism contain the same DNA sequence, they can have different patterns of gene expression due to epigenetic modifications and differential regulation of gene transcription.
Cell differentiation is the process by which cells become specialized in structure and function during development, allowing them to perform specific roles within an organism.
Different phenotypes can result from different levels of gene expression because gene expression levels influence the production of proteins and other molecules that determine the characteristics and functions of cells. Even small changes in gene expression can lead to significant differences in phenotype.
Transcription factors are proteins that bind to specific DNA sequences within regulatory regions of genes and control the rate of transcription by recruiting RNA polymerase and other transcriptional machinery. They play a crucial role in regulating gene expression by activating or inhibiting the transcription of target genes in response to various signals and stimuli.
An operon is a unit of genetic regulation found in prokaryotic cells consisting of a cluster of genes under the control of a single promoter. It typically includes structural genes, an operator region, and a regulatory gene.
A repressor is a protein that binds to the operator region of an operon, preventing RNA polymerase from transcribing the structural genes, thereby inhibiting gene expression.
A promoter is a DNA sequence located upstream of a gene or operon that serves as the binding site for RNA polymerase and transcription factors, initiating the transcription process.
The repressor interacts with the promoter by binding to the operator region, which is adjacent to the promoter. When the repressor is bound to the operator, it physically blocks the access of RNA polymerase to the promoter, preventing transcription of the genes in the operon.
The lac operon is an example of an inducible operon found in E. coli bacteria that controls the metabolism of lactose. It consists of three structural genes (lacZ, lacY, and lacA) encoding proteins involved in lactose metabolism, an operator region, a promoter, and a regulatory gene (lacI) encoding the lac repressor.
When lactose is present, it binds to the lac repressor, causing a conformational change that prevents the repressor from binding to the operator. As a result, RNA polymerase can access the promoter and transcribe the structural genes, leading to the metabolism of lactose.
When lactose is absent, the lac repressor binds to the operator, blocking RNA polymerase from transcribing the structural genes. This prevents unnecessary expression of genes involved in lactose metabolism when lactose is not available.
The lac operon is inducible because the presence of lactose induces the expression of the genes in the operon.
The trp operon is an example of a repressible operon found in E. coli bacteria that controls the biosynthesis of tryptophan. It consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) encoding enzymes involved in tryptophan biosynthesis, an operator region, a promoter, and a regulatory gene (trpR) encoding the trp repressor.
When tryptophan is present, it binds to the trp repressor, causing a conformational change that enables the repressor to bind to the operator. This blocks RNA polymerase from transcribing the structural genes, preventing the unnecessary synthesis of tryptophan.
When tryptophan is absent, the trp repressor cannot bind to the operator, allowing RNA polymerase to transcribe the structural genes. This leads to the synthesis of tryptophan to fulfill the cellular need.
The trp operon is repressible because the presence of tryptophan represses the expression of the genes in the operon.
Topic 6.6: Gene Expression and Cell Specialization
The function of the promoter is to serve as the binding site for RNA polymerase and transcription factors, initiating the process of transcription. It helps position the RNA polymerase at the beginning of the gene or operon, allowing it to unwind the DNA and begin transcribing the DNA sequence into RNA.
Transcription factors are proteins that regulate gene expression by binding to specific DNA sequences near the promoter region of genes. They can either activate or inhibit transcription by promoting or blocking the recruitment of RNA polymerase to the promoter, thus modulating the rate of transcription.
Transcription factors affect the binding at the promoter by binding to specific DNA sequences called enhancers or silencers, which are located either upstream or downstream of the promoter region. By binding to these regulatory sequences, transcription factors can either enhance or inhibit the binding of RNA polymerase to the promoter, thereby influencing gene expression.
The function of RNA polymerase is to catalyze the synthesis of RNA from a DNA template during the process of transcription. It unwinds the DNA double helix, reads the DNA sequence, and assembles the corresponding RNA strand by adding complementary nucleotides.
Negative regulatory molecules inhibit gene expression by blocking the binding of RNA polymerase to the promoter or by interfering with the activity of transcription factors. For example, repressor proteins can bind to the operator region near the promoter, preventing RNA polymerase from initiating transcription. Additionally, negative regulatory molecules can modify the chromatin structure or recruit chromatin-modifying enzymes to inhibit access to the promoter, thereby suppressing gene expression.
What is differential gene expression?
How can differential gene expression affect the cellular products?
How can differential gene expression affect the cellular functions?
What is siRNA?
What is mrRNA?
How do siRNA and miRNA affect gene expression?
Differential gene expression refers to the phenomenon where different genes are expressed at varying levels in different cell types, at different developmental stages, or in response to environmental cues. It is a fundamental mechanism that allows cells to specialize and perform specific functions.
Differential gene expression can affect cellular products by determining the types and amounts of proteins and other gene products produced by a cell. For example, cells with high expression of genes involved in insulin production will produce more insulin, while cells with low expression of those genes will produce less insulin.
Differential gene expression can affect cellular functions by influencing the activities of proteins and other gene products that are essential for various cellular processes. For instance, cells with high expression of genes involved in cell division will have a higher rate of proliferation compared to cells with low expression of those genes.
siRNA (small interfering RNA) is a class of double-stranded RNA molecules that can regulate gene expression by targeting specific mRNA molecules for degradation or by inhibiting their translation. siRNAs are typically introduced into cells exogenously or are generated endogenously from longer double-stranded RNA precursors.
mRNA (messenger RNA) is a single-stranded RNA molecule that carries the genetic information from DNA to the ribosome, where it is translated into protein. mRNA molecules are transcribed from genes and undergo various modifications before being translated into protein.
Both siRNA and miRNA (microRNA) can affect gene expression by binding to complementary sequences on target mRNA molecules. This binding can lead to mRNA degradation or translational repression, thereby reducing the levels of specific proteins encoded by the targeted genes. While siRNAs are typically exogenous and derived from longer double-stranded RNA precursors, miRNAs are endogenously produced small RNA molecules that regulate gene expression as part of the cell's natural regulatory machinery.
Topic 6.7: Mutations
The genotype influences the phenotype through the expression of genes and the interactions between genes and the environment. The genotype refers to an individual's genetic makeup, including alleles inherited from parents, whereas the phenotype refers to the observable traits or characteristics of an organism, such as physical appearance, behavior, and biochemical properties.
New phenotypes can originate through various mechanisms, including mutations, genetic recombination, and changes in gene regulation. Mutations, in particular, introduce changes to the DNA sequence, leading to alterations in gene expression or protein function, which can result in novel phenotypic traits.
Mutations can affect gene products by altering the amino acid sequence of proteins, changing protein structure or function, or affecting the level of gene expression.
The three types of substitution point mutations are:
Silent mutations: These mutations do not result in any change to the amino acid sequence of the protein. They occur when the mutated codon still codes for the same amino acid due to the redundancy of the genetic code.
Missense mutations: These mutations result in the substitution of one amino acid for another in the protein sequence. This can alter protein structure and function, depending on the specific amino acid change.
Nonsense mutations: These mutations result in the conversion of a codon that encodes an amino acid into a premature stop codon. This leads to the premature termination of protein synthesis, resulting in a truncated, often non-functional protein.
Each type of substitution point mutation can affect the protein product differently. Silent mutations typically have no effect on the protein product or its function. Missense mutations can alter protein structure and function to varying degrees, depending on the specific amino acid change and its location within the protein. Nonsense mutations usually result in the production of a truncated protein that is non-functional. Mutations such as insertions or deletions at a nucleotide base pair can cause a frameshift mutation, where the reading frame of the mRNA sequence is altered. This can lead to changes in the amino acid sequence downstream of the mutation, potentially resulting in a non-functional protein. Additionally, insertions or deletions can also lead to premature stop codons, resulting in truncated protein products.
Mutations can have a neutral effect on the protein product if they occur in non-coding regions of the gene or if they result in synonymous codons that do not alter the amino acid sequence of the protein. In such cases, the mutation does not affect protein structure or function.
A mutation can have a positive effect on the protein product if it confers a selective advantage, such as increased protein function or efficiency, improved adaptation to environmental conditions, or resistance to pathogens.
A mutation can have a negative effect on the protein product if it impairs protein structure or function, leading to loss of protein activity, dysfunction, or disease. Negative effects can include loss of enzyme activity, disruption of protein-protein interactions, or interference with protein folding and stability.
Errors in DNA replication can be caused by various factors, including:
DNA polymerase errors: DNA polymerase can occasionally make mistakes during DNA synthesis, leading to mismatches or insertion/deletion errors in the newly synthesized DNA strand.
Environmental factors: Exposure to mutagenic agents such as UV radiation, chemicals, and certain drugs can induce DNA damage, including nucleotide modifications or strand breaks, which can lead to replication errors.
Replication fork stalling: DNA replication forks can encounter obstacles or damage, such as DNA lesions or secondary structures, which can result in replication fork stalling and errors in DNA replication.
Replication slippage: During replication, DNA polymerase can slip or loop out, leading to the insertion or deletion of repetitive sequences, particularly in regions with repetitive DNA sequences.
Spontaneous DNA damage: Spontaneous hydrolysis or deamination of nucleotides, as well as oxidative damage, can occur naturally and result in errors during DNA replication.
The cell's DNA repair mechanisms include several pathways to correct errors and damage in DNA, such as:
Mismatch repair: Corrects errors that occur during DNA replication, such as mismatches or small insertion/deletion loops.
Nucleotide excision repair: Removes bulky lesions or distortions in the DNA helix, such as those caused by UV radiation or chemical carcinogens.
Base excision repair: Repairs damaged or modified bases, such as those resulting from oxidation or deamination.
Double-strand break repair: Fixes breaks in both strands of the DNA double helix, which can occur spontaneously or due to external factors.
Mutations can be detrimental if they disrupt essential cellular processes, impair protein function, or lead to diseases or disorders. For example, mutations in tumor suppressor genes or oncogenes can contribute to cancer development. Mutations can be beneficial if they confer a selective advantage, such as improved adaptation to environmental conditions, resistance to pathogens, or increased reproductive success. Mutations can be neutral if they occur in non-coding regions of the genome, do not affect gene function or protein structure, or if they result in synonymous codons that do not change the amino acid sequence of the protein.
New genetic variation arises through mechanisms such as mutation, genetic recombination during meiosis, and horizontal gene transfer. Mutation is a primary source of genetic variation by introducing new alleles and altering existing ones within a population.
An error in mitosis that leads to a change in phenotype could be nondisjunction, where chromosomes fail to separate properly during cell division, resulting in an abnormal chromosome number in daughter cells. This can lead to conditions such as trisomy or monosomy, which can affect phenotype.
An error in meiosis that leads to a change in phenotype could also be nondisjunction during meiosis I or II, resulting in gametes with an abnormal chromosome number. When fertilization occurs with one of these abnormal gametes, it can lead to conditions such as trisomy or monosomy in the offspring.
An organism that is triploid has three sets of chromosomes instead of the usual two sets (diploid). Triploidy can arise due to errors in chromosome segregation during meiosis or fertilization, resulting in the presence of an extra set of chromosomes in the genome.
Triploid organisms are usually sterile because they have an odd number of chromosome sets, leading to problems with chromosome pairing and segregation during meiosis, which can result in the production of inviable or non-functional gametes.
Down syndrome, also known as Trisomy 21, is caused by the presence of an extra copy of chromosome 21, typically resulting from nondisjunction during meiosis I in one of the parents.
Turner syndrome is caused by the complete or partial absence of one of the X chromosomes in females, typically resulting from nondisjunction during meiosis in one of the parents.
A change in genotype can affect the phenotype by altering the expression of genes or the structure and function of proteins encoded by those genes. Genotype refers to the genetic makeup of an organism, while phenotype refers to the observable traits or characteristics of an organism. Changes in the DNA sequence, such as mutations, genetic recombination, or epigenetic modifications, can lead to changes in gene expression, protein structure, or cellular processes, ultimately resulting in phenotypic variation.
False. Natural selection acts on phenotypes, not genotypes. It is the process by which organisms with traits that confer advantages in a particular environment tend to survive and reproduce more successfully than those without such traits. Over time, natural selection can lead to changes in allele frequencies within a population, as individuals with advantageous phenotypes are more likely to pass on their genes to the next generation.
Natural selection affects phenotypes by favoring traits that enhance survival and reproductive success in a given environment. Individuals with advantageous phenotypes are more likely to survive, reproduce, and pass on their genes to future generations, leading to an increase in the frequency of those traits within the population over time.
Natural selection affects genotypes indirectly by influencing the frequency of alleles that code for advantageous phenotypic traits. As individuals with advantageous phenotypes reproduce more successfully, the alleles responsible for those traits become more prevalent in the population over successive generations.
A genetic change can enhance survival if it confers a selective advantage, such as increased adaptation to environmental conditions, improved ability to acquire resources, resistance to pathogens or predators, or increased reproductive success. Such changes increase an organism's chances of surviving and reproducing in its environment, leading to the propagation of the advantageous genetic variation within the population.
Horizontal transfer, also known as lateral gene transfer, is the transfer of genetic material between different organisms that are not parent and offspring. It can occur through mechanisms such as transformation, transduction, conjugation, and transposition.
Horizontal transfer increases variation by introducing new genetic material into a recipient organism's genome, potentially providing novel traits or adaptive advantages. This can lead to increased genetic diversity within a population or even across different species.
Transformation is the process by which a bacterium takes up free DNA from its environment and incorporates it into its own genome, potentially acquiring new genetic traits.
Transduction is a process in which genetic material is transferred from one bacterium to another by a bacteriophage (a virus that infects bacteria) during the viral replication cycle.
Conjugation is a mechanism of horizontal gene transfer in bacteria where genetic material is transferred directly from one bacterium to another through physical contact facilitated by a conjugation pilus. This process typically involves the transfer of plasmids, which can carry genes encoding antibiotic resistance or other adaptive traits.
Transposition is the movement of genetic elements, such as transposable elements or transposons, within a genome. These elements can insert themselves into new locations within the genome, potentially altering gene expression or causing mutations.
Viruses can recombine genetic information through processes such as reassortment or recombination during viral replication. These mechanisms involve the exchange or mixing of genetic material between different viral strains, leading to the generation of new viral variants with potentially altered phenotypic traits.
Reproductive processes that increase genetic variation include sexual reproduction, meiosis, and genetic recombination. These processes shuffle and recombine genetic material between individuals, leading to the production of genetically diverse offspring with unique combinations of alleles.
Topic 6.8: Biotechnology
Genetic engineering is used to analyze DNA by various methods such as gel electrophoresis, polymerase chain reaction (PCR), bacterial transformation, and DNA sequencing.
Genetic engineering is a powerful tool used to manipulate DNA in various ways. Some common techniques and methods used in genetic engineering to manipulate DNA include:
Recombinant DNA technology: This involves the insertion of DNA fragments from one organism into the DNA of another organism, resulting in the creation of recombinant DNA molecules. Recombinant DNA technology allows for the manipulation of specific genes or genetic elements to alter or introduce desired traits in organisms.
Gene cloning: Gene cloning involves the isolation and amplification of specific DNA sequences using techniques such as polymerase chain reaction (PCR) or restriction enzyme digestion and ligation. Cloning allows researchers to produce multiple copies of a gene of interest for further analysis or manipulation.
Gene editing: Gene editing techniques, such as CRISPR-Cas9, allow for precise modifications to be made to the DNA sequence of an organism. CRISPR-Cas9 can be used to insert, delete, or alter specific DNA sequences, enabling targeted genetic modifications with high efficiency and precision.
Site-directed mutagenesis: This technique allows for the introduction of specific mutations into a DNA sequence at desired locations. Site-directed mutagenesis can be used to study the effects of specific mutations on gene function or to engineer proteins with altered properties.
DNA synthesis: Advances in DNA synthesis technology enable the synthesis of custom-designed DNA sequences, including entire genes or genetic elements. Synthetic DNA can be used to create novel genes, genetic circuits, or synthetic organisms with desired traits.
Gene knockout: Gene knockout involves the targeted disruption or inactivation of a specific gene within an organism's genome. This can be achieved using techniques such as homologous recombination, CRISPR-Cas9-mediated gene editing, or RNA interference (RNAi). Gene knockout studies are valuable for understanding gene function and the effects of gene loss on phenotype.
Gene insertion: Gene insertion involves the introduction of foreign DNA sequences into an organism's genome to add new traits or functions. This can be achieved using viral vectors, plasmid DNA, or other delivery methods to transfer the desired DNA sequence into the host organism's cells.
Gel electrophoresis is a technique used to separate DNA fragments based on their size and charge. DNA molecules are loaded onto a gel matrix and subjected to an electric field, causing them to migrate through the gel. Smaller DNA fragments move faster and travel farther through the gel than larger fragments. Gel electrophoresis is used to visualize and analyze DNA fragments, such as those obtained from PCR reactions, restriction enzyme digests, or genomic DNA samples. It allows researchers to determine the size of DNA fragments, assess the purity of DNA samples, and analyze genetic variation or mutations. Gel electrophoresis should be done, for example, when analyzing PCR products to verify successful amplification, when determining the size of DNA fragments after restriction enzyme digestion, or when examining genetic polymorphisms in DNA samples.
PCR (polymerase chain reaction) is a technique used to amplify specific DNA sequences from a complex mixture of DNA. It involves repeated cycles of DNA denaturation, primer annealing, and DNA synthesis using a DNA polymerase enzyme. PCR is used to amplify DNA fragments for various applications, such as cloning, sequencing, genetic testing, and forensic analysis. It allows researchers to generate large quantities of specific DNA sequences from minimal starting material. PCR should be done, for example, when amplifying a target gene for cloning, when detecting pathogens or genetic mutations in clinical samples, or when analyzing DNA from ancient or degraded specimens.
Bacterial transformation is a technique used to introduce foreign DNA into bacterial cells. It involves the uptake and incorporation of exogenous DNA, often in the form of plasmids, by competent bacterial cells.
Bacterial transformation allows researchers to genetically engineer bacteria for various purposes, such as gene expression studies, protein production, or the creation of genetically modified organisms (GMOs).
During bacterial transformation, foreign DNA is introduced into bacterial cells, where it may integrate into the bacterial genome or exist as extrachromosomal DNA (plasmids). Transformed cells are selected and identified based on antibiotic resistance markers or other selectable traits encoded by the introduced DNA.
Bacterial transformation should be done, for example, when introducing a gene of interest into bacteria for protein expression, when creating bacterial strains with specific genetic modifications, or when studying gene function in bacterial systems.
DNA sequencing is a technique used to determine the precise order of nucleotides in a DNA molecule. It involves sequencing a DNA template using methods such as Sanger sequencing or next-generation sequencing (NGS). DNA sequencing provides information about the sequence of nucleotides in a DNA molecule, allowing researchers to identify genes, detect mutations, characterize genetic variation, or analyze genomic structures. During DNA sequencing, the DNA molecule is enzymatically or chemically fragmented, and the sequence of nucleotides is determined by synthesizing complementary DNA strands or detecting fluorescently labeled nucleotides. DNA sequencing should be done, for example, when determining the genetic basis of a disease or disorder, when characterizing the genome of an organism, or when studying the evolutionary relationships between species.
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 1 -
Name _______________________ Period ___________
Chapter 17: From Gene to Protein
This is going to be a very long journey, but it is crucial to your understanding of biology. Work on this
chapter a single concept at a time, and expect to spend at least 6 hours to truly master the material. To
give you an idea of the depth and time required, we have spent over 5 hours writing this Reading
Guide! You will need even longer to complete it and learn the information. Good luck, and take your
time.
Overview
1. What is gene expression?
Concept 17.1 Genes specify proteins via transcription and translation
2. What situation did Archibald Garrod suggest caused inborn errors of metabolism?
3. Describe one example Garrod used to illustrate his hypothesis.
4. State the hypothesis formulated by George Beadle while studying eye color mutations in
Drosophila.
5. What strategy did Beadle and Tatum adopt to test this hypothesis?
6. Which organism did Beadle and Tatum use in their research? How did this organism’s
nutritional requirements facilitate this research?
7. How were Neurospora spores treated to increase the mutation rate?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 2 -
8. Study Figure 17.2 carefully. On the figure below, outline the technique used to identify and
isolate mutant fungi.
9. Cite two significant findings that resulted from the research of Beadle and Tatum.
10. What revision of detail (but not of basic principle) did this hypothesis undergo as more
information was gained? Write this restatement and then box or highlight it. This is an
important concept!
Basic Principles of Transcription and Translation
This section will introduce you to the processes and associated terminology in the form of an
overview. Once you have the big picture, you will take a closer look in the next few concepts.
11. From the first paragraph in this section, find three ways in which RNA differs from DNA.
12. What are the monomers of DNA and RNA? Of proteins?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 3 -
13. Define each of these processes that are essential to the formation of a protein:
transcription
translation
14. Complete the following table to summarize each process.
Template Product Synthesized Location in Eukaryotic Cell
Transcription
Translation
15. In eukaryotes, what is the pre-mRNA called?
16. Write the central dogma of molecular genetics, as proclaimed by Francis Crick, in the box
below.
17. How many nucleotide bases are there? _______________ How many amino acids?
__________
18. How many nucleotides are required to code for these 20 amino acids? ___________________
19. So, the language of DNA is a triplet code. How many unique triplets exist? ______________
20. DNA is double-stranded, but for each protein, only one of these two strands is used to produce
an mRNA transcript. What is the coding strand called?
21. Here is a short DNA template. Below it, assemble the complementary mRNA strand.
3'A C G A C C A G T A A A 5'
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 4 -
22. How many codons are there above? ________ Label one codon.
23. Describe Nirenberg’s experiment in which he identified the first codon.
24. What was the first codon–amino acid pair to be identified? __________________________
25. Of the 64 possible codons, how many code for amino acids? _________________________
26. What event is coded fro by UAA, UAG and UGA? ________________________________
27. What is the start codon? ____________________________________________________
28. Why is the genetic code said to be redundant but not ambiguous?
29. Explain the concept of reading frame.
30. Now here is an important idea: DNA is DNA is DNA. By this we mean that the code is nearly
universal, and because of this, jellyfish genes can be inserted into pigs, or firefly genes can
make a tobacco plant glow. Enjoy a look at Figure 17.6 in your text . . . and no question to
answer here!
Concept 17.2 Transcription is the DNA-directed synthesis of RNA: A closer look
31. Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand.
32. You will recall from Chapter 16 that DNA polymerase III adds new nucleotides to the template
DNA strand to assemble each new strand of DNA. Both enzymes can assemble a new
polynucleotide only in the 5' Æ direction. Which enzyme, DNA polymerase III or RNA
polymerase, does not require a primer to begin synthesis?
33. What is a transcription unit?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 5 -
34. Figure 17.7 in your text will require a bit of study. Use it to label the following elements on the
figure below: promoter, RNA polymerase, transcription unit, DNA template, nontemplate DNA,
and RNA transcript. Then, to the right of the figure, name the three stages of transcription and
briefly describe each stage.
35. Let’s now take a closer look at initiation. Read the paragraph titled “RNA Polymerase Binding
and Initiation of Transcription” carefully. List three important facts about the promoter here.
(1)
(2)
(3)
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 6 -
36. Use Figure 17.8 in your text to label the following elements of the figure below: TATA box,
RNA polymerase II, transcription factors, template DNA strand, start point, 5' and 3', and
mRNA transcript. To the right of the figure, explain the three stages of initiation that are shown.
37. What is the TATA box? How do you think it got this name?
38. What comprises a transcription initiation complex?
39. Now it is time to put all of the elements of transcription together. Write an essay below to
describe the process by which mRNA is formed. Use these terms correctly in your essay, and
underline each one: TATA box, gene, terminator, promoter, elongation, 5’ to 3', termination,
initiation RNA, polymerase RNA nucleotides, template, start point, termination signal, and
transcription factors. This essay is typical of what you might be asked to write on the AP
Biology exam.
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 7 -
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
__________________________________________________________________________________
Concept 17.3 Eukaryotic cells modify RNA after transcription
40. RNA processing occurs only in eukaryotic cells. The primary transcript is altered at both ends,
and sections in the middle are removed.
a. What happens at the 5' end?
b. What happens at the 3' end?
41. What are three important functions of the 5' cap and poly-A tail?
42. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are
expressed.
43. On the figure below, label: pre-mRNA, 5' cap, poly-A tail, introns, and exons.
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 8 -
44. What are snRNPs? What two types of molecules make up a snurp? (We like the word snurp! It
reminds us of little cartoon characters that wore blue hoods and were called smurfs.
45. You will be introduced to a number of small RNAs in this course. What type is the RNA in a
snRNP?
46. Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work?
47. On the figure below, label the following: pre-mRNA, snRNPs, snRNA, protein, spliceosomes,
intron, and other proteins.
48. Study the figure and text carefully to explain how the splice sites are recognized.
49. What is a ribozyme?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 9 -
50. What commonly held idea was rendered obsolete by the discovery of ribozymes?
51. What are three properties of RNA that allow it to function as an enzyme?
(1)
(2)
(3)
52. What is the consequence of alternative splicing of identical mRNA transcripts?
Concept 17.4 Translation is the RNA-directed synthesis of a polypeptide: A closer look
53. You may need to read on in this section in order to answer this question as well as think back to
earlier information about mRNA. Come back to this question later if you wish. Three types of
RNA are needed for protein synthesis. Complete the chart below.
Type of RNA Description Function
mRNA
tRNA
rRNA
54. What is an anticodon?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 10 -
55. Transfer RNA has two attachment sites. What binds at each site? Sketch tRNA, indicate the 2
attachment sites, and note where complementary base pairing and hydrogen bonding occur to
give tRNA its shape.
56. How many different aminoacyl-tRNA synthetases are there? ____________________________
57. Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have been
discovered. How does wobble explain this?
58. Use the figure below to explain the process of a specific amino acid being joined to a tRNA.
Also add these labels: aminoacyl-tRNA synthetase, ATP, amino acid, and tRNA.
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 11 -
59. Describe the structure of a eukaryotic ribosome.
60. How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical
significance of this difference?
61. On this figure, label the large subunit, small subunit, A, P, and E sites, mRNA binding site. To
the right of the figure, explain the functions of the A, P, and E sites.
62. Much like transcription, we can divide translation into three stages. List them.
63. Summarize the events of initiation. Include these components: small ribosomal subunit, large
ribosomal subunit, mRNA, initiator codon, tRNA, Met, initiation complex, P site, and GTP. The
figure below may help you.
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 12 -
64. What is always the first amino acid in the new polypeptide?
65. Now, summarize the events of elongation. Include these components: mRNA, A site, tRNA,
codon, anticodon, ribozyme, P site, and E site. Again, the figure may help you.
66. What is a release factor? By what mechanism is termination accomplished?
67. What is a polyribosome?
68. What are some of the things that will result in a final-form functional protein?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 13 -
69. Describe at least three types of post-translational modifications.
70. Use the following figure to explain how proteins are targeted for the ER.
Concept 17.5 Point mutations can affect protein structure and function
71. Define a mutation in terms of molecular genetics.
72. Define point mutations.
73. What are frameshift mutations?
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 14 -
74. Identify two mechanisms by which frameshifts may occur.
75. What is the difference between a nonsense and missense mutation?
76. How can a base-pair substitution result in a silent mutation?
77. What are the two categories of mutagens?
78. Describe the action of difference types of chemical mutagens.
Concept 17.6 Although gene expression differs among the domains of life, the concept of a gene is
universal
79. Describe two important ways in which bacterial and eukaryotic gene expression differ.
80. What is a gene? It used to be simply stated that one gene codes for one polypeptide. That
definition has now been modified. Write below the broader molecular definition in use today.
AP Biology Reading Guide Chapter 17: From Gene to Protein
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 15 -
81. Finally, use this summary figure to put together all that you have learned in this chapter.
Testing Your Knowledge: Self-Quiz Answers
Now you should be ready to test your knowledge. Place your answers here:
1. __________2.__________3. __________4. __________5. __________6. __________7. _________
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 1 -
Name_______________________ Period___________
Chapter 20: Biotechnology
The AP Biology exam has reached into this chapter for essay questions on a regular basis over the past
15 years. Student responses show that biotechnology is a difficult topic. This chapter requires a strong
conceptual understanding of the technological processes and the underlying biology that guides the
procedure. With a little careful work, this chapter will give you insights into the incredible
advancements already made and a basis for understanding the new marvels yet to be discovered in
biotechnology.
Overview
1. It is important to understand the meaning of the three terms in bold to start this chapter.
recombinant DNA
biotechnology
genetic engineering
Concept 20.1 DNA cloning yields multiple copies of a gene or other DNA segment
2. Plasmids are important in biotechnology. Give a full and complete definition of plasmid.
3. The production of multiple copies of a single gene is called ____________________________.
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 2 -
4. Using Figure 20.2, label and explain the four steps in this preview of gene cloning.
5. Read the description of restriction enzymes on page 398 carefully. Then draw and explain each
step of Figure 20.3. When you finish, you should have recreated Figure 20.3 in the space
below.
6. What is a cloning vector?
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 3 -
7. Figure 20.4 is a more detailed discussion of the gene cloning procedure shown in Figure 20.2.
Explain the following key points.
a) Explain why the plasmid is engineered with amp
R and lacZ.
b) After transformation has occurred, why are some colonies blue?
c) Why are some colonies white? Why is this important?
8. The cloning procedure described in question 7 and Figure 20.4 will produce many different
fragments of hummingbird DNA. These fragments may be stored in a genomic library.
a) What is the purpose of a genomic library?
b) Explain how a bacterial artificial library (BAC) and a cDNA library are formed.
9. Once the hummingbird DNA is cloned, we have the problem of finding the piece of DNA that
holds our gene of interest. Explain how nucleic acid hybridization will accomplish this task.
10. Describe how a radioactively labeled nucleic acid probe can locate the gene of interest on a
multiwell plate. (Use Figure 20.7 to guide your response.)
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 4 -
11. What are two problems with bacterial gene expression systems?
12. The polymerase chain reaction (PCR) is a Nobel Prize–winning idea that is used by scientists
to amplify DNA, particularly when the quantity of DNA is very small or contaminated. Explain
the three initial steps that occur in cycle 1 of PCR.
13. How many molecules will be produced by four PCR cycles?
Concept 20.2 DNA technology allows us to study the sequence, expression, and function of a gene
This section begins with a discussion of gel electrophoresis, a technique covered in AP Biology Lab 6.
It is important to understand the principles of gel electrophoresis.
14. ____________________ is a technique used to separate nucleic acids or proteins that differ in
size or electrical charge.
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 5 -
15. Why is the DNA sample to be separated by gel electrophoresis always loaded at the cathode
or negative end of the power source?
16. Explain why shorter DNA molecules travel farther down the gel than larger molecules.
17. To the right of the β-globin alleles, draw a gel showing the different pattern obtained from a
normal patient and a sickle-cell patient. For help, examine Figure 20.10.
18. A patient who is a carrier for sickle-cell anemia would have a gel electrophoresis pattern
showing four bands. Add this pattern to your gel in number 17 and explain why the gel shows a
four-band pattern.
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc.
19. What is the purpose of a Southern blot?
20. What two techniques discussed earlier in this chapter are used in performing a Southern blot?
21. In working toward the general idea of how DNA sequencing was mechanized, look at Figure
20.12 to answer the following general questions about the dideoxy chain termination method
for sequencing DNA.
a) Why does a dideoxyribonucleotide terminate a growing DNA strand? (You may need to
refer to Figure 16.14, as suggested in the text, to answer this question).
b) Why are the four nucleotides in DNA each labeled with a different color of fluorescent
tag?
Use unlabeled Figure 20.15 to explain the four steps of DNA microarray assays.
- 6 -
(1)
(2)
(3)
(4)
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 7 -
22. Explain how microarrays are used in understanding patterns of gene expression in normal and
cancerous tissue.
Concept 20.3 Cloning organisms may lead to production of stem cells for research and other
applications
23. What is a totipotent cell?
24. How is nuclear transplantation performed in animals?
25. Use unlabeled Figure 20.18 to explain the six steps in reproductive cloning for mammals.
(1)
(2)
(3)
(4)
(5)
(6)
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 8 -
26. What are stem cells?
27. What is the major difference between embryonic stem cells (ES) and adult stem cells?
28. How might induced pluripotent stem cells (iPS) resolve the debate about using stem cells for
medical treatments?
Concept 20.4 The practical applications of DNA technology affect our lives in many ways
29. In question 17, you used two ideas that are featured in the first part of this concept. Explain
how single-nucleotide polymorphisms (SNPs) and restriction fragment length polymorphisms
(RFLPs) were demonstrated in analyzing sickle-cell alleles.
30. Explain the idea of gene therapy, and discuss the problems with this technique as demonstrated
in the treatment of SCID.
31. Explain how transgenic “pharm” animals might be able to produce human proteins.
AP Biology Reading Guide Chapter 20: Biotechnology
Fred and Theresa Holtzclaw
Copyright © 2010 Pearson Education, Inc. - 9 -
32. Describe how short tandem repeats can produce a sensitive genetic profile.
33. How does the Ti plasmid make genetic engineering in plants a possibility?
34. What are genetically modified organisms, and why are they controversial?
Testing Your Knowledge: Self-Quiz Answers
Now you should be ready to test your knowledge. Place your answers here:
1._______2._______3._______4._______5._______6._______7._______ 8._______
9. Use the space below for the drawing.