Assignment Prompt & Instructions
Answer all questions
– ## Genetic.docx
**## Genetic.docx**
_BIOL-2416 Baggett – Unit 04 – Study Tips_
## Study Suggestions for Exam #4 over Chapters 14-16 & 18
### General Exam Format and Information
**What to bring:** knowledge and understanding, your signed 4×6 notecard, at least 2 sharpened pencils and a calculator if you have one (can borrow from me if needed during exam, but no phones allowed)
**The exam will be administered from 6:00 p.m. to 8:00 p.m.** **No need to return after the exam this time**.
**Question breakdown** (test total is 100 points)
·
**40 regular multiple-choice questions** (2 pts each x 40 = 80 pts)
· 4 chapters is ~8-12 questions per chapter for Ch. 14, 15, 16 and 18
· you should go back and review the cell cycle (Ch. 2), chromosome mapping (Ch.5), chromosome structure and variation (Ch.6) and bacterial plasmids, transformation and immune-like defense (Ch. 7) as you study this unit since must of this content builds on topics from those chapters.
· 2 or 3 of the multiple-choice questions will be from Genetics in Practice openers
·
**3 short essay questions** (5-8 pts each)
**plus 1 bonus short essay question** –
***For this exam, I have noted the concept most likely to show up in the short essay questions for you (see chapter headings)**
### Topics and Key Terms by Chapter –
#### What to Study for Chapter 14 – _expect a short essay on combined: #5, #6 and #10_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**recombinant DNA, transgenic organism, nuclease, agarose, methylene blue, ethidium bromide (EtBr), SYBR Green, anneal / annealing, primer, antibiotic, antibiotic resistance**
3. Describe the normal cellular origin and role of
**restriction enzymes**, what types of sequences they recognize, how they cut DNA and what scientists use them for in the laboratory
3.1. Distinguish between the type of cut that makes a cohesive (sticky) end versus a
**blunt end**.
3.2. Identify which restriction enzymes will produce larger fragments (cut less often) based on length of the
**recognition sequence.**
_**You will NOT be tested on the engineered nuclease section (no questions on this)._
4. For
**CRISPR-Cas** systems:
4.1. Describe the normal cellular origin and role of CRISPR-Cas systems, how they know which sequences to recognize (
**crRNA**), which part has nuclease activity to cut the DNA
4.2. Explain how scientists have engineered this system to cut and modify any specific sequence they desire, including what
**sgRNA** is and how
**Non-Homologous End-Joining (NHEJ)** and
**Homology Directed Repair** (
**HDR**) enzymes are involved.
5. Explain what
**gel electrophoresis** is, what creates the gel matrix for DNA gels and how we use it to separate and visualize DNA.
6. Describe the three steps of
**Polymerase Chain Reaction (PCR)**, including why they are repeated, how primers are involved, where they bind (why just
_outside_ the region you want to amplify?) & the key role of
**_Taq_ polymerase.**
7. Define “
**gene cloning**” and describe the 3 requirements for any
**cloning vector** to work
7.1. Identify key characteristics of
**plasmid vectors**, the basic
**transformation** process and the two common hosts scientists use by the scientific names (which specific bacteria and yeast from Ch. 1)
7.2. Describe the unique characteristics of
**expression vectors** and how scientists obtain eukaryotic DNA that can be used with them (see next item)
8. Describe how a
**DNA library** is made, stored and the differences between making and using a
**genomic library** versus a
**cDNA library**
9. Describe how
**Sanger sequencing** (
**dideoxy sequencing**) works and what is special about dideoxy nucleotides (
**ddNTPs**) that allows them to be used in this method.
10. Describe
**microsatellites**(
**short tandem repeats, STRs**) in DNA and explain how they are used in DNA fingerprinting or profiling to identify DNA samples.
_Be able to relate this to #5 and #6 in a complete crime scene analysis procedure._
11. Define or recognize examples of
**forward genetics** versus
**reverse genetics** methodologies.
#### What to Study for Chapter 15 – _likely no short essay on this chapter since Ch. 18 has two_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Differentiate between
**genomics** and
**proteomics**.
2.1. Describe the differences between the
**Human Genome Project (HGP)** and the
**Human Proteome Project (HPP)** in both their purpose and who they are examining humans (HGP focused on humans as whole organisms, while HPP is looking at different cell types
_within_ humans)
2.2. Define
**structural genomics** and
**functional** genomics in relation to these two terms.
3. Describe the approach to sequencing a complex genome that ended up working for the HGP, including the role of
**genetic linkage mapping, physical mapping, map-based sequencing** and whole genome
**shotgun sequencing.**
_**You will NOT be tested on NextGen or newer sequencing methods (no questions on this)._
4. Describe what a
**Single Nucleotide Polymorphism (SNP)** is and why a single SNP does not provide much information about a person or group of people, but a
**haplotype** can.
4.1. Explain how a
**Genome-Wide Association Study (GWAS)** uses genome sequence and SNP information to being to analyze possible causes of a genetic condition, including the limitations of these studies.
5. Identify the interdisciplinary fields involved in
**bioinformatics** and why.
6. Describe what
**metagenomics** is and that it primarily focuses on microbial communities (and why helpful there)
_**You will NOT be tested on using BLAST to analyze homologues or orthologs or RNA-seq (no questions on this)._
7. Describe what a
**microarray** is and how it is used by scientists to analyze gene expression differences between cell types or groups of individuals to identify genes involved in a process (such as cancer patients or developmental changes)
8. For
**comparative genomics**, review and be able to discuss basic features of prokaryotic versus eukaryotic genomes (general size of genome, # of genes and gene “density”) and the impact of
**transposons** in repetitive DNA in eukaryotic genomes.
#### What to Study for Chapter 16 – _expect a short essay on combined #3, #4 and #6_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**cell cycle checkpoints, contact inhibition, density dependent inhibition, metastasis / metastasize / metastatic, benign, malignant**
3. Describe the primary characteristics of
**cancer** (differentiating it from normal cells) and explain why it is a
_group_ of genetic diseases, not just one.
4. Explain why cancer is not typically inherited and why most non-inherited cancer arises later in life rather than in young people
5. Identify the environmental factor that contributes
**_most_** to the development of cancer (
**tobacco**) as well as the relative
**_overall impact_** of environmental factors on cancer development (
**around 40%** of cancer cases).
6. Describe how cancer develops, including what
**clonal evolution** means and the genetic changes involved in developing a
**tumor**, how it becomes
**malignant** and how
**metastasis** occurs.
7. Identify what the proteins encoded by
**proto-oncogenes** normally do in the cell and why mutations in these genes are often dominant alleles (why are most
**oncogenes** dominant?)
7.1. Recognize the proto-oncogene example
**_ras_** has an oncogene mutant version present in 1/3 of all tumors
8. Identify what roles the proteins encoded by
**tumor suppressor genes** normally play in the cell and why mutations in these genes are often recessive
8.1. Recognize the key examples of tumor suppressor genes discussed and their normal functions:
**p53**,
**RB**,
**BRCA1** (and not listed in chart, but there is also a BRCA2 with similar function)
8.2. Explain what
**haploinsuffiency** is and how it might affect a heterozygote who inherited one knock-out allele for a tumor suppressor gene
8.3. Describe how inheriting one knock-out allele for a tumor suppressor gene might lead to increased development of cancer even though the allele is recessive (i.e. explain
**loss of heterozygosity** cause & effect)
_**You will NOT be tested on cyclins and cdks, though I may mention them in a question, so recognize that they are involved in checkpoints and forward/stop signals so you aren’t confused by the mention._
9. Describe how
**retinoblastoma (Rb) cancer** develops, including which cell cycle checkpoint fails (G1-to-S) and what the
**2-hit hypothesis** explains about inherited versus sporadic (non-inherited) retinoblastoma tumors (which are almost always
**unilateral** and which are often
**bilateral** and why).
10. Recognize and identify the role of secondary mutations in genes for
**telomerase**,
**angiogenesis** and
**cytoskeletal** and
**ECM structure** as well as
**aneuploidy** and large chromosomal mutations on tumor development and cancer progression.
11. Identify the 2 key ways that
**viruses**, especially
**retroviruses** like HPV, can cause cancer after infection.
#### What to Study for Chapter 18 – _expect a short essay on #3_ _or #5 AND also on #7, including 7.1_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**evolution, gene pool, genotypic frequency, allelic frequency, pre-zygotic, post-zygotic, speciation**
3. Calculate genotypic and allelic frequencies for an autosomal locus with two alleles given population information (total number of individuals and number of individuals with each phenotype).
4. Describe the
**Hardy-Weinberg law** (i.e. equations) and the conditions required for
**genetic** **equilibrium** to exist in a population.
5. Apply the predictions of the Hardy-Weinberg law to calculate genotypic and allelic frequencies for populations in HW equilibrium given one piece of information (such as q2)
6. Describe the forces that drive evolution (
**genetic drift**,
**nonrandom mating**,
**mutation**,
**migration**, and
**natural selection**) and their effects on allelic frequencies of a population.
6.1. For genetic drift, also explain the causes of genetic drift (
**sampling error**, randomness), what factors influence the magnitude of drift and what
**bottleneck** **effect** and
**founder effect** are.
6.2. For natural selection, explain how evolutionary change of this type differs from the others
6.3. Identify which forces increase diversity and which decrease diversity WITHIN a population
6.4. Identify which forces increase diversity and which decrease diversity BETWEEN SEPARATE populations
7. Recite the
**biological species** **definition** and describe its
**limitations**.
7.1. Be ready to define
**Reproductive Isolating Mechanism (RIM)** and describe at least two examples.
8. Explain the difference between
**allopatric** and
**sympatric speciation**
8.1. Identify the forces that drive evolution in each type of speciation.
9. Explain how
**phylogenetic trees** are used to show evolutionary relationships and the difference between
**anagenesis** and
**cladogenesis** in evolutionary relationships and appearance on the tree.
10. Explain why rates of
**nucleotide substitutions** vary among different parts of the genome and within a gene.
11. Define the
**molecular clock**, including the key assumption it makes and how scientists apply it to evolutionary studies.
_Page 2 of 2_
**## Genetic.docx**
_BIOL-2416 Baggett – Unit 04 – Study Tips_
## Study Suggestions for Exam #4 over Chapters 14-16 & 18
### General Exam Format and Information
**What to bring:** knowledge and understanding, your signed 4×6 notecard, at least 2 sharpened pencils and a calculator if you have one (can borrow from me if needed during exam, but no phones allowed)
**The exam will be administered from 6:00 p.m. to 8:00 p.m.** **No need to return after the exam this time**.
**Question breakdown** (test total is 100 points)
·
**40 regular multiple-choice questions** (2 pts each x 40 = 80 pts)
· 4 chapters is ~8-12 questions per chapter for Ch. 14, 15, 16 and 18
· you should go back and review the cell cycle (Ch. 2), chromosome mapping (Ch.5), chromosome structure and variation (Ch.6) and bacterial plasmids, transformation and immune-like defense (Ch. 7) as you study this unit since must of this content builds on topics from those chapters.
· 2 or 3 of the multiple-choice questions will be from Genetics in Practice openers
·
**3 short essay questions** (5-8 pts each)
**plus 1 bonus short essay question** –
***For this exam, I have noted the concept most likely to show up in the short essay questions for you (see chapter headings)**
### Topics and Key Terms by Chapter –
#### What to Study for Chapter 14 – _expect a short essay on combined: #5, #6 and #10_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**recombinant DNA, transgenic organism, nuclease, agarose, methylene blue, ethidium bromide (EtBr), SYBR Green, anneal / annealing, primer, antibiotic, antibiotic resistance**
3. Describe the normal cellular origin and role of
**restriction enzymes**, what types of sequences they recognize, how they cut DNA and what scientists use them for in the laboratory
3.1. Distinguish between the type of cut that makes a cohesive (sticky) end versus a
**blunt end**.
3.2. Identify which restriction enzymes will produce larger fragments (cut less often) based on length of the
**recognition sequence.**
_**You will NOT be tested on the engineered nuclease section (no questions on this)._
4. For
**CRISPR-Cas** systems:
4.1. Describe the normal cellular origin and role of CRISPR-Cas systems, how they know which sequences to recognize (
**crRNA**), which part has nuclease activity to cut the DNA
4.2. Explain how scientists have engineered this system to cut and modify any specific sequence they desire, including what
**sgRNA** is and how
**Non-Homologous End-Joining (NHEJ)** and
**Homology Directed Repair** (
**HDR**) enzymes are involved.
5. Explain what
**gel electrophoresis** is, what creates the gel matrix for DNA gels and how we use it to separate and visualize DNA.
6. Describe the three steps of
**Polymerase Chain Reaction (PCR)**, including why they are repeated, how primers are involved, where they bind (why just
_outside_ the region you want to amplify?) & the key role of
**_Taq_ polymerase.**
7. Define “
**gene cloning**” and describe the 3 requirements for any
**cloning vector** to work
7.1. Identify key characteristics of
**plasmid vectors**, the basic
**transformation** process and the two common hosts scientists use by the scientific names (which specific bacteria and yeast from Ch. 1)
7.2. Describe the unique characteristics of
**expression vectors** and how scientists obtain eukaryotic DNA that can be used with them (see next item)
8. Describe how a
**DNA library** is made, stored and the differences between making and using a
**genomic library** versus a
**cDNA library**
9. Describe how
**Sanger sequencing** (
**dideoxy sequencing**) works and what is special about dideoxy nucleotides (
**ddNTPs**) that allows them to be used in this method.
10. Describe
**microsatellites**(
**short tandem repeats, STRs**) in DNA and explain how they are used in DNA fingerprinting or profiling to identify DNA samples.
_Be able to relate this to #5 and #6 in a complete crime scene analysis procedure._
11. Define or recognize examples of
**forward genetics** versus
**reverse genetics** methodologies.
#### What to Study for Chapter 15 – _likely no short essay on this chapter since Ch. 18 has two_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Differentiate between
**genomics** and
**proteomics**.
2.1. Describe the differences between the
**Human Genome Project (HGP)** and the
**Human Proteome Project (HPP)** in both their purpose and who they are examining humans (HGP focused on humans as whole organisms, while HPP is looking at different cell types
_within_ humans)
2.2. Define
**structural genomics** and
**functional** genomics in relation to these two terms.
3. Describe the approach to sequencing a complex genome that ended up working for the HGP, including the role of
**genetic linkage mapping, physical mapping, map-based sequencing** and whole genome
**shotgun sequencing.**
_**You will NOT be tested on NextGen or newer sequencing methods (no questions on this)._
4. Describe what a
**Single Nucleotide Polymorphism (SNP)** is and why a single SNP does not provide much information about a person or group of people, but a
**haplotype** can.
4.1. Explain how a
**Genome-Wide Association Study (GWAS)** uses genome sequence and SNP information to being to analyze possible causes of a genetic condition, including the limitations of these studies.
5. Identify the interdisciplinary fields involved in
**bioinformatics** and why.
6. Describe what
**metagenomics** is and that it primarily focuses on microbial communities (and why helpful there)
_**You will NOT be tested on using BLAST to analyze homologues or orthologs or RNA-seq (no questions on this)._
7. Describe what a
**microarray** is and how it is used by scientists to analyze gene expression differences between cell types or groups of individuals to identify genes involved in a process (such as cancer patients or developmental changes)
8. For
**comparative genomics**, review and be able to discuss basic features of prokaryotic versus eukaryotic genomes (general size of genome, # of genes and gene “density”) and the impact of
**transposons** in repetitive DNA in eukaryotic genomes.
#### What to Study for Chapter 16 – _expect a short essay on combined #3, #4 and #6_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**cell cycle checkpoints, contact inhibition, density dependent inhibition, metastasis / metastasize / metastatic, benign, malignant**
3. Describe the primary characteristics of
**cancer** (differentiating it from normal cells) and explain why it is a
_group_ of genetic diseases, not just one.
4. Explain why cancer is not typically inherited and why most non-inherited cancer arises later in life rather than in young people
5. Identify the environmental factor that contributes
**_most_** to the development of cancer (
**tobacco**) as well as the relative
**_overall impact_** of environmental factors on cancer development (
**around 40%** of cancer cases).
6. Describe how cancer develops, including what
**clonal evolution** means and the genetic changes involved in developing a
**tumor**, how it becomes
**malignant** and how
**metastasis** occurs.
7. Identify what the proteins encoded by
**proto-oncogenes** normally do in the cell and why mutations in these genes are often dominant alleles (why are most
**oncogenes** dominant?)
7.1. Recognize the proto-oncogene example
**_ras_** has an oncogene mutant version present in 1/3 of all tumors
8. Identify what roles the proteins encoded by
**tumor suppressor genes** normally play in the cell and why mutations in these genes are often recessive
8.1. Recognize the key examples of tumor suppressor genes discussed and their normal functions:
**p53**,
**RB**,
**BRCA1** (and not listed in chart, but there is also a BRCA2 with similar function)
8.2. Explain what
**haploinsuffiency** is and how it might affect a heterozygote who inherited one knock-out allele for a tumor suppressor gene
8.3. Describe how inheriting one knock-out allele for a tumor suppressor gene might lead to increased development of cancer even though the allele is recessive (i.e. explain
**loss of heterozygosity** cause & effect)
_**You will NOT be tested on cyclins and cdks, though I may mention them in a question, so recognize that they are involved in checkpoints and forward/stop signals so you aren’t confused by the mention._
9. Describe how
**retinoblastoma (Rb) cancer** develops, including which cell cycle checkpoint fails (G1-to-S) and what the
**2-hit hypothesis** explains about inherited versus sporadic (non-inherited) retinoblastoma tumors (which are almost always
**unilateral** and which are often
**bilateral** and why).
10. Recognize and identify the role of secondary mutations in genes for
**telomerase**,
**angiogenesis** and
**cytoskeletal** and
**ECM structure** as well as
**aneuploidy** and large chromosomal mutations on tumor development and cancer progression.
11. Identify the 2 key ways that
**viruses**, especially
**retroviruses** like HPV, can cause cancer after infection.
#### What to Study for Chapter 18 – _expect a short essay on #3_ _or #5 AND also on #7, including 7.1_
1. Genetics in Practice – make sure you know the answers to the questions I asked in the chapter PowerPoint.
2. Terms from chapter to review (in addition to those directly mentioned in specific topics below):
**evolution, gene pool, genotypic frequency, allelic frequency, pre-zygotic, post-zygotic, speciation**
3. Calculate genotypic and allelic frequencies for an autosomal locus with two alleles given population information (total number of individuals and number of individuals with each phenotype).
4. Describe the
**Hardy-Weinberg law** (i.e. equations) and the conditions required for
**genetic** **equilibrium** to exist in a population.
5. Apply the predictions of the Hardy-Weinberg law to calculate genotypic and allelic frequencies for populations in HW equilibrium given one piece of information (such as q2)
6. Describe the forces that drive evolution (
**genetic drift**,
**nonrandom mating**,
**mutation**,
**migration**, and
**natural selection**) and their effects on allelic frequencies of a population.
6.1. For genetic drift, also explain the causes of genetic drift (
**sampling error**, randomness), what factors influence the magnitude of drift and what
**bottleneck** **effect** and
**founder effect** are.
6.2. For natural selection, explain how evolutionary change of this type differs from the others
6.3. Identify which forces increase diversity and which decrease diversity WITHIN a population
6.4. Identify which forces increase diversity and which decrease diversity BETWEEN SEPARATE populations
7. Recite the
**biological species** **definition** and describe its
**limitations**.
7.1. Be ready to define
**Reproductive Isolating Mechanism (RIM)** and describe at least two examples.
8. Explain the difference between
**allopatric** and
**sympatric speciation**
8.1. Identify the forces that drive evolution in each type of speciation.
9. Explain how
**phylogenetic trees** are used to show evolutionary relationships and the difference between
**anagenesis** and
**cladogenesis** in evolutionary relationships and appearance on the tree.
10. Explain why rates of
**nucleotide substitutions** vary among different parts of the genome and within a gene.
11. Define the
**molecular clock**, including the key assumption it makes and how scientists apply it to evolutionary studies.
_Page 2 of 2_