Download Examination 3

Examination 3 Learning Objectives
Thursday April 5, 2012 at 6:00 PM in Campbell Auditorium. Bring a number 2 pencil and your ID. There
will be 56 questions – the exam is worth 112 points.
Make sure you can do the genetics problems posted on Moodle! Use the Cell Division Summary, Cell
Division Worksheet, Molecular Genetics I and II Worksheets and the Intron Exercise.
The material in the textbook: Chapters 12, 13, 14, 15, 16 and 17. Focus on the material covered in lecture.
Cell Division
• Fig. 12.4, 12.5, 12.6, 12.7, 12.8, 12.10 and 12.15
• Fig. 13.7,13.8 and 13.9
• Be sure you can complete the worksheets on Cell Division.
• Review the material in the Cell Division Summary sheet.
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Centromeres
o Area of attachment between 2 sister chromatids
Kinetochores
o Structure of proteins and specific sections of chromosomal DNA at the centromere; point of
attachment for microtubules of the spindle
Chromatids
o Two copies of a duplicated chromosome
Spindle apparatus
o Formed from microtubules extending from the two centrosomes; as centrosomes move away
from each other the microtubules lengthen
Cell cycle and control checkpoints – Why are there checkpoints? What do they check for? Figure
12.15
o Checkpoints – stop and go-ahead signals that help regulate the cycle
o Checks for:
- G1 checkpoint – checks to see if DNA is damaged
- G2 checkpoint – checks to see if DNA is replicated properly
- M checkpoint – spindle assembly checkpoint, checks for alignment of chromosomes
Interphase
o What occurs in G1, S and G2 phases?
- G1 – synthesis of cell components; increase in number of organelles
- S – synthesis (replication) of DNA; doubling of the genetic material
- G2 – centrioles replicate in animal cells; structure for cytokinesis is put in place
o What is Go?
- Non-dividing phase
- Most cells in the human body are non-dividing
What is the purpose of the different types of cell division?
o Mitosis
- Produces “daughter” cells that have identical genetic complements
- Occurs in somatic cells
o Meiosis
- Cell division for gamete production
- In specialized tissues
- Produces cell with the 1n chromosome number (haploid)
Haploid
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o One set of chromosomes; 1n
Diploid
o Two sets of chromosomes (one from each parent); 2n
Mitosis
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Mitosis – Events in each phase – What are the number of chromatids, DNA content, number of
chromosomes – Figure 12.7a, 12.7b
o Prophase
- Nucleoli disappear
- Chromatic condenses
- Mitotic spindle form from microtubules in cytoplasm
- Centrosome move away from each other
- Mitotic spindle:
• Formed from microtubules extending form the two centrosomes
• As the centrosome move away from each other the microtubules lengthen
o Pro-metaphase
- Nuclear envelope fragments
- Microtubules of the spindle invade the nuclear region and interact with the
chromosomes via the kinetochore
o Metaphase
- Centrosomes at opposite poles
- Chromosomes arrange at the mid-plane of the spindle
o Anaphase
- Sister chromatids separate and move towards the poles
o Telophase
- Nuclear envelope reforms
- Spindle breaks down
- Nucleoli reform
- Chromatids become less densely coiled
o Cytokinesis – Figure 12.10
- Division of cytoplasm
- Mechanism differs between plants and animal cells because plants have a cell wall
Questions on Moodle
Meiosist
• Meiosis – Events in each phase – What are the number of chromatids, DNA content, number of
chromosomes – Figure 13.8
o Interphase
- As in mitosis
- During S phase, DNA is replicated giving rise to chromosomes consisting of two
sister chromatids
o Prophase 1
- Spindle formation
- Breakdown of nuclear envelope
- Nucleoli disappear
- Chromosomes condense
- Each chromosome consists of two chromatid from S phase of interphase
- Homologous chromosome pairs lie next to one another
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- Crossing over of chromatids between pairs (chiasma formation)
o Metaphase 1
- Chromosome pairs align on equator of spindle
- Kinetochore of sister chromatids are attached to fibers going to the same pole
o Anaphase 1
- Homologous chromosome pairs separate
- Sister chromatids remain together
o Telophase 1
- Depending on the species:
• Nuclear membrane my reform
• Cytokinesis occurs
Meiosis II
o Cell division is like mitosis but starts with haploid chromosome complement
o Sister chromatids are separated
o Figure 13.8b
Questions on Moodle
Figure 13.9 – A comparison of mitosis and meiosis
Blood Groups
• ABO and Rh blood groups figure 14.11
o Multiple alleles (Ia, Ib, i (Io))
o Phenotypes (A, B, AB, O)
o Ia is co-dominant with Ib
o Ia is dominant to Io
o Ib is dominant to Io
• Know the genetics/inheritance of these phenotypes.
• Are the genes for the ABO and Rh blood groups on the same chromosome?
o No
• Be able to do problems on paternity exclusion
• Transfusions – which combinations of donor and recipient blood groups are compatible?
• Fig. 14.11, p. 946
o A  A, O
o B  B, O
o AB  A, B, AB, O (universal recipient)
o O  O (universal donor)
• Rh Factor genetics
o Rh Factor is an antigen on RBC’s
o D is dominant
o d is recessive
o Genotypes DD or Dd
- Phenotype Rh+
o Genotype dd
- Phenotype Rh- Lacks the Rh antigen
Questions on Moodle
seX-Linkage
• Fig. 15.6, 15.7, 15.8
• Inheritance of X-linked and Y-linked traits
o Y – always passed from father to son
o X – inherited from mother (sons and daughters) or father (daughters)
o Father – determines sex of child
o Mother – determines whether a son displays an X-linked trait
o Examples from lecture, e.g. color blindness, hairy ear rims, hemophilia
• What are the differences between X and Y-chromosomes? Do they each have the same genes?
o Do not have same genes:
o Estimated 78 genes on Y
- Testis determining factor, hairy ear rims
o Estimated 1100 genes on X
- Color blindness, hemophilia
• Know how to do Punnet squares for X-linked traits.
o You need to keep track of the sex chromosomes whereas for autosomal traits the sex
chromosomes can be ignored.
• Sex determination and inheritance
• Barr bodies / Inactivated X chromosomes (heterochromatin). Be able to relate the number of Barr
bodies observed to the number of X chromosomes an individual has.
o Barr body
- Inactivation of one X chromosome
• Heterochromatin – tightly coiled inactive DNA
• Only one x chromosome is active in any given cell
- Cell of women are a mosaic for genes on the X chromosome
• Random
• What are karyotypes? Be able to identify different conditions based on viewing the karyotype
o Somebody that is XO is missing one X
o A male that is XXY is a klinefelters syndrome
• Examples of X-chromosome inactivation and the fur color patterns of tortoiseshell cats (for example
Fig. 15.8). What is the sex of most cats displaying the tortoiseshell pattern? Why?
o Females: 2 X chromosomes
o Males would have to have more than 1 X chromosome
Questions on Moodle
Mendelian Inheritance
• The terminology for the generations that are followed in the crosses: P, F1 and F2
o P – parental
o F1 – filial one – offspring of the parental generation – hybrids
o F2 – filial two – offspring of cross between F1 (hybrid) individuals
• What is meant by a true-breeding lineage?
o Organisms that produce offspring of the same variety over many generations of selfpollination
• Mendelian segregation, inheritance
o Fig. 15.2
o Two Laws
Test Crosses
• Know what a test cross is and why it is performed. What is the phenotype of the unknown individual
and what are the possible genotypes. What is the genotype of the individual that the individual with
the unknown genotype is crossed with? Be able to perform testcrosses.
o Performed because genotype is unknown, when the dominant phenotype – the second one is
unknown
o How do you determine whether an individual is homozygous dominant or heterozygous?
- Phenotype is P
- Genotype is P(–)… (Could be PP or Pp)
- Cross the individual with an unknown genotype with a homozygous recessive (pp)
individual
o Fig. 14.7
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What is meant by dominant, co-dominant, and incomplete dominance? Figure 14.10
o Dominant – allele that is fully expressed in the phenotype of a heterozygote; only a single
copy is required to express the trait
o Co-dominant – heterozygous individuals express traits of both alleles; human blood types
o Incomplete dominance – heterozygous individuals are intermediate between the dominant
and recessive traits; three phenotypes
What is pleiotropy? What is an example of this?
o Multiple phenotypic effects due to a single allele
o Sickle cell
Sickle cell – what is the difference being a heterozygote and homozygous for the sickle allele?
o Figure 5.21
o Heterozygous
- Exertional (strenuous and low oxygen environments) sickling
- Have the trait
o Homozygous
- Sickle cell anemia
- 10% of red cells are destroyed
- Causes anemia
Dihybrid crosses Fig. 14.8. What does it mean if two genes are linked? What is the pattern of
phenotypes seen in the offspring in a cross of two individuals who are heterozygous at the two genes
being followed – 1) if the two genes are linked or 2) if they are on separate chromosomes? Answers
on figure 14.8
o Two different genes involved (dihybrid)
o Independent assortment
- Four different phenotypes
- Color and shape alleles are on different chromosomes
o Linkage
- Two genes
- Physically located on the same chromosome are linked
- The alleles linked on the chromosome will the be transmitted to the same gamete
- Different expectation for the phenotypes of offspring
• Fig. 14.3, 14.5, 14.6 and 14.10
Question on Moodle
Pedigrees
• Be able to identify the type of inheritance based on a pedigree.
o Dominant vs. recessive, x linked
o Dominant does not skip generations
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What are the symbols for male and female? How are affected individuals (individuals displaying the
trait in question) indicated?
o Squares are male
o Circles are female
o Dark is affected
o Light is unaffected
Know the characteristics of transmission of different types of traits (autosomal dominant, autosomal
recessive, sex-linked recessive)?
o Autosomal recessive
- Generation are often skipped
- Almost equal distributions among sexes
- If both parents are affected, all children should be affected
o Autosomal dominant
- Generations are not skipped
- Almost equal distribution among sexes
- Not all the children of parents who display the trait, will not display trait – means
they are heterozygous and the kids are recessive
o Sex linked recessive
- Most affected are males
- Affected males have carrier mothers (have affected brothers, father, or maternal
uncles)
- Approximately half of son should be affected
What is meant by skipping generations?
Why is it that mostly males display an X-linked recessive trait?
Figure 14.15
Human genetics
• Autosomal vs. Sex-linked
o What is the difference between autosomal and sex-linked inheritance?
o Sex linked
- The gene is carried through the X chromosome
- Primarily concerned with X linked traits
- Must track sex chromosomes from each parent
o Autosomal
- Genes are non-sex chromosomes
- Get 1 copy from each parent
- Gene is on a chromosome on a chromosome that is not a sex chromosome
• Sickle cell – Fig. 5.21, Fig. 23.17
o Trait
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- External sickling
o Anemia
- Homozygous recessive (autosomal)
- 10% of red blood cells are destroyed prematurely
Phenylketonuria (PKU)
o Homozygous recessive (autosomal) trait
o Defect in metabolism of the amino acid phenylalanine
o Diagnosed by testing newborns
• Screening new born babies
o Today every US baby is tested for two rare diseases that can cause retardation:
hypothyroidism and PKU
o Benefits – costs saved through preventing hospitalization for diagnosis or long term
disability are significant
• Chromosomal abnormalities:
o Triploid
- 3n number, bananas
o Hexaploid
- 6n number, wheat
o Monosomic
- One missing chromosome
o Trisomic
- One extra chromosome
o Polyploidy (euploidy)
- Multiple of the complete (haploid) set of chromosomes
o Aneuploidy
- Down syndrome (trisomic (3 copies) of chromosome 21)
- Turner females (XO) (monosomic)
- Kleinfelter males (XXY, XXXXY)
- XYY
- XXX
• Extra-chromosomal inheritance
o Mitochondria inherited from mother
Questions on Moodle
DNA synthesis
• Know what experiments were performed to show that DNA rather than protein was the genetic
material.
o Transforming bacteria
o Cause non-virulent bacteria to become virulent (bacterial transformation)
o Figure 16.2
o Live bacteria took up pieces of DNA from dead bacteria
• The transforming principle in bacteria– Griffith – caused ; Avery, MacCleod and McCarty
o Griffith
- Streptococcus pneumonia transforming principle
o Avery, MacCleod, and McCarty
- Demonstrated that DNA was the transforming principle
• DNA as the genetic material
o Hershey and Chase – Figure 16.4
- Used the bacteriophage T2, bacteria eater
- Sulfur in proteins
- Phosphate in DNA
o Mirsky in 1950
- Equal amounts of DNA in each somatic cell of a species
- Constancy of DNA in somatic cells
o Chargaff
- A=T
- G=C
o What information was available to Watson and Crick that helped them to correctly model the
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structure of DNA?
- Chargaff- 1950 A/T and G/C ratios
- 1953, DNA structure and the implication for DNA replication
- Insights from Wilkins and Franklin x-ray date: DNA is a double helix of uniform
witdth
Wilkinson and Franklin’s x-ray crystallography
o Data showing that DNA was a double helix of uniform width
What is meant by anti-parallel?
o Figure 16.7 – strands run opposite of each other
Base pairing between strands of DNA - How many H-bonds stabilize A-T base pairs? How many
stabilize the G-C base pair?
o A-T = two hydrogen bonds
o G-C = three hydrogen bonds
Know which enzymes are involved in DNA replication - Pay attention to Figure 16.17
How does DNA synthesis start? What serves as the primer for DNA synthesis?
o Polymer synthesized by monomer
o DNA synthesis is primed with a short segment of RNA synthesized by the enzyme primase
o DNA polymerase
- Only works in the 5 to 3 direction (from 5 to 3)
- Adds new nucleotide triphosphate to the 3 OH of the growing chain
- Proof reading ability
What is meant by the leading and lagging strands?
o Leading strand synthesized in the 5 to 3 direction of the replication fork
o Lagging strand synthesize 5 to 3 away from the replication fork
Why are the details of DNA synthesis different between these two strands?
o Because DNA is synthesized by 5 to 3
What is meant by 5’ to 3’?
What are Okazaki fragments?
o Linked together by the enzyme ligase
Telomeres and telomerase Fig. 16.20 and 16.21
o Telomeres
- Non-coding repetitive DNA sequence laid down by telomerase
- Protects the ends of the chromosomes from deterioration
o Telomerase
- Enzyme with a short sequence of RNA
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Adds non-coding sequence of DNA to the template strand (in some tissues)
The usual enzymes can not extend the new DNA strand
The telomere prevents erosion of chromosome ends during rounds of replication
Uses RNA, made of protein, to add to the chromosome
Why is telomerase an important enzyme? What does it use as a template for adding additional DNA
bases?
Base pairing (Fig. 16.7, 16.8 and 16.14)
o A-T – two hydrogen bonds between them
o G-C – three hydrogen bonds between them
Know how AZT (from your lecture notes) blocks the synthesis of HIV DNA by reverse transcriptase.
Why does the addition of an AZT molecule stop further nucleotides from being added? Why does
AZT affect viral DNA synthesis but not human DNA replication?
o Blocks the production of viral DNA (by reverse transcriptase)
o AZT
- 3 azido (n3) group instead of 3’OH group
- When AZT is added to growing viral DNA strand the azido group stops the addition
of further nucleotides
- The azido group cannot form a covalent bond with a 5’ phosphate
o Human DNA polymerase has a good proof-reading ability compared to the viral reverse
transcriptase so AZT is not incorporated
Ends of chromosomes are protected
o Telomeres – non-coding repetitive DNA sequence laid down by telomerase
o Protects the ends of the chromosome from deterioration
o Like the protective tips on shoe laces
See the worksheet Molecular Genetics on Moodle
Transcription and translation – Figure 17.4
• What is the Central Dogma? What are the exceptions to the Central Dogma?
o DNA is transcribed into mRNA
o mRNA is translated into protein
o Exceptions:
- Reverse transcriptase: RNA is used as template to make DNA
- Telomerase
• What is transcription? What is translation?
o Transcription – Figure 17.26- taking DNA and making RNA (transcribed to mRNA)
o Translation- taking RNA to proteins (mRNA is translated into protein with help of rRNA and
tRNA)
• What are the differences between these processes in prokaryotes and eukaryotes? What are the
similarities? Figure 17.3
o Differences:
- Prokaryotes
• Transcription and translation occur contemporaneously in same
compartment
• No RNA processing
- Eukaryotes
• Transcription and translation occur in different compartments
• RNA processing
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What are the types and functions of RNA? Figure 17.14
o rRNA – serves as the scaffolding for the proteins of the ribosome
o tRNA – serves as an adapter molecule to bring in the appropriate amino acid in protein
synthesis. Figures 17.15 and 17.16-4
- Key features:
- Attachment site for the appropriate amino acid
• Amino acyl tRNA synthase
- Single strand of RNA
• Anticodon base pairs with the codon mRNA
o mRNA – single strand, specifies the sequence of amino acids to be added to the polypeptide
which will be synthesized
RNA synthesis
o Figure 17.26
o RNA polymerase
o Formed on the template strand of DNA
o The RNA is anti parallel to the DNA
o RNA polymer grow in the 5’ to 3’ direction
- Monomer added to the 3’ OH of the polymer
What components are involved in the translation process? Figure 17.14 and 17.19
o Ribosome RNA
o mRNA
o tRNA
o Amino acids
Codons and the correspondence to amino acids – Why do we need 3 bases per codon to specify 20
amino acids?
o How many amino acids would 1 base per codon code for? – 4
o How many amino acids would 2 bases per codon for? – 4 bases x 4bases = 16 amino acids
o How many amino acids would 3 bases per codon code for? – 4 x4 x 4 = 64
What is a mutation? What are the types of mutations?
o Mutation is
- A change in DNA
o Point mutations, Figure 17.23, 17.24
- Change in a single nucleotide
- Silent mutation – no effect on amino acid sequence
- Missense mutation – mutation has different amino acid
- Nonsense mutation – mutation leads to a stop codon
o DNA damage by ultraviolet light
- Leads to thymine dimers from
o Insertions/deletions - Frameshift mutations – 17.24
- Codons are read incorrectly
- Frame shift – adding or taking away one or two nucleotides causing a shift in the
way the message is read
- Frameshift can cause immediate nonsense or can cause extensive missense
- No frameshift just leaves one amino acid missing
o How many insertions/deletions result in a shift in the reading frame?
- Codons have three bases, taking out one or two letters will scramble the message.
- Taking out or putting in three letters/bases will not make that much difference
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Processing of mRNA
o What are the differences between prokaryotes and eukaryotes? Figure 17.10
- Prokaryotes:
• RNA processing is not seen in prokaryotes
- In the nucleus of eukaryotes:
• Addition of a 5’ GTP gap
• Addition of a poly-A tail
• Removal of introns (intervening sequences)
o 5’GTP cap, 3’poly A tail
o Introns and exons
- Intron – intervening sequence, is the non-coding sequence and is removed from the
mature mRNA
- Exon – expressed sequence, codes for a sequence of amino acids; codes for protein
domains
o Protein domains – Figure 17.13
- Modular architecture
- Functional units of the protein
- E.g. substrate binding site, coenzyme binding site
o Splicing and alternative splicing – see the examples we did in class (also posted on Moodle)
- Splicing – removing introns and adding exons
- Alternative splicing – in different tissues, different parts of the gene might be
expressed; important because you can have the same gene coding for proteins
expressed in different tissues
Questions on Moodle
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Figures: 17.3, 17.4, 17.8, 17.9, 17.10, 17.11, 17.13, 17.14, 17.15, 17.16, 17.19, 17.23, 17.24 and
17.26.
See worksheet Molecular Genetics II on Moodle
Polyploidy in plants
• What are some examples of polyploid plants?
o Corn, cotton, sugarcane, apples, watermelons, bananas, wheat, and many flowers
• How do plants that have unpaired homologous chromosomes reproduce?
o By mitosis (asexual)