Final Exam Review Sheet Flashcards
What is the product rule?
The product rule states that the probability of 2 (or more) independent events occurring together can be calculated by multiplying the individual probabilities of the events. With independent events:
Probability of event 1 AND event 2 = Probability of event 1 * probability of event 2
For example, the probability that both coins
will turn up heads is: 1/2 * 1/2 = 1/4 or 0.25
What is the sum rule?
Probability of event 1 OR event 2 = Probability of event 1 + probability of event 2
For example, from the product rule the probability that both coins
will turn up heads is: 1/2 * 1/2 = 1/4 and the probability that
both coins will turn up tails is also: 1/2 * 1/2 = 1/4
In the sum rule, we have 1/4 + 1/4 = 2/4 = 1/2 or 0.5
What are the types of Mendel’s Laws of Inheritance.
They are: the Law of Segregation and the Law of Independent Assortment
What is the Law of Segregation?
Law of segregation: the two alleles for each trait separate (segregate) during gamete formation, and then they unite at random, one from each parent, at fertilization
What is the Law of Independent Assortment?
Law of independent assortment: during gamete formation, different pairs of alleles segregate (separate) independently of each other
What is the Pleiotrophy?
Pleiotrophy is a single gene that determines several different and unrelated characteristics. The gene has different effects on different tissues. One gene contributes to several phenotypes/characteristics
For example. Marfan syndrome
What is a polygenic trait?
A polygenic trait is the characteristic, such as height or skin color, which is controlled by multiple genes (2 or more genes)
What are the environmental effects on the genes?
Expression of phenotype depends on the environment and genes. The environmental effects are: temperature, phenocopy and epigenetics
Haploid vs Diploid
Haploid - State of a cell with one copy of each chromosome. Human gametes have one copy of 23 chromosomes. (meiosis)
Diploid - State of a cell with 2 copies of homologous chromosomes. Humans have 23 pairs of chromosomes, which is total 46 chromosomes. (mitosis, meiosis)
Haploid meaning
Haploid - is a cell that has a half of the set (one copy) of unpaired chromosomes.
Diploid meaning
Diploid - is a cell that contains 2 complete sets (copies) of chromosomes, one from each parent.
Sister chromatids definition
Sister chromatids are identical copies of a replicated chromosome
What are the homologous chromosomes (homologs)?
Homologs contain the same set of genes, but can have different alleles for some genes.
One copy from mom and the other from dad.
Nonhomologs chromosomes definition
Nonhomologs carry completely unrelated sets of genes
Metacentric vs Acrocentric chromosomes
Metacentric chromosomes (with long arms) - centromere position is middle at the centre of the chromosome Acrocentric chromosomes (with short arms) - centromere position is very close to the end
What are the stages of the cell cycle? Describe the brief function of each.
1) G1 Phase, 2) S Phase, 3) G2 Phase, 4) M (Mitosis or Meiosis) phase
What are the phases (stages) of mitosis?
Interphase, Prophase, (Prometaphase), Metaphase, Anaphase, Telophase
What are the phases (stages) of meiosis I?
Prophase I, Metaphase I, Anaphase I, Telophase I and (Interkinesis - not actual stage)
What are the phases (stages) of meiosis II?
Prophase II, Metaphase II, Anaphase II, Telophase II and (Cytokinesis - division of cytoplasm, which ends with 4 non-identical haploid cells)
What is the purpose of cell cycle checkpoints? Which checkpoints do we have?
The cell cycle checkpoints ensure that cell is able to move from
one phase to another in the cell cycle. They are G1, G2 and M checkpoints
Mitosis Vs Meiosis.
What is mitosis?
Mitosis is the nuclear cell division that generates two daughter cells.
What is meiosis?
Meiosis is the nuclear cell division that generates gametes (egg and sperm) and results in 4 daughter cells
Describe the 2 ways of how meiosis contributes to genetic diversity.
a) Independent assortment of nonhomologous chromosomes create different combinations of alleles.
b) Crossing-over (recombination) between homologous chromosomes, which create different combinations of alleles. After recombination, homologs segregate to different daughter cells.
Gametogenesis. Oogenesis vs Spermatogenesis
- Male gametes are produced by spermatogenesis in the testes
o Diploid Spermatogonium (germ cells in testes) are divided by mitosis to form
Primary spermatocyte.
o After puberty, undergoes Meiosis I for secondary Spermatocyte.
o Undergoes Meiosis II to create spermatids.
o Developmental changes occur to make spermatozoa into mobile sperm. - Female gametes are produced by oogenesis in the ovary.
o Oogonium (germ cells in ovaries) are divided by mitosis to form primary oocyte.
o Primary oocyte begins Meiosis I, which arrests at Prophase I
o Secondary oocyte & first polar body, ovulation occurs —–> 1 egg released each month.
o Fertilization, sperm fuses with egg, as sperm nucleus is traveling to egg nucleus (Meiosis II) to develop 1 ovum and 2nd polar body.
Explain how sex is determined in humans
In humans, presence or absence of Y chromosome determines
gender —> XY male, XX female (sex chromosomes)
Difference between sex chromosomes and autosomes.
The key difference between autosomes (22 pairs) and sex chromosomes (1 pair) is that the autosomes contain genes that are responsible for the determination of somatic characteristics while the sex chromosomes contain genes that determine sex and sex-related characteristics of an organism.
• Sex Chromosomes – pair 23-d, still considered homologs
• Autosome – pairs 1-22 that are non-sex
What is aneuploidy?
Aneuploidy is the variation in chromosome number, so that an organism gains or
loses one or more chromosomes
What is monosomy? Which disease it causes?
Loss of a single chromosome (2n-1)
Turner syndrome - a condition that affects only females, results when one of the X chromosomes (sex chromosomes) is missing or partially missing
What is Klinefelter Syndrome?
Klinefelter syndrome is a common genetic condition where a male is born with an extra X chromosome. (XXY)
What is Down Syndrome?
Down syndrome, also known as trisomy 21, is a genetic disorder caused by a chromosomal abnormality with the presence of all or part of a third additional copy of chromosome 21.
Sex-linked genes definiton
Sex-linked genes are those found on one of the two types of sex chromosomes, but not both (X-linked or Y-linked).
Recognize genetic diseases that are inherited in a sex-linked dominant and sex-linked recessive manner
- X-linked (recessive or dominant)
– Many human disorders including hemophilia and
colorblindness (recessive diseases). Males are more likely to be affected.. Why?
Hemizygous (a single copy of allele instead of 2) - Y-linked (holandric, which means located on Y chromosome)
Rare, relatively few genes in humans
– Transmitted from father to son
Sex-limited inheritance vs Sex-influenced inheritance (pic)
Sex-limited inheritance occurs in cases where the expression of a
specific phenotype is absolutely limited to one sex.
Sex-influenced inheritance is when the sex of an individual influences the expression of a phenotype that is not limited to one sex or the other.
Explain how linked genes differ from unlinked genes. What is the ratio in testcross?
In a testcross if TWO genes assort independently (dihybrid
cross) we expect a __1:1:1:1____ ratio.
Null hypothesis: Two genes are unlinked.
Deviation from this 1:1:1:1 suggests linkage
• Linked genes – nonrecombinant & recombinant gametes are produced. They are found on the same chromosomes.
• Unlinked genes are found on different chromosomes. They have 2 genes that assort into gametes independently of each other (nonrecombinant -parentals)
Connect the percent recombination to a genetic map distance (formula)
Recombination frequency f-la?
Recombination frequency = # of recombinant progeny/ Total # of progeny X 100%
• The map distance gives us info on the distance between genes. It tells us the proportions
of recombinant & non-recombinant gametes produced.
What is the coefficient of coincidence?
The expected frequency of multiple exchanges between two genes can be predicted from the distance between them # of observed D.C.O (double cross-over) / # of expected D.C.O
What is the Interference? What is the formula?
Interference= 1- coefficient of coincidence
I = 1-.62= 0.38
Interference – tells the percentage of double cross over progeny expected that will not be
observed due to the interference in crossing over.
-positive if fewer double-crossovers than expected
-negative if more double-crossovers than expected
Double crossover are the smallest numbers in the progeny
What is the s-re of the DNA?
Two strands (of nucleotides) are twisted together around a common axis to form a spiral called a double helix
How the strands of the DNA directed and run which direction?
The two strands are antiparallel. One runs in the 5’ (free phosphate) to 3’ direction (free sugar) and the other 3’ (free sugar) to 5’ (free phosphate) direction.
The helix of the DNA is right-handed or left-handed? Why?
The helix is right-handed in a clockwise direction giving 10 bases & 3.4 nm per complete turn of the helix. As it spirals away from you, the helix turns in a clockwise direction
The double-bonded strand of DNA is stabilized by?
a. Hydrogen bonding between complementary bases.
A bonded to T by 2 hydrogen bonds,
C bonded to G by 3 hydrogen bonds
What are the 3 modes of DNA replication
They are
- Semi-conservative
- Conservative
- Dispersive
Leading vs Lagging Strands
a. Leading Strand – new stranded that is synthesized in the 5’ —–> 3’direction, which grows continuously during DNA replication, left to right unwinding
DNA can only be synthesized in the 5’ to 3’ direction.
b. Lagging strand- is the DNA strand, which grows discontinuously by forming short segments known as Okazaki fragments. It’s synthesized in the 5’ —-> 3’direction, opposite right to left unwinding
Describe the process of bidirectional replication
It’s a type of DNA replication, where replication is moving along in both directions from the starting point. This creates 2 replication forks, moving in opposite directions. When the 2 replication forks move to opposite directions, DNA can get ready to replicate DNA quickly (to make complementary DNA strand)
Wild-type VS Mutant alleles
Wildtype alleles is a term used to refer to most
common allele in the population, which is displayed as (+)
Mutant allele is a rare allele (less than 1% of pop.), which usually result from a mutation.
Forward vs Reverse mutation
a. Forward – changes wild type allele to a mutant allele.
For example, e+ —> e
b. Reverse – changes a mutant allele back to a wild type.
For example, e –> e+ (more rare)
What is substitution (point) mutation? What are the 2 types of base substitutions?
It’s a change in the single base pair in DNA.
There are 2 types of base substitutions: transition and transversion
Transition vs Transversion substitution
1) Transition:
- pyrimidine replaces a pyrimidine (T —-> C) or
- purine replaces a purine (A –> G)
2) Transversion (rare):
- purine / a pyrimidine are interchanged
T —> A or G, C —-> G or A, A —–> T or C,
G —-> C or T
Insertion vs Deletion
adding or removal of a base pair in the DNA
Translocations definition
Translocation means that a piece of chromosome move from one chromosome to another
Conservative –> Cut and paste
Replicative —> Copy and paste
Mutagens vs Carcinogen
Mutagens are natural or artificial environmental agents that cause mutation and increase the rate of mutation
Carcinogen - any substance that causes cancer.
Mutagens cause changes in the genetic information of an organism, which may sometimes cause cancers. Carcinogens cause cancers through formation of tumors.
What is the Central Dogma?
The ‘Central Dogma’ (gene expression) is the process by which the instructions in DNA are converted into a functional product, such as a protein.
What is the difference between DNA and RNA? What is the sugar for each?
The sugar in RNA is ribose. The sugar in DNA is deoxyribose.
The nitrogenous bases used in DNA are: Adenine, Guanine, Cytosine, and Thymine.
The nitrogenous bases used in RNA are: Adenine, Guanine, Cytosine, and Uracil.
In eukaryotes: initial transcript destined for translation is called? Where processing occurs?
In eukaryotes: initial transcript destined for translation is called
pre-mRNA processing —–> processing occurs in nucleus
What mRNA (type of RNA) processing includes?
mRNA processing includes:
RNA splicing, the addition of a modified (methylated) nucleotide 5’ cap to the 5’ end, and the addition of a poly-A tail to the 3’ end.
What is poly-A tail?
it’s the repeating sequence of Adenine (A) nucleotides, which is added to the 3’ end
What is RNA splicing? (Hint: introns)
Introns (RNA transcript) are removed by splicing (cut) and exons are joined.
What are the levels of protein s-re?
They are primary, secondary, tertiary, and quaternary structures of a protein.
What is the primary s-re of the protein?
The linear chain of amino acids
What is the secondary s-re of the protein?
The regions are stabilized by hydrogen bonds between atoms of the polypeptide backbone; beta pleated sheets & alpha helices
What is the tertiary s-re of the protein?
3D shape stabilized by interactions between side chains
What is the Quaternary s-re?
The association of two or more polypeptides of a protein
What are the mutations in DNA that affect proteins?
They are silent, missense, nonsense, and frameshift mutations
What is the silent mutation?
Silent mutation – doesn’t alter the amino acid sequence, so it stays in the same box of the codon chart. Redundancy (amino acid can be specified by more than 1 codon)
What is the missense mutation?
Missense mutation - alter the amino acid sequence, so it goes from one box of the codon chart to another.
Base substitution for which codon on transcribed mRNA specifies wrong amino acid.
ex sickle cell anemia
What is the Nonsense mutation?
Nonsense mutation - codon is changed from the amino acid to a stop codon, which forms the incomplete polypeptide (amino acid chain - nonfunctional protein)
What is the Frameshift mutation?
Frameshift mutation means that we insert or delete a single nucleotide, which causes the disruption in the reading frame of mRNA, so that the resulting protein will be shorter. The function of proteins is inhibited.
Chemically defined media vs complex media
Chemically defined media are culture media that contain a known chemical composition. Composed of exact amounts of chemically pure inorganic or organic components.
o Ex: glucose salt broth, inorganic synthetic broth
Complex media are culture media that contain unknown chemical composition. Composed of organic materials that are not chemically pure
o Ex: nutrient broth, agar, blood agar
Selection vs Screen
a. Selection – establish conditions in which only the desired mutant will grow.
b. Screen – growth condition where both mutant and wild type are able to grow, but we can distinguish them phenotypically. We can look on the bacterial colony for a particular phenotype.
Vertical gene transfer vs Horizontal gene transfer
1) Vertical gene transfer – binary fission (divides into 2), going from one generation to the next.
2) Horizontal gene transfer – transfer genes to members of the same generation.
What are the mechanisms of horizontal gene transfer?
They are transformation, conjugation and transduction
What is the transformation mechanism of horizontal gene transfer?
Transformation: cells must be competent (be able to take in DNA fragments) from the environment and incorporate into own DNA
Natural transformation vs Artificial transformation
Natural transformation: when bacteria take up DNA fragments spontaneously from their surroundings
Artificial: accomplished in the lab by making cells competent (treat cells with calcium or use electroporation)
What is the conjugation mechanism of horizontal gene transfer?
Conjugation: is the process by which one bacterium transfers genetic material to another through direct contact; requires cell-to-cell contact, must be opposite mating type, involves F plasmid and formation of Hfr (high frequency of recombination for chromosomal genes) cell.
What are the 2 opposite mating types in conjugation?
Donor cell carries plasmid (F+)
Recipient cell lacks plasmid (F-)
What is the transduction mechanism of horizontal gene transfer?
Transduction: transfer of DNA from host (bacterial) cell to another bacterial cell via bacteriophage (virus).
F plasmid vs F’ plasmid
F plasmid: a conjugative plasmid that carries many genes required for the transfer of DNA.
F’ plasmids: F plasmid variants + some bacterial genomic DNA
Transfer of F+ plasmid from a F+ to F- through a sex pilus results in a newly formed F+
cell. The plasmid then gets integrated into the host chromosome and converts and F+ to
Hfr. Excision of the F plasmid can convert Hfr back to F+. Excision of F plasmid plus
host DNA results in F’.
• Hfr allows recombination for plasmid DNA & main bacterial chromosome. Increases
diversity in bacteria. Occurs on conjugation.
Why Hfr bacteria produce a high frequency of recombinants for chromosomal genes?
Because their chromosomes contain an integrated F plasmid.
What is operon?
Operon (operator) – an area of DNA (upstream) that controls whether or not DNA gets transcribed
What is gene regulation?
Gene regulation is the process of turning genes on and off
What is the Lac operon? (the sequence of DNA)
Lac operon: an inducible operon (active in induction - beginning the process), which utilizes lactose (sugar) by E.coli.
This is an example of gene regulation
What is trp (tryptophan) operon? (the sequence of DNA)
Trp operon is the repressible operon (activates repressor protein, inhibiting transcription); responsible for the production of the amino acid tryptophan.
Identify the levels of DNA compaction.
Helical (spiral) → nucleosome “beads on a string” (first level) —-> 30nm fiber (second level) ——> fiber is organized into loops, scaffolds, domains (third level - 300 nm fiber) —–> metaphase chromosome
What is telomere? It’s function.
It’s a compound s-re at the end of eukaryotic chromosome, which contain specific repetitive base pair sequences. They shorten each division
They protect the ends of the chromosome from being digested (broken down) by preventing the loss of base pairs during replication
What is kinetochore?
It’s the protein unit (mixture of DNA and proteins), which are found in the centromere (black dots - kinetochores) to which spindle fibers attach to in the chromosome
What is centromere?
Structure in the chromosome that holds 2 sister chromatids together by cohesion proteins, which are part of the centromere. Centromeres also contain kinetochore proteins, which help the attachment of spindle fibers.
Euchromatin vs. Heterochromatin
a. Euchromatin: less condensed regions = transcriptionally active
b. Heterochromatin: more condensed regions= transcriptionally inactive (RNA polymerase can’t read them)
What are the types of heterochromatin?
(1) Constitutive heterochromatin - regions that are always permanently inactive (for transcription).
Usually contains highly repetitive sequences.
(2) Facultative heterochromatin - regions that can go between Euchromatin & Heterochromatin
This means that heterochromatin can become euchromatin, and vice versa.
Define a Barr body
it’s the highly condensed (inactive) X chromosome, which can be seen in females.
Females have only one active sex chromosome, because they have XX, and one of the X’s is a barr body (which is inactive).
o Number of X Chromosomes – 1 = # of Barr Bodies
o Ex: Trisomy XXX would have 2 Barr Bodies (3-1 = 2)
Bacterial (prokaryotic) VS Eukaryotic chromosome
Bacterial (prokaryotic) - short, circular DNA molecules
Eukaryotic chromosome - long, linear DNA molecules
What are the 3 main RNA polymerase enzymes?
- RNA Polymerase I- produces rRNA
- Polymerase II- produces mRNA
- Polymerase III- produces tRNA
What are the basal transcription factors?
Basal transcription factors produce low levels of transcription. It requires 3 factors:
1) RNA polymerase II enzyme to make mRNA
2) 5 different proteins called general transcription factors (GTFs) act as a protein helper, which bind to promoter
3) A protein complex called mediator - to switch between transcription initiation and elongation.
Transcription factors definition
Transcription factors are proteins (activators, enhancer, promoter, mediators) that interact directly through DNA binding
Transcriptional activators definition
Transcriptional activators (transcription factors) are proteins that bind to DNA and stimulate transcription of nearby genes (turn genes on)
Repressor definition
A repressor is a protein, which is produced by the regulatory gene and binds to the DNA, inhibiting the expression of one or more genes (turn off transcription).
Explain how chromatin structure affects gene expression
a group of proteins bind to the DNA (in the chromatin) and change the structure of the chromatin (to expose the promoter). Promoters of inactive genes are hidden in nucleosomes. To activate a gene, transcription factors (proteins) bind to enhancers (DNA sequence) and attract chromatin remodeling proteins. The chromatin remodeling proteins: 1. change the location of nucleosomes 2. remove histones from the DNA; 3. replace core histones with variants (coactivators). As a result, the promoter (the sequence of DNA) becomes more accessible, so that RNA polymerase II can bind to the promoter and transcription can occur.
Contrast prokaryotic and eukaryotic gene expression.
Prokaryotes: no nucleus, no nucleosomes
But Eukaryotes have nucleus and nucleosomes
What is the Genomic Imprinting? (Monoallelic expression)
the expression of a gene, which depends on whether it is inherited from the male or the female parent. This means that one allele was epigenetically silenced - meaning turned off.
Maternally expressed (paternally imprinted —> paternal gene silenced) —> suppress
growth.
Paternally expressed (maternally imprinted
—-> maternal gene silenced) —-> enhance growth.
What are Tumor Suppressor genes?
Tumor Suppressor genes are genes whose products block cell cycle progression at checkpoints and stop progression of non-functional cells (Negative regulation). Tumor Suppressor gene prevent cancer under normal conditions, stopping the progression of checkpoints followed by DNA repair or apoptosis.
What is the role of oncogenes?
Oncogenes have the potential to cause cancer
They are mutated forms. They are the altered gene, whose product can act to help make a cell cancerous.
Explain why cancer risk increases with age
cancer risk increase with age because with every replication of cells (cell division) we lose telomeres, so there is a chance for mutation. As we age, we are exposed to more mutagens (hazardous environments), which eventually can lead to cancer.
Do we have maternal or paternal inheritance of mitochondria in humans? Explain.
We have maternal Inheritance of mitochondria in humans.
1. Develop from the original small amount of mtDNA in the original egg cell
2. inherited through the mother only (maternal inheritance), not the father.
This means that the mitochondrial DNA is passed only from mother to offspring.
3. Because of this they provide a way to trace ancestry through an unbroken chain of female ancestors.
What is Endosymbiotic theory?
Endosymbiotic theory states that mitochondria and chloroplasts are descended from bacteria (prokaryotic cells) that fused with nucleated cells (any cell with a nucleus).
Hardy-Weinberg proportions can be expressed as equations. What are the 2 equations?
p + q = 1
p = frequency (A) q = frequency (a)
p^2 + 2pq+ q^2 = 1
So then… p^2 = AA 2pq= Aa q^2 = aa
What is the purpose of Polymerase Chain Reaction (PCR)?
PCR multiplies specific segments of DNA
Purpose: digestion of DNA with restriction enzymes
Restriction enzymes splice (cut) the plasmid (circle)
gel electrophoresis definition
Gel electrophoresis is a method for separation mostly DNA, rarely RNA and protein based on size and charge.
What is ligation?
Ligation is the binding gene of interest (specific gene) to the plasmid, so that it can be transformed to the living cells (bacteria).
What is transformation
Transformation is the process of incorporating DNA segment into the chromosome (from the plasmid)
What gives rise to aneuploidy?
The abnormalities of aneuploidy occur due to non-disjunction in Meiosis.
Nondisjunction – chromosome number abnormalities
What is the meiotic recombination?
Occurs in Meiosis, which allows for new combination as compared to the parent. This happens through crossing over and independent assortment
Telomerase definition
It’s an enzyme made up of protein and RNA, which allows for replication at the end of chromosomes. We find this in fetal germ and cancer cells
What is spontaneous mutation?
Spontaneous mutations happen naturally and randomly, which are linked to normal biological or chemical processes in the organism.
What is induced mutation?
Induced (activated) mutations result from the influence of an outside factor, either natural or artificial. For example, natural like UV light or sunlight, which can cause mutation and artificial, such as chemicals in the lab, which also cause mutation.
What is proofreading?
Proofreading – looking for the mistakes by DNA polymerase, which is able to recognize and correct errors that occur during replication. Exonuclease activity functions in proofreading.
Mismatch repair function
Mismatch repair – fix errors that remain after proofreading.
What are the 2 types of Excision repair?
Excision repair: base excision repair and nucleotide excision repair.
Base excision repair
A modified base is removed from DNA strand by base excision repair
What are kinds of gene interactions. Provide brief description of each
Epistasis definition
Epistasis is a circumstance where the expression of one gene is modified (e.g., masked, inhibited or suppressed) by the expression of one or more other genes.
o Gene that is doing the masking
o Ex: blood typing, Labrador retrievers
What is incomplete dominance?
Neither trait is dominant, an intermediate phenotype exists that is a blending
ex. flowers in snapdragons
What is codominance?
Codominance phenotypic detection of both gene products
ex. Lentils (spotted or dotted)
Complete dominance VS Incomplete dominance VS Codominance
Complete dominance: Hybrid resembles one of the two parents
Incomplete dominance: Hybrid resembles neither parent, blending
Codominance: Hybrid shows traits from both parents
What is the cleavage furrow?
It’s the hollow that appears in a cell’s surface when the cell undergoes cytokines (cytoplasm division) in the process of cell division.
What bond is formed between the nucleotides on the DNA?
Covalently linked together by phosphodiester bonds.
This means that nucleotides are bonded together by phosphodiester bonds, which are covalent (non-metal groups).
– A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of another
Recognize genetic diseases that are inherited in an autosomal
dominant and autosomal recessive manner.
Recessive Autosomal Allele o Sickle-cell anemia o Cystic Fibrosis o Tay-Sachs • Dominant Autosomal Allele o Huntington disease
Interpret the symbols used in a pedigree.
Explain extensions to Mendelian genetics about multiple alleles
- The number of alleles within a population can be greater than two.
o Can only have 2 alleles per locus because we have only a pair of chromosomes.
o Multiple alleles arise via spontaneous mutations.
Complementary gene action?
when 2 different genes work together to contribute to one single trait.
What is the effect of temperature on genes?
o Temperature
- Can play a role in an organism’s fur color, as well as survivability.
1) Warm temp —–> no melanin —-> light fur
2) Cooler temp —–> melanin —–> dark fur
What is phenocopy?
- It’s the phenotype arising from an environment agent (such as radiation) that mimics the effect of a mutant gene.
- Ex: PKU disease, missing an enzyme —-> brain damage
Epigenetics meaning?
Epigenetics is the study of how the factors (such as environment, inheritance) can cause changes that affect the way your genes work. When our genes are affected (activated or deactivated) it will change the gene expression without changing the DNA sequence (no mutation). You have a change in the phenotype through the activation or repression of the gene without changing the gene sequence.
Chromosome definition
a threadlike condensed s-re made of protein (histones) and a single DNA molecule that carry the genetic information from cell to cell
Trisomy definition
Trisomy – gain a single chromosome (2n+1)
3 copies of one chromosome are present
o Klinefelter’s —> XXY
o Down syndrome
Distinguish between meiotic and mitotic recombination.
Meiotic recombination serves as accurate chromosome segregation, which requires crossovers
Mitotic recombination - repair of DNA damage, which typically generates non-crossovers
What are the grooves of DNA? It’s function?
Major & minor grooves that are located outside of the helix for allowing proteins to bind to and recognize DNA sequences from outside of the helix.
The group of nucleotides joined together are called?
Nucleic acids, which are the building blocks of DNA or RNA
Nucleotides (DNA vs RNA). + s-re difference?
Nucleotides consist of
1) A nitrogenous base: Adenine, thymine, cytosine, guanine (DNA) & uracil (in RNA)
2) 5- Carbon (Pentose) sugar- ribose (RNA), or deoxyribose (DNA).
NOTE: We lack Oxygen in the s-re of DNA
3) Phosphate group
Describe the process of transcription (in steps)
• Transcription (occurs in nucleus)
o Step 1: Initiation: RNA polymerase binds to promoter of DNA
o Step 2: Elongation: RNA polymerase moves along the template DNA, linking
RNA nucleotides together, forming a complementary mRNA molecule
(but RNA uses U instead of T)
o Step 3: When RNA polymerase reaches termination sequence, it stops
o Step 4: RNA is removed from DNA template strand
o Step 5: mRNA molecule is released
o Step 6: Separated DNA strand forms back into double helix
o Step 7: mRNA is further processed before leaving nucleus to become mature
(5’ meytlated cap, 3’ poly tail, RNA splicing)
Describe the main points of translation (in steps)
Translation (occurs in cytoplasm)
o Step 1: AUG (start codon) encodes for methionine (1st amino acid)
o Step 2: 2nd amino acid is in position and an enzyme forms a peptide bond
between the two amino acids
o Step 3: tRNA for first amino acid is released
o Step 4: Ribosome moves to next codon and repeats, adding 3rd amino acid to chain
o Step 5: Protein synthesis continues until ribosome reaches a stop codon (UAA,
UAG, and UGA)
o Step 6: Ribosome detaches from mRNA
o Step 7: Amino acid chain (polypeptide) released, folds into a 3D structure
What are the types of RNA?
Types of RNA
o Ribosomal rRNA – structural component of ribosomes for protein synthesis (mRNA translation)
o Messenger mRNA – template for protein synthesis, carries genetic info (mRNA strand) from DNA to the ribosome.
o Transfer tRNA – carries amino acids to ribosome for protein synthesis, so that each amino acid corresponds the specific codon of mRNA
DNA vs RNA
List 3 events that happen to pre-mRNA to form mature mRNA in eukaryotes? Describe the modifications made to eukaryotic mRNA during RNA processing?
1) 5’ methylated cap (methyl group CH3 is added to Guanine)
2) 3’ Poly- A tail (Polyadenylation - adding A nucleotides)
3) RNA splicing (introns are removed by splicing and exons are joined)
Be able to use the Genetic Code to translate a sequence of mRNA into a polypeptide.
mRNA contains codons, which correspond to a particular amino acid. We can have the same amino acid for several codons (redundancy).
Uracil replaces Thymine in mRNA
Contrast gene interactions definitions & ratios
Describe how to use Hardy Weinberg to calculate genotype/allele
frequencies. What are the formulas?
- Only works if you have 2 alleles!
• Purpose is to correlate allele & genotype frequency.
• Useful in estimating population changes through a few generations.
• Not useful for predicting long-term changes but does provide a foundation for modeling.
Horizontal gene transfer. Donor cell vs Recipient cell
- Donor cell – organism gives up its entire DNA.
- Recipient cell – receives portion of donor cell’s DNA and incorporates into its own DNA.
Explain the end of chromosome replication problem (telomere) & how cells solve it.
An enzyme called telomerase (made of protein and RNA) fix the telomere by adding base pairs, so that telomere sequences will not disappear.
The RNA is complementary to the DNA in that repeat telomeric region. This allows for these sections (telomeres) to not be shorter each time.
mtDNA vs cpDNA
Genetic material of the mitochondria is referred to as mtDNA. The mitochondrial
proteins are encoded by genes in the nucleus. The proteins are made in the cytoplasm, then transported into the mitochondria. MtDNA is developed only in the egg cell —> maternal inheritance.
Genetic material of the chloroplast is referred to as cpDNA. They have compact gene arrangement (includes introns and exons), contains more genes than the mitochondria. Many chloroplasts’ proteins are also encoded by genes in the nucleus.
What are the 3 reasons for evidence of endosymbiont theory for mitochondria and chloroplasts?
- They have their own DNA
- Like in bacteria, mtDNA (mitochondrial DNA) and cpDNA (chloroplast DNA) are not arranged into nucleosomes
- Comparisons of rRNA gene sequences suggest mitochondrial and chloroplast genomes derive from a common ancestor of nonsulfur and cyanobacteria (types of ancient bacteria – prokaryotic cell)
What is DNA ligase?
a) After DNA polymerase 1 has removed and replaced the primer, a nick remains in
the sugar-phosphate linkage.
b) DNA ligase seals the nick in the sugar by catalyzing the formation of phosphodiester bond without adding another nucelotide
What are the causes of spontaneous mutation?
DNA replication errors, Tautomeric Shifts, Depurination & Deamination, Oxidative
Damages, Replication Slippage
What is DNA replication error? Exonuclease activity?
If DNA repair occur before replication, we can fix it.
If DNA repair doesn’t occur before replication, we get a spontaneous mutation
DNA polymerase in rare cases may incorporate a non-complementary base (instead of A-T, it can be G-T), which can lead to the mutation.
Exonuclease activity checks the mistakes from 5’ to 3’ by DNA polymerase 1 before replication.
Exonuclease is the ability to remove nucleotides one at a time from the end of a chain, fixing it.
Exonuclease activity functions in proofreading.
What are the Tautomeric Shifts?
When tautomers form, in which nitrogenous bases are the shifts from common form keto to rare form enol?
Which common form amino to rare form imino (All or nothing)
Tautomeric shift is the spontaneous mutation, when N base attaches to another chemical element.
For example, Thymine and Guanine - a spontaneous proton shift, when H moves from N to O (keto to enol)
Cytosine and Adenine - H moves from one N to another N. (amino to imino)
As a result, the molecular formula doesn’t change: the keto and enol forms are tautomers of each other, as well as amino and imino. This change can occur during the DNA replication.
Depurination & Deamination
Depurination is the loss of a purine base from a nucleotide.
When we lose the bond between the sugar and nitrogenous base, the base pair, such as Guanine (G) will release and instead we get the apurinic site.
Deamination is the loss of an amino group (NH2) from a nitrogenous base. For example, when Cytosine loses NH2, it will become Uracil. So, we get a sequence C-G –> U-A –> T-A (mutant sequence), which is easier for DNA to detect, because of Uracil base pair. But, this can be sometimes recognized and repaired because of the change to uracil, so that we add NH2 back (easy process).
Oxidative Damages?
Normal byproducts of cellular respiration.
The reactive oxygen species: free radicals (such as superoxide, hydroxide, and hydrogen peroxide).
It often occurs to Guanine (G), forming mispairing with A, which cause T to A mutant sequence. (G-C —> GO-C —-> T-A)
Replication Slippage
During replication slippage, one strand loops out, so that it alters (changes) the newly laid strand causing either trinucleotide repeat expansion or contraction.
Trinucleotide repeats are hotspots for mutation.
What are the causes of Induced Mutations?
Base Analogs, Alkylating Agents, Intercalating Agents, Ultraviolet Light,
Ionizing Radiation
Base Analogs?
Base analogs are chemicals with structures similar to our 4 standard base pairs, so that DNA polymerase can’t recognize the difference between them. When our base analog 5-Bromouracil (5 BU) is incorporated during DNA replication, we get the mutation.
5 BU: one tautomer resembling T pairs with A, other tautomer resembling C pairs with G, so that we get
T:A —-> C:G substitution.
Alkylating Agents
Alkylating agents are chemicals that add an alkyl group, such as methyl (CH3) or ethyl (CH3-CH2) to nitrogenous bases, which change the base pairing. For example, Ethylmethylsulfonate (Mustard gas) adds an ethyl group to the Guanine (G), so that we get 6-Ethylguanine, which pairs with Thymine (T) instead of Cytosine (C). Here, we get G:C —-> A:T substitution.
Intercalating agents?
Intercalating (additive) agents interfere with DNA replication process. They are acridine dyes, which cause insertions and deletions between purines and pyrimidines leading to frameshift mutations. For example, Proflavin, acridine orange and ethidium bromide – the acridine dyes.
UV light?
Purines and pyrimidines readily accept UV light, which results in formation of covalent bonds forming between bases molecules on the same DNA strand. For example, when 2 Thymine on the same strand get exposed to UV light, we get Thymine dimers (means the same), which distort the DNA, blocking replication and cell division.
UV light works to kill bacteria and can cause skin cancer.
Ionizing Radiation?
Ionizing radiations – radiations, which have short wavelengths and high energy.
For example, X-rays is ionizing radiation.
The radiation breaks covalent bonds between sugar-phosphate backbones, which leads to a lot of chromosomal mutations. High doses of radiation kill cells, while lower doses produce point mutations.
What are the 2 double-stranded break repairs?
1) Non-homologous end-joining happens, when the break ends are directly ligated (come together) without the need for a homologous template, so that it repairs itself without the help of sister chromatids. This is messy (mutagenic), removing some base pairs and ligating (bonding) the 2 strands back together. As a result, we often get some base pairs that end up being deleted there, which were removed.
2) Homologous recombinant repair uses the DNA strands either from homologous chromosomes (DNA is not replicated) or sister chromatid (if DNA has been replicated) to repair a lesion on the other sister chromatid.
