Exam 3 Review
1. Meiosis
Sexual vs. Asexual Reproduction:
Sexual reproduction promotes genetic diversity but requires significant resources.
Asexual reproduction is energy-efficient but produces genetically identical offspring.
Advantages vs. Disadvantages
Sexual Reproduction Advantages
Variation → if environment changes
No advantage if environment stays the same
Sexual Reproduction Disadvantages
Requires more than one cell (needs to find another gamete) → requires a lot of energy and time
Asexual Reproduction advantages
Requires 1 cell (no need for a mate) → uses less energy, quicker and faster reproduction
Asexual Reproduction Disadvantages
No variation → cannot adapt to environment
Purpose of Meiosis:
Reduces chromosome number from diploid (2N) to haploid (N).
Get 4 daughter cells at the end of meiosis
Each daughter cell has 23 chromosomes
Introduces genetic diversity through crossing over and independent assortment.
Stages of Meiosis:
Meiosis I (Reductional Division):
Prophase I: Homologous chromosomes held together tightly at synaptonemal complex, chromosomes begin condensing,
Crossing over occurs at chiasmata. (segments of chromosomes are exchanged through crossing over)
Prometaphase I: spindle fibers attach to kinetochore, homologs still held together at chiasmata, nuclear envelope is completely broken down, chromosomes continue to condense
Metaphase I: Homologous pairs align at the metaphase plate;
independent assortment occurs. (maternal and paternal chromosomes orient randomly when they migrate to poles)
Anaphase I: Homologous chromosomes are pulled to opposite poles, independent assortment still occurs here
Telophase I and Cytokinesis: Two haploid cells form, each containing duplicated chromosomes.
Meiosis II (Equational Division):
Interkinesis- happens before but no s phase (no replication occurs)
Prophase II: Chromosomes re-condense; spindle fibers reform
Prometaphase II: nuclear envelope disappears, spindles fully formed, each sister chromatid attaches a kinetochore and attaches to microtubules from opposite poles
Metaphase II: Chromosomes align individually at the metaphase plate.
Anaphase II: Sister chromatids are pulled apart to opposite poles, nonkinetochore microtubules lengthen the cell
Telophase II and Cytokinesis: Four haploid cells are produced, each genetically unique. ( so we get a haploid number of chromosomes)
Key Processes that result in genetic variation:
Crossing Over: Exchange of genetic material between homologous chromatids in Prophase I.
Recombinant nodule- enzyme that cuts and makes sure genetic info equal length facilitates transfer and reattaches them
Chiamata- visible site of crossing over
Crossing over produces recombinant chromosomes (which are a mix of both parents)
Further genes are apart the more likely to cross over
Independent Assortment: Random orientation of chromosome pairs during Metaphase I and in Anaphase I the chromosomes get separated.
Random fertilization: Any unfertilized egg can fuse with any unfertilized sperm
Key Terms
Gene- unit of heredity that codes for RNA
Locus- location of a gene on a chromosome
Allele- versions of a gene
Homologous chromosomes:
1 chromosome from each parent
Same size and shape
Same location of centromere
Genes controlling the same inherited characteristics (maybe different versions of the same genes)
Ploidy- # of set of chromosomes in a cell of an organism
Humans are diploid (2n) has two sets of chromosomes
Diagram:
Meiosis I and II: Key Events
[Illustration of the stages of meiosis I and II, showing chromosome behavior during each phase.]
Crossing over:
[crossing over illustration]
Independent assortment: (2n=4)
[Independent assortment illustration]
Conclusion:
Meiosis ensures genetic diversity and accurate chromosome distribution in sexually reproducing organisms. Its mechanisms, such as crossing over and independent assortment, provide variation crucial for evolution.
2. Genetics I
Mendel’s Experiments:
Mendel’s experiments with pea plants demonstrated patterns of inheritance in P, F1, and F2 generations.
Pea plants were used because:
Have a lot of simple traits, monoecious (male/female in 1 flower - easy to manipulate), short generation times, produce many seeds
Concluded that translate transmitted from parent to offspring independently of other traits and ion dominant and recessive patterns
Established:
Principle of Segregation: Each organism carries two alleles per gene, which separate during gamete formation.
Principle of Independent Assortment: Genes on different chromosomes assort independently. Applies to genes on different homologous chromosomes.
Mendel’s Concepts
1. Heredity is particulate, and alternative version of genes (alleles) account for variation in inherited traits
2. An organism inherits two alleles for each trait, one from each parent
3. There is a dominant allele which is expressed, and a recessive allele that has no noticeable effect on appearance
4. Principle of segregation: two alleles for a heritable trait separate to different gametes. A gamete only gets one of the two alleles
Pre-Mendel Belief:
Believed in blending hypothesis- offsprings were an average of both traits
Key Concepts:
Monohybrid Cross: Examines inheritance of one trait; 3:1 phenotypic ratio.
Dihybrid Cross: Examines two traits; 9:3:3:1 phenotypic ratio.
Punnett Squares: Predict offspring genotypic and phenotypic ratios.
Non-Mendelian Inheritance:
Incomplete Dominance: Phenotype is an intermediate blend (e.g., red and white flowers produce pink).
Codominance: Both alleles are fully expressed (e.g., AB blood type).
Overdominance: no dominant or recessive heterozygous is more adaptive
Pleiotropy: A single gene affects multiple traits (e.g., Marfan syndrome).
Epistasis: One gene modifies or masks the expression of another gene.
Polygenic Inheritance: Traits influenced by multiple genes (e.g., skin color, height).
Andirdria:
It is a dominantly inherited disorder, where eye vision is impaired. Small towns in Michigan children have the disease but parents do not. Bc she met a man with aniridia and got with him. Reason for the actual mutation is possibly water pollution.
Important Key Terms:
Phenotype- physical trait (observable trait)
Genotype-underlying genetic makeup
Genes- hereditary unit factor
Locus- location of a gene
Testcross- used when we don't know the individual (mystery) so we cross with a homozygous recessive
Diagram:
Punnett Squares: Monohybrid and Dihybrid Crosses
[Illustration of Punnett squares showing examples of monohybrid and dihybrid crosses.]
Conclusion:
Mendel’s principles provided the foundation for understanding inheritance. Modern genetics incorporates complexities like non-Mendelian inheritance and polygenic traits, explaining real-world diversity.
3. Genetics Part 2, Nondisjunction, and Chromosomal Errors
Chromosomal Theory of Inheritance
Hypothesis that chromosomes carry genes
Boveri- found that there was an equal importance of maternal and paternal genetic material using sea urchins
Sutton- chromosomes occur in homologous pairs and segregate into daughter cells in meiosis using grasshoppers
Morgan- provided actual evidence that specific genes on a specific chromosome
Morgan's Experiment with Fruit Flies:
White eyes were the mutant allele; red eyes were the normal allele
Found that the gene was on the x chromosome so could reason why the f1 and f2 generations were the way they were.
F1 generation
Morgan crossed a red-eyed female (w⁺w⁺) with a white-eyed male (wY).
Result: All F1 offspring have red eyes. This showed that the white-eye mutation is sex-linked.
F2 generation
Morgan then allowed the F1 generation to interbreed (w⁺w × w⁺Y):
Result: White-eyed flies reappear in the F2 generation, but only in males. This confirmed that the gene for eye color is located on the X chromosome.
Key reasoning
Males inherit their X chromosome from their mothers and their Y chromosome from their fathers.
The white-eye mutation in males (wY) appears because they have no second X chromosome to mask the recessive trait.
Females require two copies of the mutation (w⁺w) to express the white-eye phenotype, which is why no white-eyed females appeared in the F2 generation.
Below there is a picture for how the generations happened.
Barr Body:
One of the two chromosomes in each cell is randomly inactivated during embryonic development. The inactive x condenses into a tightly coiled Barr Body and genes can be expressed.
This is done so that no overexpression of the x gene.
Linked Genes:
Linked genes are usually inherited together
If genes are linked than they are on the same chromosome
If we cross two organisms with 2 linked genes they should have 2 gamete possibilities.
If genes are not linked they are not on the same chromosome
If we cross two organisms with that are not linked linked with 2 different genes they should have 4 gamete possibilities
If genes are located on separate chromosomes we predict a 1:1:1:1 ratio. If genes are located on the same chromosome and are inherited together we predict there to be a 1: 1 ratio
The problem is that this didn't happen. This is because linkage is incomplete and you get recombinants due to crossing over. (so they are not assorting independently and they are not on different chromosomes)
(illustration below)
Definitions:
Euploidy- normal set of chromosomes
Aneuploidy- missing or having an extra chromosomes
Monosomic zygote- missing one chromosome, only has one copy of particular gene
Trisomic zygote- has 3 copies instead of a pair (ex. Down syndrome)
Nondisjunction- occurs when homologous chromosomes fail to separate (during Meiosis I) or when sister chromatids fail to separate (during Meiosis II)
Results of Nondisjunction:
Monosomy: Missing one chromosome (e.g., Turner syndrome).
Trisomy: Extra chromosome (e.g., Down syndrome, Trisomy 21).
Disorders Caused by Structurally Altered Chromosomes:
Cri du chat- Specific deletion in chromosome 5; caused by defective sperm
Duplication on chromosome 17- leads to overexpression, which leads to abnormal myelin, which affects transduction in neurons so it wont work properly
Inversions
They affect linkage and may disrupt genes
Paracentric- does not include the centromere
Pericentric- does include the centromere
Can change the relative length of the chromosome arms
Philadelphia Chromosome- chromosome 22 is broken off and moved to chromosome 9, now chromosome 9 is much longer
Brings two genes that are not supposed to be together leading to overactivation and overregulation of gene , which can cause cancer
Uniparental disomy
Have 2 chromosome (both coming from the same parent); extra copy of the same chromosome
*Know mice example
PWS (Prader Willi Syndrome)- egg has an extra copy of the same chromosome
AS (Angelman Syndrome)- sperm has extra copy of the same chromosome
Chromosomal Structural Changes:
Deletion: Loss of a chromosome segment.
Duplication: Repetition of a segment.
Translocation: Movement of a segment to a non-homologous chromosome.
Inversion: Reversal of a chromosome segment.
Diagram:
[Morgan’s fruit fly experiment illustration]
[Illustration of Gene Linkage]
Nondisjunction in Meiosis I vs. Meiosis II
[Illustration of nondisjunction processes showing the outcomes of errors during Meiosis I and II.]
Conclusion:
Errors in meiosis, such as nondisjunction, highlight the importance of precise chromosomal segregation. These errors can result in significant genetic disorders.
4. DNA Structure and Replication
Historical Experiments:
Prehistory: Morgans experiment showed that genes are located on chromosomes, so they questioned which one is genetic material DNA or proteins
Most people at the time believed proteins were the carriers of genetic information because proteins are made up of 20 different amino acids, offering a greater variety for encoding information, whereas DNA is composed of only four nucleotides.
Griffith’s Experiment
Two strains of bacterium, one pathogenic (virulent= disease causing) and one virulent
R cell injected into mice → mice lived
Heat killed S cells injected into mice → mice lived
R cell + Heat killed S cells injected into mice → mice dead; they found S strain in heart
reasoned that a 'transforming principle' from the dead S cells enabled the R cells to transform into virulent S cells.
Question: What is the transformation factor?
Avery, McCarty, and MacLeod confirmed DNA as the genetic material.
Experimental Design
Question- What is the transforming agent made up of?
Hypothesis (3)- The transforming agent is made up of RNA; The transforming agent is made up of proteins; The transforming agent is made up of DNA
Prediction: If we were to take S strain cells and kill them in heat filter them out and put them into 3 batches and add RNAse in one batch (which removes rna), add Proteinase in another batch (which removes proteins) , and DNAse in another batch (which removes DNA), we expect to see virulent S strain and R strain bacteria in the batches where RNA and Protein was removed, but only the R strain bacteria in the batch where DNA was removed.
Proved that DNA was the transforming substance
Hershey and Chase used bacteriophages to prove DNA's role.
Structure of DNA:
Watson and Crick
Double-helix structure with base pairing (A-T, C-G).
Antiparallel strands with 5’ and 3’ ends.
Chargaff's Rules
Amount of adenine is equal to the amount of thymine. Amount of Cytosine is equal to the amount of Guanine.
The amount of Purines equals the amount of Pyrimidines
In same species concentration for bases are the same, but differ among species
DNA Replication:
Read DNA IN 3’ to 5’
Synthesize DNA from 5’ to 3’
Polymerase removes hydroxyl group
To add nucleotide we have to remove hydroxyl group
Base pairing in DNA
One purine and 1 pyrimidine
The two dna are complementary
Each strand acts as a template
DNA Replication Hypothesis
Semi conservative Replication
In semi-conservative replication, each DNA molecule consists of one original (parental) strand and one newly synthesized strand. The original strands come apart and a complementary strand gets added to each of the original strands.
After one generation, the DNA is intermediate in density (one parent + one new strand per molecule). By the second generation, half the DNA molecules are light (two new strands) and half are intermediate, and this pattern continues in subsequent generations.
Conservative Replication
In conservative replication, the entire parental DNA molecule remains intact, and a completely new DNA molecule is synthesized.
After one generation, two distinct types of DNA are present: heavy parental DNA and light newly synthesized DNA. Over successive generations, the proportion of light DNA increases, but the original heavy DNA remains unchanged.
Dispersive Replication
In dispersive replication, both DNA strands are broken into fragments, and the new and old DNA fragments are reassembled into hybrid strands. (chops off DNA into bits and pieces)
After one generation, the DNA is intermediate in density, but unlike semi-conservative replication, all molecules are a uniform mix of old and new DNA. In subsequent generations, the DNA becomes progressively lighter as more new DNA is incorporated.
Meselson and Stahl Experiment
Wanted to see which DNA replication hypothesis was correct
Experimental Design
In the Meselson and Stahl experiment, they grew bacteria in heavy nitrogen (N-15) so the DNA would become "heavy," then switched the bacteria to light nitrogen (N-14) and allowed the DNA to replicate. They used centrifugation to separate DNA by density and tracked how the DNA changed over generations. After one replication cycle, all DNA was intermediate in density, ruling out conservative replication. After two cycles, there was both intermediate and light DNA, confirming that DNA replication is semi-conservative.
Semi-Conservative Model was proven by Meselson-Stahl.
illustration below
Origin of Replication
Eukaryotes
Multiple points of replication
Prokaryotes
1 origin of replication
Key enzymes:
Helicase: Unwinds DNA.
Topoisomerase: Relieves tension.
Ligase: Joins Okazaki fragments on the lagging strand.
(NOT KEY) DNA polymerase 2- plays a role in proofreading
DNA REPLICATION STEPS (Leading Strand)
1. Helicase separates two strands that are hydrogen bonded; and unwinds the strands
2. Single stranded binding proteins prevent it from hydrogen bonding to itself again
3. As helicase unwinding it will supercoil downstream, so topoisomerase will cut and rejoin the backbone to relieve the tension (if we don't do this then it will supercoil and eventually break)
4.Need a primer for DNA to work
5.Primase will make a primer (RNA)
6. Primase makes an RNA copy
7. 3’ hydroxyl group from which DNA Polymerase can add DNA nucleotide going forward
DNA REPLICATION STEPS (Lagging Strand)
1. Primase will add primer
2. DNA polymerase 3 will extend the primer
3. DNA polymerase 1 will remove the primer RNA nucleotides will be removed and replaced with DNA nucleotides
4. DNA ligase will join the sugar phosphate backbone of the Okazaki fragments together at the end.
Leading vs Lagging Strand
Leading Strand
If DNA polymerase is moving in same direction as helicase
Lagging Strand
If DNA polymerase is moving in opposite direction as helicase
Repeated rounds of replication produce shorter DNA molecules
Not a problem for Prokaryotes because
Prokaryotes DNA is circular, meaning there are no ends to replicate—each strand is continuous and complete, avoiding the shortening problem entirely.
Problem for eukaryotes
Linear, so there is an end, so you can remove the primer but cant replace it so tips of your chromosome will be missing segments of double stranded DNA, everytime you replicate DNA will continue to get shorter
Telomeres were the fix to this problem for eukaryotes
Telomeres- Nucleotide sequences at the end of eukaryotic chromosomes
There will be no short chromosomes passed onto the next generation because of telomerase
Telomerase is an enzyme that lengthens the telomeres when they divide.
Diagram:
[Illustration of Meselson and Stahl Experiment and DNA Replication Hypothesis]
Replication Fork and Key Enzymes
[Illustration showing DNA replication with leading and lagging strands.]
Conclusion:
DNA replication ensures accurate genetic transfer during cell division. Its semi-conservative mechanism maintains genetic stability.
5. Transcription and Translation
GENETIC INFORMATION OVERVIEW
DNA → RNA → Protein → Phenotype
Ribosomes are the sites of translation
Genetic Code
Written for mRNA
Why must there be 3 nucleotides
2 nucleotides → only gives you 16 unique combinations not enough
3 nucleotides – gives you 64 combinations
Genetic code is redundant/degenerate
More than one code for one amino acid → some mutations will have no affect
Found what it codes for by starting with the simple codon (UUU) finding out the amino acid it codes for nd continued until figured out all the combinations
Nearly Universal
You can take genes from one eukaryote and plop them into another eukaryote and the gene will be translate the protein
Example
pig and jellyfish gene
tobacco plant and firefly gene
Gene Expression in Prokaryotes
Transcription and translation happen simultaneously because there is no nucleus
Gene Expression in Eukaryotes
Transcription and translation do not happen simultaneously. There is a physical separation between transcription (occurs in nucleus) and translation (occurs in cytosol) that makes it so that it doesn't happen simultaneously.
Transcription (DNA to RNA):
General Overview
RNA polymerase binds to promoters, synthesizing mRNA.
mRNA undergoes processing (5’ cap, poly-A tail, splicing).
3 stages
Initiation
The TFIID is the first thing that binds. Part of the TFIID is the TBP which recognizes the TATA box sequences, and tells TFIID to bind to the promoter, then it will detach. As other factors join, it further stabilizes the pre initiation complex and contributes to the recruition of the RNA polymerase II when RNA polymerase II is added initiation is complete and the transcription initiation complex is created.
Elongation
The next step is elongation, in order for it to start the transcription factors must leave. The polymerase will proceed along the DNA template. It will unwind the two strands of DNA, synthesize complementary RNA going from 5’ to 3’.We need to move histones everytime RNA polymerase encounters a nucleosome. So with the help of FACt a histone chaperone. FAct will pull histines away from the dna template as the RNA polymerase moves along it. Once pre rna is synthesized the FAct complex will replace the histones to recreate the nucleosome.
Termination
Eukaryotes don't have terminator sequences (only prokaryotes). Soa signal sequence in the DNA, called the polyadenylation signal sequence (ex. AAUAAA), will trigger the termination of transcription.
Pre mRNA processing in eukaryotes
Key terms
exons - code for amino acids
introns - do not code for amino acids but will be transcribed because it is in the middle of the gene
premRNA will be much longer than mature RNA because has extra info
RNA polymerase will start at the promoter sequence and keep going towards 3’ end
The complex protein will cut extra rna at the cleavage site. Then a g cap will be added to the 5' end. A poly tail will get added to the 3' end.
Introns will be cut out of the preRNA to get mature RNA (this process is called splicing). Spliceosomes will be used to put the exons together.
Functions of the poly a tail and G cap
Poly a tail-facilitates the export of mRNA out of the nucleus
5’ cap- helps the ribosomes attach to the 5’ end and start translation
Both- protect mRNA from hydrolytic enzymes → sp mRNA can last a long time
Alternative splicing
Multiple traits produced the same gene through alternative splicing
Example: different exons were removed from the same gene and got different characteristics (smooth muscle and skeletal muscle)
Functional Importance of introns
Alternative RNA splicing
Genes nestled inside introns of other genes
Regulate ribosomal protein gene s
Translation (RNA to Protein):
General Overview
Ribosomes translate mRNA codons into amino acids.
tRNA
Is one strand that is hydrogen bonded and folds on itself
It has an anticodon on the bottom
3d shape matter bc has to fit in ribosome when it fits the anticodon of trna has to match the codon of mrna
Steps:
Initiation: Ribosome assembles at the start codon (AUG).
Translation begins when the mRNA binds to the small ribosomal subunit, aligning the start codon (AUG) in the proper position. The initiator tRNA, carrying methionine (Met) and equipped with a complementary anticodon (UAC), pairs with the start codon in the P site. GTP provides energy for this process, facilitating the attachment of initiation factors and the joining of the large ribosomal subunit. Once the large subunit binds, the ribosome is fully assembled, and the initiator tRNA is correctly positioned in the P site to start polypeptide synthesis.
Elongation: Amino acids are added sequentially.
Codon Recognition: A charged tRNA with an anticodon complementary to the codon in the open A site enters the ribosome
Peptide Bond Formation: The ribosome catalyzes the formation of a peptide bond between the growing polypeptide chain (held by the tRNA in the P site) and the amino acid on the tRNA in the A site.
Translocation: The ribosome moves along the mRNA, shifting the tRNA from the A site to the P site, and the tRNA in the P site moves to the E site, where it is released. This leaves the A site open for the next tRNA, and the process repeats for each codon in the mRNA.
Termination: Stop codon signals release of the polypeptide chain.
Termination begins when a stop codon (UAA, UAG, or UGA) appears in the A site. Since there are no tRNAs with anticodons complementary to stop codons, a release factor binds to the A site instead. The release factor uses GTP to help cleave the bond between the polypeptide and the tRNA in the P site, freeing the newly synthesized polypeptide. Finally, the ribosomal subunits, release factor, and mRNA dissociate, completing the process of translation.
Termination requires the hydrolysis of a GTP molecule.
Diagram:
Transcription Process:
Translation Process: Codons and Ribosomal Sites
[Illustration showing ribosomal sites (A, P, E) and polypeptide elongation.]
Conclusion:
Transcription and translation are crucial for gene expression, converting genetic information into functional proteins.
7. Mutations
Mutations- changes in the genetic material of a cell
Point mutations- are chemical changes in just one base pair of a gene
Types
Base pair Deletion or insertions
Base pair substitutions
Silent Mutation- Codon has changed but we have the same amino acid
No effect on polypeptide
Shows the positive side of redundancy in genetic code
Missense Mutation- middle nucleotide changed, causing amino acid to change
May or may not have effect on protein
Sickle cell affects only one change in amino acid
Nonsense Mutation- single base pair changed that causes codon to become a stop codon
More severe → could have tiny polypeptide that does nothing if stop codon happens during the beginning
Frameshift Mutation- base pair addition or deletion → changes reading frame → them everything is being shifted
Shifts everything so amino acids after it are changing
Other Frameshift Mutations
ex) Frameshift leading to nonsense mutation
2 base pairs missing → codes for a stop codon
* add or delete three base pairs does not change the whole thing, you just add an amino acid or loose one
Conclusion:
Mutations are changes in the genetic material that can affect protein synthesis and function in various ways. Point mutations, such as substitutions, deletions, or insertions, can lead to silent (no effect), missense (amino acid change), or nonsense mutations (premature stop codons). Frameshift mutations, caused by insertions or deletions that alter the reading frame, can significantly disrupt protein structure. While some mutations are neutral or even beneficial, others can result in severe consequences, such as genetic disorders.