Chapter 7: RNA, The Genetic Code, Mitosis/Meiosis, and Mendelian Genetics Flashcards Preview

MCAT Biochemistry > Chapter 7: RNA, The Genetic Code, Mitosis/Meiosis, and Mendelian Genetics > Flashcards

Flashcards in Chapter 7: RNA, The Genetic Code, Mitosis/Meiosis, and Mendelian Genetics Deck (66):
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Control of Gene Expression in Prokaryotes

Operon

operon components?

operon purpose?

how does it work?

 

How do the following work:

Positive Control Operon System?

Negative Control Operon System?

  • Operon = a cluster of genes that are transcribed as a single mRNA.
    • Operons control the gene expression in prokaryotes
    • Allows gene expression to be controlled
  • Components:
    • Structural genes: code for proteins of interest
    • Promoter site: site where the RNA polymerase begins transcription
    • Operator site: site where repressor protein binds to prevent transcription
    • Regulator gene: codes for the Repressor protein

 

Positive Control Operon System

[This results in transcription being turned on]

  • Transcription is turned off at default.
    • The repressor protein blocks the operon, so that RNA polymerase cannot transcribe the mRNA.
  • Presence of an inducer molecule turns on transcription by blocking the repressor protein.
    • Thus, transcription of the structural genes occurs.

 

Negative Control Operon System

[This results in transcription being turned off]

  • Transcription is turned on at default.
    • A repressor protein is inactive.
  • When a Corepressor molecule is present, it activates the repressor protein, which turns off transcription.

 

 

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In what direction does transcription and translation occur?

 

5' ⇒ 3'

or 

3' ⇒ 5'

Transcription:

The template strand of DNA is 3' ⇒ 5'

mRNA is transcribed from the template strand in the 5' ⇒ 3' direction.

 

Translation:

In the ribosome, mRNA is translated into protein in the 5' ⇒ 3' direction

 

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Frameshift mutation

Frameshift mutation

  • Mutation of the mRNA sequence that is translated into protein
  • Occurs when nucleotides are added to or deleted from the mRNA sequence.
  • This shifts the way codons are read.

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Translation Mechanism and Steps

(Initiation, Elongation, Termination, and Post-translational Processing)

Include the few differences for prokaryotes and eukaryotes

How are peptide bonds formed? Ribozyme?

 

Translation

mRNA ⇒ Protein

in the cytoplasm

Steps: (Initiation, Elongation, Termination)

  1. Initiation: (Assisted by Initiation Factors)
    1. Small rRNA subunit binds to the front of mRNA.
      • Prokaryotes:
        • Small rRNA (30S) subunit binds to the Shine-Dalgarno sequence of the 5' front of mRNA
      • Eukaryotes:
        • Small rRNA (40S) subunit binds to the 5' methylated cap of mRNA
    2. The anticodon sequence of initiator tRNA binds to the AUG stat codon in the P-site of the ribosome, bringing in the initial amino acid.
      • Prokaryotes: 
        • Initial amino acid: N-formylmethionine (fMet)
      • Eukaryotes:
        • Initial amino acid: Methionine
    3. Large subunit binds to small subunit 
      • Prokaryotes (50S); Eukaryotes (60S)
  2. Elongation: (Assisted by Elongation Factors)
    1. Ribosome moves in the 5' ⇒ 3' direction along the mRNA, making the protein from its amino (N) to carboxyl (C) terminus.
    2. tRNA brings amino acids to the A-site
    3. The peptide chain grows from the P-site
    4. Ribozyme activity (part of large subunit)
      • Peptidyl transferase uses GTP to form peptide bonds between the amino acids as the A-site tRNA moves to the P-site and adds more amino acids
        • Peptidyl transferase is part of the large subunit of ribosomes
    5. After attaching amino acids to the grow peptide chain, tRNA leaves at the E-site
  3. Termination: (Assisted by Termination Factors)
    1. Stop codon reaches the A-site.
    2. Release-factor protein binds to the stop codon, causing the peptide chain to be hydrolyzed off of the ribosome and tRNA.
    3. Both ribosomal subunits separate.
  4. Post-Translational Processing:
    1. In the endoplasmic reticulum (ER), the peptide chain is folded in by chaperone proteins.
    2. Proteins can also be phosphorylated, carboxylated, glycosylated (sugar added), methylated, etc.
    3. Proteins are transferred to the Golgi for further modification and export

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Where does transcription and translation take place?

 

Transcription occurs in the nucleus

(DNA ⇒ mRNA)

 

Translation occurs in the cytoplasm

(mRNA ⇒ Protein)

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Transcription Mechanism and Steps

Include Post-Translational Processing

 

TATA box?

snRNA and snRNPs?

 

Does post-Translational Processing occur in both eukaryotes and prokaryotes?

Transcription and Post-Translational Processing

In the nucleus

DNA ⇒ mRNA

 

Transcription Steps (Nucleus):

  1. Topoisomerase gets rid of the supercoiling and Helicase separates the two DNA strands.
    • Coding strand + Template strand
  2. RNA polymerase locates certain genes by identifying promoter regions of DNA.
    • TATA Box = promoter region in eukaryotes
      • Has a lot of thymine and adenine bases because they have weaker bonds and can be separated easily
      • Located 25 bases before the first base of the desired gene.
    • Transcription factors help RNA polymerase find and bind to the promoter regions
  3. RNA polymerase travels and reads from 3' ⇒ 5' on the template strand to transcribe the mRNA in the 5' ⇒ 3' direction.
    • Does not need RNA primer and does not proofread its work.
  4. RNA polymerase continues to transcribe the mRNA in the 5' ⇒ 3' direction until a stop sequence is reached.
  5. DNA double helix reforms and the transcription product is pre-mRNA that undergoes post-transcriptional processing.

 

Post-Transcriptional Processing Steps (Nucleus of Eukaryotes only)

  1. In the spliceosome of the nucleus, introns are removed as lariat loops (lasso-shapes) and exons are spliced together.
    • Spliceosome complex is made up of:
      • snRNA: small nuclear RNA molecule
      • snRNP: small nuclear ribonucleoproteins
  2. A Methylated cap is added to the 5' front of the mRNA.
  3. A Poly-A tail is added to the 3' end of the mRNA.
  4. Mature mRNA has now been formed and it exists the nucleus to the cytoplasm.

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Transcription Factors

what are they?

what are they involved in?

domains (2) and their functions?

 

In eukaryotes or prokaryotes?

Transcription Factors proteins

They regulate gene expression in Eukaryotes

Proteins that activate transcription at certain regions of DNA

 

Transcription factor proteins have 2 domains:

  1. DNA-binding domain - binds to specific DNA sequences to help recruit transcription machinery.
  2. Activation domain - allows transcription machinery to bind (ex: RNA polymerase).

 

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hnRNA is another term for the pre-mRNA

heterogeneous nuclear mRNA

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Where are ribosomes made?

 

Where do they function?

Made in the nucleus

 

In the cytoplasm, they translate mRNA into proteins 

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tRNA

 

what does it do? where?

anticodon? how does it match the mRNA?

where is the amino acid held?

 

Also, what is aminoacyl-tRNA Synthetase?

Transfer RNA (tRNA)

  • In the cytoplasm, tRNA brings and matches amino acids to their respective codons on the mRNA of the ribosome. 
    • It builds the peptide chain of amino acids
  • tRNA has an anticodon (3 base) sequence on it which is complementary to the codon on mRNA
    • This is how the tRNA knows where to put the amino acid
  • Each amino acid is attached to the 3' hydroxyl of tRNA

Aminoacyl-tRNA Synthetase

enzyme that uses ATP to bind the amino acid to 3' hydroxyl of tRNA

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What is the start codon for every eukaryotic protein?

 

what amino acid does it code for?

Methionine (AUG)

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Point mutation

 

what if it occurs at the wobble position?

 

3 types:

Silent Point Mutation?

Missense Mutation?

Nonsense Mutation?

Point mutation

  • A mutation that affects one of the nucleotides in a codon
  • Silent point mutation:
    • If it occurs at the wobble position (3rd base of codon), it will be silent and not affect the amino acid selected.
      • This is because the first two bases of a codon determine the amino acid, not the third base
  • Missense mutation:
    • A point mutation that changes a codon and results in a different amino acid
  • Nonsense mutation:
    • A point mutation that changes a codon into a premature stop codon, ending the protein translation

 

 

 

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What are the 3 stop codons

 

what do they do?

UGA

UAA

UAG

 

U Go Away

U Are Away

U Are Gone

 

They end translation of mRNA to protein

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Control of Gene Expression in Eukaryotes 

(via regulation of chromatin structure and Methylation)

 

Heterochromatin vs Euchromatin?

Histone Acetylation vs Histone Deacetylation?

DNA Methylation?

Control of Gene Expression in Eukaryotes 

(via regulation of chromatin structure and methylation)

  • Heterochromatin = tightly packed chromatin that is transcriptionally inactive
  • Euchromatin = loosely packed chromatin that is transcriptionally active

 

  • Histone Acetylation = makes chromatin transcriptionally active
    • Histone Acetylase adds acetyl to histone proteins, causing the chromatin to become looser Euchromatin form.
  • Histone Deacetylation = makes chromatin transcriptionally inactive
    • Histone deacetylases remove acetyl from histone proteins, causing the chromatin to become tighter Heterochromatin form.

 

  • DNA Methylation = DNA methylase adds methyl groups to DNA, causing chromatin to wrap tightly and become transcriptionally inactive

 

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mRNA

 

how is it made?

what does it do?

 

monocistronic mRNA?

polycistronic mRNA?

Messenger RNA

  • In the nucleus, RNA polymerase transcribes mRNA from template DNA strands 
  • Carries information to the ribosome that specifies the amino acid sequence of the protein.
    • Has codons (3 bases) that code for certain amino acids
  • Monocistronic mRNA = Eukaryotic mRNA that translates into one protein
  • Polycistronic mRNA = Prokaryotic mRNA that translates into multiple proteins

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rRNA

 

what is it?

where is it made?

what size make up prokaryote ribosomes and eukaryote ribosomes?

Ribosomal RNA

  • It is a major component of ribosomes
    • Ribosomes are made of rRNA and proteins
  • It has enzymatic activity
  • It is made in the nucleus and goes to the cytoplasm to become ribosomes
  • The subunits bind together only when mRNA is translated to protein

 

  • Eukaryotic ribosomes = 80S ribosome
    • Small subunit: 40S rRNA
    • Large subunit: 60S rRNA
  • Prokaryotic ribosomes = 70S ribosome
    • Small subunit: 30S rRNA
    • Large subunit: 50S rRNA

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Purpose of introns?

 

And alternative splicing?

  • Introns are the regions of the mRNA precursor that are removed to form the mature mRNA.
  • Intron functions:
    1. Regulate cell gene expression.
    2. Separate exons so that a single mRNA can be spliced in different ways to form different proteins (alternate splicing).
    3. Can be included in the mature mRNA transcript to promote protein production.
  • Introns allow eukaryotic cells to evolve new genes readily.

 

Alternative Splicing

One gene can make many proteins.

Because, a single gene can be spliced in multiple ways to yield different mature mRNAs; thus, different proteins.

 

 

 

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Central Dogma of Molecular Biology

DNA ⇒ RNA ⇒ Protein

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Control of Gene Expression in Eukaryotes

via Enhancers and Transcription factors

 

components?

mechanism and steps?

 

Control of Gene Expression in Eukaryotes

Enhancer Regions + Transcription Factors

they control gene expression in eukaryotes

 

  • Transcription factors = proteins that activate transcription by binding to promoter regions of DNA and allowing transcription enzymes to bind (ex: RNA polymerase).
    • Have 2 domains:
      • DNA-binding domain =  binds to the enhancer and promoter regions of DNA
      • Activation domain = allows transcription enzymes to bind
  • Enhancer = a region of DNA where transcription factors bind and activate the RNA polymerase for transcription.

 

Mechanism:

  1. Transcription factors bind to the promoter site and recruit RNA polymerase
  2. Transcription factors bind to the enhancer site way upstream of the promoter site.
  3. The DNA bends so that the enhancer site can touch and activate the RNA polymerase at the promoter site.
  4. Transcription begins.

 

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Why is the genetic code considered degenerate?

 

Wobble position? Evolutionary advantage of it?

  • The genetic code is degenerate
    • because more than one codon can specify a single amino acid.
    • Example: All the following codons code for Alanine (wobble position underlined)

      GCU, GCC, GCA, GCG

  • Each amino acid is encoded by multiple codons.
  • The first two bases are the same for each amino acid, except the third base is different.
  • Wobble position = the third base of a codon, which varies for multiple codons of a single amino acid.
    • It is an advantage, because if a mutation occurs to the third base, the correct amino acid will still be selected.

 

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chromosomes vs chromatin

Chromosomes - compactly wrapped chromatin (DNA) with histone proteins that wrap it with supercoils

 

 

Chromatin - all of the DNA with histones that wrap it around

 

 

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Non-coding RNA (ncRNA)

RNA that does not code for protein products

 

it contributes to the regulation of gene expression by affecting the chemical changes that alter chromatin structure

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How many double stranded DNA molecules do we have?

 

How many of them code for the same traits?

 

How many homologous pairs of chromosomes do we have?

We have 46 double-stranded DNA molecules (chromosomes)

 

Half of them code for the same traits as the other half

 

Thus, we have 23 homologous pairs of chromosomes,

each with a chromosome from our mom and from our dad

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what makes up the genome?

DNA, histones, and some RNA

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nucleosomes

complex of DNA wrapped around histones

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During transcription,

 

which strand is transcribed to mRNA (coding strand or template strand)?

 

which one is the same as the mRNA? 

which one is complementary to the mRNA?

RNA polymerase transcribes mRNA from the template strand

 

mRNA and the coding strand are the same, other than the uracil and thymine differences between DNA and RNA

 

thus, the mRNA and coding strand are complementary to the template strand.

 

 

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does prokaryotic mRNA have introns?

 

does prokaryotic mRNA undergo post-transcriptional modification?

No, prokaryotic mRNA does not have introns

 

prokaryotic mRNA does not undergo post-transcriptional modification

 

in prokaryotes, as soon as transcription occurs, translation also occurs.

They occur at the same time

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Spliceosome

and its components

Spliceosome = a complex that is involved in post-transcriptional modification of mRNA in eukaryotes

  • It removes introns as lariats and splicing exons together.
  • It is a ribozyme = RNA molecule that acts as an enzyme

Components: 

  • small nuclear RNA (snRNA)
  • small nuclear ribonucleoproteins (snRNP)

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In Eukaryotes,

where does transcription and post-transcriptional mRNA modification occur?

Both transcription and post-transcriptional mRNA modification occur in the nucleus of eukaryotic cells

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nucleolus

Found in eukaryotes

Region of the nucleus that makes ribosomes

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what are the stages of the cell cycle?

 

what stage of the cell cycle does DNA replication occur?

 

 

Cell cycle stages:

G0 ⇒ G1 ⇒ S ⇒ G2 ⇒ M

 

S: DNA replication occurs

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Describe the steps of mitosis

What is created?

 

Components of spindle apparatus?

Asters?

Kinetochores?

Mitosis = Cell divides once to produce 2 diploid cells, each with identical genetic information

 

Prophase, Metaphase, Anaphase, Cytokinesis, Telophase (PMAT)

  1. Prophase
    • Chromatin is condensed into chromosomes.
    • The two identical copies of DNA from replication are joined together as sister chromatids by centromere proteins.
    • Nucleus and nucleolus disappear.
    • Spindle apparatus forms and consists of:
      • Asters - microtubules of the spindle
      • Centrosomes move to opposite sides of the cell
  2. Metaphase
    • Centrosomes send their centrioles (bands of microtubules) to the centromeres of the chromosomes.
    • This aligns the chromosomes in one row at the middle of the cell
    • Kinetochores = structure of protein and DNA at the centromere of two joined sister chromatids
  3. Anaphase
    • The spindle apparatus of centrosomes and centrioles pulls the sister chromatids apart.
    • They move towards opposite sides of the cell
  4. Cytokinesis
    • The cell splits into two
  5. Telophase
    • Opposite of prophase
    • Nucleus and nucleolus of each daughter cell forms
    • Spindle apparatus disappears
    • Chromosomes become looser chromatin

 

 

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Define the following & what are they all involved in?

Centrosomes

Centrioles

Asters

Centromeres

Kinetochores

All are involved in Mitosis

 

  • Centrosomes -  organelle that contains bundles of microtubules (centrioles) that form the spindle apparatus.
  • Centrioles - bundles of microtubules of the spindle apparatus.
  • Asters - another name for the microtubules that radiate out of the centrosome.
  • Centromere - proteins that hold sister chromatids together
  • Kinetochores - structure of proteins and DNA at the centromere of joined sister chromatids

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START CODON: AUG 

Methionine

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the mRNA is the same as the coding strand

 

both the mRNA and coding strand are complementary to the template strand

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mutagen

physical or chemical agents that can damage DNA and cause mutations

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transposon

DNA segments that can leave chromosomes and re-enter at a different location

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Define the following types of chromosomal mutations:

 

Deletion

Duplication

Translocation

Inversion

Chromosomal Mutations

 

  • Deletion - when a segment of a chromosome breaks off
  • Duplication - when a segment of a chromosome breaks off and goes to its homologous chromosome, forming a duplicate in the homologue
  • Translocation - when a segment of a chromosome switches places with a segment from another chromosome
  • Inversion - when a segment of DNA flips orientations
  •  

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Can RNA polymerase proofread?

no it cannot

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define gamete

gamete

 

haploid male (sperm) or female (egg) germ cell

 

each has one set of chromosomes (haploid)

no pairs

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Meiosis

occurs in what types of cells? (males vs females)

steps?

synaptonemal complex?

genetic recombination?

 

Products in males vs products in females?

Meiosis

process for making haploid gametes (sperm or eggs) for sexual reproduction

A diploid cell divides twice to produce 4 haploid cells, each with different genetic information.

Occurs in spermatogonium cells (males) and oogonium cells (females)

 

Steps:

  1. Meiosis 1 = diploid cell's homologous chromosomes are separated to produce 2 haploid cells
    • Prophase 1 =
      • Chromosomes line up, matching their genes exactly.
      • Then they form the synaptonemal complex, in which they cross over and exchange segments of DNA
      • Genetic recombination = production of offspring with a combination of traits that are different than the parent's traits.
      • Nucleus/nucleulous dissapear, spindle apparatus forms)
    • Metaphase 1
      • The homologous chromosomes line up in two rows at the middle of the cell
    • Anaphase 1
      • The homologous chromosomes from each parent go to each side, becoming haploid chromosomes
    • Telophase 1 and cytokinesis
      • Two new haploid cells are formed
      • Nucleus/nucleolus appears and the spindle apparatus disappears
  2. Meiosis 2 : 2 haploid cells become 4 haploid cells (pretty much the same process as mitosis)
    • Prophase 2 = nucleus/nucleolus disappears, spindle apparatus forms
    • Metaphase 2 = chromosomes line up at the middle of the cell
    • Anaphase 2 = the sister chromatids are pulled apart 
    • Telophase 2 and cytokinesis = 4 haploid cells are formed
      • Female product = 1 ovum and 3 polar bodies that are waste products
      • Male product = 4 sperm cells

 

 

 

 

 

 

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Describe gametogenesis for each:

Spermatogonium

Oogonium

 

Stages, their ploidy level, and when each stage was made? (5 stages)

Gametogenesis = production of gametes (haploid sex cells) via meiosis 

  • Spermatogonium = cell where meiosis occurs in males to make 4 haploid sperm
    • Stages:
      1. Spermatogonium (diploid)
        • present at birth.
      2. Primary spermatocyte (diploid)
        • after mitosis cell division
      3. Secondary spermatocyte (haploid)
        • after meiosis 1
      4. Spermatid (haploid)
        • after meiosis 2
      5. Mature sperm
        • after maturation process
  • Oogonium = cell where meiosis occurs in females to make a haploid egg 
    • Stages:
      1. Oogonium (diploid) 
        • present at birth
      2. Primary oocyte (diploid)
        • after mitosis
      3. Secondary oocyte (haploid)
        • after meiosis 1
      4. Ootid (haploid)
        • after meiosis 2
      5. Mature ovum (haploid)
        • after maturation process

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List the ploidy level and # chromosomes/chromatids for the start and finish of the following processes:

 

Replication (start and finish)

Mitosis (start and finish)

Meiosis 1 (start and finish)

Meiosis 2 (start and finish)

Replication

  • Start: Diploid (46 chromosomes; 46 chromatids)
  • Finish: Diploid (46 chromosomes; 92 chromatids)

 

Mitosis

  • Start: Diploid (46 chromosomes; 92 chromatids)
  • Finish: 2 Diploid (46 chromosomes; 46 chromatids)

 

Meiosis 1

  • Start: Diploid (46 chromosomes; 96 chromatids)
  • Finish: 2 Haploid (23 chromosomes; 46 chromatids)

Meiosis 2

  • Start: 2 Haploid (23 chromosomes; 46 chromatids)
  • Finish: 4 Haploid (23 chromosomes; 23 chromatidS)

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Law of independent assortment

states that genes located on different chromosomes assort independently of each other

 

Genes that code for different traits on different chromosomes do not affect each other during gamete formation

 

summary: genes for different traits don't affect each other

Example: Gene for black skin does not affect the gene for height

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what chromosomes are sex chromosomes?

the 23rd pair of chromosomes

 

chromosomes 45 and 46

 

Female: 2 X chromosomes

Male: X and Y chromosomes

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4/16

 

= 25% chance

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Hardy-Weinberg equilibrium

what are the 5 conditions?

 

and equations (2)

explain the variables

 

solve the following question

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Hardy-Weinberg equilibrium

  • states that evolution is not occurring in a population that does not have a net change in allele frequencies.
  • 5 conditions for no change in allele frequencies (no evolution):
  1. No gene flow
  2. No natural selection
  3. No mutations
  4. Random mating
  5. Extremely large population size
    • larger population sizes are more likely to have constant alelle frequencies

 

p2 + 2pq + q2 = 1            p + q = 1

  • Variables
    • p: % of dominant alleles in a population (decimal form)
    • q: % of heterozygous alleles in a population (decimal form)
  • prefers to homozygous dominant alleles
  • 2pq refers to heterozygous alleles
  • q2 refers to homozygous recessive alleles

 

 

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they all contain the recessive allele

thus, all their kids must at least be carriers

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Tetrads are made in prophase 1 of meiosis 1

 

tetrads = side by side homologues, thus, there are 4 sister chromatids total

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