Genetics Fundamentals: DNA, Replication, Transcription, Translation, and Mutations, Study notes of Genetics

genetics_study_guide The first half of the study guide is basically all the AB stuff. Bio (2021-22):

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2022/2023

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Genetics!
How is this all one unitโ€ฆ
DNA
โ—Purine Bases (Ag for Silver)
โ—‹Adenine & Guanine
โ—‹Two-Ring
โ—Pyrimidine Bases
โ—‹Thymine (Uracil) &
Cytosine
โ—‹Single-Ring
โ—DNA Denaturation
โ—‹Separating the strands by the H bonds
โ—‹NOT harmful & reversible
โ—Directionality
โ—‹5โ€™ end is top of nucleotide (where the Phosphate
sticks up)
โ– Five = phosphate
โ—Organized in tightly wounded chromosomes
โ—‹Circular in prokaryotes
โ—‹Linear in eukaryotes
pf3
pf4
pf5
pf8
pf9

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Genetics!

How is this all one unitโ€ฆ

DNA

โ— Purine Bases (Ag for Silver) โ—‹ Adenine & Guanine โ—‹ Two-Ring โ— Pyrimidine Bases โ—‹ Thymine (Uracil) & Cytosine โ—‹ Single-Ring โ— DNA Denaturation โ—‹ Separating the strands by the H bonds โ—‹ NOT harmful & reversible โ— Directionality โ—‹ 5โ€™ end is top of nucleotide (where the Phosphate sticks up) โ–  Five = phosphate โ— Organized in tightly wounded chromosomes โ—‹ Circular in prokaryotes โ—‹ Linear in eukaryotes

REPLICATION

โ—‹ In both strands: ยฝ is new DNA and ยฝ is the parent template strand โ–  Semi-conservative process

  1. Topoisomerase relaxes supercoiling of the chromosome
  2. 2 Replication Complexes attach to the Origin of Replication (ORI Sequence) a. Replication Complex: Enzymes ATTACHED to each other and maintain the same speed of operations b. Each chromosome will have more than one i. Simultaneous process at dierent points in the chromosome
  3. The Replication Complexes travel in opposite directions creating Replication Bubbles
  4. Helicase breaks hydrogen bonds creating separate strands a. Stabilized by single-stranded binding proteins
  5. RNA Primase places RNA primers at the beginning of each building chunk where DNA Polymerase III can continue adding nucleotides
  6. DNA Polymerase III builds daughter strand by adding complementary bases a. Polymerization: an ANABOLIC process i. Every additional base pair is an endergonic reaction 1. Energy is used from the exergonic reaction of reducing ATP to Adenine (GTP, CTP, & TTP too!) b. Strand only grows in 5โ€™ โ†’ 3โ€™ direction

โ— The one and only enzyme that does all: RNA Polymerase (RNAP) โ—‹ NO EDITING: unnecessary โ—‹ Transcription bubble contained in RNAP โ— RNAP binds to the promoter region โ—‹ TATA Box in any direction โ— Enhancer region โ—‹ Transcription factors โ—‹ Initiation complex binds to promoter region and triggers transcription โ— Terminator Region POST-TRANSCRIPTIONAL PROCESSING โ— Splicing: cut out the introns to make mature mRNA transcripts โ—‹ Eukaryotic genes are not continuous โ—‹ Exons = the โ€œreal geneโ€ โ–  expressed/coding โ—‹ Introns = the โ€œjunkโ€ โ–  In between โ—‹ Alternative splicing โ–  One gene can code for more than one protein โ— Dierent introns within the same gene โ— Protecting the ends of the mRNA as it travels from the nucleus through the cytoplasm โ—‹ Add 5โ€™ GTP cap โ—‹ Add poly-A tail on 3โ€™ end โ—‹ mRNA will last longer and produce more protein

Translation: Creating a Polypeptide

โ— Codon: each group of consecutive 3 nucleotides that code for 1 amino acid โ— Directionality โ†’ โ—‹ N-AA 1 -AA 2 -AA 3 -AAi-C

โ— Highly conserved genetic code: a 3 base combination will code for the same amino acid across ALL species โ— Defense against mutation: more than 1 codon for the same Amino Acid โ— Start Codon: 5โ€™ AUG 3โ€™ (methionine) โ— Stop Codons (5โ€™ โ†’ 3โ€™): UAA, UAG, UGA โ—‹ Stop translation as there is no tRNA to bind to here โ— Transfer RNA Structure (tRNA): โ—‹ โ€œClover leafโ€ โ—‹ Anticodon determines amino acid โ— Ribosomes facilitate coupling of tRNA anticodon to mRNA codon

  1. Initiation a. Ribosomes latches onto mRNA where it sees 5โ€™ AUG 3โ€™ first at P site i. First anticodon is 3โ€™ UAC 5โ€™
  2. Elongation a. Ribosome will move down one codon b. tRNA will enter through A site and latch onto the codon c. The Amino Acid from the tRNA in the P site will detach and create a polypeptide bond with the amino acid in the A site d. The tRNA without an Amino Acid will leave in the E site i. E for Exit
  3. Termination a. Reach a stop codon and no tRNA attaches

The Exception to the Central Dogma: Viruses

โ— Virus: Genetic material within a protein capsid/envelope/capsule

Prokaryotes

โ— No nucleus (or other organelles) โ— No post transcriptional processing โ— Direct translation โ—‹ As mRNA gets made, it is fed into a ribosome

General Gene Stuff

โ— Phenotype: Version of a trait โ— Allele: Version of a Gene โ— Genotype: Combination of Alleles โ— 2 Chromosomes = 2 Copies of each gene = 2 alleles for each trait โ— Dominant allele renders 2nd^ allele irrelevant (will be expressed no matter what) โ—‹ Functioning Protein โ— Recessive Allele typically makes a malfunctioning allele โ— True-Breeding: Homozygous โ— Carrier: Heterozygous โ— Punnett Squares โ—‹ Dihybrid Cross: Maintain Gene Order and FOIL for gametes โ—‹ Polyhybrid Cross: figure out probability of each trait and then x โ€˜em all โ— Autosomal Chromosomes (Regular, 2 of each #) & Sex Chromosomes (X, Y) โ— Pedigree โ—‹ Square = Genetically Male โ—‹ Circle = Genetically Female โ—‹ Shaded = Has Phenotype โ—‹ Skipped Generation: when children have the trait, but the parents donโ€™t โ—‹ Can use? or _ for second allele when dominant and indertiminable โ— Determining Inheritance Patterns โ—‹ Skipped Generation? = Autosomal Recessive, X-Linked Recessive โ—‹ Sex Distribution? โ–  Only Males (all dads with sons) = Y-linked โ–  All moms with sons = X-linked recessive โ–  All females with dads = X-linked dominant

Mendelโ€™s Laws

  1. Law of Dominance a. Dominant Allele? Dominant Phenotype!
  2. Law of Segregation

a. During meiosis, alleles segregate i. Homologous chromosomes separate b. Each allele for a trait is packaged into a separate gamete i. Can only give 1 allele per gene to your kiddo

  1. Law of Independent Assortment a. Dierent loci (genes) separate into gametes independently b. Each gene is going to randomly out its allele i. Many possibilities for gametes 1. Ex. YyRr โ†’ YR, Yr, yR, yr c. Exception: if genes are on same chromosome & close together i. Will usually be inherited together ii. Rarely crossover separately

Non-Mendelian Inheritance

โ— Incomplete Dominance: 2 Dominant Alleles โ—‹ Heterozygote shows a novel, intermediate, blended phenotype โ—‹ Ex. RR = Red, WW = White, RW = Pink โ— Codominance: 2 Dominant Alleles โ—‹ New Phenotype that is BOTH simultaneously (SEPARATE BUT EQUAL) โ— Multiallelic Trait: has more than 2 alleles coding for 1 gene โ—‹ Ex. Blood Type Phenotype Genotype Antigens Antibodies Donation Status To From A AA, AO A Anti-B A, AB A, O B BB, BO B Anti-A B, AB B, O AB AB A & B None AB A, B, O, AB O OO None Anti-A, Anti-B A, B, O, AB O โ— Pleiotropy: 1 Gene aects many traits โ—‹ Most genes! โ— Lethality โ—‹ Presence of 2 specific alleles is LETHAL even if the phenotype is possible โ— Polygenic Inheritance: Many genes aect 1 trait โ— Epistasis: One gene can completely mask another gene