Pre-AP Semester 2 Final Exam Study Guide (Unit 4) - DNA Structure, Synthesis, Protein Synthesis, Mutations, Inheritance

Structure of DNA

• Contributions to DNA Structure:

  • Rosalind Franklin: Discovered DNA's helix shape using X-ray images.

  • Erwin Chargaff: Found that adenine (A) equals thymine (T) and guanine (G) equals cytosine (C) in DNA (Chargaff's rules).

  • Watson and Crick: Created the double helix model of DNA using Franklin's and Chargaff's information.

• Chargaff's 1:1 Ratios:

  • Adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C) in a 1:1 ratio. This is key to DNA base pairing.

• Base Proportions in DNA:

  • The amounts of A, T, G, and C vary between organisms but always follow Chargaff's rules (A=T, C=G).

DNA Organization

• Prokaryotes vs. Eukaryotes:

  • Prokaryotes: DNA is a single, circular chromosome in the cytoplasm's nucleoid region. They may also have small DNA circles called plasmids.

  • Eukaryotes: DNA is in multiple linear chromosomes inside the nucleus. DNA is packed with histone proteins to form chromatin.

DNA Monomers and Nitrogen Source

• Monomers for DNA:

  • DNA is built from deoxyribonucleotides, each with a deoxyribose sugar, a phosphate group, and a nitrogenous base (A, G, C, or T).

• Nitrogen Source:

  • Living things get nitrogen to build DNA from their diet and environment. Nitrogen is reused in ecosystems and added to nitrogenous bases during DNA creation.

DNA Structure Phrases

• DNA as a Double Helix:

  • DNA has two strands twisted into a helix, like a spiral staircase.

• Antiparallel Strands:

  • The two DNA strands run in opposite directions (5' to 3' and 3' to 5').

• Sugar-Phosphate Backbone:

  • The DNA structure is made of alternating deoxyribose sugar and phosphate groups, forming a backbone.

• Hydrogen Bonds:

  • Nitrogen bases connect with hydrogen bonds: A with T (two bonds) and G with C (three bonds).

DNA Synthesis/Replication

• Importance of DNA Synthesis/Replication:

  • DNA replication is needed for cell division (mitosis and meiosis). It ensures each new cell gets an identical copy of the genetic material.

• DNA Synthesis Model:

  • Replication starts at origins of replication. Helicase unwinds the DNA, creating a replication fork. DNA polymerase adds matching nucleotides to the template, building new strands from 5' to 3'. The leading strand is made continuously, while the lagging strand is made in Okazaki fragments, joined by DNA ligase.

• Semi-Conservative Replication:

  • DNA replication is semi-conservative because each new DNA molecule has one original and one new strand.

• Role of DNA Helicase:

  • Helicase unwinds DNA by breaking hydrogen bonds between base pairs, forming a replication fork.

• Role of DNA Polymerase:

  • DNA polymerase builds new DNA strands by adding nucleotides to the 3' end of a strand or primer. It also proofreads the new DNA.

Protein Synthesis

• DNA vs. RNA:

  • Sugar: DNA has deoxyribose, RNA has ribose.

  • Bases: DNA uses thymine (T), RNA uses uracil (U).

  • Structure: DNA is double-stranded, RNA is single-stranded.

• Transcription:

  • Genetic information in DNA is copied into RNA by RNA polymerase.

• Transcription Location:

  • Prokaryotes: In the cytoplasm.

  • Eukaryotes: In the nucleus.

• Template Strand:

  • The DNA strand used to make RNA is the template strand.

• End Result of Transcription:

  • Transcription produces messenger RNA (mRNA), which carries genetic information to ribosomes for protein synthesis.

• Types of RNA:

  • mRNA: Carries information from DNA to the ribosome.

  • tRNA: Transfers amino acids to the ribosome during protein synthesis.

  • rRNA: Part of the ribosome, helps make proteins.

• Genes and Gene Expression:

  • Genes are DNA segments that code for proteins. Gene expression is how the information in a gene is used to make a protein.

• Genotype vs. Phenotype:

  • Genotype is the genetic makeup; phenotype is the observable traits.

• Translation of mRNA:

  • The information in mRNA is used to assemble a protein. Ribosomes read mRNA codons to assemble amino acids into a polypeptide chain.

• Translation Location:

  • On ribosomes in the cytoplasm or endoplasmic reticulum.

• mRNA Reading and Amino Acid Incorporation:

  • Ribosomes read mRNA in codons (three nucleotides). Each codon specifies an amino acid. tRNA brings the amino acids to the ribosome, adding them to the protein until a stop codon is reached.

• Start and Stop Codons:

  • Start codons (AUG) begin translation and specify methionine. Stop codons (UAA, UAG, UGA) end translation.

• Protein Shape and Function:

  • A protein's shape and function depend on its amino acid sequence, which dictates how it folds into a 3D structure.

• Mutations:

  • Changes in the DNA nucleotide sequence.

• Mutagens:

  • Agents that cause mutations, like radiation and chemicals.

Point Mutations

• Substitution:

  • One nucleotide is replaced.

  • Missense: Changes the amino acid in the protein.

  • Nonsense: Creates a stop codon, shortening the protein.

• Insertion:

  • Adding nucleotides to the DNA sequence.

• Deletion:

  • Removing nucleotides from the DNA sequence.

• Frameshift Mutations:

  • Insertions and deletions that change the genetic code's reading frame, leading to a nonfunctional protein.

• Mutation Effects:

  • Mutations can be neutral, bad, or good, depending on their impact on protein function.

Asexual and Sexual Passing of Traits

• Binary Fission:

  • Asexual reproduction where a cell divides into two identical cells.

• Asexual Reproduction and Genetic Diversity:

  • Asexual reproduction reduces genetic diversity because offspring are identical to the parent.

• Parthenogenesis:

  • Asexual reproduction where an egg develops without fertilization.

• Advantages and Disadvantages of Asexual Reproduction:

  • Advantages: Fast reproduction, no mate needed, good for stable environments.

  • Disadvantages: Low genetic diversity, less adaptable to change.

• Meiosis:

  • Cell division that halves the chromosome number from diploid (2n) to haploid (n).

• Meiosis Divisions:

  • Two divisions are needed to produce haploid gametes.

• Meiosis Events:

  • Homologous Chromosomes in Tetrad: Chromosomes pair up in prophase I to form a tetrad.

  • Crossing Over: Homologous chromosomes exchange genetic material in prophase I.

  • Homologous Chromosome Separation: Homologous chromosomes separate in anaphase I.

  • Sister Chromatid Separation: Sister chromatids separate in anaphase II.

• Sources of Genetic Variation During Meiosis:

  • Crossing Over: Exchange of genes between chromosomes.

  • Independent Assortment: Random separation of chromosomes during meiosis I.

  • Random Fertilization: Random combination of sperm and egg.

• End Result of Meiosis:

  • Four haploid gametes (sperm or egg) with unique genetic combinations.

• Gametes and Sexual Reproduction:

  • Gametes (sperm and egg) fuse during fertilization to form a diploid zygote.

Chromosome Numbers

• n and 2n:

  • n: haploid number (gamete chromosomes).

  • 2n: diploid number (somatic cell chromosomes).

  • If n = 23, then 2n = 46.

  • If 2n = 80, then n = 40.

• Zygote Formation:

  • A zygote is formed by sperm and egg fusion; it is diploid.

• Nondisjunction:

  • Failure of chromosomes to separate during meiosis, leading to genetic disorders like Down syndrome.

Karyotypes

• Chromosome Pairs:

  • Homologous chromosomes.

• Autosomes:

  • Non-sex chromosomes (22 pairs in humans).

• Sex Determination:

  • Females: XX; males: XY.

• Karyotype Analysis:

  • Karyotypes can show genetic conditions.

  • Trisomy 21 (Down syndrome): extra chromosome 21.

  • Nondisjunction can cause extra chromosomes.

Inheritance Patterns

• Genotype and Phenotype:

  • Genotype: genetic makeup; phenotype: observable traits.

• Alleles:

  • Different versions of a gene.

• Somatic vs. Sex Cells:

  • Somatic cells: body cells (diploid); sex cells: gametes (haploid).

• Simple Dominance:

  • One allele (dominant) hides the other (recessive). AA and Aa show the dominant trait, aa shows the recessive trait.

• Codominance:

  • Both alleles are equally expressed (e.g., blood type AB).

• Incomplete Dominance:

  • Heterozygous phenotype is intermediate (e.g., red + white = pink flowers).

• Sex-Linked Traits:

  • Traits on sex chromosomes (usually X) (e.g., hemophilia).

• Probability and Punnett Squares:

  • Predict allele passage using probability and Punnett squares.

Monohybrid Cross

• Monohybrid cross: one trait.

• Use Punnett squares to find offspring genotypes and phenotypes.

Dihybrid Cross

• Dihybrid cross: two traits.

• Use Punnett squares to find offspring genotypes and phenotypes.

• Example: heterozygous parents

• Solve dihybrid crosses with Punnett squares or by multiplying monohybrid probabilities.

• Example: Mice with running (R) dominant over waltzing (r), black hair (B) dominant over brown (b).

• Cross RrBb x Rrbb

  • Probability of running, black mouse:

  • Running: 3/4 (RR, Rr, Rr)

  • Black: 1/2 (Bb)

  • Probability: (3/4) * (1/2) = 3/8

  • Probability of running, brown mouse:

  • Running: 3/4

  • Brown: 1/2 (bb)

  • Probability: (3/4) * (1/2) = 3/8

  • Why no waltzing mice?

  • Both parents have at least one R allele, so no rr offspring are possible.

Pedigrees

• Pedigrees predict trait inheritance across generations.

Exam Preparation

• Mathematics: Use math to understand biology, interpret data, calculate %, nucleotides, chromosome numbers, probabilities from crosses, etc.

• Reading and Writing: Read carefully, answer questions with evidence and biological concepts.

• Attention to Modeling: Label diagrams, create/revise models to explain biological relationships.