AP Bio: Molecular Genetics Notes

DNA and RNA Structure

• DNA is a double-stranded helical molecule made of nucleotide monomers.

• Each nucleotide consists of:

  • A five-carbon sugar called deoxyribose.

  • A phosphate group.

  • One of four nitrogenous bases.

• Each strand has a sugar-phosphate backbone formed by covalent bonds between deoxyribose sugars and phosphate groups.

• Complementary base pairing occurs within the helix via hydrogen bonds:

  • Adenine (A) pairs with Thymine (T).

  • Guanine (G) pairs with Cytosine (C).

• Base pairing rules:

  • A binds with T.

  • G binds with C.

• For nucleotides to bind, they must be oriented in opposite directions, making the two strands antiparallel.

DNA as the Molecule of Heredity

• Information Storage:

  • The sequence of bases (A, C, T, G) is not determined by DNA's chemistry, allowing it to serve as an informational code.

  • This code specifies sequences of RNA and protein.

• Replicability:

  • Base pairing (A with T, G with C) allows each strand to serve as a template for synthesizing a complementary strand during DNA replication.

  • Ensures high-fidelity transmission of genetic information from parent to daughter cells.

• Stability:

  • The double helical structure protects the sequence of bases.

• Mutability:

  • A low level of mutation allows for change in the code, enabling evolution.

Functions of DNA and RNA

• DNA:

  • The molecule of heredity in all cell-based organisms.

• RNA:

  • Hereditary molecule in some viruses (e.g., HIV, SARS).

  • Involved in information transfer related to protein synthesis in all organisms.

    • Includes mRNA, tRNA, and rRNA.

  • In eukaryotes also regulates gene expression.

    • Splicing out introns (non-coding DNA) from pre-mRNA to create mRNA.

    • Regulating protein synthesis.

Genetic Information Storage in Prokaryotes and Eukaryotes

• Prokaryotes:

  • Store DNA in looped circular chromosomes.

  • Genomes range from approximately 100,000 to 10,000,000 base pairs.

  • DNA is naked (not wrapped around a protein scaffold).

• Eukaryotes:

  • DNA organized into multiple linear chromosomes with ends.

  • DNA wrapped around proteins called histones.

  • Eukaryotic genomes are much larger.

    • e.g. Human genome consists of 3,200,000,000 base pairs.

    • Some plant genomes consist of 150,000,000,000 base pairs.

Plasmids

• Small, extra-chromosomal loops of DNA found in bacteria (less commonly in archaea, rarely in eukaryotes).

• Involved in horizontal gene transfer between bacterial cells through conjugation.

• Often carry genes for antibiotic resistance.

• Used in genetic engineering to replicate DNA and express engineered genes within bacterial cells.

DNA Replication

• DNA replication involves a team of enzymes that use each strand of the double helix as a template to synthesize new daughter strands.

• Nucleotides bind to the exposed strand following base pairing rules (A with T, C with G).

• Each daughter DNA double helix consists of one conserved strand from the parent molecule and one newly synthesized strand (semi-conservative replication).

Starting DNA Replication

• Helicase enzyme finds the origin of replication and separates the double-stranded DNA by breaking hydrogen bonds.

• This exposes single strands and creates a replication fork.

Roles of DNA Polymerase, Primase, and Primers

• DNA Helicase opens up the parent strand exposing nucleotides in the two daughter strands.

• DNA polymerase is the key enzyme involved in creating new DNA.

• Nucleotides bind based on base pairing rules; DNA polymerase binds new nucleotides to the 3' end of a growing strand via sugar-phosphate bonds.

• DNA polymerase requires an RNA primer (a few bases of RNA) to start adding nucleotides to an existing strand.

• Primase is the enzyme that lays down the RNA primer at the open replication fork.

Single-Strand Binding Proteins

• Keep the double helix from rewinding so that enzymes can get into place and carry out replication.

Leading vs. Lagging Strand Replication

• Leading Strand:

  • DNA replication is continuous because DNA polymerase follows the opening replication fork created by helicase.

• Lagging Strand:

  • DNA polymerase synthesizes in the opposite direction from the opening replication fork.

  • Replication is discontinuous and built from short sequences called Okazaki fragments.

DNA Polymerase I and Ligase

• DNA polymerase I removes RNA primers and replaces them with DNA.

• DNA ligase seals the gaps between fragments with sugar-phosphate bonds to create complete daughter strands.

Transcription

• The central dogma of molecular genetics: DNA makes RNA makes protein.

• Information flows from DNA triplets to mRNA codons to amino acids.

Gene Definition

• A gene is the basic unit of heredity passed from parent to offspring; it determines a trait.

• In molecular genetics, it's a sequence of DNA nucleotides that codes for RNA, which codes for protein.

Forms of RNA

• mRNA (messenger RNA):

  • A linear molecule that brings instructions from DNA to ribosomes.

• rRNA (ribosomal RNA):

  • Makes up the catalytic part of ribosomes and binds amino acids together during protein synthesis.

• tRNA (transfer RNA):

  • Brings specific amino acids to the ribosomes for protein synthesis.

• Small RNAs:

  • Involved in eukaryotic gene regulation.

The Process of Transcription

• RNA (in blue) is created from DNA.

• Every gene begins with a promoter region where the gene starts.

• RNA polymerase binds with the promoter on DNA and transcribes the DNA sequence into RNA using the template strand.

• RNA polymerase reads DNA from 3' to 5' and synthesizes RNA from 5' to 3'.

• When RNA polymerase reaches a terminator region at the end of the gene, it dissociates from the DNA, ending transcription.

Terminology

• Template Strand:

  • Also known as the non-coding strand, antisense strand, or minus strand.

  • The strand that gets transcribed from DNA into RNA.

• Coding Strand:

  • Complementary to the template strand.

  • Has the same sequence of nucleotides as the mRNA (except U replaces T).

  • Also called the sense strand or positive strand.

Prokaryotic Transcription

• Prokaryotes lack a nucleus, meaning no separation between genetic material and cytoplasm.

• Transcribed RNA can immediately be translated by ribosomes into protein.

• Multiple ribosomes often read the same RNA strand (polysomes).

Genetic Code

• The code used by living things to translate nucleotide sequences into amino acid sequences (RNA to protein).

• Groups of three RNA nucleotides (codons) code for one amino acid.

• The code is nearly universal, specific, and redundant.

• First nucleotide, second nucleotide, and third nucleotide. Work from outside in.

Tabular genetic code

• More commonly chart representation.

Translation

• mRNA contains the codons that specify the order of amino acids.

• The ribosome connects amino acids to create a polypeptide.

• tRNAs bring specific amino acids to the ribosome-mRNA complex.

• tRNAs have an anticodon and an amino acid binding site.

Ribosomes

• Ribosomes are general-purpose proteins that convert mRNA to sequences of amino acids.

• They have a large and small subunit with three tRNA binding sites: E (exit), P (polypeptide), and A (amino acid).

Beginning of Translation

• Processed mRNA leaves the nucleus through a nuclear pore.

• The small ribosomal subunit binds with the mRNA and moves to the start codon (AUG).

• A tRNA with a matching anticodon (UAC) binds with the start codon carrying methionine.

• The large subunit binds with the small subunit, placing the tRNA with methionine in the ribosome's P site.

Elongation Phase

• The next tRNA comes to the A site bearing a new amino acid.

• The ribosome catalyzes a peptide bond between the P and A site amino acids.

• The ribosome translocates, moving over one more codon.

• The tRNA in the E site exits while a new tRNA enters at the A site.

• The process continues along the length of the mRNA.

Termination Phase

• The ribosome reaches a stop codon, which codes for a release factor instead of a tRNA.

• The release factor binds with the stop codon, causing the ribosome to dissociate and the polypeptide to be released.

• The polypeptide folds up into a functional protein.

Regulation of Gene Expression

• E. coli has about 4,000 genes.

• Regulation is required and controlled through gene on an of.

• An operon is a cluster of genes transcribed as a single RNA that primarily exists in prokaryotes; it consists of structural genes, an operator, a promoter, and a regulatory gene that produces a regulatory protein.

TRP Operon

• The TRP operon codes for enzymes that synthesize tryptophan and is regulated to control enzyme production.

• If no tryptophan is in the environment, the regulatory protein cannot bind with the operator, allowing RNA polymerase to transcribe the structural genes.

• When tryptophan is present, it binds with the repressor protein, causing it to change shape and bind with the operator, blocking RNA polymerase.

• The TRP is called a repressible operon and tryptophan is the co-repressor, shutting down the repression of tranlscritpion.

Lac Operon

• The lac operon is an inducible operon, coding for enzymes that digest lactose.

• Lactose Diffuses into E. coli, the lactose molecules binds with repressor proteins preventing the formation operator-r polymerase bonds.

• Absent lactose promotes default repressor shapes.

• It is an inducible operon, triggered by lactose.

Systems Analysis Comparison

• LAC Turns on and removes lactose.

• Both, LAC and TRIP are examples of negative feedback systems.

E. coli Culture Growth with Glucose and Lactose

• E. coli prefers to metabolize glucose, because glucose is the easier-to-digest monosaccharide.

• Followed by the lactoperon, churning enzymes to break down lactose into monosaccharides.

• Glucose will be metabolized first, followed by lactose.

Gene Regulation

• Multicellular eukaryotes are composed of organized tissues of trillions of cells.

• Encoded with 46 chromosomes, 3 billion base pairs, and 20,000+ genes.

Coding vs. Non Coding

• Every single cell has the same DNA, but cells need to know which genes to express during developmental gene regulation. In which cells are determined by factors.

• Genes contain introns.

  • In some cells, a small number of genes are turned on, while genes are tightly packaged.

  • Methylation prevents transcription.

  • Acetylation loosens DNA making transcriptions manageable in enzymes.

Epigenetics

• Changes in DNA expression that involve reversible chemical modifications of DNA packaging.

• Responsible for differentiation of tissues during development.

• Can be transmitted through generations.

• All cells in the same organism are genomically equivalent with a single zygote.
  DNA differentiates because they express different genes relating to epigenetic modifications. Previously, operons were covered, which is how genes can be turned on and off in relation to environmental changes.

Eukarytoic Cell Regulation

• Eukarytoic cells possess regulatory DNA sequences for transcriptions.

• Interacting with proteins.
  Exons, enhancers, interactions enable RNA polymerase to bind.

Gene expression coordination

• During development, different tissues express different genes. But coordination through shared sequences promotes transcription via hormones.

• Introns are sequences of DNA within genes that are transcribed into pre mRNA.

• Translatable mRNA requires that this pre mRNA have gone through eukaryotic processing.

• A bit of pre mRNA has already been processed to get into this tranlatable state.

5' GTP & 3' Poly modifications

• Before translation into protein, eukaryotic cell pre mRNA is processed through 5' prime ends, and three prime poly A, spliced exon is connected.

  • It has to get addition on is five prime end.

Genetic Organization

• Exons are used.

• Intron sequences are spliced.

• Alternative splicing uses other fragments to make diverse modifications on gene and protein function.

• Additional variations come from eukaryotes that don't have the intron exon organization of their coding genes involved.

Small RNAs

• Micro RNas lead to post transcriptional control of translation.

• This process involves sequences where DNAs can code the RNAs and modify mature RNA to have other elements involved.

• RNA will be destroyed to stop complex actions.

• RNA in post-transcriptional control genes come from RNA silence that is matched.

Mutation

• Random change in DNA or chromosome.

• A point mutation is a change nucleotide and bases.
  Distinguished between silent mutation, nonsense and missense mutation.

Frameshift mutations

• Mutations in genetic data can shift codons.

  • Extensive missense or nonsense can be produced.

• Sickle cell is caused by sub mutation relating.

  • Single substitution causes the expression to be mutated.

  • They are depended on environment positively and negatively.

• The effect always depends on environment, not the type of mutation.

  • Is contextual.

    • Increased evolution.

    • Is adaptive.

Neutral mutation

• No effect on phenotype.

• Becuase does not happen on coding/regulating DNAs.

• Results on silent mutation where acid doesn't change.

• Mutations are important to evolution, is used by Darwinism process.

• Germline mutations are in cells the make gammets, transmitted to embryo.

• Any genetic diesease would be found here, but adaptation too.

• Somatic mutation is on emergence on tissue in development.

• They are found to evolve into environmental exposures such as cancer.

Horizontal Gene Transfer

• Vertical gen transfer uses transmission of half genom. By offspring vs horizontal DNA transfer where DNA transfers not be its own offspring.

Horizontal Gene Transfer Forms

• Bacterial conjunction.

• Bacterial transformation.

• Viral transduction.

Bacterial Transformations.

• Bacteria pick up DNA from from environment become incorporated the genome.

• Transfer foreign genes into humans in bacterial.

• Mistakes in viral replications inject DNA in cells.

• Viral recombination emerges in the same host.

Biotechnology

• Recombitant Dna from more than one source.

• Using restriction enzyme one from a restriction site.

• Cut strand DNA to create exposure nucleotides.

  • DNA ligase bonds creates creating recombant DNA.

  • Create a new gene insert.

• Extracted a plasma cell, cut open, recombine enzyme.

• For gene expression on human DNA must introns removed for protein translation to avoid confusion.

Gene Expression and Modification Methods

• Determine the amino acids and reverse engineer DNA with enzyme.

• Extract MRNA and insert reverse transcriptase to form complex.

• Gel electrophoresis is sorting molecules by size by using DNA fingerprints.

Electrophoresis Analysis

• Placing molecules in porous gel device with electricity source.

• Run eletic current that push side repels charge. Small fragements impedeted less larger fragements to be sorted by size. BAM H1 is enzyme to cut plasmid with restriction points.

Post Analysis Manipulation

• B would your answer if were multiple answer.

• Polymerase chain reaction (PCR) makes test tube clone copies.

  • Requires sample, primer, to begin analysis in tubes.

• DNA sequencing involved taking sample DNA such gene code expression.

• Cancers and diseases identified by evoltionary process.