DNA Structure & Function Notes

DNA Structure & Function

The Blueprint of Life

• DNA (Deoxyribonucleic Acid) is the blueprint of life.

What We Know

• Questions to consider:

  • What does DNA stand for?

  • What type of molecule is DNA?

  • What is the monomer of DNA?

Deoxyribonucleic Acid

• Deoxyribose is a sugar found in DNA.

• DNA contains the bases Adenine (A), Thymine (T), Cytosine (C) and Guanine (G).

DNA History

• Hershey and Chase: Experiments with viruses confirmed that DNA was the molecule of heredity.

• James Watson and Frances Crick: Established the structure of DNA.

• Rosalind Franklin: Contributed significantly with Photo 51.

Functions of DNA

• Codes for traits.

• Stores and transmits genetic information.

• Provides instructions for protein synthesis:

  • DNA → RNA → Protein

Nucleotide Structure

• A nucleotide consists of three parts:

  • Phosphate group

  • Sugar (deoxyribose)

  • Nitrogenous base (A, T, C, G)

Base Pairing Rules (Chargaff's Rule)

• Adenine (A) pairs with Thymine (T).

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

• Represented as: A=T and C≡G

Purines and Pyrimidines

• Purines: Adenine (A) and Guanine (G)

• Pyrimidines: Thymine (T) and Cytosine (C)

Chargaff's Rule (cont.)

• The total percentage of Adenine and Thymine plus Guanine and Cytosine equals 100%.

• $(A + T) + (G + C) = 100\%$

Recap

• Which parts of a nucleotide remain the same?

• Which parts change?

DNA Structure

• The sides of the DNA molecule are composed of phosphate and sugar.

• The insides are nitrogenous bases.

• Strands are held together by hydrogen bonds.

• DNA has anti-parallel strands.

Check for Understanding

• What are nucleic acids made of?

• What are the three parts of a nucleotide?

• What are the base pairs?

  • Adenine pairs with Thymine

  • Thymine pairs with Adenine

  • Guanine pairs with Cytosine

  • Cytosine pairs with Guanine

Labeling Exercise

• Label the following parts of a DNA model:

  • Phosphate

  • Hydrogen Bond

  • Nucleotide

  • Deoxyribose (sugar)

  • Nitrogen base

Extra Resources

• CK12 DNA Structure and Replication (provides visuals).

DNA and Chromosomes

• In prokaryotic cells, DNA is located in the cytoplasm.

• Most prokaryotes have a single DNA molecule containing nearly all the cell’s genetic information.

• Eukaryotes have 1000 times more DNA than prokaryotes.

• Eukaryotic DNA is located in the cell nucleus inside chromosomes.

• The number of chromosomes varies from one species to another.

Chromosome Structure

• Depiction of DNA double helix, coils, supercoils, nucleosomes, histones, and chromosome.

Chromosome Structure (cont.)

• Eukaryotic chromosomes contain DNA and protein, tightly packed together to form chromatin.

• Chromatin consists of DNA tightly coiled around proteins called histones.

• DNA and histone molecules form nucleosomes.

• Nucleosomes pack together, forming a thick fiber.

Directionality in Nucleic Acids

• DNA is read from 3' to 5'.

• DNA is created from 5' to 3'.

DNA Diagram

• Detailed diagram of a DNA nucleotide showing phosphate, deoxyribose sugar, and nitrogenous base.

• Labeled 5' and 3' ends.

Sugar-phosphate Backbone

• Illustration of the sugar-phosphate backbone with nitrogenous bases.

• Labeled 3' and 5' ends.

DNA Structure Models

• Key features of DNA structure, partial chemical structure, and space-filling model.

• Measurements provided: 3.4 nm, 1 nm, 0.34 nm.

• Hydrogen bonds between base pairs are shown.

DNA Replication

• DNA replication is the process where DNA makes a copy of itself.

• This is essential for cell division, growth, and reproduction.

• Every new cell needs a copy of the DNA or instructions to know how to function.

• Replication ensures that each resulting cell will have a complete set of DNA.

DNA Replication: Semi-Conservative

• DNA Replication is semi-conservative, meaning that when a new copy is made, one half of the old strand is always kept in the new strand.

DNA Replication (cont.)

• Each strand of the DNA double helix has all the information needed to reconstruct the other half by base pairing.

• In most prokaryotes, DNA replication begins at a single point and continues in two directions.

DNA Replication in Eukaryotes

• In eukaryotic chromosomes, DNA replication occurs at hundreds of places.

• Replication proceeds in both directions until each chromosome is completely copied.

• The sites where separation and replication occur are called replication forks.

DNA Replication: The Steps

1. The DNA molecule separates into two strands by the helicase enzyme.

2. DNA polymerase builds new complementary strands following the base pairing rules (A=T, G=C).

DNA Replication: The Steps (cont.)

3. The two strands of DNA are joined together by the enzyme ligase.

4. DNA polymerase “proofreads” each new DNA strand.

Leading/Lagging Strand

• Illustration of leading and lagging strands during DNA replication.

• Includes DNA polymerase, helicase, topoisomerase, Okazaki fragments, and RNA primer.

Important Enzymes in DNA Replication

• Helicase: Untwists the double helix at the replication forks.

• Single-strand binding proteins (SSBs): Bind to and stabilize single-stranded DNA.

• Topoisomerase: Relieves the strain caused by tight twisting ahead of the replication fork by breaking, swiveling, and rejoining DNA strands.

• Primase: Puts down an RNA primer.

• DNA Polymerase: Builds the new strand & proofreads DNA.

• DNA Ligase: Ligates (joins) the strands.

DNA Replication Process

• Visual representation of DNA replication with nitrogen bases, replication fork, DNA polymerase, new strand, and original strand.

Fun Fact

• The rate of elongation is about $500$ nucleotides per second in bacteria and $50$ per second in human cells.

Part 2: RNA

RNA

• Important role in protein synthesis.

• Sugar = ribose.

• Short chains.

• Bases = Adenosine, Uracil, Guanine, and Cytosine (no thymine).

• A bonds with U.

• G bonds with C.

Three Types of RNA

1. Messenger RNA (mRNA): Carries the instruction (code) from a gene to make a protein (Letter).

2. Ribosomal RNA (rRNA): Makes up ribosomes, synthesizes protein.

3. Transfer RNA (tRNA): Transfers amino acids to the ribosome to make a protein.

DNA vs. RNA

• Comparison of DNA and RNA.

Structure of DNA & RNA

• Diagram comparing Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).

• Includes nucleobases, base pairs, and the helix of sugar-phosphates.

Genes and Genetic Messages

• Genes are coded DNA instructions that control the production of proteins.

• Genetic messages can be decoded by copying part of the nucleotide sequence from DNA into RNA.

• RNA contains coded information for making proteins.

Protein Synthesis

• Protein Synthesis: The formation of proteins by using information contained in DNA.

• DNA → RNA → Protein

• DNA is transcribed into an RNA code that signals or is translated into different amino acids that synthesize different proteins.

Overview of Replication, Transcription, and Translation

• Visual representation of the flow of genetic information: Replication, Transcription, and Translation.

Transcription

• DNA is copied in the form of RNA.

• This first process is called transcription.

• The process begins at a section of DNA called a promoter.

RNA Editing

• Some DNA within a gene is not needed to produce a protein. These areas are called introns.

• The DNA sequences that code for proteins are called exons.

  • Introns- interrupted sequences.

  • Exons- expressed sequences.

Exons and Introns

• Diagram illustrating Exons and Introns.

Transcription (DNA → RNA)

1. Initiation: The enzyme RNA polymerase binds to the promoter region of DNA and unwinds the DNA strand.

2. Elongation: RNA Polymerase assembles mRNA bases to the DNA strand.

3. Termination: RNA Polymerase reaches a stop signal.

   • Example: TACTTGGCGATT (DNA) → AUGAACCGCUAA (mRNA)

Check in: Transcription

• Transcribe the following DNA strand: TAC GAC GGG CAT TTA CCC

mRNA Translation

• RNA → Protein

• Translation is the decoding of an mRNA message into a polypeptide chain (protein).

• Translation takes place on ribosomes.

• During translation, the cell uses information from messenger RNA to produce proteins.

Codons

• A codon consists of three consecutive nucleotides on mRNA that specify a particular amino acid.

• Example: AUG

Amino Acids

• Chart displaying various amino acids and their properties (non-polar, polar, + charge, - charge).

Using a Decoder

• Explains use of mRNA codon chart.

mRNA Codon Chart

• mRNA codon chart.

Translation Process

• The ribosome binds new tRNA molecules and amino acids as it moves along the mRNA.

Protein Synthesis

• Visual representation of translation with mRNA, ribosome, tRNA, and amino acids.

Termination of Translation

• The process continues until the ribosome reaches a stop codon.

Translation (RNA → Protein)

• mRNA codons signal different amino acids.

1. Initiation: Ribosome binds to the mRNA. The amino acid (Methionine) binds with the start codon (AUG).

2. Elongation: Amino acids attach to the tRNA and are matched up with the mRNA strand.

3. Termination: The ribosome reaches a stop codon (UAG, UGA, UAA) and a protein is released.

Protein Synthesis Break Down

• DNA → RNA → Protein

• DNA is transcribed into RNA codons.

• RNA is translated into amino acids that signal different proteins.

Recap of Protein Synthesis

1. Newly transcribed mRNA is sent out to ribosome.

2. Translation begins at the “start” codon: AUG.

3. Each tRNA (w/amino acid), matches up with the pairing codon from the mRNA.

4. Ribosome joins the new amino acid to the polypeptide chain & lets go of the tRNA.

5. The process continues until a “stop” codon: UAG.

6. Polypeptide Chain is folded into the final protein structure.

Check for Understanding (Translation)

1. What is the purpose of translation?

2. What is a codon?

3. What is the start codon?

4. How does tRNA know where to put the amino acids?

5. Where in a cell does translation take place?

Part 2: Mutations

Turn and Talk: Mutations

• What are mutations? Are they good, bad, or neutral?

Types of Mutations

• Germline mutations: Occur in gametes and can be transmitted to offspring, affecting every cell in the offspring.

• Somatic mutations: Occur in other cells of the body and may have little effect on the organism; cannot be passed on to offspring.

Mutations

• Mutations are changes in the genetic material.

1. Gene mutations: Produce changes in a single gene.

2. Chromosomal mutations: Produce changes in whole chromosomes.

Kinds of Gene Mutations: Point Mutations

• Gene mutations: Point Mutation change in one or a few nucleotides and include:

  • Substitution

  • Insertion

  • Deletion

Kinds of Mutations: Substitutions

• Substitutions usually affect no more than a single amino acid.

Types of Substitutions

Kinds of Mutations: Insertions or Deletions

• The effects of insertions or deletions are more dramatic.

• The addition or deletion of a nucleotide causes a shift in the grouping of codons.

• Changes like these are called frameshift mutations.

Kinds of Mutations: Insertion

• In an insertion, an extra base is inserted into a base sequence.

Kinds of Mutations: Deletion

• In a deletion, the loss of a single base is deleted and the reading frame is shifted.

Chromosomal Mutations

• Chromosomal mutations involve changes in the number or structure of chromosomes. Chromosomal mutations include:

  • Deletions

  • Duplications

  • Inversions

  • Translocations.

Kinds of Mutations: Deletions (Chromosomal)

• Deletions involve the loss of all or part of a chromosome.

Kinds of Mutations: Duplications (Chromosomal)

• Duplications produce extra copies of parts of a chromosome.

Kinds of Mutations: Inversions (Chromosomal)

• Inversions reverse the direction of parts of chromosomes.

Significance of Mutations

• Many mutations have little or no effect on gene expression.

• Some mutations are the cause of genetic disorders.

Genetic Testing

• Methods include PCR, Cycle Sequencing, Analysis, and Next Gen Sequencing.

Genetic Testing Example: TSC2

• TSC2 provides instructions to make protein tuberin which helps control cell division.

Genetic Disease Example: Duchenne’s Muscular Dystrophy

• Genetic disease that primarily affects males because it is found on the X chromosome.

• Weakens skeletal and heart muscle.

• New Treatments are being developed.

Part 3: Gene Regulation

Turn and Talk: Gene Regulation

• Do all the following cells have the same function? Do they need the same proteins?

Gene Regulation

• An expressed gene is a gene that is transcribed into RNA.

• Certain DNA sequences = promoters.

• Binding sites for RNA polymerase serve as transcription initiation sites.

• Others serve as stop and start signals for transcription.

• Regulatory sites = places where other proteins bind directly to DNA – regulates transcription (turn gene off or on).

A Typical Gene

• Illustration of a typical gene with promoter sites, regulatory sites, start transcription, and stop transcription signals.

Gene Regulation: E. coli Example

• E. coli provides an example of how gene expression can be regulated.

• An operon is a group of genes that operate together.

• In E. coli, these genes must be turned on so the bacterium can use lactose as food. Therefore, they are called the lac operon.

• The lac genes are turned off by repressors and turned on by the presence of lactose.

The lac Operon

• On one side of the operon's three genes are two regulatory regions.

• In the promoter (P) region, RNA polymerase binds and then begins transcription.

Operator Region

• The other region is the operator (O).

Repressor Binding

• When the lac repressor binds to the O region, transcription is not possible.

Lactose Interaction

• When lactose is added, sugar binds to the repressor proteins.

Gene Expression Repressed

• The repressor protein changes shape and falls off the operator and transcription is made possible.

Gene Regulation (cont.)

• Many genes are regulated by repressor proteins.

• Some genes use proteins that speed transcription.

• Sometimes regulation occurs at the level of protein synthesis.

Eukaryotic Gene Regulation

• Operons are generally not found in eukaryotes.

• Most eukaryotic genes are controlled individually and have regulatory sequences that are much more complex than those of the lac operon.

TATA Box

• Many eukaryotic genes have a sequence called the TATA box.

TATA Box Function

• The TATA box seems to help position RNA polymerase.

Eukaryotic Promoters

• Eukaryotic promoters are usually found just before the TATA box and consist of short DNA sequences.

Enhancer Sequences

• Genes are regulated in a variety of ways by enhancer sequences.

• Many proteins can bind to different enhancer sequences.

• Some DNA-binding proteins enhance transcription by:

  • Opening up tightly packed chromatin.

  • Helping to attract RNA polymerase.

  • Blocking access to genes.

Development and Differentiation

• As cells grow and divide, they undergo differentiation, meaning they become specialized in structure and function.

• Hox genes control the differentiation of cells and tissues in the embryo.

• Careful control of expression in hox genes is essential for normal development.

• All hox genes are descended from the genes of common ancestors.

Hox Genes

• Comparison of Hox Genes between fruit flies and mice.