DNA and RNA Structure

Chapter 3.1 - DNA and RNA

• Focuses on nucleic acids as information molecules for protein synthesis
• Involves the structure of DNA, three main forms of RNA--mRNA, rRNA, and tRNA--and the comparison of DNA and RNA
• Success requires outlining nucleotide structural features, explaining DNA condensation into chromosomes, and comparing DNA

Nucleic Acids

• All life contains nucleic acids
• Nucleic acids are responsible for storing genetic information and producing proteins
• There are two types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA)

DNA Structure

• Two DNA chains make up the helix
• The two chains are linked via hydrogen bonds between bases

DNA Chains Backbone

• Backbone of the chains are made from covalent bonds known as phosphodiester bonds
• The DNA strand runs antiparallel

Key Components

• Consists of a phosphate group (PO₄), which is negatively charged
• Also includes a sugar group called deoxyribose, which is a 5-carbon pentose
• Also includes a nitrogen base including Adenine, Thymine, Cytosine, Guanine

Primer Numbers

• DNA chains are arranged antiparallel
• One chain is set up 5' to 3', and the other one its 3' to 5'

Nitrogen Bases

• Adenine always binds to Thymine with 2 hydrogen bonds, and vice versa
• Cytosine always binds to Guanine with 3 hydrogen bonds, and vice versa
• For example, if you have a DNA chain that was ATT CGA GGA, then the complementary chain would be TAA GCT CCA

Nucleic Acids (RNA)

• RNA shares similarities with DNA, such as similar sugar groups and phosphate backbone arrangement, but there are differences

RNA vs DNA

• RNA uses ribose as its sugar group, while DNA uses deoxyribose
• RNA uses Uracil, while DNA uses Thymine
• RNA is single-stranded, while DNA is double-stranded
• RNA is created when needed for protein synthesis and comes in three forms: mRNA, tRNA, and rRNA
• DNA is always found in each cell

Chromosomes

• DNA wraps around histones which make coils, supercoils, nucleosomes and chromosomes

Gene Structure and Expression

• The genetic code as a universal triplet code that is degenerate and the steps in gene expression, including transcription, RNA processing in eukaryotic cells and translation by ribosomes
• It explores the structure of genes, including exons, introns, promoter, and operator regions
• Also discusses the role of rough endoplasmic reticulum, Golgi apparatus, and associated vesicles in exporting proteins from a cell via the protein secretory pathway

Success Criteria

• To outline the three stages of transcription and of translation
• To distinguish between introns and exons

RNA

• RNAs role is as a nucleic acid used during gene expression
• Proteins repair and build muscle but is mainly used in creating hormones and enzymes that control bodily functions.

Gene Expression

• Gene Expression consists of three steps: transcription, RNA processing, and translation

Transcription:

• RNA is produced from the DNA in the nucleus
• Has 3 stages: Initiation, Elongation, Termination

RNA processing:

• RNA that is copied from DNA is refined into mRNA

Translation:

• mRNA enters ribosomes and becomes a protein

Transcription Process

• RNA is produced from a DNA strand in three stages: initiation, elongation, and termination

Transcription: Initiation

• Transcription factors (specific proteins) bind to the promoter region
• This directs the polymerase on where it needs to bind
• Then RNA polymerase binds to the promoter region
• Presence of RNA polymerase signals hydrogen bonds to weaken and break down
• DNA strand will then unwind, exposing its nitrogen bases

Transcription: Elongation

• RNA polymerase forms pre-mRNA
• The pre-mRNA molecule is synthesised in a 5' to 3' direction using the template strand.
• New RNA nucleotides are added to the exposed 3' end.
• Pre-mRNA strand has a complementary nucleotide sequence to the DNA template strand.
• The strand of DNA that is not read by RNA polymerase is called the coding strand.

Transcription: Termination

• Transcription ends when RNA polymerase reaches the termination sequence
• RNA polymerase detaches, releasing the pre mRNA molecule, and the DNA molecule winds up
• The pre-mRNA molecule is then processed to become mRNA

RNA Processing

• RNA produced from transcription needs to be modified before becoming mRNA
• RNA processing requires: addition of 5' cap, addition of a poly-A tail, and splicing
• The end result is a single-stranded mature RNA that leaves the nucleus and moves on to the translation step of protein synthesis

Splicing

• Splicing involves required parts (exons) and unnecessary regions (introns)
• Splicing happens through the removal of introns from RNA to form mature RNA
• A spliceosome removes introns and joins together remaining exons
• Alternative splicing means that different mRNAs can form, depending on how exons are joined or even if exons are cut

Translation

• mRNA produced from RNA processing now interacts with a ribosome
• This will begin the creation of polypeptide chains and process is in 3 stages, initiation, elongation, termination

Translation: Initiation

• A ribosomal subunit the attaches to 5' end of mRNA and along until its finds a start codon
• The translation process begins
• The result is a chain of amino acids forming a polypeptide chain
• Each set of codons codes for an amino acid, where AUG is Met
• Codons are degenerate, meaning that more than one codon can code for an amino acid
• Amino acids are transported via tRNA to form the polypeptide chain
• TRNA with the anticondon UAC will carry the Amino Acid, Met to begin forming the chain

Translation: Elongation

• Ribosomal subunit will move down the mRNA chain to the next codon, AAA, which will cause tRNA with anti codon, UUU to carry Lys to attach to Met
• When two amino acids are next to each other, they will form a peptide bond via condensation polymerisation

Translation termination

• The process will continues until it reaches a stop cordon, UAA, UAG, UGA
• tRNA can reused to transport more amino acids in the future
• Polypeptide chain is released from ribosomes into the cytoplasm
• Either the endoplasmic reticulum or multiple polypeptide chains can also be formed simultaneously to the Golgi apparatus

Gene Regulation

• Gene regulation is either inhibiting or activating gene expression
• Prevents unnecessary production of gene products such as proteins when they are not required in order to conserve energy
• It is achieved by using structural and regulatory genes
• Regulatory genes produce regulatory proteins, repressor, proteins, and activator proteins
• Structural genes produce proteins that help in cell function, transport, receptors, and hormones

Tryptophan

• The amino acid tryptophan can be used to build complex proteins
• E. Coli can make its own tryptophan, or obtain it from the environment

Tryptophan in E.Coli: High Level

• In a high tryptophan environment, the repressor protein is produced via a regulatory gene
• Tryptophan in the environment will attach to the repressor protein, causing a conformational shape change and making it active
• The repressor protein then attaches to the operator. Meaning the RNA polymerase cannot attach to the promoter, therefore tryptophan gene expression stops

Tryptophan in E.Coli: Low Level

• In low tryptophan, the repressor protein is produced via a regulatory gene
• However, if there is no tryptophan in the environment the repressor protein is inactive
• As a result, RNA polymerase can attach to the promoter and transcribe the protiens needed that with form tryptophan

Gene Regulation: Attenuation

• Tryptophan type of gene regulation also controlled by levels of trp
• With low levels of Trp, transcribe mRNA pauses because it is responsible for coding for Trp
• When there's enough tryptophan, the mRNA is complete

Defining DNA Sequences

• TrpL gene represents the regulatory gene, which is responsible for starting and halting protein production
• Trp structural gene is responsible for producing amino acids that form the Trp protein
• DNA sequence also has some distinct sections with each section consist of a sequence of nucleotides

High Levels of Tryptophan

• Higher levels is achieved if in if this scenario the ribosome is able to easily translate the trp condons, and a Trp proteins is sysnthesized
• The ribosome can continue translation along the mRNA
  • Then the attenuator loop will causes RNA polymerase to stop transcription
  • Therefore, it ensures energy is not wasted when there is tryptophan

Low Levels of Tryptophan

• Ribosome will translate, However, lack of trp will stall it at the trp codons
• Then This loop does not affect RNA polymerase