Nucleic Acids: DNA and RNA Structure & Functions

Nucleic Acids

• Nucleic acids include DNA and RNA
• The building block of Nucleic acid is the Nucleotide
• A Nucleotide consists of:
• A sugar
• A nitrogenous base
• A phosphate group

DNA Functions

• Carries the genetic instructions for development, functioning, and reproduction of organisms and some viruses

RNA Functions

• Viruses may carry genetic information as RNA only
• Involved in converting DNA code into polypeptides or proteins
• Acts as a catalyst
• Regulates gene expression and modifies other RNA

DNA Structure

• Nitrogen-containing bases project from the backbone
• Bases are linked to a carbon in the sugar by a glycosidic bond
• A phosphodiester bond links sugar to form the backbone of a DNA strand
• DNA is a huge polymer with chromosome 1 in humans having 249 million base pairs

The Sugars

• Sugars are 5-carbon sugars or 5C sugars
• DNA contains deoxyribose
• RNA contains ribose
• The phosphate group at the 5' carbon bonds to the 3' carbon of the next sugar
• Bonds to nitrogenous bases at 1' carbon

Nitrogenous Bases

• DNA has four bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C)
• Adenine (A) hydrogen bonds to Thymine (T)
• Guanine (G) hydrogen bonds to Cytosine (C)
• RNA also has 4 bases, but Uracil (U) replaces Thymine (T) in RNA

DNA Antiparallel Strands

• Two strands are parallel but run in opposite directions
• One strand runs 5' to 3', and the other runs 3' to 5'
• The 5' sugar bonds to a phosphate
• The 3' hydroxyl group is on the sugar
• DNA can be single-stranded but is most stable when double-stranded
• DNA twists into a 3-D helix
• Antiparallel strands allow hydrogen bonding between bases and provide stability for the DNA molecule

Packaging DNA

• In eukaryotes, DNA wraps around proteins called histones, forming a coiled structure called chromatin
• This structure is further compressed by supercoiling to form chromosomes
• Most prokaryotes lack histones, but have supercoiled forms of DNA held together by special proteins

RNA Structure

• RNA is single-stranded
• It can form double-stranded structures important to its function
• By folding, RNA can form secondary structures stabilized by hydrogen bonds between the nitrogenous bases

DNA Replication

• DNA replication is the process of copying DNA
• The three key processes are:
• Separating DNA
• Building a complementary strand
• Quality control and DNA repair

Separating DNA During Replication

• DNA helicase functions as an enzyme that unzips the DNA by breaking hydrogen bonds between complementary pairs
• The junction is called a replication fork
• Single-stranded binding proteins bind to exposed DNA single strands to prevent hydrogen bonding between base pairs
• Topoisomerase regulates the unwinding of the DNA

Building Complementary Strands

• DNA polymerase creates a new strand by pairing complementary bases to the separated strands or template strands
• It always travels in the 3' to 5' direction on the template strand and builds a complementary strand in the 5' to 3' direction
• DNA polymerase cannot initiate a strand, so primase must first add a primer or a short segment of nucleotides to the 3' end of the template strand
• The primers are later removed by DNA polymerase, and replaced with DNA
• Primase belongs to a family of enzymes called RNA polymerase

DNA Polymerase

• A family of enzymes involved in DNA replication and contains 7 different subgroups
• DNA polymerases I, II, and III are specific enzymes from E. coli, where DNA replication was studied first

DNA Replication Strands

• Leading strand follows the 3' to 5' template strand and moves toward the replication fork and is replicated continuously
• Lagging strand moves from the replication fork to the 5' end of the template strand, so replication is discontinuous.
• The resulting fragments are called Okazaki fragments
• DNA ligase catalyze the reaction to join the Okazaki fragments together

Semiconservative replication

• The replication process is called semi-conservative to describe that one half of the original strand is always saved or conserved in the daughter DNA molecules

Editing and Proofreading DNA

• DNA polymerase also checks the complementary strand for errors.
• DNA polymerase proofreads and corrects typos, repairs mismatched bases, and removes abnormal bases

Gene Regulation

• Gene regulation is the process that determines which genes are expressed and at what levels.
• Cells must have the ability to turn genes on and off
• Cells can adjust the "volume" of each gene by controlling how many proteins are produced

Gene Regulation Prokaryotes Vs Eukaryotes

• Prokaryotes Utilize a feedback model called an operon system
• Operons are clusters of coregulated genes that share a promoter and operator
• Gene control is more complex in eukaryotes than in prokaryotes

Operon Structure

• Consists of a promoter, which is the site where DNA transcription begins
• Has an operator, which is a sequence of bases that control transcription
• A repressor binds to the operator and stops transcription of that gene
• Contains structural genes that code for the protein(s), and they are transcribed as a unit

The lac Operon

• The lac operon is always present, so genes are normally off
• The operon contains a CAP site, promoter, operator, lacZ, lacY, and lacA
• The repressor is always bound to the operator region, preventing RNA polymerase from transcribing DNA
• Lactose or the inducer binds to the repressor protein, which is then released from DNA
• As lactose levels drop, the repressor binds to the operator region again, stopping the production of proteins

Proteins Produced by the lac Operon

• B-galactosidase is used to split bond in lactose
• Galactoside Permease acts as a transport protein that embeds in the cell membrane and pumps lactose into the cell
• Transacetylase which transfers an acetyl group from one molecule to another

Tryptophan(Trp) Operon

• Genes turn on and will continue to produce tryptophan
• If tryptophan is present it binds to the repressor, and prevents more tryptophan from being made

Eukaryotic Categories of Gene Regulation

• Transcriptional regulation by synthesizing mRNA
• Post-transcriptional regulation by making mRNA available to ribosomes
• Translation by synthesizing proteins
• Post-translation by regulating proteins after synthesis

Transcriptional Regulation

• This type of regulation regulated the transcription rate of genes
• Enhancement or decresed access to promoters
• Ex, is the methylation of genes

Post Transcriptional Regulation

• Controls the availability of mRNA to ribosomes
• Example: Alternative splicing. 75% of human genes may undergo alternative splicing

Translational Regulation

• Regulation of translation focuses on controlling the rate and manner in which mRNA is translated to create a protein
• Ex, length in the poly-A tail.

Post-Translation Regulation

• Regulating proteins after their synthesis can vary according to functional state, or level of degradation.
• Ex, activation of p53.

Mutations

• Mutations are simply changes in the DNA and can have no effect, a positive effect, or a negative effect
• The mut at ion may cause a change in phenotype, a slight change, or a large change, especially when the gene controls other genes
• Chromosomal mutations can result in part of the chromosome being flipped and reinserted, or a loss of part of the chromosome

Classes of Mutations

• Small scale mutations is a changes in single or small group of base pairs
• Large scale mutations is large chunks of DNA, inserted, lost or repeated, or duplication of genes
• Large Scale mutations are in the 10,000 to 5,000,000 bases long

Small Scale mutation types

• Point Mutations - single-base changes
• Types are substitutions where one base is is replaced by another
• Insertion where one or more is added in the sequence
• Deletion where one or more are removed from the sequence
• Inversion where two adjacent trade place
• Change of small group of base pairs
• Types of small scale are substitutions insertions deletions inversions
• Deletion and insertion casues changes to reading frame codons

Effect of Mutations

• Silent mutations does not change the amino acid coded for.

• Nonsense mutations: converts a codon into a stop signal.

• Missenses mutations: Results in the single substitution of one amino acid

What is Frameshift mutation

• Insertion or Deletion of one or more base pairs causes the reading frame to shift in one direction or the other

Important of Mutations

• Mutations provide the raw material for genetic diversity and thus are essential for evolution.
• They may be beneficial, harmful, or neutral.
• Mutation rates may be increased by the external environment.
• However, they are random in that whether a particular mutation happens or are not related to how useful that mutation would be.

Mutation Causes

• Spontaneous: caused naturally like errors during DNA copying
• Induced: caused by an impact from UV light X-ray or certain chemicals

Genetic Material

• A gene is a sequence of DNA that codes for a protein
• Protein coding genes account for less than 2% of the nucleotides.
• Each 3 nucleotide base pairs code for an amino acid and is referred to as a codon.
• Some part of in the gene do not code for a protein
• All other part provide additional info, that control to make

Genetic Code

• Almost begins protein coding regions the AUG that encodes for amino acid Methionine(Met)

• 3 stop condons that mark the end

• All multiple cordons can code for the code

Translation and Transcription

• Transcription copying infoDNA to messenger RNA(mRNA)
• Transltion assemble amino in the form protein
• translation assemble amino in the form protein

Types of DNA Replication

• Only one strand of DNA serves as a template
• The sequence is New messenge DNA
• Templete strand or not non coding structure

The Three stages of the replication process?

• Initiation or RNA polymerase binds to template DNA

• Elongation or RNA pollymearse redsDNA adds nulesotides direction mRNA

• Templetess 3s end to 2 the direction RNATranscriptless is less cempxes the prokartons

Initiation DNA Replication

• RNA polymerase attaches Up-Screen

RNA

Elongation

Elongation

• Double helix Unwinds
• RNA Polymerase reds end

• Template transribeds helix is

Gene Regulation Termmation and Transcription

• RNA Polymerase reaches a terminal