Nucleic Acids: DNA vs RNA

The Central Dogma of Molecular Biology

• The central dogma defines the flow of information from DNA to RNA and then to protein in all organisms
• In most organisms, DNA is stored as genetic information; however, some viruses use RNA as their genome
• The information flow in a mammalian cell is DNA to RNA to protein
• Retroviruses, such as HIV, use the flow of RNA to DNA to RNA to protein

Nucleic Acids: DNA and RNA

• Nucleic acids are linear polymers of nucleotides or polynucleotides that facilitate genetic information storage and expression
• There are two chemically unique types of nucleic acids
• Deoxyribonucleic acid or DNA is a polymer of deoxyribonucleotides that is covalently linked by a 3' to 5' phosphodiester bond that carries genetic information in all cellular organism and some viruses
• Ribonucleic acid or RNA is a polymer of ribonucleotides covalently linked by a 5' to 3' phosphodiester bond that functions as an intermediary in the transfer of genetic information from DNA to protein

Nucleotides

• Nucleotides are essential building components of RNA and DNA
• Each nucleotide has three component
• A nitrogenous base
• A pentose sugar
• A phosphate molecule
• A nucleoside consists of two components
• A nitrogenous base
• Pentose sugar

Nucleotides Components

• There are two types of nitrogenous bases
• The two types of nitrogenous bases are:
  • Pyrimidine
  • Purine
• The structure share similarity between the 6-membered rings
• The stuctures are planar due to the double bonds, and are also unsaturated

Nucleotides Components Types

• Nitrogenous bases come in two types
• Purine: has a two-ring structure such as Adenine (A) and Guanine (G)
• Pyrimidine: has a one-ring structure such as Thymine (T), Cytosine (C), and Uracil (U)
• The structure share similarity between the 6-membered rings
• The structures are planar because of the double bonds, are also unsaturated
• DNA has A, G, T, and C, while RNA has A, G, U, and C

Nucleotides Component Types

• There are two types of Pentose sugars
• Phosphate groups: are strongly acidic and it's a resoning for calling DNA and RNA as acids

Nucleotides Structure

• Nucleotides are formed by covalent bonding of the phosphate, base, and sugar

Nucleotides Structure: Base/Nucleosides/Nucleotides

• In RNA the "base" is, the "nucleoside" is, and the "nucleotide" is adenosine monophosphate(AMP)
• In RNA the "base" is guanine, the "nucleoside" is guanosine, and the "nucleotide" is guanosine monophosphate (GMP)
• In RNA the "base" is uracil, the "nucleosides" is uridine, and the "nucleotide" is uridine monophosphate (UMP)
• In RNA the "base" is cytosine, the "nucleoside" is cytidine, and the "nucleotide" is cytidine monophosphate (CMP)
• In DNA the "base" is: Adenine, the "nucleoside" is deoxyadenosine, and the "nucleotide" is deoxyadenosine monophosphate(dAMP)
• In DNA the "base" is guanine, the "nucleoside" is deoxyguanosine, and the "nucleotide" is deoxyguanosine monophosphate (dGMP)
• In DNA the "base" is thymine, the "nucleoside" is deoxythymidine, and the "nucleotide" is deoxythymidine monophosphate (dTMP)
• In DNA the "base" is cytosine, the "nucleoside" is deoxycytidine, and the "nucleotide" is deoxycytidine monophosphate (dCMP)

Polynucleotide Chains

• Nucleotides are covalently linked via 3'→5' phosphodiester bonds to form polynucleotides chains
• The resulting chain has polarity
• A 5'-end has a free phosphate and a 3'-end has a free hyroxyl group, that results in a chain with a 5'→3' direction
• Bases are written in the conventional 5'→3' direction and abbreviated, for example 5'-AGCT-3'
• DNA has two polynucleotides chains while RNA has only one
• Each single-strand nucleic acid chain has a polarity

Key Features of Double Helix DNA

• Double helix DNA follows the Watson-Crick Model (1953)
• DNA typically exits as double-stranded helix molecule
• DNA is composed of two polynucleotide chains running in opposite directions -One chain typically runs in 5'→3' direction, and the other in 3'→5' direction
• Base pairing is highly specific such that adenine (A) in one chain pairs with thymine (T) in the opposite chain by two hydrogen bonds, and cytosine (C) pairs with guanine (G) by three bonds

Double Helix DNA: Watson-Crick Model

• The base pairing makes the two polynucleotide chains of DNA complementary in base composition
• If one strand has the sequence 5'-ACGTC-3', then the oppossite strand should be 3'-TGCAG-5'
• The double-stranded structure would be written as 5'-ACGTC-3'/3'-TGCAG-5'
• Chargaff Rule: A=T, G=C, Total purines=Total pyrimidines

More on Double Helix DNA: Watson-Crick Model

• Double helix DNA uses complementary base pairing and hydrogen bonds formation
• Secondary Structure: the two chains twist around each other in a right-handed to form a double helix (B-form)
• One complete turn happens in 10 base pairs and has a space between of 0.34 nm

More on Features of Double Helix DNA

• The third OH-group on the phosphate is free and dissociates a hydrogen ion at physiologic pH, giving a negative charge
• DNA helix has negative charges coating its surface that facilitate the binding of specific proteins, such as histones and non-histones
• DNA Denaturation and Renaturation: the doube strands separate into single strands by disruption of the hydrogen bonds between the paired bases using acidic or alkaline pH or heating
• The phosphodiester bonds are not broken by such treatment
• Complementary DNA stands reform the double helix under appropriate conditions
• DNA degradation occurs through phosphodiester bonds via chemical or enzymatic reactions

Structural forms of DNA double helix

• There are three major structural forms of DNA that uses a Watson and Crick complementary base paring and anti-parallel
  • A, B, and Z forms

Ribonucleic Acid (RNA)

• RNA is a polymer of ribonucleotides covalently linked by 3'-> 5 phosphodiester bonds
• RNA is a single strand that has polarity in a direction from 5'->3' direction
• The bases sequence is always written from 5' to 3' e.g., 5'-AGCU-3'
• Phosphodiester bonds can be broken with chemicals

DNA Condensation

• A cell's genetic information, or DNA, is stored its nucleus.
• DNA must be highly organized and condensed do to space concerns
• DNA coils around proteins called histones, forming beads-on-a-string-like structures called nucleosomes.
• DNA is wraps at several level; until, compacted into chromasomes
• Eight histone proteins will form nucleosome
• A fifth type of histone protein attach to nucleosomes to linker regions of DNA

Condensation and Chromatin

• Further condensing results in chromatin fibers
• The chromatin fibers condense to form chromosomes during cell division
• Chromatin is packed by special proteins known as histones to make complex called chromatic
• Chromatin undergoes for the condensation to chromosomes
• Chromatin is observable in interphase nucleus
• Chromosomes are known as a compact structure of proteins and genetic information
• Genes make chromosomes in observable in M-phase of nucleus division

Cell Division and Replication

• When a cell goes through DNA synthesis or replication
• Chromosomes are duplicated and its consists of two identical "sister" chromosome
• DNA replication occurs before mitosis

DNA Replication

• DNA replication is know a biological process for basis of genetic information
• DNA replications in occur is the S phase of cell cycle
• DNA replication is a semi-conservative process that results to produce two new double strand molecule
• DNA is paired with one made strand

Semiconservative Replication

• Semiconservative Replication will create copies with the origin

More About Replication

Replication begins when a DNA molecule creates: - Origins of replication - Origins are specifically based on origin site

• Mammalian has many origins

Replication Fork

• The replication fork is structure in the nucleus where DNA replication occurs, broken down into two DNA strands
• The fork is where there parentral DNA strans haven't untwist
• Untwisted DNA would not enzyme during replicating, thus; speed of DNA is increased
• The helicase unwinds the double strand DNA for creating forked structure
• Primase makes a chain of RNA to start the DNA
• DNA polymers III only works in 5' to 3' direction. Continuous strands form by continuous replication

Replication Strands

• The leading strand is new DNA strand that synthesized countinously
• The legging strand is a new strand that synthesized discontinously

Helicase in DNA Replication

• Also known as helix destabilizing enzyme
• Helicase's function to is unwind the DNA using the replication fork

Polymerase

• DNA Polymerase: Builds a new duplex of DNA strands
• Nucleotides must be in 5' to 3' for it to perfom functions
• Single Strand Binding Protein: It allows helps prevent DNA and helps maintain strand formation
• Toporsomerase: It relaxes it from super coiled force
• Primase: Provies starting and synthesis for the start formation
• Ligase: Help reannewl semi conservative

DNA Polymerase

• Three DNA polymerase are in the e.Coli
• DNA is needed to function through the DNA
• II is what is what is required to the repairs
• 50 base and added during Mammals per second

Cell Cycle

• Cell cycle or cell division if series of event for cell division
• DNA is replicated to the daughter cells
  • The following occurs in the cell cycle
    • Interphase
      • Phase
        • G1 (Gap 1)- Stage begin after mitotis Proteins; RNA and Organelles are synthesized
        • S- Replicated proteins are synthesized
        • Divide: Precuous fibers are formed.
    • Mitosis
      • Phrophase- Nuclear forms are desynathies
      • Metaphase- Is form is form
      • Anapahse- Chromosme are separated -Teophase; Chrosmone has new from -Cytokenisis- Divides the Cytomplasm -A cell has 46 chrosmones, but the human had 23
• Mitosis will go the copy of original
• The cell cycles time is measured as such - G1 ( 6-12) - S (6-8) - G2 ( 3-4) - M (1)
• Genotypes
  • Some haploid and diploid divide by Mitosis
  • Produces 2 cells that are new and genitical

Explore the differences between DNA and RNA, including nitrogenous base composition and genetic information flow. Covers retrovirus integration, phosphodiester bonds, and the central dogma. The role and structure of nucleotides and nucleosides are explained.