DNA Structure and Replication Quiz

Molecular Biology

• Coined by James Watson
• Focuses on the study of biological phenomena involving molecules such as DNA, RNA, and proteins.
• Molecular diagnostics is the use of molecular biology techniques to detect diseases.

History

• Friedrich Meischer published a paper on nuclein, and isolated nuclein from WBC nuclei.
• Nuclein was a viscous, nonprotein substance extracted from cell nuclei and was renamed DNA once the chemical composition was found.
• Walther Flemming described the nucleus in 1882.
• James Watson and Francis Crick first described the double helical structure of DNA in its hydrated form, with 10.5 base pairs per turn.
• Rosalind Franklin performed diffraction analyses of Watson and Crick's molecular model and acted as physical evidence.
• Francis Crick proposed the central dogma, which decribes the flow of genetic information from DNA to RNA to proteins

Deoxyribonucleic Acid (DNA) Structure

• The physicochemical demands of the linear array of nucleotides determine its helical structure.
• DNA is a polymer which is made up of subunits called monomers
• The name comes from deoxyribo (a sugar) + nucleic acid
• Nucleic acid is composed of nucleotides, and the nucleic acid chain grows when the 5' phosphate group is bound to the 3' hydoxyl group on the last nucleotide
• The Anti-parallel arrangement of DNA has the 5' end of one strand aligns with the 3' end of the other strand
• DNA's sequence is read in the 5' to 3' direction.
• DNA is primarily composed of carbon, nitrogen, oxygen, phosphorous and hydrogen atoms (CHONP).
• 2 strands of nucleotides are linked together by nucleotides that create a polynucleotide.

Nucleotide

• A nucleotides, the basic unit of DNA, consist of a phosphate group, deoxyribose sugar, and nitrogenous base.
• 1st C of sugar is joined to a nitrogen base
• 5th C of sugar is joined to a phosphate group
• When an unphosphorylated sugar is attached to a nitrogen base, it becomes a nucleoside
• All nucleotides are chemically identical, except for the nitrogen base

Nucleotide vs. Nucleoside

• Nucleotide: nitrogenous base + pentose sugar + phosphate group, polymerizes to form DNA/RNA
• Nucleoside: nitrogenous base + sugar; cannot form DNA or RNA
• Examples of nucleotides: 2'-deoxyadenosine 5'-triphosphate (dATP), 2'-deoxyguanosine 5'-triphosphate (dGTP), etc.
• Examples of nucleosides: Adenosine (A), Guanosine (G), Cytidine (C), Thymidine (T)
• Function of nucleotides: building blocks of DNA & RNA, energy carriers ( ATP, GTP), and signaling molecules (cAMP).
• Function of nucleosides: Precursor to nucleotides, involved in metabolic pathway
• Polynucleotide forms when nucleotides attach to one another and have linkage between nucleotides in a polynucleotide.
• Nucleotide monomers are linked through a phosphate group which attaches to the 5' carbon of one nucleotide, to the 3' carbon of the next.

Components of Nucleotide

• 2' deoxyribose is a pentose sugar that has lost the hydroxyl (-OH) group on its 2' carbon.
• 2' deoxyribose has no oxygen attached on its 2' carbon, versus a ribose which has an OH group.
• The hydroxyl group on the 3rd carbon is important for forming the phosphodiester bond that is the backbone of the DNA strand.
• Nitrogen bases are planar carbon-nitrogen ring structures which form rungs of the DNA.
• B-N-glycosidic bond is a covalent bond that connects a nitrogenous base to the deoxyribose sugar in nucleotides.
• Hydrogen bonds link two nitrogen bases

Complementary Base Pairing

• DNA bases pair predictably: Adenine with Thymine, Cytosine with Guanine.
• Hydrogen pairing is a weak electrostatic attraction between an electronegative atom, and a hydrogen atom.
• Base pairing occurs as the sequences for polynucleotides are determined by each sides sequence
• Hybridization is when there is formation of hydrogen bonds between two complementary strands of DNA

Summary of Bonds in DNA

• Phosphodiester Bond: links nucleotides together via sugar and phosphate groups
• 3'-OH of one sugar and 5'-phosphate of the next nucleotide
• Beta N-Glycosidic Bond: connects nitrogen base with the sugar
• C1' of sugar and N1 pyrimidine or N9 purine
• Hydrogen Bond: Connects the complementary bases together
• The hydrogen bond acts as a facilitator in base pairing and allows for the the DNA double helix stability.

DNA Replication

• DNA creates a copy in this process by the name of DNA replication
• The process is considered conservative - for maintaining the sequence of nucleotides
• Semoconservative entails that when a molecule is copied, the molecules consist of one original strand and one newly synthesized strand
• DNA synthesis happens in the 5' to 3' direction
• In semiconservative replication, DNA polymerase - is the enzyme that determines which nucleotide is added to the chain
• Replication apparatus copies DNA strands in an orderly way before cell division

DNA Replication Process

• DNA replication begins at the Origin of Replication (ORI) at a specific DNA sequence/location

• At the origin the duoble helix is unwinding, and forming a replication bubble

• Further separation of strands is caused by the enzyme, Helicase

• Helicase breaks the hydrogen bonds, and the resulting effect produces 2 template strands

• Gyrase assists helicase and reduces torsional strain and positive supercoil ahead of the replication fork

• Single-strand binding proteins (SSB) are located after the helicase coats, they prevent the strands/single strand DNA from rewinding into a double helix

• RNA Primers are short segments of RNA produced by primase to come bind to start the process

• The RNA Primer strand is attached by DNA Polymerase III (in prokaryotes) or DNA Polymerase δ/ε (in eukaryotes)

• DNA Polymerase III adds nucleotides with its 5'-phosphate group to the 3' end of the last nucleotide of the primer

• During synthesis of a growing strand occurs in the in the 5'-to-3' direction while complementing the template strand.

• DNA polymerase will add nucleotides continuously to the leading strand in the same direction as synthesis of the replication fork

• While the leading strand is synthesized, the DNA polymerase will synthesize discontinuously in the opposite directiion, while forming short fragments called Okazaki Fragments

• When the gaps are filled, RNAse H (DNA polymerase I) removes the RNA primer and approaches to catalyze

• Finally to seal the DNA strand a DNA ligase is used to joins Okazaki fragments on the lagging strand by forming phosphodiester bonds

Recombination

• The mixture and assembly of new genetic combinations, through the molecular process of physical exchange between molecules
• When a molecule holds a new combination of DNA sequences, can be coined as a recombinant molecule
• Sexually reproducing create genetic diversity
• At prophase of meiosis, there is separation of chromosomes. The non sister chromatids separate and form a recombinant chromosome in one of the four DNA duplexes
• Each gamete contains one set of chromosomes, so they are randomly assorted into new gametes
• The gamete will merge with another one from a new set from recominant chromosomes

Recombination in Asexual Reproduction

• Refers to the movement of genetic material between organisms, other than through vertical transmission
• Conjugation involves F+ (had a “fertility factor”) and F- (does not carry a genetic facto)
• The fertility factor also carries the responsibility for establishing the physical connection between the mating bacteria
• F factor was shown to be an extrachromosomal circle of dsDNA carries the code for creating the mating bridge
• Process often involves the transfer of plasmids and a direct transfer of bacterial cell

Transduction

• Francois Jacob and Elie Wollman studied the transmission of units of heredity carried by viruses (transduction)
• Alfred Hershey and Martha Chase confirmed that that the DNA of a bacterial virus was the carrier of its genetic
• This involves the transfer of genetic material from one bacterium to another via bacteriophages (viruses infecting bacteria).
• The phages inadvertently package bacterial DNA into their viral, introduced to a new bacterial host.
• Useful for genetic recombination

Transformation

• Observed by Frederick Griffith, becoming the modern basis
• A process when a bacterium takes up free, naked DNA fragments from a surrounding environment.
• Enacting that the transfer of DNA occurs from one organism to another

Ribonucleic Acid (RNA)

• A polymer of nucleotides
• Having uracil instead of thymine
• Single strand rather than double helix
• Can pair with single strands of DNA to form a double helix

Types of RNA

• mRNA: Messenger RNA
  • Carries genetic information from DNA template
  • Eukaryotic mRNA are monocistronic
  • Undergoes a series of transcriptional events before the translated in proteins
  • Constitutive and Inducible Transcription are present
• rRNA: Ribosomal RNA
  • Largest component of cellular RNA
  • Part of the ribosomes where proteins are synthesized
    • 16S - small ribosome
    • 23S; and 5s - large ribosome
• tRNA: Transfer RNA
  • Translation requires requires reading of mRNA by ribosomes, with adaptor molecules
  • Relatively short sequence from 73 to 93 bases in length
  • Cruiform structure present

Transcription Process

• DNA goes to mRNA in the nucleus and cytoplasm
• RNA poylmerse its supporting accesor proteins assemble on DNA at a prompter sequence
• Transcriptional factors binds to DNA sequencs
• Codified coding region is then transcribe

Phases of RNA Processing

• Elongation has to have a region to control transcription levels
• Termination sequence is for notifying end portion
• RNA requires priming, but requires Rho Protiens to facilitate Rho leaving
• INTRONS get exits nucleus

Proteins

• Abundant for the macromolecule
• Express phenotype Proteome: collection of protein-encoded DNA from an organism
• Proteins serve as Enzyme, Transport, Storage, Defese, and Regulatory and Conjugate

Amino Acids

• Grouped according to Polarity

Genetic Code

• Language that expresses Amino Acids, and universal
• Codons have sequences of consecutive nucleodies
• Stop Codons: UAG,UAA, UGA
• Mutations can be silent or drastic

Translation

• Involves synthesis of Protein and involves in Eukaryotic and Bacterial Cells
• 3 RNA present
• Two steps amino activation with ATP addition and amyno group combined with TRNA
• 20 amino acids present

Protein Synthesis

• Initiation, Elongation, Termonation helps fold and bond peptide
• Involves Chaperones

Sequence of Amino Acids

• Primary, Secondary
• tertiary, quaternary

I hope this helps!

Test your knowledge of DNA structure, components, and replication. This quiz covers key concepts such as the double helix, nucleotide composition, and the directionality of DNA. Learn about the scientists involved in DNA discovery and the processes that ensure genetic information is accurately copied.