DNA Structure and Properties

DNA Structure (Nucleotides)

DNA is a double-helical molecule composed of nucleotides, each consisting of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (A, T, G, C). The structure and pairing of these bases are fundamental to genetic information storage and transmission.

• Nucleotide Composition: Each nucleotide contains a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, guanine).

• Phosphodiester Bonds: Nucleotides are linked by covalent phosphodiester bonds between the 3' hydroxyl of one sugar and the 5' phosphate of the next.

• Base Pairing: Hydrogen bonds hold complementary bases together: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds).

• Antiparallel Strands: The two DNA strands run in opposite directions (5' to 3' and 3' to 5').

• Chargaff's Rules: In double-stranded DNA, %A = %T and %G = %C.

Example: If a DNA sample contains 35% A, it must also contain 35% T, and the remaining 30% is divided equally between G and C (15% each).

DNA Replication

DNA replication ensures that each new cell receives an exact copy of the genome. The process is semi-conservative, meaning each daughter DNA molecule contains one parental and one newly synthesized strand.

• Purpose: To duplicate the genetic material before cell division.

• Enzymes Involved: DNA helicase (unwinds the helix), DNA polymerase (synthesizes new DNA), primase (synthesizes RNA primers), ligase (joins Okazaki fragments).

• Directionality: DNA polymerase adds nucleotides in the 5' to 3' direction.

• Leading and Lagging Strands: The leading strand is synthesized continuously; the lagging strand is synthesized in short fragments (Okazaki fragments).

DNA Organization and Chromatin Structure

Chromosome Structure

DNA is packaged into chromosomes to fit within the nucleus and regulate gene expression.

• Chromatin: DNA wrapped around histone proteins forms nucleosomes, further compacted into chromatin fibers.

• Chromosome Forms: Tightly coiled DNA is visible during cell division as chromosomes; loosely packed chromatin is present during interphase.

Historical Discoveries

• Watson and Crick: Proposed the double helix model of DNA structure.

• Rosalind Franklin: Provided X-ray crystallography data crucial for elucidating DNA's helical structure.

DNA vs. RNA Structure Differences

• Sugar: DNA contains deoxyribose; RNA contains ribose.

• Bases: DNA uses thymine; RNA uses uracil instead of thymine.

• Strandedness: DNA is typically double-stranded; RNA is usually single-stranded.

• Function: DNA stores genetic information; RNA functions in gene expression and regulation.

Transcription

Process of Transcription

Transcription is the synthesis of RNA from a DNA template. Only one DNA strand (the template strand) is transcribed for each gene.

• Enzyme: RNA polymerase synthesizes RNA in the 5' to 3' direction.

• Initiation: RNA polymerase binds to the promoter region upstream of the gene.

• Elongation: RNA polymerase adds complementary RNA nucleotides.

• Termination: Transcription ends at specific termination sequences; the RNA transcript is released.

• Product: The primary transcript (pre-mRNA in eukaryotes) is produced.

Note: Promoter regions are not transcribed into RNA.

mRNA Processing (Eukaryotes)

Post-Transcriptional Modifications

Before mRNA can be translated, it undergoes several modifications:

• 5' Capping: Addition of a modified guanine nucleotide to the 5' end.

• Polyadenylation: Addition of a poly(A) tail to the 3' end.

• Splicing: Removal of non-coding introns and joining of coding exons.

Example: The mature mRNA transcript contains only exons, a 5' cap, and a poly(A) tail.

Translation and Protein Synthesis

Translation Process

Translation is the process by which ribosomes synthesize proteins using the sequence of codons in mRNA as a template.

• mRNA: Provides the codon sequence for amino acid assembly.

• tRNA (Transfer RNA): Brings specific amino acids to the ribosome; each tRNA has an anticodon complementary to an mRNA codon.

• rRNA (Ribosomal RNA): Structural and catalytic component of ribosomes.

• Initiation: Ribosome assembles at the start codon (AUG) on mRNA.

• Elongation: tRNAs bring amino acids to the ribosome, and peptide bonds form between them.

• Termination: Occurs when a stop codon is reached; the completed polypeptide is released.

Example: The codon UUU codes for phenylalanine; the process continues until a stop codon (UAA, UAG, UGA) is encountered.

Proteins

Amino Acids and Protein Structure

Proteins are polymers of amino acids, which are linked by peptide bonds. The sequence and properties of amino acids determine protein structure and function.

• 20 Standard Amino Acids: Each has a unique side chain (R group) that determines its chemical properties.

• Peptide Bond: Covalent bond formed between the amino group of one amino acid and the carboxyl group of another.

• Levels of Protein Structure:

  • Primary: Linear sequence of amino acids.

  • Secondary: Local folding into alpha helices and beta sheets (stabilized by hydrogen bonds).

  • Tertiary: Overall 3D shape formed by interactions among R groups.

  • Quaternary: Association of multiple polypeptide chains (subunits).

• R Group Properties: Amino acids can be nonpolar (hydrophobic), polar (hydrophilic), acidic (negatively charged), or basic (positively charged).

Mutations

Definition and Types

A mutation is a change in the nucleotide sequence of DNA. Mutations can be neutral, harmful, or beneficial, depending on their effect on protein function.

• Point Mutation: Change in a single nucleotide; may result in a different amino acid (missense), a stop codon (nonsense), or no change (silent).

• Insertions/Deletions: Addition or loss of nucleotides; may cause frameshift mutations, altering the reading frame.

Effect on Proteins: Mutations in coding regions can change the amino acid sequence, potentially altering protein structure and function.

Example: Sickle cell anemia is caused by a single nucleotide substitution in the beta-globin gene, resulting in a defective hemoglobin protein.

Summary Table: DNA vs. RNA

Key Equations

• Chargaff's Rule:

• Calculating Base Percentages: If %A = 35%, then %T = 35%, and %G + %C = 30% (so %G = %C = 15%).

Additional info:

• These notes cover core topics in nucleic acids, gene expression, protein structure, and mutations, which are foundational for biochemistry students.

• For further study, consult recommended videos and articles on DNA replication, transcription, translation, and protein structure.