Nucleic Acids and DNA Structure

Nucleic Acids and DNA Structure

• DNA and RNA are nucleic acids composed of nucleotides.
• Nucleotides consist of a phosphate group, a sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.
• DNA contains four nitrogenous bases: adenine (A), thymine (T), guanine (G), and cytosine (C).
• A always bonds with T, and G always bonds with C.
• RNA has uracil (U) instead of thymine (T), which bonds with adenine (A).
• Both DNA and RNA have a covalently bonded sugar-phosphate backbone.
• DNA is double-stranded, forming a double helix. RNA is single-stranded.
• The sugar-phosphate backbone forms the sides of the DNA "ladder," while the nitrogenous bases form the rungs, held together by hydrogen bonds.

DNA Replication

• DNA replicates during cell division, using each strand as a template to create a new strand.
• The resulting DNA molecule contains one original (parent) strand and one new (daughter) strand (semiconservative replication).
• DNA strands run antiparallel (3' to 5' and 5' to 3').
• One end of a DNA strand has a phosphate group, and the other has a sugar.

Leading Strand Replication

• DNA helicase unwinds the DNA double helix.
• RNA primase creates a short RNA primer.
• DNA polymerase reads the template strand in the 3' to 5' direction and builds the new strand in the 5' to 3' direction.
• This allows for continuous replication on the leading strand.

Lagging Strand Replication

• DNA polymerase cannot continuously replicate the lagging strand (which runs 5' to 3'), so it moves in short fragments called Okazaki fragments.
• RNA primase adds primers to initiate each Okazaki fragment.
• DNA polymerase adds DNA nucleotides to each Okazaki fragment.
• DNA ligase joins the Okazaki fragments to form a complete new strand.

Replication Initiation Sites

• Replication begins at multiple sites along the DNA molecule to increase speed. These sites create replication bubbles.

Transcription

• Genes contain the code for proteins.
• DNA, which contains the genetic code, cannot leave the nucleus.
• RNA carries the genetic code from the nucleus to the ribosomes.
• Transcription analogous to copying architectural plans for a new construction.
• The process is initiated, elongated, and terminated. These three phases are: Initiation, elongation, and termination.

Transcription Initiation

• DNA helicase unwinds the DNA helix.
• RNA polymerase binds to the promoter (a region of DNA at the gene's start).

Transcription Elongation

• RNA polymerase moves along the template strand, building a complementary RNA strand.
• RNA uses uracil (U) instead of thymine (T).

Transcription Termination

• RNA polymerase reaches the terminator sequence (end of the gene).
• RNA polymerase detaches, and the DNA rewinds

Post-transcriptional Modifications

• mRNA capping: A modified guanine is added to the 5' end.
• Polyadenylation: A poly-A tail (~250 adenine nucleotides) is added to the 3' end for protection from cellular enzymes.
• Alternative splicing: Introns (non-coding regions) are removed from the mRNA, and exons (coding regions) are joined.

Translation

• RNA (mRNA) nucleotides are translated into amino acids.
• mRNA, in sets of three nucleotides called codons, provides the instructions.
• Transfer RNA (tRNA) carries amino acids to the ribosomes.
• A codon is a sequence of three nucleotides specifying an amino acid. Each codon corresponds to a single amino acid
• A codon wheel is used to determine the amino acid sequence
• Translation occurs in ribosomes and involves three phases: Initiation, elongation, and termination.

Translation Initiation

• mRNA binds to a ribosome.
• The start codon (usually AUG) initiates translation.
• A tRNA molecule with the corresponding amino acid binds to the start codon.

Translation Elongation

• tRNA bringing the next amino acid binds to the A site of the ribosome
• Peptide bonds form between the amino acids connected to the tRNA
• The ribosome moves along the mRNA, adding amino acids to the growing polypeptide chain.

Translation Termination

• When a stop codon is reached, translation stops,
• The polypeptide chain is released.

Gene Regulation

• Gene expression is the process of turning genes on or off to control protein production.
• Gene regulation does not change DNA sequence (genotype).
• It controls whether or not a protein is produced (phenotype).
• Gene regulation is crucial and a precise control mechanism. Gene expression helps coordinate cellular activities and processes in many different organisms.

Cell Differentiation

• Cells differentiate to become specialized cell types during development.
• All cells have the same DNA, but different genes are expressed in different cells.
• Gene regulation is essential for differentiation.

Eukaryotic Transcription Regulation

• Transcription in eukaryotic cells relies on transcription factors which bind to the DNA enhancer sequence.
• The DNA folds, locking RNA polymerase into position on the promoter to start transcription.

Post-Transcriptional Gene Regulation

• mRNA can be broken down or last for a while depending on how often that protein's gene needs to be expressed.
• Some proteins have inactive and active forms changing how they function.