DNA Structure and Replication

• Hereditary information, also known as genetic information, includes traits and characteristics passed from parents to offspring via genes.

DNA Composition

• DNA consists of nucleotides.

Watson and Crick's DNA Model

• Proposed in 1953, it describes DNA as a double helix.
• The double helix is composed of two nucleotide strands twisted around each other.
• The strands are connected by hydrogen bonds between specific base pairs.
• Adenine pairs with thymine, and guanine pairs with cytosine.
• The two strands run in opposite directions, described as antiparallel.

DNA Replication and Repair

• DNA replication duplicates DNA strands, ensuring genetic material is accurately transmitted during cell division.
• DNA repair mechanisms correct errors during replication and prevent mutations.
• DNA replication is a semi-conservative process.

Nitrogenous Bases

• Nitrogenous bases are organic molecules that are the building blocks of DNA and RNA.
• They are classified into purines (double ring structure) and pyrimidines (single ring structure).

Erwin Chargaff's Discoveries

• Established Chargaff's rules: the amount of adenine (A) equals the amount of thymine (T), and the amount of guanine (G) equals the amount of cytosine (C).
• This disproved the tetranucleotide hypothesis.
• His work paved the way for Watson and Crick's double helix model of DNA.

Origin of Replication

• The origin of replication is a site where DNA molecule replication begins.
• It consists of a specific sequence of nucleotides.

Enzyme Functions

Helicases

• Function by unwinding and "unzipping" the DNA double helix.

DNA Polymerases

• Function by building new DNA strands.

Primase

• Lays down a short RNA primer to begin replication.

RNA Polymerase

• Builds RNA from a DNA template.

DNA Ligase

• Joins DNA fragments together.

Nuclease

• Cuts out damaged or incorrect DNA or RNA.

Okazaki Fragments

• Okazaki fragments are short, newly synthesized DNA strands about 150-200 base pairs long.
• They form during discontinuous synthesis of the lagging strand of DNA during replication.

DNA Polymerase Proofreading

• DNA polymerases proofread newly made DNA.
• They replace any incorrect nucleotides.

Telomeres

• Telomeres are protective caps at the ends of chromosomes that prevent DNA degradation and fusion.
• They ensure genomic stability.
• They act as a biological clock for cell aging, regulating cell division frequency and preventing cancer by limiting uncontrolled cell growth.

Histones

• Histones are positively charged proteins.
• These play a crucial role in organizing DNA within the nucleus of eukaryotic cells.

Euchromatin vs. Heterochromatin

• Euchromatin is loosely packed and transcriptionally active.
• Heterochromatin is tightly packed and transcriptionally inactive.

DNA and Traits

• DNA is related to specific traits because it contains genes.
• Genes provide instructions for building proteins.

Genotype and Phenotype

• Genotype provides the genetic instructions.
• Phenotype is the observable expression of those instructions.

Gene Expression

• Gene expression is the process by which genetic information encoded in a gene is used to create a functional product, typically a protein.

Transcription and Translation

• Transcription creates an RNA copy from a DNA sequence.
• Translation uses that RNA copy to assemble a protein.

Ribosomes

• Ribosomes are essential cellular structures responsible for protein synthesis.
• They translate genetic information from mRNA into proteins.
• They are found in both prokaryotic and eukaryotic cells.

Central Dogma of Cell Biology

• The central dogma of molecular biology describes the flow of genetic information within a cell, primarily from DNA to RNA to protein.

DNA Encoding

• DNA instructions for assembling amino acids into proteins are encoded using a specific sequence of nucleotides.
• Nucleotides are grouped into three-nucleotide units called codons.

Nucleotides and Amino Acids

• Three nucleotides correspond to an amino acid.

Triplet Code

• Codons are triplets of nucleotides (3-letter code).
• Dictates which amino acid will be added to a growing protein chain.

Template Strand

• In molecular biology, a template strand is a DNA strand that serves as the pattern for making a complementary RNA strand during transcription.

Codon Function

• Codons are three-nucleotide sequences in mRNA.
• Specify the order of amino acids in a protein during translation.
• They are read from 5' to 3' along the mRNA molecule.
• The 5' end contains the start codon, and the 3' end contains the stop codon.

RNA Synthesis

• RNA synthesis, also known as transcription, involves the creation of an RNA molecule from a DNA template.
• This process is catalyzed by RNA polymerase, which binds to a specific DNA sequence called a promoter.

Promoter

• A promoter is a region of DNA where RNA polymerase binds to initiate transcription.

Terminator

• A terminator is a sequence of DNA that signals RNA polymerase to stop transcription and release the newly synthesized RNA.

Transcription Unit

• The transcription unit is a segment of DNA that is transcribed into RNA.
• It encompasses the regions needed for the transcription process.
• Includes a promoter, a structural gene, and a terminator.

Stages of Transcription

• The three main stages of transcription are initiation, elongation, and termination.
• Initiation involves RNA polymerase binding to a promoter region and unwinding the DNA.
• Elongation is the process where RNA polymerase moves along the DNA, adding RNA nucleotides to the growing transcript.
• Termination occurs when RNA polymerase reaches a termination sequence, and the new RNA transcript is released.

RNA Processing

• RNA processing differs significantly between prokaryotes and eukaryotes.
• Prokaryotes, lacking a nucleus, translate mRNA directly while it is being transcribed.
• Eukaryotes, however, have a nucleus, and their pre-mRNA must undergo extensive modifications like capping, tailing, and splicing before translation can occur.

Introns vs. Exons

• Exons are the coding regions of a gene that are transcribed into mRNA and translated into proteins.
• Introns are non-coding regions that are transcribed but are then removed from the mRNA before it is translated.

Replication Bubble

• The replication bubble is a region of DNA, in front of the replication fork, where helicase has unwound the double helix.

Replication Fork

• The replication fork is a Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are being synthesized.

Direction of Replication

• DNA polymerases add nucleotides only to the free 3' end of growing strands.
• DNA can only elongate in the 5' to 3' direction.

Chromatin

• Chromatin is the complex where DNA and protein are precisely combined.
• It is usually loosely packed in the nucleus during interphase and condenses prior to mitosis.

Leading Strand Formation

• DNA polymerase synthesizes from the origin, continuously, towards the replication fork in one direction.

Mismatch DNA Repair

• Repair enzymes replace incorrectly nucleotides that have evaded the proofreading process.

Lagging Strand Formation

• DNA polymerase synthesizes from the replication fork, in pieces, towards the origin.

Primer Function

• Primers used in PCR provide a site for DNA polymerase to start adding nucleotides.
• Cells use RNA as primers.

RNA Polymerase Function

• RNA polymerase separates the DNA strands and joins together RNA nucleotides.
• It is complementary to the DNA strand.

Semiconservative Model

• Each newly formed DNA molecule consists of one original (parental) strand and one newly synthesized strand.
• When DNA replicates, the original double helix splits, and each single strand serves as a template for the synthesis of a new complementary strand.
• The result is two new DNA molecules, each containing one old and one new strand.

Antiparallel Model

• The two strands making up DNA run in opposite directions, i.e., antiparallel.
• The head of one strand is always against the tail of the other strand.

RNA Splicing

• Removed introns and joins exons, creating an mRNA molecule with a continuous coding sequence.

Alternative RNA Splicing

• Some introns contain sequences that regulate gene expression and many affect gene products.
• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.

Transfer RNA (tRNA) Function

• Used by the cell to translate an mRNA message into protein.
• Transfers the amino acid to the growing polypeptide in a ribosome.

Anticodon

• This is a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA.

Ribosomal RNA (rRNA) Function

• Large and small structural components of the ribosome that function primarily in protein synthesis by binding tRNA and mRNA.
• Binds to ensure the codon sequence of the mRNA is translated accurately.

Ribosomes in Medicine

• Differences between Bacterial and eukaryotic ribosomes can be used to create antibiotics.

Special Codons

• Start and stop codons are special.

Post-Translation Protein Processing

• Translation is not always enough to make a functional protein.
• Proteins have specific functions, so it has to go to the right location.
• Polypeptide chains are targeted to specific sites in the cell.
• Some proteins are modified.

Populations of Ribosomes

Free Ribosomes

• Located in the cytosol.
• Synthesize proteins that function in the cytosol.

Bound Ribosomes

• Attached to the ER.
• Make proteins of the endomembrane system and proteins that are secreted from the cell.
• These ribosomes are identical and can switch from free to bound.

Polyribosome (Polysome)

• Multiple ribosomes can translate a single mRNA simultaneously, enabling a cell to make many copies of a polypeptide very quickly.

Mutation

• Mutation is changes in the genetic information of a cell.

Point Mutation

• Point mutation is changes in just one nucleotide pair of a gene.

Genetic Disorder/Hereditary Disease

• This a mutation that has an adverse effect on the phenotype of the organism

Possible Point Mutations

Silent Mutations

• Have no effect on the amino acid produced by a codon because of the redundancy in the genetic code.

Missense Mutations

• Still code for an amino acid, but not the right amino acid.

Nonsense Mutations

• Change an amino acid codon into a stop codon; most lead to a nonfunctional protein.

Frameshift Mutation

• Mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide.

Mutagen and Carcinogen

• A mutagen is a physical or chemical agent that can cause mutations.
• A carcinogen is cancer causing chemicals, are mutagens and most mutagens are carcinogenic.

Gene

• A discrete unit of inheritance.
• A region of a specific nucleotide sequence in a chromosome.
• A DNA sequence that codes for a specific polypeptide chain or RNA molecule.
• A region of DNA that can be expressed to produce a final functional product.