Genetics: DNA and Cell Division

DNA Structure

• E. coli has a genome of ~5 million base pairs
• Histones are found in eukaryotes and archaea
• Bacteria do not have histones
• DNA consists of two strands twisted into a double helix
• DNA molecules and proteins are organized into chromosomes
• DNA can coil in two directions: positive and negative
• Positive supercoiling is more "stressful" and happens in most archaea
• Negative supercoiling is more relaxed and allows for easier unwinding of the molecule, this occurs in the majority of prokaryotes and bacteria

Cell Division and Chromosomes

• During cell division, the entire chromosome is duplicated, forming sister chromatids
• Daughter cells receive identical copies of the chromosomes
• Each eukaryotic cell has a characteristic number of chromosomes
• Diploid cells have two pairs of each type of chromosome
• Humans have 46 chromosomes
• Trisomy is a condition where an individual has an extra chromosome, most cases are fatal, trisomy 21 is Down syndrome
• Chromosomes are organized into autosomes (non-sex chromosomes) and sex chromosomes
• Sex chromosomes differ between males and females, the last pair

Karyotyping

• Karyotyping reveals the characteristics of an individual's chromosomes
• It is a visual representation of the chromosomes
• Genome size shows the complexity of an organism, larger genomes are more complex

Genetic Elements

• Plasmids are found in many bacteria and archaea
• Plasmids contain genetic information that is not essential for cell function, but it might give an advantage to the cell
• Plasmids can confer a selective growth advantage
• Plasmids range in size from 1kbp to more than 1mbp
• R plasmids are resistance plasmids that confer antibiotic resistance
• R plasmids contain many antibiotic resistance genes

Cloning

• Dolly the sheep was the first successfully cloned mammal
• Dolly was cloned by removing the nucleus from an egg cell and implanting the nucleus from a donor cell
• In humans, partial cloning is more accepted, it is used to synthesize organs and uses somatic stem cells

Antibiotic Resistance

• Penicillin and other beta-lactam antibiotics inhibit penicillin-binding proteins
• Resistance to penicillin occurs due to modified cross-linking enzymes
• Antibiotic resistance can mis-spread via plasmids, which can transfer from one bacteria to another via horizontal gene transfer

The Central Dogma

• The flow of genetic information includes replication, transcription, and translation
• This flow is known as the central dogma
• The central dogma describes how genetic information is turned into proteins

Transcription

• Transcription is the process of DNA to RNA
• RNA polymerase is the main enzyme involved

Translation

• Translation is the process of RNA to protein
• Ribosomes are the main enzyme involved
• Viruses are also involved in replication, transcription, and translation, but they can violate the central dogma

DNA Replication

• There are 5 DNA polymerases involved in DNA replication
• DNA Polymerase I: plays a lesser role in DNA replication
• DNA Polymerase II: repairs DNA damage
• DNA Polymerase III: primary enzyme for replication of chromosomal DNA
• DNA Polymerase IV: repairs DNA damage
• DNA Polymerase V: repairs DNA damage
• Replication occurs ONLY from the 5' end to the 3' end of the DNA strand
• DNA replication requires extraordinary fidelity to prevent gene mutations
• Gene mutations can cause irregularities in an organism
• Gene mutations can also render genes useless or different
• The origin of replication in prokaryotes is a specific DNA sequence where replication begins
• Replisomes move to the origin of replication and initiate replication
• Replisomes contain the enzymes necessary to replicate DNA
• Helicase unwinds the DNA double helix to create the replication fork
• Single-strand binding proteins (Ssbp) help to stabilize the unwound DNA strand, preventing it from rewinding
• The replication fork is the point on the DNA where replication occurs
• DNA polymerase III adds nucleotides at a rate of 1000 per second
• Primase creates a short RNA primer to initiate DNA synthesis.
• DNA polymerase III synthesizes the majority of the new DNA sequence
• DNA polymerase I removes the RNA primer and replaces it with DNA
• DNA ligase seals the gaps left by the removal of the RNA primer
• DNA replication is antiparallel, with one strand running from 5’ to 3’ and the other from 3’ to 5’
• The leading strand is synthesized continuously in a 5’ to 3’ direction
• The lagging strand is synthesized discontinuously in a 5’ to 3’ direction
• Synthesis of the lagging strand requires the creation of Okazaki fragments
• Okazaki fragments are short segments of DNA that are ligated together to form the complete lagging strand
• DNA is supercoiled to maximize space inside the cell and allow for compacting into a small space
• Supercoiling is relaxed during replication to allow for proper unwinding and replication
• Replication is done on BOTH STRANDS of DNA

Applications

• Understanding DNA replication helps to develop new treatments for diseases caused by gene mutations
• Replication errors are a major cause of cancer initiation and progression
• DNA polymerase inhibitors are commonly used in chemotherapy to prevent cancer cell replication.

DNA Replication

• DNA polymerase adds 1000 nucleotides per second.
• It takes 76 minutes to complete replication of a 4.6mbp coli genome.
• Leading and lagging strands are replicated simultaneously during DNA replication.
• Replication is bidirectional in prokaryotes due to their circular chromosome structure.
• The replisome is a complex of proteins involved in replication, including enzymes that move as one.
• DNA ligase seals the nicks in DNA fragments on the lagging strand.

Transcription

• Transcription is the process of synthesizing RNA from a DNA template strand.
• RNA polymerase is the primary enzyme responsible for transcribing DNA to mRNA.
• The sigma factor identifies the promoter region and determines the direction of transcription.
• The sigma factor attaches RNA polymerase to the promoter region and is then released allowing transcription to start.
• Transcription occurs from 5' to 3', similar to DNA replication, with the template strand oriented in the 3' to 5' direction.
• RNA polymerase does not require a primer to initiate transcription.
• Transcription uses ribonucleotides (NTPs) instead of deoxyribonucleotides (dNTPs).
• RNA polymerase can transcribe both strands of DNA, resulting in different amino acid sequences, hence the need for a single strand template.

Transcription Initiation

• The sigma factor recognizes the promoter region on DNA, including the Pribnow box (-10 region) and TTGACA (-35 region).
• The Pribnow box (-10 region) is located 10 bases before the start of transcription and is also known as a TATA box.
• The TTGACA (-35 region) is located 35 bases before the start of transcription.
• Different sigma factors recognize different promoter sequences.

Transcription Elongation

• RNA polymerase makes copies of DNA using RNA.
• The RNA polymerase employs A-U and G-C base pairing, as opposed to DNA's A-T and G-C pairing.

Transcription Termination

• Transcription terminates when RNA polymerase reaches a specific sequence that signals the end of the process.
• The RNA transcript is released, and the process allows for translation.

Transcription in Bacteria

• Bacteria transcribe genes into operons (DNA segments transcribed into one RNA molecule bounded by initiation and termination sites).
• Operons ensure efficient expression of genes needed for a specific function.
• Most genes encode proteins, but some genes produce non-protein-coding RNAs like rRNA and tRNA, which are involved in protein synthesis.
• The process of transcription involves the production of a primary transcript containing intervening sequences that need to be removed before translation.
• These intervening sequences do not code for proteins, are known as jumping genes, and are removed from the sequence.
• The final RNA product corresponds to the RNAs involved in the translation process.

This quiz covers key concepts in genetics related to DNA structure and the processes of cell division. Understand the differences in chromosome organization between prokaryotes and eukaryotes, as well as the implications of genetic conditions like trisomy. Test your knowledge of these fundamental biological principles.