A Comprehensive Review of DNA Structure, Replication, Transcription

SBI4U – Grade 12 Biology – Molecular Genetics MOLECULAR GENETICS REVIEW ● DNA Structure Deoxyribonucleic acid is a polymer of nucleotide, Nucleotides have a 5-carbon sugar, a phosphate group (phospho-diester bond) and a nitrogenous base (A,T,G,C ) (H-bond) ● Purines 6-membered ring joined to a 5-membered ring (A,G) ● Pyrimidines single 6-membered ring (C,T) *A-T are double bonded, while G-C are triple bond (stronger)* DNA consist of two antiparallel strands curled around in a double helix (like a spiral) 5’ to 3’ and 3’ to 5’ *The 5’ end is the one that stars with a phosphate, and the 3’ ends with a OH* *The right handed helix turns CLOCKWISE* ● DNA Replication ● Semiconservative model the daughter DNA molecule is made up of one parental strand and one new strand (parental strand serves as a template) Chromosome is 60% proteins (Histone is a protein that prevents DNA from tangling) DNA replicates itself during the interphase of cell division. The double helix is divided into two parts as the first step. New DNA is continuously replicated on the 3' to 5' strand in the direction of the replication fork. Replication is interrupted on the 5' to 3', away from the fork. 1. 2. 3. 4. DNA Helicase– Uncoils the 2 strands by breaking H-bonds b/w nitrogen bases. DNA Gyrase– Relieves tension in untwisted strands. Single Stranded Binding Proteins (SSBPs) – Protein that keeps the two strands apart. Primase- Enzyme that makes Primer (indicates DNA Polymerase 3 where replication start) 5. DNA Polymerase 3- Bonds free nucleotides on the strand (From 5’ to 3’) Okazaki fragments fragments of the laggings strand 1. Polymerase 1- Removes primers and replace them with right nucleotides 2. DNA Ligase- Joins fragments together (forming Ester bonds) 3. Exonucleases– Proofread & correct any errors (Poly 3&1) ● Telomeres is a region of repetitive nucleotide sequences at each end of a chromatid, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes *When a cell is out of telomeres, the cells are senescence (period of decline)* ● Help prevent chromosomes from fusing to other chromosomes ● Prevents DNA degradation ● May have a role determining life spam Some cells that produce telomeres: STEM CELLS & CANCER CELLS ● Protein synthesis “The central dogma” (DNA>mRNA>protein) is the sequence of events that occur from a gene in DNA to a protein DNA carries the instructions to build and manufacture all the proteins needed but it cannot leave the nucleus, therefore it needs messenger RNA. Ribosomes translate mRNA message into a polypeptide sequence Two main processes involved: –Transcription (making of mRNA) 3 stages: initiation, elongation & termination –Translation (making of polypeptide chain) Also 3 stages RNA DNA Single polynucleotide chain Two polynucleotide strands (double helix) Ribose Deoxyribose Uracil Thymine Found in ribosome nucleus, cytoplasm and Only found in nucleus 3 classes of RNA ● mRNA (messenger) ● tRNA (Transfer proper amino acids to build a protein *leaves after peptide bonds form b/w amino acids*) ● rRNA ( structural component of a ribosome, along with proteins) ● Genetic code There are 20 amino acids found in proteins, each amino acid is coded by 3 DNA nucleotides. Each triplet of nucleotides is called a CODON (64, 44 extra) More than one codon can code for a single amino acid ● Transcription occurs in the nucleus of eukaryotic cell ● Initiation RNA polymerase binds to the promoter region (promoter is located upstream of the gene) Promoter is a TATA sequence; RNA polymerase opens the double helix ● Elongation RNA polymerase starts to build the mRNA molecule in 5’ to 3’ direction using DNA as a template Primer is not needed, promoter sequence is NOT transcribed Template strand is used as a template, the other one is called coding strand mRNA sequence is complementary to the template strand and therefore identical to the coding strand (except mRNA contains uracil instead of thymine) ● Termination RNA polymerase reaches termination sequence which signals it to stop mRNA detaches from DNA template strand, RNA synthesis stops and RNA polymerase is released ● Post-transcriptional modifications Primary transcript must go through 3 modifications: 1. 5’ cap is added to the start of the primary transcript (7-methylguanosine) needed to initiate translation and to prevent mRNA from being digested 2. Poly-A-tail is added by poly-A-polymerase that consists of 200 adenine RNA nucleotides (Protect from degradation, possibly related with movement) 3. Splicing coding sections called EXONS and noncoding called INTRONS Spliceosomes are responsible for cutting the introns out of the mRNA (If the introns are translated, the protein gene codes will not fold properly and therefore will not perform its function properly) Pre-mRNA combines with snRNPs and other proteins to form a spliceosome , within the spliceosome, snRNA base-pairs with nucleotides at the ends of the introns. The RNA transcript is cut to release the intron, and the exons are spliced together. Spliceosome comes apart and releases mRna. ● Translation (the ribosome) consist of 2 subunits (large 60s, small40s) mRNA is clumped by the subunits Ribosomes move toward de 3’ end, it read codons and adds aminoacids. The reading frame determines the sequence in which the codons are read tRNA delivers the amino acids to the ribosome. When AUG is in P site of ribosome and everything else is in A position tRNA joins the ribosome. The anticodons of some tRNAs recognize more than one codon (wobble hypothesis) the rules for base pairing between the third base of the codon and anticodon are relaxed. This is beneficial to avoid mutation 3erd base of the tRNA anticodon “wobbles”: it can H-bond with more than one type of base in the 3er position of the codon ● Elongation the ribosome has three sites for tRNA: A site (acceptor), P site (peptide), E site (exit). The charged tRNA Carrying the next amino acid in sequence enters the A site , then ribosome moves to next codon and uncharged tRNA moves to P, a peptide bond forms b/w the amino acids and the uncharged tRNA is recycled back to the cytoplasm ● Termination once the stop codon is reached, a protein release factor comes to aid the release of the polypeptide chain GENE PRODUCTS ARE NOT ALWAYS PROTEINS SINCE tRNA AND rRNA GENES DO NOT CODE POLYPEPTIDES ● Gene control mechanism Genes ultimately code for proteins, proteins: enzymes, transport molecules (hemoglobin), immune system *20 thousand genes encode for proteins* ● Control mechanisms Transcription factors turn genes ON when required (gene regulation) Proteins always needed are called housekeeping genes Transcriptional control blocks DNA from becoming mRNA Translational control blocks mRNA from becoming protein There are 4 levels of gene regulation (EUKARYOTE) ● ● ● ● Transcriptional- regulates rate of transcription Post transcriptional- modifications of mRNA can be regulated Translational- how often and how quickly mRNA is translated Post translational-regulate modifications to newly formed proteins Lac operon (only in prokaryote) code for enzymes that break down lactose (glucose + galactose) An operon is a region of bacterial DNA that codes for genes that are transcribed into one RNA transcript (promoter and an operator) E.Coli uses glucose as primary source of energy (can use carbon when glucose is absent). It can obtain glucose by the enzyme β-galactosidase (lac genes code for it), which is only made when lactose is present *when is needed* Followed by the operon are a cluster of genes that code for proteins involved in breakdown of lactose: ● lacZ encodes β-galactosidase ● lacY encodes galactoside permease a membrane-bound transport protein that pumps lactose into the cell. ● lacA encodes transacetylase ● lacI is a gene that is part of the operon but codes for a repressor protein (it has own promoter). This repressor blocks transcription of β-galactosidase by binding to lactose operator ( prevents RNA polymerase to bind) Lactose binds with the repressor and causes it to change shape and release from its binding site (lactose is called inducer) MAXIMAL TRANSCRIPTION OF LAC OPERON WHEN LACTOSE IS PRESENT. THE ACTION OF A CYCLIC AMP AND A CAMP RECEPTOR PROTEIN ARE RESPONSIBLE FOR THIS. ● Point mutations Are spontaneous(error in DNA replication), can be induced by radiation, mutagen or chemical ● ● ● ● ● substitution (replacement of base pair silent (does not alter sequence) missense (changes single aa sequence) nonsense (results in premature stop codon) insertion/deletion of a base pair (there is a frame shift in coding sequence) BIOTECH (finish) ● ● ● ● ● ● ● Cloning using restriction enzymes, gel electrophoresis, plasmids and transformations Genetic engineering Polymerase chain reactions Human genome project Genetic screening and gene therapy Genetically modified organisms Forensics