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DNA = phosphate + deoxyribose sugar + A/T/C/G o Contains two strands. The strands are antiparallel (opposite each other). o 5’ → 3’ 3’ ← 5’ RNA = phosphate + ribose sugar + A/U/C/G o Single strand, can fold back onto itself and form pairs between itself (stem‐loop). Each nucleic acid is made up of polymers (many monomers) that are called nucleotides. o Nucleotides contain one or more phosphates, a five‐carbon sugar, and a nitrogen base. o Nucleotides are always made in the 5’ to 3’ direction. o 5 is always the beginning of the strand, 3 is the end where nucleotides are added. DNA organization: DNA is wrapped around proteins called histones → nucleosome → chromatin fiber→ chromosomes
Steps to the central dogma: o Coding DNA → template DNA → mRNA → tRNA (amino acid) o DNA → transcribed to mRNA → translated to protein o Each step is complementary (opposite) to the previous step, but if you skip a step it will be identical to the previous step. o Example 1. Coding DNA strand 5’ AAA TTT GGG CCC 3’
2. Template DNA strand 3’ TTT AAA CCC GGG 5’ 3. mRNA 5’ AAA UUU GGG CCC 3’ 4. tRNA Lys Phe Gly Pro Pairing: o DNA: A → T o RNA: A → U DNA replication: o Because DNA is a double helix, one strand can be separated and serve as a template for synthesis of a new strand. o Semi‐conservative : each copy of DNA contains a template strand and a new strand. o Steps of replication:
o Elongation: One strand of DNA, the template strand , acts as a template for RNA polymerase. As it "reads" this template one base at a time, the polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5' to 3'. The RNA transcript carries the same information as the non‐ template ( coding ) strand of DNA, but it contains the base uracil (U) instead of thymine (T).
o Termination. Sequences called terminators signal that the RNA transcript is
complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase. o Pre‐mRNA must go through extra processing before it can direct translation. They must have their ends modified, by addition of a 5' cap (at the beginning) and 3' poly‐A tail (at the end).
Translation occurs in the cytoplasm: o Initiation: The ribosome assembles around the mRNA to be read and tRNA brings in its perspective protein, decoding 3 bases at a time, beginning with the start codon, AUG. o These 3 base pairs of mRNA are called codons. The mRNA base pairs are complementary to the base pairs of the tRNA, called anticodons. o Elongation : The amino acid chain gets longer. The mRNA is read one codon at a time, and the amino acid matching each codon is added to a growing protein chain. When the complementary pairs are formed, they are added to the protein chain by peptide bonds, the result is polypeptides. o Termination: The finished polypeptide chain is released when a stop codon (UAG, UAA, or UGA) enters the ribosome.
Gene regulation o Promotor sites : can be turned off or on, enabling or disabling a gene from being replicated. o Alternative splicing : Exons are used to code for protein, introns are clipped out. The order of exons can determine different mature mRNA strands which result in different proteins. o Epigenetics : involves packaging of DNA. DNA is round around histones. These packages are called nucleosomes. How tightly packed they are determines whether or not the gene is on or off.
Repairing Mutations o Damage to single nucleotide bases from harmful molecules (chemicals or oxygen). o Repair: Base excision ‐ replace with a base that isn’t damaged. 1. DNA repair enzymes recognize the damaged base, removes it. 2. DNA polymerase fills the gap with a new base. 3. Ligase seals the gap. o Damage from UV causes multiple damaged nucleotides, ie causing two thymine’s to fuse together (called thymine dimers). o Repair: Nucleotide excision repair ‐ removes 20‐30 nucleotides to fix damage. 1. DNA repair enzymes recognize damage, cuts out damage and surrounding area. 2. DNA polymerase fills in the gap with new bases. 3. Ligase seals the gap. o Base mismatch due to errors in replication. o Repair #1: DNA polymerase proof reading. Removes incorrect base, inserts correct base. o Repair #2: Mismatch repair ‐ fixes the mismatch 1. DNA repair enzymes recognize mistake, and remove several
bases surrounding the mismatch. 2. DNA polymerase inserts correct bases. 3. Ligase seals the gap. o Double stranded breaks in the DNA from radiation, can lead to cell death o Repair:
o Females are indicated by circles; males are indicated by squares. o Unaffected individuals are indicated by open shapes; affected individuals are indicated by filled shapes. o Recessive vs Dominant o If two unaffected parents have an affected child, they are carrier parents. o Carrier parents = recessive trait o No carrier parents = dominant trait o Autosomal vs Sex linked o Males and females affected equally = autosomal o Only males = sex linked o Autosomal dominant vs sex linked dominant
o Affected males with a sex linked dominant trait will pass it on to all of their daughters (females do not inherit father’s Y chromosome, therefore only getting affected X chromosome)
Co‐dominance‐ both equally share dominance (red and white) Incomplete dominance ‐ neither really stand out (pink) Complete dominance‐ either one or the other is dominant (red OR white)
Visual representation with chromosomes
Remember that chromosomes come in pairs of two, eliminate the answers that don’t include pairs. Carriers have one of each allele (Rr). If the person actually has the disease, they will have both alleles (rr) or (RR). Autosomal is chromosomes 1‐22, sex linked is chromsomes X and Y.
Epigenetics is the result of making different proteins and gene expression. It determines what genes function and which do not. o Increased expression means you make more proteins. o Decreased expression means you stop making proteins. o 5 required parts, the first three parts are required to turn a gene on. Promoter ‐ Start line for making the protein. Transcription factors ‐ foot blocks for the runner (RNA polymerase) to start with. RNA polymerase ‐ the runner, makes the mRNA Need all three of the above to turn gene on (increase expression) Nucleosomes‐ the packaging of DNA. Spacing determines whether or not the promoter is visible for a gene to be turned on or off. If it is loosely packed, the promoter is visible and can be accessed by RNA polymerase =Increased expression. If it is tightly packed, the promoter cannot be accessed and therefore the gene will remain turned off= Decreased expression. Methylation ‐ CH3 (Methyl) is added to DNA or nucleosomes. Turns gene off by causing nucleosome to become tightly packed. Without it, gene remains on. Acetylation ‐ Gene expression is turned on because nucleosomes are widely spaced apart and transcription factors can get in to start transcription.
