TL - IB HL BIO YR 1 UNIT SEVEN

  • DNA Structure: double helix, antiparallel

    • Nucleotide: monomer of DNA

      • Phosphate group

      • Deoxyribose sugar

      • Nitrogenous Bases: either adenine, thymine, guanine, or cytosine

    • Polynucleotide: polymer of DNA, multiple nucleotides connected by phosphodiester bonds

      • 5’ End: carbon with phosphate group, typically top left carbon

      • 3’ End: carbon with a hydroxyl group, typically bottom left carbon

    • Phosphodiester Bond: connect nucleotides together

    • Hydrogen Bonding: connect the nitrogenous bases

    • Antiparallel: equal distances apart but run in opposite directions

    • Double Helix: two linked strands that wind around each other

    • DNA Complementary Base Pairing: adenine & thymine, guanine &  cytosine

  • Purpose of DNA replication: produce two identical copies of a DNA molecule, cell division, growth or repair of damaged tissues

  • Meselson and Stahl

    • Experimental Procedure: grew e coli cells in presence of special N15 (to make DNA heavier) and in second round- N14 (to make DNA lighter)

    • Results: after two cell divisions, the DNA was half heavy and half light

    • Conclusion: DNA is semi-conservative

    • Semi-conservative: both new DNA strands have 1 original DNA strand and one newly synthesized DNA strand

      • Template Strand: The DNA sequence that is transcribed to make RNA

      • Complementary Strand: other DNA strand

  • Helicase: helps first step of DNA replication, unwinds double helix (creates replication fork) and separates 2 DNA strands by breaking hydrogen bonds between the bases, exposes bases and allows them to be paired

  • Replication Fork: site where helicase separates/unwinds DNA

  • Gyrase: moves in front of helicase to relieve tension from supercoils before replication fork to prevent breakage/damage

  • Single Strand Binding Proteins: bind to single stranded DNA to keep strands apart and prevent hydrogen bonds from reforming

  • Primase: creates an existing strand for DNA polymerase III to add to 3’ end, done by adding a primer made of a short sequence of RNA nucleotides

  • DNA Polymerase III: enzyme that reads single strand and builds a complementary strand, can only add nucleotides to 3’ end, proofreads new DNA to limit mistakes

    • Directionality of DNA Synthesis: 5’ to 3’

    • 3’ Sticky End: 3’ end of DNA is “sticky” because that is where DNA polymerase III adds nucleotides 

    • Proofreading: read DNA bases ahead of time to make sure that correct complementary base is placed

  • DNA Polymerase I: removes RNA nucleotides (primers) and replaces them with correct nucleotides

  • Ligase: catalyzes formation of phosphodiester bonds between Okazaki fragment

  • Leading Strand: single strand after fork, follows same direction as helicase, can be continually synthesized by DNA polymerase III, only needs one primer

  • Lagging Strand: single strand after fork, is discontinuously synthesized away from replication fork, each okazaki fragment needs own primer to attach DNA polymerase III to it

  • Okazaki Fragments: fragments of synthesis on lagging strand

  • Polymerase Chain Reaction (PCR): used to amplify small DNA fragments, DNA replication in a test tube

    • Denaturation: heated to 98°C to break hydrogen bonds between strands

    • Annealing: cooled to 60°C, primers bind to complementary DNA

    • Extension: about 72°C, taq polymerase replicates DNA

    • Taq Polymerase: does the same thing as DNA polymerase III but is heat stable and can work in high temperatures

  • Gel Electrophoresis: usually done after PCR, uses electrical currents to move DNA fragments through the gel

    • DNA Fingerprint: DNA fragment lines on the gel

    • Single Nucleotide Polymorphisms (SNPs): can change cut sites of restriction enzymes, changes banding pattern (DNA fingerprint)

    • Uses of Gel Electrophoresis: paternity tests

  • Restriction Enzymes (Restriction Endonucleases): cuts DNA into fragments

  • The Central Dogma: describes flow of genetic information, DNA is transcribed into mRNA and mRNA is translated into protein

  • Transcription: producing mRNA using DNA as a template, only a portion of genome is copied (resource efficiency), allows DNA to stay protected in nucleus

    • Location in eukaryotes and prokaryotes: nucleus and cytoplasm

    • RNA Polymerase: synthesizes mRNA strand 5’-> 3’, binds to promoter

    • Initiation: first phase, RNA polymerase begins to temporarily unzip small DNA section to expose bases

      • Transcription Factors: proteins that bind to promoter, recruit RNA polymerase to promoter

      • Promoter: non-coding region of DNA in front of a gene of interest

      • TATA Box: start of promoter, thymine, adenine, thymine, adenine, adenine…

    • Elongation: second phase, growing mRNA strand exits RNA polymerase and DNA rezips

      • Template Strand (Antisense Strand): read by RNA polymerase, complementary to coding strand

      • Coding Strand (Sense Strand): complementary to template strand

      • Directionality of mRNA synthesis: 

      • RNA Complementary Base Pairing: A & U, G & C, same as DNA but swap U and T

      • Hydrogen bonding: RNA nucleotides temporarily hydrogen bond with the template strand while mRNA is synthesized

    • Termination: third phase, terminator sequence at the end of the gene is reached, signals for RNA polymerase to release mRNA and detach from DNA

  • Post-Transcriptional Modification (mRNA Processing): only done in eukaryotic cells, done after transcription before mRNA can leave nucleus

    • 5’ Cap: modified nucleotide that is added to the 5’ end of mRNA, helps with ribosome binding during translation

    • Poly-A Tail: string of adenines attached to the 3’ end of mRNA, aid in export of mature mRNA from nucleus and protect mRNA from degradation in cytoplasm

    • mRNA Splicing: removing all the introns and splicing back together exons, take pre-mRNA and make it mature mRNA

      • snRNPs: small nuclear ribonucleoproteins, catalyze mRNA splicing, bind to either side of introns and assemble into spliceosomes

      • Spliceosome: remove introns, join exons together

      • Intron: base sequences removed before translation (during mRNA splicing), stay in nucleus

      • Exon: base sequences that are expressed, coding regions within a gene

      • Alternative splicing: different combinations of exons within a gene can be spliced together to generate multiple mRNA isoforms and increase protein diversity, allows for production of multiple proteins from a single gene

  • Translation: 

    • Location in eukaryotes and prokaryotes: cytoplasm, free and bound ribosomes

    • Speed in prokaryotes and eukaryotes: faster in prokaryotes than eukaryotes because mRNA processing has to happen in eukaryotes

    • Genetic Code: how mRNA is decoded into amino acids 

      • Codon: three bases together, each one codes for specific amino acid

      • Universal: every organism uses the same genetic code, evidence for LUCA, allows for genetically modified organisms

      • Degenerate (redundant): some amino acids are coded for by more than one codon

      • Unambiguous: no codon codes for more than one amino acid 

      • Start Codon: AUG, translation starts here

      • Stop Codons: UGA, UAA, UAG, if one of these is read, translation stops

    • tRNA: transfer rna, carries amino acids to ribosomes, single strand of RNA folded into 3D structure held together by hydrogen bonds, when represented in 2D form - looks like a clover

      • Anticodon: bottom of trna, binds to mRNA codon

      • Amino Acid Binding Site: top of trna, where amino acid is attached

        • Aminoacyl-tRNA synthetase: attaches correct amino acid to trna

        • Charged tRNA: tRNA with amino acid, full

        • Discharged tRNA: tRNA without amino acid, empty

    • Ribosome: made of RNA and proteins, small and large subunits, mRNA attaches to small subunit, tRNA binds to 3 binding sites on large subunit

      • rRNA: ribosomal RNA, structural component of ribosomes

      • Small Subunit: binding site of mRNA

      • Large Subunit: 3 binding sites where tRNA binds

      • A Site: aminoacyl-tRNA binding site, for incoming tRNA with amino acid

      • P Site: peptidyl-tRNA, for tRNA holding growing polypeptide chain to bind

      • E Site: exit site, for discharged/empty tRNA to leave ribosome 

    • Initiation: 5’ end of mRNA binds to small ribosomal subunit, small ribosomal subunit moves from 5’ -> 3’ and scans for start codon, once it finds start codon, large ribosomal subunit assembles and the initiator tRNA binds to P site 

      • Small ribosomal subunit: moves from 5’ -> 3’ direction and scans for start codons

      • 5’ end: binds to small ribosomal subunit

      • Start codon: where initiator tRNA binds

      • Initiator tRNA: binds to start codon

      • Met (Methionine): amino acid for start codon (AUG)

      • P site: where initiator tRNA goes once large ribosomal subunit is formed

    • Elongation: ribosome reads mRNA in codons and a cycle occurs

      • Codon Recognition: incoming tRNA’s anticodon binds to mRNA codon at the A site, ensures correct amino acid is in the polypeptide sequence

      • Peptide Bond Formation: peptide bonds forms between polypeptide chain and new amino acid, transfers polypeptide chain from the tRNA in the P site to the tRNA in the A site

      • Translocation: ribosome shifts over one codon, discharged tRNA in P site moves to the E site and leaves the ribosome, tRNA in the A site moves to the P site and leaves the A site empty for a new tRNA

    • Termination: when a stop codon is in the A site, no new tRNA will enter, a release factor will enter instead and perform a hydrolysis reaction to break bond between the polypeptide chain and the tRNA in the P site, the released polypeptide chain’s translation complex disassembles and polypeptide chain is modified/folded into its final form

  • Post-Translational Modification: often in golgi, can involve addition of chemical groups or cleavage of specific peptide bonds

    • Pre-proinsulin to Proinsulin: pre-proinsulin is 110 amino acids in length and has 4 sections (signal peptide, A chain, B chain, and C-peptide), in the RER, the signal peptide is removed

    • Proinsulin to Insulin: in the RER, disulfide bridges are formed between A chain and B chain, they are packaged into vesicles and sent to golgi, while in golgi, the C-peptide is removed and insulin is formed

  • Proteome: total of all of the proteins made and used in the body, is dynamic (the body is constantly synthesizing and hydrolysing proteins)

    • Proteasome: protein complex that hydrolyzes damaged/unused proteins 

  • Genetically modified organisms: any organism whose genetic material has been altered using genetic engineering techniques

    • How they are made: Splice the gene(s) of interest into another organism, allows for protein synthesis of the gene(s) of interest by the new organism

    • Why it is possible: genetic code is universal

    • Example of uses of GMOs: insulin gene in bacteria allows for mass production of insulin protein, pesticide gene in crops allows crops to produce protein that acts as pesticide so bugs don't eat crops