EXAM 1 Material From Exam 1 Outline Fill in on your own CENTRAL DOGMA DNA transcribed to RNA mRNA and translated to protein A Nucleic Acids in general 1 Nucleotides 2 Sugar 3 phosphate Base pairing AT CG DOUBLE HELIX A DNA Structure groups This is how genetic info is passed double helix Polymer made of deoxyribose and phosphate Phosphodiester bond link the sugars of the nucleic acids A Key Properties Long polymer made of 4 monomers Approximately 20 angstroms wide They are anti parallel but complimentary Antiparallel opposite directionality Covalent bonds phosphodiester bonds sugars linked this way These interactions lead to the backbone Negatively charged and polar The nitrogen bases are facing one direction The bases are hydrophobic and the sugars and phosphates are hydrophilic 1 turn in the helix equates to approx 10 base pairs 2 grooves major and minor groove has to do with the width This allows for HBB What is directionality DNA runs antiparallel 3 ends with OH to 5 phosphate group Grooves have a specific sequence B How does DNA db strand stick Sticks due to hydrophobic interactions and Van Der Waals forces these are also called stacking forces New Information 1 DNA deoxyribonucleic acid Missing an OH 2 RNA Ribonucleic acid single strand of AGCU A Nucleobase just the nitrogen base Purines pyrimidines Nitrogen containing heteroaromatic molecule B Nucleoside nitrogen base sugar group Intermediate product N group C1 pyrimidine C Nucleotide all of the components ATP is a nucleotide ATCG Nitrogen bases are always C1 purine N9 attaches C 1 Structure Nitrogenous base pyrimidine cytosine urasil thymine 2 rings purine adenine guanine Pentose sugar ribose Draw carbons 5 membered not 5 carbon attach to base off of C1 DNA deoxyribose 2 C missing O2 RNA oxyribose 2 C indicates that it has oxygen Phosphate all DNA RNA have phosphate groups negatively charged Attach to fifth C5 is attachment point on both If it is on any other will not bind D NUCLEIC ACIDS 1 phosphodiester bonds get thru condensation between 2 nucleotides 2 base pairing bond 2 strands through base pairing result thru hydrogen bonding 3 SEMICONSERVATIVE REPLICATION A Meselson and Stahl demonstrated and supported semiconservative replication in bacteria B Semiconservative replication Theorized by meselson and stahl This theory states that the sequence of another Strands can be separated and synthesized Make one copy of each 4 3 FORMS OF DNA 1 B form base pairs per turn Most common form of DNA Also called Watson and crick helix 10 2 A form Shorter and wider 11 base pairs per turn Turn at a 20 degree angle This form occurs when DNA is not in an aqueous solution 3 Z form seen as a form of gene expression zig zag Left handed turn 12 base pairs per turn In some cells this is 5 PACKAGING OF DNA IN CELL supercoiling this is how we can fit DNA in a cell DNA double helix gets packaged and wrapped around itself HISTONES NUCLEOSOMES A Histones highly basic proteins These are important for gene expression package DNA They are compacted DNA in complex with DNA core These are made up of many histones There are a total of 8 in the core with about 200 base pairs Form ionic bonds and hydrogen bonds What must occur in order for DNA to be replicated The DNA must be disessembled B Nuclosomes C Solenoid Nucleosomes coiled together Further compaction of DNA What level is higher than this Chromosomes Other info What is chromatin This is DNA with all associated proteins E Variations of RNA structure Can have elaborate structures that are inaccessible for DNA replication Sometimes these can look like they are double but they are single stranded Look out for that because the bitch will probably try and trick you Loops form in the complimentary structure 6 OTHER FUNCTIONS OF NUCLEOTIDES A Carry chemical E ADP 3 Repulsion carry in the form of ATP Remember 1 Resonance 2 Ionization of B Enzyme Cofactors many cofactors can incorporate Adenine nucleotide B Regulatory molecules high levels of energy in our system will hinder ATP production CAMP cell signaling DNA Replication Chapter 34 I TERMS 1 origin of replication this is the point at which DNA first separates 2 polymerization replication 3 replication fork parent strands separate 4 factory model of rep consists of stationary proteins DNA moves through Like a factory II PROTEIN PLAYERS 1 helicase around 1 strand Pushes the two strands apart protein enzyme Unwinds double strands at replication fork Hexamer forms Warner syndrome mutation in helicase 2 single stranded binding protein ssb from becoming complimentary ATP is needed for this to work grab on to the lagging strand This prevents it 3 topoisomerases prepares the helix for unwinding and prevents super coiling Many drugs target this What is the most common DNA gyrase there is type 1 and type 2 gyrase is a type 1 Type 2 would induce stress and cause coiling 4 DNA polymerase III KEY CHARACTERISTICS OF DNA SYNTHESIS ARE 1 2 3 4 IV DNA POLYMERASE A Shape B Specificity C Origin of Replication D General Structure of DNA polymerase E coli processive E Two problems Primer 1 2 Leading strand Lagging strand Trombone Model How to connect Okazaki Fragments 1 RNase H 2 DNA poly 3 RNase H DNA poly 4 DNA ligase F Proofreading Ability 3 5 exonuclease activity V DNA SYNTHESIS IN EUKARYOTES VI TELOMERES A telomere B telomerase reverse transcriptase