BIOLOGY NOTES FOR EXAM 3- Molecular Basis of Inheritanceo What is the structure of the genome? Chromosome and DNA structureo How is the genome copied? DNA replicationo What is the genome used for? Protein synthesis- Chromosome Structureo Eukaryotic chromosome structure DNA (linear molecule) Histone proteins- DNA replication occurs in a semi-conservative mechanism.- Ultimately, the information in DNA is used to make proteins.- DNA structureo Four nucleotideso Complementary base pairing (hydrogen bond) Adenine bonds to Thymine Guanine bonds to Cytosine Purine + pyrimidineo Double helixo Anti-parallel backbones (held together by covalent sugar-phosphate bonds)- How is DNA Copied?o How do you make exact copies?o What does the structure of DNA tell you about how to copy it?o Replication The parent molecule’s strands separate. New molecules are added to each piece, forming “daughter” DNA molecules, each consisting of one parental strand and one new strand. Begins at many origins (could be thousands) Strands must separate and unwind- Helicase (untwists at replication fork), SSB proteins (keeps DNA from re-pairing)[causes strain and tither winding further down strand], and topoisomerases (relieves strain by breaking, swiveling, and rejoining DNA strands Add primer (RNA chain)- Synthesized by primase- Uses DNA as template Replication- DNA polymerase (add nucleotides to a preexisting chain) Fuse sections/fragments of lagging/Okazaki fragments- DNA ligase New sections built 5`-3` and anti-parallel What happens if the wrong base is added?- Proofreading Where does the energy come from?- From nucleotides themselves (before added, have three phosphate groups; when joined, release two phosphate groups, releasing energy) Why does DNA polymerase only build 5` to 3`?- It must be important- Be able to proofread, and nucleotides bring energy Can errors in DNA be repaired after replication?- Yes, nuclease (takes it), polymerase (replaces it), and ligase (glues it all together)o Semi-conservative Because the new molecule is a piece of the original DNA and a piece of new backbone.- Central Dogmao Flow of information within a cello The flow is largely in one direction DNA <--> DNA (replication) DNA RNA (transcription) RNA protein (translation) RNA DNA (reverse transcription) [retroviruses]- RNAo Differs from DNA in that: Ribose sugar Single stranded Uracil instead of thymine- A- U- C- Go Types of RNA Messenger RNA – mRNA- Transcribed from DNA (true for all RNAs)- Contains the code to build one polypeptide chain- Specific- Contains exons and codons (mRNA nucleotide triplets)- Specifies the amino acid sequence for a protein Ribosomal RNA – rRNA- Is the most abundant form of RNA- Is a component of ribosomes Transfer RNA – tRNA- Contains an anticodon (base-pairs with complementary mRNA sequence)[at one end of tRNA]- Has amino acids covalently attached- Transcriptiono RNA polymerase binds to the promoter site (TATA box [not the strand to be coded])o RNA polymerase builds the new strand 5` to 3` with complementary RNA nucleotideso Anti-parallelo When RNA polymerase reaches the termination sequence, it leaves the DNA and so does the RNA- Prokaryotes vs. Eukaryoteso Eukaryotes 3 types of RNA polymerase mRNA produced during transcription must be processed prior to translation- RNA processingo Cappingo Poly-A tail (pull several hundred adenines in a row)o Editing (how our genes are structured. Editing by reducing and rearranging information) Exons final message Introns removed (final message is just exons with a cap and a tail)- Genetic Codeo mRNA nucleotideso Triplets (codons)o Degenerate code- Translationo Occurs in the cytoplasm at a ribosomeo mRNA to polypeptide (nucleotide sequence to amino acid sequence)o Steps to Translation Initiation- Small subunit binds to 5` end of RNA- Moves to start codon (AUG)- tRNA binds and then large subunit Chain elongation- Ribosomes binds 2 tRNA moleculeso A siteo P siteo E site- Moves 3 nucleotides at a time Termination- Reach stop codon- Insert releasing factor:o Ribosome breaks aparto Polypeptide released- Bacterial Genome Organizationo Singular circular chromosomeo Naked DNAo No intronso Located in the cytoplasmo Plasmids Separate from chromosome Not necessary for survival- Do the differences in organization lead to functional differences?o Transcription and translation can occur simultaneouslyo Easy for prokaryotes to take up foreign DNA (transformation)- Gene Regulationo Why regulate? Energetics Control- Bacterial Operono Only exists in prokaryotic cellso Promotero Operatoro Structural geneso Regulator produces repressor Wants to attach to the operator Prevents polymerase from transcribing structural geneso Repressible operon Trp operon- Repressor produced in an inactive form- Binds with co-repressor- Complex blocks transcriptiono Inducible operon Lac operon- Repressor produced in an active form- Blocks transcription- Binds with inducer- Repressor/inducer complex inactive- Positive Gene Regulationo cAMPo cAMP Receptor Protein (CRP)- Eukaryotic Gene Regulationo Genome structure, genes, DNA and chromosomes Complete genome DNA sequence known- Humans, chimps, flies, worms, and plants- Exact AGCT base order is known- Genes are known- Functions are being determined Human genome- Genes are at set positions on the chromosomeso ~5000 expressed in each cell typeo ~1000 “housekeeping” geneso Prokaryotic gene regulation occurs at the level of transcriptiono Eukaryotic gene regulation occurs at many levelso Levels of regulation Chromosomal- DNA packing- DNA Methylation- Gene Amplification Transcriptional- Promoters, enhancers- Regulatory proteins- Increase rate of transcription of single gene Post-transcriptional- mRNA processing – make many proteins but one gene- mRNA degradation – message degrades and breaks apart Translational- Regulatory proteins Post-translational- Cleavage and modification- Transport and degradationo In a repressible operon the repressor protein is made in an inactive form and does not bind to the operator preventing transcription.- Cell Cycleo The life of a cello G1 – gap one DNA remains unreplicatedo S – synthesis of DNA After, twice as much DNA (DNA replicated)o G2 – gap two Chromosomes remain replicated through this stageo Cell division
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