Main functions of DNA Cells use the genetic information stores in DNA in 2 ways: 1. Heredity complete copy of genetic information physically passed from one generation to the next during reproduction a. DNA must be replicated (copied) b. Copies passed to the daughter cells when a cell divides c. DNA passed from parent to offspringIf you want to learn more check out What is a dominant allele?
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during sexual reproduction 2. Control DNA controls cell structure and function a. DNA codes for proteins b. Proteins in a cell determines its structure and function c. All of the cells in an organism (human) determine the structure and function of the organism! The Watson and Crick model of DNA suggested a mechanism for DNA replication A parental molecule >The parental strands separate> Two Identical daughter cells of DNA and serve as templates DNA replication is semiconservative ● Each original strand is used a template ● The new daughter molecules are made up of one original (old/blue) strand and one “new” strand (gray) DNA Helicase ● Unwinds and separates the DNA strands DNA Polymerase protein that ensures right DNA joins together forming a covalent bond ● Covalently links the free nucleotides to the 3’ end of the newly forming daughter strand ○ Polymerization always occurs in the 5’ to 3’ direction DNA Primase ● Adds primers to the template strand Leading Strand replication is continuous Lagging Strand replication is discontinuous ● Synthesized in pieces called Okazaki fragments ● Fragments are then joined together by DNA ligase ○ Ligate to bind together ○ (think ligature) DNA Replication 1. Helicase unwinds and separates the DNA strands 2. Primers are added to the single stranded template strands 3. Free deoxyribonucleotides form Hbonds with the nucleotides in the template strands 4. DNA polymerase covalently links the free nucleotides to the 3’ end of the newly forming stands (works only in the 5’ to 3’ direction of the NEW strand) 5. The leading strand is synthesized continuously while the lagging strand is synthesized in fragments (discontinuous) 6. Primers are removed and replaced with deoxyribonucleotides (DNA polymerase must link) 7. Ligase covalently links the fragments 8. DNA polymerase proofreads and fixes mistakes DNA Polymerase has 2 roles 1. Covalently links free nucleotides to form a new DNA strand 2. Proofreads fixes mismatched base pairs Before proofreading 1 in 10,000 base pairs are mismatched After proofreading 1 in 1 billion base pairs are mismatched For each replication event, approx 3 mistakes remain unfixed these are mutations DNA Replication Error ● Extremely accurate ○ 1 error in several billion bases ● DNA polymerases and DNA ligase correct errors and DNA damage ○ Errors in DNA (mutations) can lead to cancer cells ● Mutations are the raw material for evolution REVIEW: 1. Explain how the structure of DNA facilitates its replication 2. Describe the process of DNA replication Different cells express different genes! Leads to…. ● Differentiation individual cells become specialized in structure and function ● Gene regulation is the turning on and off of genes ○ Turned on when it needs to be made ○ Turned off when does not need to be made ● Gene expression is the overall process of information flow from genes to proteins ○ Taking a code and turning it into something physical ● Cells only produce the produce needed by the cell ● Our earliest understanding of gene control came from the study of E. coli Jacob and Monod ● 1961 ● Observed E. coli (bacteria, a prokaryote) ○ Bacteria cultured with lactose (sugar found in milk) produced 3 enzymes (proteins) needed to “digest” lactose ○ Bacteria cultures without lactose did not produce the 3 enzymes Lac Operon in bacteria ● lac= lactose (sugar found in milk) ● operon= a series genes under the control of the same promoter Operon turned off (lactose absent) ● Repressor binds operator prevents transcription Operon turned on (lactose inactivates repressor) Regulation of Eukaryotic Genes Enhancers and Specific Transcription Factors ● Genes are only transcribed when the right factors are present ● Regulates how much of a specific mRNA is made Mechanisms of Post Transcriptional Regulation ● Regulatory mechanisms can operate at various stages after transcription ○ Alternative splicing ○ Breakdown of mRNA ○ Initiation of translation ○ Protein activation ○ Protein breakdown Alternative RNA splicing ● Different mRNA molecules are produced from the same primary transcript ● Depending on which RNA segments are treated as exons and which as introns Effects of mRNAs by MicroRNAs and Small Interfering RNAs ● MicroRNAs (miRNAs) small single stranded RNA molecules that can bind to mRNA ○ Can degrade mRNA or block its translation ● RNA interference (RNAi) use of miRNA to artificially control gene ○ Turn off specific genes Gene Mutation ● A permanent change in the nucleotide sequence of a gene Causes ● Environmental xrays, viruses, UV light, chemicals ● Mistakes during DNA replication DNA polymerase doesn’t fix all mismatches Mutations ● A change in the DNA sequence ○ Substitution one base is substituted for another ■ Affects just the amino acid that codon codes for ● Silent mutation does not affect the amino acid strand (protein) ● Missense codes for a different amino acid ● Nonsense causes a premature stop codon ○ Deletion one base is deleted ○ Insertion an extra base is inserted ■ insertions/ deletions change the entire reading frame for the codons ● Results in a very different amino acid sequence ● Most likely nonfunctional Heritability of Mutations Mutations affect the individual cell that they are found in, and any progeny of that cell Somatic cells ordinary body cells (skin, muscle, blood) Germ cells cells that will divide to make gametes (sperm, egg)DNA ● Deoxyribonucleic acid ● Deoxyribose sugar ● Bases A, T, C, G ● Double Stranded RNA ● Ribonucleic acid ● Ribose sugar ● Bases A, U, C, G ● Generally single stranded Transcription= copy: synthesis of RNA under the direction of DNA Translation= changing: synthesis of proteins under the direction of RNA What are genes? ● Segments of the DNA in each chromosome ● Each chromosome has a different set of genes ● Each gene 1,000’s to 100,000’s of basepairs long ○ Sequence of bases ● Code for a specific gene product; ○ Mostly protein; some RNA ○ Often separated by noncoding regions of DNA ******AUG is always the start of a reading codon Promoter ● Where transcription begins (starts) ● Binding site for RNA polymerase ● Determines which strand will be used as a template for transcription Coding Sequence ● Series of codons (three base code for an amino acid) Terminator ● Where transcription end ● RNA polymerase detaches THREE PARTS OF GENE: Promoter, Coding Sequence, Terminator Gene a segment of DNA that codes for a specific product, usually a polypeptide (protein) ● 10% of genes are transcribed into ○ Ribosomal RNA (rRNA) ○ Transfer RNA (tRNA) ● 90% of genes are transcribed into messenger RNA (mRNA) ○ Translated into a polypeptide (protein) mRNA processing: If the gene codes for messenger RNA (mRNA): ● Cap and tail added ● Introns removed ● Exons spliced together rRNA processing: If the gene codes for ribosomal RNA (rRNA): rRNA + “imported” proteins= RIBOSOMAL SUBUNITS 1 Ribosome: ● 60% RNA ● 40% protein ● Assembled in the cytoplasm tRNA processing: If the gene codes for Transfer RNA (tRNA) ● H bonding between complementary ribonucleotides results in 3D “L”shape ○ Amino acid binding site at one end ○ Anticodon at the other end (3 ribonucleotides that can base pair with mRNA codons) The Genetic Code ● Triplet (codons) ● Redundant Translation (as it would happen inside a cell) Initiation ● mRNA binds to small subunit of ribosome ● tRNA binds to start codon AUG When the large ribosomal subunit binds to the small subunit initiation is complete Elongation ● Another tRNA binds to the next codon in A site ● tRNA in P site emptied of amino acid when the amino acids covalently linked= peptide bond ● mRNA moves through ribosome Termination ● STOP codon reached ● Polypeptide released ● mRNA released DNA Structure and Function What is a genetic molecule? ● Scientists knew ○ Genetic material was in the nucleus ○ Pieces of genetic material chromosomes ○ Chromosomes were made of protein and DNA ● Hershey and Chase, 1952 ○ DNA? ■ Composed of 4 nucleotides (too simple?) ○ Protein? ■ Composed of 20 amino acids (seemed more likely) Hershey Chase Experiment ● Phage (bacteriophage) virus that infcts bacterial cells ○ How does a virus reproduce ■ Example in humans: flu virus ● Virus must get genetic material inside cells *** Viruses made up of DNA and PROTEIN Radioactive Labeling ● Radioactive phosphorous (32P) ○ Incorporated into phosphate groups of DNA ● Radioactive sulfur (35P) ○ Incorporated into protein (not DNA) Results Summary the Hershey chase experiments ● Phage inject their DNA into bacterial cells to infect them ● The injected DNA contained all of the genetic information needed for directing the synthesis of new virus particles ● The protein part of the phage didn’t enter the bacterial cells, its not needed for infection ● CONCLUSION: DNA (not protein) is the genetic molecule DNA Structure ● Determine that for any sample ○ The number of adenine is equal to the number of thymine ■ A=T ○ The number of cytosine is equal to the number of guanine ■ C=G ● Heilical Shape● Rosalind Franklin (19201958) ○ 2nm wide ○ Complete turn every 3.4 nm Watson and Crick’s contributions ● Double stranded ○ A pairs with T ○ C pairs with G ● Complementary molecule Pyrimidines Thymine (T) Cytosine (C) (longer name) Purines Adenine (A) Guanine (G) (PURe As Gold) QUIZ: 1. The epigenome switches or tags that E: are changes “above the genome,” that influence gene expression 2. Which of the following is TRUE about identical twins? B: As they age their epigenomes become more distinct 3. Which of the following is not true E: No diseases are caused by epigenetics 4. Which of the following is a TRUE statement regarding epigenetics and cancer 5. Changes in your epigenome C. Are permanent From Genes to Proteins (the control function of DNA) ● If a gene is expressed, it is used to direct the synthesis of a protein Epigenetic Inheritance ● Epigenetics is a way of preparing a fetus for the world it will be born into ● The egg that made you was produced inside of your grandmother Initial Research Assignment….. Epigenome relates to the Control function of DNA From Greek (epi= above) means “above the genome” Environmental effect on gene expression ● Lifestyle choices Influence whether or not a given gene is expressed ● DNA methylation ○ Direct effect of DNA ○ Methyl groups (CH3) attached to DNA in specific places ○ Turn genes off/ on ● Chemical tags on proteins (histones) associated with DNA ○ Indirect effect on DNA ○ After how tightly or loosely DNA is packaged ■ Tightly packed DNA; reduces expression ■ Loosely packed DNA; increases expression What is a molecule? ● DNA How do you know this? ● Double Helix, Bases List structural features of a molecule ● Nucleotides ○ Phosphate group ○ Sugar group ○ Nitrogen base ■ Adenine (A) ■ Thymine (T) ■ Guanine (G) ■ Cytosine (C) ● G & C > 3 bonds ● A & T > 2 bonds ● C = carbon ● H = hydrogen Two strands in DNA molecule ● Each made up of repeating nucleotide subunits ● Containing PO4 and sugar and base ● Stands oriented in opposite directions ○ Antiparallel Twisted into a double helix Base pairs link strands to each other ● Big base & small base ● Hbonded ● AT (2x) ● GC (3x) DNA nucleotide (repeating subunit of DNA) ● Sugar (deoxyribose) ● Phosphate group ● Base (can be A,T,C,G) How are strands connected to form a DNA molecule ● Complementary base pairing ○ A with T ○ C with G ○ Connected with 2 or 3 Hydrogen bonds ● Complementary = always go together “complement” each other What is the function of DNA ● Holds our genes (genetic code) ● Pass genes on (hereditary) ● DNA is used to make protein What aspect of DNA structure allows it to carry the coded (genetic) information? ● Sequence of ATGC is different in everyone and every living thing ○ Sugar? ○ Phosphate group? ○ Sugar Phosphate backbone? ○ Complementary base pairs? ○ Sequence of bases on each strand? ■ This is what is unique about each DNA molecule (sequence of it) Why learn about DNA? ● Cell function ○ DNA controls cell type ● Proteins ○ DNA contains instructions for making proteins ● Genetics/ Inheritance ○ DNA is inherited and determines characteristics ○ (cell to cell and parent to offspring) ● Evolution and Ecology ○ Organisms that live in a desert are different than organisms that live in a rainforest with the characteristics they have and then pass on ○ Most effective genes are passed on ○ DNA determines what organisms look like and what they do ■ Cactus in a desert needs the type of body and hardness it has ● Exercise changes our DNA