DNA STRUCTURE FUNCTION What is DNA DNA Deoxyribonucleic
DNA STRUCTURE & FUNCTION
What is DNA? • DNA – Deoxyribonucleic Acid • A chemical substance that encodes our genetic make-up
Why have DNA? • Why do we have DNA? – DNA carries instructions for all of life’s processes
Early Discoveries • Fredrick Griffith – – Tried to develop a vaccine against pneumonia • He was one of the first to prove that inheritable characteristics are from DNA
Confirmation of DNA • Use of Bacteriophages – Alfred Hershey and Martha Chase • Bacteriophages are made up of a protein coat and has DNA inside. – They placed fluorescents on both the protein and the DNA to see with would shine in the viruses » Phosphorus in DNA » Sulfur in Proteins
What is DNA made up of? • Subunits are Nucleotides – 5 carbon sugar (deoxyribose)=DNA – Phosphate Group – Nitrogen Bases = 4 • Adenine • Guanine • Thymine • Cytosine * Purines (double ring) * Pyrimidines (single ring)
Nucleotide
Chargaff’s Rule • 1949 - Erwin Chargaff – Noticed that… • A’s paired with T’s • C’s paired with G’s – A = T (double bond) – C = G (triple bond)
Nitrogen Bases
DNA Structure & Shape • Double stranded – 2 strands of DNA hydrogen bonded together • Helical Shape (helix) – DNA shape resembling a spiral staircase or a twisted ladder • Watson and Crick
• What is the orientation of DNA? – Antiparallel 5’ 3’ 3’ 5’
Other Terms • Double Helix • Anti-parallel
DNA Replication • When does this happen? – Think back to Mitosis… • Synthesis “S” phase
Replication • DNA uses enzymes to help unwind and copy the complimentary base strands – Helicase – DNA Polymerase – Ligase
Enzymes • Helicase – Unwinds (unzips) a portion of DNA – Separates the 2 strands by breaking the hydrogen bonds holding them together • DNA polymerase – Enzyme that adds complementary (A-T, CG) nitrogen bases to the empty (exposed) strand • Ligase – Enzyme that links copied sections together on the lagging strand
Replication cont… • Replication fork – The point where the 2 strands are separated • Template strand – The strand that copies are made from
Replication cont… • Leading strand – The strand being copied in the 5’ to 3’ direction (only continuous replication) • Lagging strand – The strand being copied in short segments because the enzyme works in the 5’ to 3’ direction • Okazaki fragments – The short segments created in the lagging strand that will be linked by an enzyme called ligase
Okazaki fragments • DNA is always replicated in a 5’ 3’ direction
Review … Steps of Replication • Step 1 DNA must be Unzipped (Unwound). – – – Helicase binds to the Double helix. Helicase unwinds the 2 strands and separates them into separate strands. Nitrogen bases are now separated and unpaired
Step 2 • DNA Polymerase binds to DNA and starts adding complementary nucleotides to the unzipped strands. • The enzyme works in one direction: 5’ to 3’ • The two strands of DNA are antiparallel 5’ 3’ 3’ 5’
Step 2 cont… • On the leading strand (5’ to 3’), DNA polymerase synthesizes a continuous complementary strand • On the lagging strand, DNA polymerase adds bases in small segments at a time • The segments are called Okazaki fragments
Step 3 • Ligase (GLUE) must piece together the lagging strand pieces (Okazaki Fragments). To make a continuous strand.
Result of Replication: • An EXACT copy of each original strand of DNA is produced. • Cells can now divide through the process of Mitosis (to make body cells) or Meiosis (to make sex cells).
Mistakes • Do mistakes happen during replication? – Extremely rarely because DNA polymerase is able to proof-read to make sure any mistakes are corrected • If mistakes happen, it would result in a mutation – Some are good and some are not!
Central Dogma
Transcription & Translation • Transcription occurs in the Nucleus – Makes RNA (m. RNA) • Decodes the DNA into RNA • Translation occurs in the cytoplasm – Making of proteins from m. RNA molecule
Transcription & Translation • Transcription – DNA to RNA • Translation – RNA to Proteins
3 Types of RNA Type of RNA Messenger RNA (m. RNA) Ribosomal RNA (r. RNA) Function • Copies the DNA sequence • Carries the message from the nucleus out to the cytoplasm where the protein synthesis occurs • Central component of ribosomes • Machinery that makes protein from the message encoded by m. RNA • Small RNA chain that transfers a Transfer RNA specific amino acid to the growing (t. RNA) polypeptide chain during protein synthesis
RNA • Copied from DNA in the nucleus • Has ribose instead of deoxyribose • Complementary bases – G pairs with C – A pairs with U • Single stranded • Leaves the nucleus to go out into the cytoplasm
RNA composition • Nitrogen bases – – Adenine Cytosine Guanine Uracil • Ribose • Phosphate group • Sugar-phosphate backbone
Transcription • Unlike DNA replication, only certain segments serve as a template for RNA to make proteins – Use of enzymes • RNA polymerase – adds nucleotides to the 3’ end
To start Transcription • Must have a start sequence (promotor) • Continues copying until RNA polymerase reaches a stop signal – All in the nucleus • pre-m. RNA
Process of Transcription • RNA polymerase has 3 jobs 1. Attach to the DNA 2. Open DNA 3. Add complimentary base pairs to one strand of the DNA molecule • • The subunits added have ribose instead of deoxyribose The subunits added have Uracil in place of Thymidine
Pre-m. RNA • Before it can leave out of the nucleus to find a ribosome – A “cap” is attached to the 5’ end • Cap helps bond to the ribosome – A long chain of Adenine nucleotides are added to the 3’ends • Poly – A tail
Removal of not translated parts • Introns – – Thought to have been evolutionary material that we do not need anymore • Exons – – Codes for the proteins
Introns and Exons
Transcription • Black strand: coding strand • Blue strand: template to make m. RNA • Red Strand: newly synthesized m. RNA 5’ 3’ 3’ 3’ 5’ • Result: 5’
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC U
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UC
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCG
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGG
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGA
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGAC
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGACA
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGACAC
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGACACU
Transcription • For example: DNA: m. RNA: AGCCTGTGAAC UCGGACACUUG
Transcription Review • What is transcription? • Name 3 things that are different between DNA and RNA. • What does uracil pair with? • What is the function of m. RNA?
TRANSLATION Protein Synthesis
Translation • the process of making protein from m. RNA – the m. RNA sequence determines the amino acid sequence in the protein – the protein synthesis machinery includes m. RNA, ribosome and t. RNA
Translation • Takes place in the cytoplasm • t. RNA (transfer RNA) brings amino acids to the ribosome nucleus ribosome Codon Anticodon
Translation • Ribosome – machinery that strings amino acids together to make protein • Amino acid – basic building block of protein • Peptide bond – Covalent bond between amino acids in a peptide (string of amino acids)
Genetic Code • Nucleotide base (3 at a time) – Codons • Code for a specific amino acid. (a. a. ) – 64 codons – most of the 20 different a. a. still code for more than one codon • Anticodon – the complementary 3 -nucleotide code on the t. RNA
Codon Chart
• Start codon – AUG (codes for methionine) • 3 stop codons
• Start codon – AUG (codes for methionine) • 3 stop codons - UAG
• Start codon – AUG (codes for methionine) • Stop codon – UAG, UAA,
Translation • Start codon – AUG (codes for methionine) • Stop codon – UAG, UAA, UGA
t. RNA • Has a hook that allows the a. a. to attach onto it. – They have an anticodon that pairs with the codon for the specific a. a. to form a long polypeptide chain
Translation Stages • Initiation – Elogation – Termination AUG - add a. a. - UAA, UAG, UGA
Translation cont… • Once ribosome reaches the stop codon – The protein is clipped off and floats in the cytoplasm where it will eventually be used or enters the RER • Were it is either shipped somewhere inside or outside the cell
Process of Translation 1. The m. RNA leaves the nucleus through pores in the nuclear membrane into the cytoplasm 2. A ribosome attaches to m. RNA 3. The ribosome moves along the m. RNA to find the first AUG codon 4. The correct t. RNA has the anticodon that will bind to the codon on the m. RNA 5. The correct t. RNA bring the amino acids
Process of Translation 6. The codon AUG starts the protein synthesis, and therefore, methionine is the first amino acid 7. A t. RNA with the UAC anticodon carries the amino acid methionine 8. The ribosome moves to the next codon 9. The correct t. RNA has the anticodon that will bind to the codon on the m. RNA 10. The ribosome makes the protein
Protein Synthesis • Determine the amino acid sequence of the following m. RNA using the codon chart m. RNA: CGAUGACACUUUAGAAC Hint: Find the start codon
Protein Synthesis • Determine the amino acid sequence of the following m. RNA using the codon chart m. RNA: CGAUGACACUUUAGAAC
Protein Synthesis • Determine the amino acid sequence of the following m. RNA using the codon chart m. RNA: CGAUGACACUUUAGAAC Met
Protein Synthesis • Determine the amino acid sequence of the following m. RNA using the codon chart m. RNA: CGAUGACACUUUAGAAC Met - Thr - Leu
Protein Synthesis • Determine the amino acid sequence of the following m. RNA using the codon chart m. RNA: CGAUGACACUUUAGAAC Met - Thr - Leu (stop) • The amino acid chain is released from ribosome when a stop codon is reached
Protein Synthesis • Why do we need to make protein? • How are the amino acids put together in the correct order? • How does translation start? • How does translation end?
Gene Expression
Mutations and Cancer
Genetic Change What is a mutation? • A change in the DNA sequence leading to a change in the genetic message
Types of Mutations • Point mutation – Involves one or a few bases in the DNA sequence – Could be base substitution, insertion or deletion • Frameshift mutation – Changes DNA sequence and causes codons to be read differently – Could be insertion or deletion
Base Substitution • One or few bases are replaced by different ones AGC CTA UCG GAU Ser – Asp No Change AGT CTA UCA GAU Ser – Asp DNA AGC TTA UCG UAU Ser – Tyr DNA m. RNA Protein • May or may not change amino acid at that position • Does NOT cause frameshift
Insertion • Addition of one or few bases ATG CCT AUG CCU Met – Pro ATT GCC T AUU GCC U Iso – Ala • Causes frameshift - changes how codon sequence is read • Changes amino acid sequence
Deletion • One or a few bases are removed TGC TCA G ACG AGU G Thr – Ser TG –T CAG AC A GUC Thr – Val • Causes frameshift – changes how codon sequence is read • Amino acid sequence is changed
Other Types of Mutations Inversion Duplication Transposition Translocation A section of DNA is flip-flopped and ended up backwards in the same location on the chromosome The same section of DNA appears twice on the chromosome A gene is moved to another location on the same chromosome A gene is moved to a different chromosome Chromosomal A part of a chromosome is moved to rearrangement another chromosome
Original DNA Strand DNA sequence: 1 DNA RNA 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 G C A T G T C G A T T A T G T T A G C G T A C A G C T A A T A C A A T C G C A U G U C G A U U A U G U U A G Protein: Met – Ser – Iso – Met – Cys – Stop
Base Substitution Substitute base # 6 (“T”) with a “C”. DNA sequence: 1 DNA RNA 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 G C A T G C C G A T T A T G T T A G C G T A C G G C T A A T A C A A T C G C A U G C C G A U U A U G U U A G Protein: Met – Pro – Iso – Met – Cys – Stop
Insertion Insert an “A” between bases 4 and 5 in the DNA sequence: 1 DNA RNA 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 G C A T A G T C G A T T A T G T T A G C G T A T C A G C T A A T A C A A T C G C A U A G U C G A U U A U G U Protein: Met – Cys – U A G Stop
Deletion Delete base # 7 (“C”) in the original DNA sequence: 1 DNA RNA 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 G C A T G T C G A T T A T G T T A G C G T A C A G C T A A T A C A A T C G C A U G U C G A U U A U G U U A G Protein: Met – Stop
Cause and Effect of Carcinogens Cancer – Disease identified by uncontrolled cell division and the ability of the cells to spread to other parts of the body Carcinogens – Agents thought to cause cancer – Examples are chemicals such as cigarette tar, pesticides, and ionizing radiation such as X rays or UV rays from the sun
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