DNA

Nucleic Acids DNA and RNA are examples Deoxyribonucleic acid

Nucleic Acids A gene is a section of DNA that provides the code to make a protein.

Nucleic Acids Built from monomers of nucleotides Consists of a phosphate group, a sugar molecule, and a nitrogenous base

Nitrogenous bases Purines – double ring -adenine, guanine A=T C=G Purines – double ring -adenine, guanine Pyrimidines – single ring thymine, cytosine

Tight helical fiber (30-nm diameter) Huge molecule over 3 billion base pairs per cell Condenses by wrapping/coiling around histones -called a chromosome Linker DNA double helix (2-nm diameter) “Beads on a string” Tight helical fiber (30-nm diameter) Metaphase chromosome Histones Nucleosome (10-nm diameter) Supercoil (300-nm diameter) 700 nm Figure 11.2a-0 DNA packing in a eukaryotic chromosome

How did we discover DNA is the genetic material? In a group or individually, read through page 182 and figure 10.1B (183) What did Fredrick Griffith discover? What did Alfred Hershey and Martha Chase discover? What was their experiment?

Hershey Chase Animation

Batch 1: Radioactive protein labeled in yellow Phage Bacterium Radioactive protein DNA Empty protein shell Phage DNA Centrifuge Pellet Batch 1: Radioactive protein labeled in yellow Radioactive DNA The radioactivity is in the pellet. The radioactivity is in the liquid. Batch 2: Radioactive DNA labeled in green Figure 10.1b-0 The Hershey-Chase experiment

How was the double helix discovered? Read pages 186 and 187

Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Pyrimidines Purines Figure 10.2b-0 The nitrogenous bases of DNA

Recall: The experiment from Hershey and Chase (1952) demonstrated DNA is the passed from parents to offspring, but what is its structure? Phage Bacterium Radioactive protein DNA Empty protein shell Phage DNA Centrifuge Pellet Batch 1: Radioactive protein labeled in yellow Radioactive DNA The radioactivity is in the pellet. The radioactivity is in the liquid. Batch 2: Radioactive DNA labeled in green Figure 10.1b-0 The Hershey-Chase experiment

Discovering the Structure of DNA Watson and Crick were the first to discover the structure of DNA. Used data x-ray crystallography data from Wilkins and Franklin without their permission

Earliest Model of DNA

Make our own models Two simple steps Label the nitrogenous bases Fold it

DNA We know the structure of DNA, and that more than 3 billion base pairs are in each cell, what about new cells?

DNA Replication Depends on specific base pairs adenine – thymine guanine – cytosine If this is one half of DNA, what would the other half be?

DNA Replication Semiconservative model The two DNA strands separate (parent strands). Each parent strand then becomes a template for a new, complementary strand (daughter strand) forming two new daughter molecules of DNA Each new DNA helix has one old strand with one new strand.

Daughter DNA molecules Figure 10.4b A T G C A T Parental DNA molecule A T T A C G G C T Daughter strand Parental strand A C C G G G C T G C T T C A A G Figure 10.4b The untwisting and replication of DNA A G T A C C A G T A T A T A G Daughter DNA molecules T C

DNA Replication Over a dozen enzymes and other proteins needed to replicate DNA DNA polymerase – adds nucleotides one at a time to the strand Other enzymes “proofread” and fix mistakes

DNA Replication Replication occurs at multiple points at the same time

DNA Replication Carbons are labeled The direction DNA polymerase moves is determined by the sugar phosphate backbone There is a 5’ end and a 3’ end Nucleotides are added onto the 3’ end, moving towards the 5’ end

DNA polymerase molecule 3′ This daughter strand is synthesized continuously 5′ Parental DNA 5′ 3′ Replication fork This daughter strand is synthesized in pieces 3′ 5′ 5′ Figure 10.5c How daughter DNA strands are synthesized 3′ DNA ligase Overall direction of replication

Recall A gene is a section of DNA that provides the code to make a protein. Genes carry different information on them Human Genome mapped it out – ethical questions

https://www. youtube. com/watch https://www.youtube.com/watch?v=zwibgNGe4aY&feature=youtube_gdata_player

Parent molecule Daughter molecules

Parent strand Daughter strand

Daughter DNA molecules Parental DNA molecule A T T A C G G Daughter strand C T Parental strand A C C G G G C T G C T C A A T G Figure 10.4b The untwisting and replication of DNA A G T A C C A G T A T A T A G Daughter DNA molecules T C

Hypothetical DNA If this is the parent strand? What is the daughter strand? A - T - C - G -

What was the main enzyme in DNA replication What was the main enzyme in DNA replication? What was unique as a result of the sugar phosphate backbone?

DNA polymerase molecule 3′ This daughter strand is synthesized continuously 5′ Parental DNA 5′ 3′ Replication fork This daughter strand is synthesized in pieces 3′ 5′ 5′ Figure 10.5c How daughter DNA strands are synthesized 3′ DNA ligase Overall direction of replication

https://www.hhmi.org/biointeractive/dna-replication-basic-detail

3’ 5’

https://www.hhmi.org/biointeractive/dna-replication-basic-detail

After DNA replicates, the cell divides Looking at that after break. Why is DNA Critical?

Transcription and Translation DNA is transcribed into RNA RNA is translated into protein DNA NUCLEUS CYTOPLASM RNA Transcription Translation Protein

DNA Ingredientes: 2 1 / 4 tazas de harina para todo uso 1 cucharadita de bicarbonato de soda 1 cucharadita de sal 1 taza (2 palos) de mantequilla, suavizada 3 / 4 taza de azúcar granulada 3 / 4 taza de azúcar morena 1 cucharadita de extracto de vainilla 2 huevos grandes 2 tazas (12 oz. Pkg.) TELEPEAJE CASA NESTLÉ ® ® semi-dulce de chocolate bocados 1 taza de nueces picadas

RNA Ingredients: To 2 1/4 cups all-purpose flour 1 teaspoon baking soda 1 teaspoon salt 1 cup (2 sticks) butter, softened 3/4 cup granulated sugar 3/4 cup brown sugar 1 teaspoon vanilla extract 2 large eggs 2 cups (12 oz. Pkg.) NESTLÉ TOLL HOUSE ® ® semi-sweet chocolate morsels 1 cup chopped walnuts

Protein

Transcription Sections of DNA called genes are used RNA polymerase attaches to the DNA at a ‘promoter’ site It moves along the gene forming a new RNA strand using the base pair rules

Transcription DNA Base pairs A-T G-C There is no thymine in RNA, a different nucleotide Uracil is used RNA Base pairs A-U G-C

DNA Transcription RNA Codon Translation Polypeptide Amino acid A A A C C G G C A A A A Transcription RNA U U U G G C C G U U U U Codon Translation Figure 10.7-1 Transcription and translation of codons (partial) Polypeptide Amino acid

Quick review

DNA replication Lots of enzymes, DNA polymerase one of them

DNA codes for protein Only part of DNA is a gene

Transcription and Translation DNA is transcribed into RNA RNA is translated into protein DNA NUCLEUS CYTOPLASM RNA Transcription Translation Protein

DNA Ingredientes: 2 1 / 4 tazas de harina para todo uso 1 cucharadita de bicarbonato de soda 1 cucharadita de sal 1 taza (2 palos) de mantequilla, suavizada 3 / 4 taza de azúcar granulada 3 / 4 taza de azúcar morena 1 cucharadita de extracto de vainilla 2 huevos grandes 2 tazas (12 oz. Pkg.) TELEPEAJE CASA NESTLÉ ® ® semi-dulce de chocolate bocados 1 taza de nueces picadas

RNA Ingredients: To 2 1/4 cups all-purpose flour 1 teaspoon baking soda 1 teaspoon salt 1 cup (2 sticks) butter, softened 3/4 cup granulated sugar 3/4 cup brown sugar 1 teaspoon vanilla extract 2 large eggs 2 cups (12 oz. Pkg.) NESTLÉ TOLL HOUSE ® ® semi-sweet chocolate morsels 1 cup chopped walnuts

Protein

Transcription Sections of DNA called genes are used RNA polymerase attaches to the DNA at a ‘promoter’ site It moves along the gene forming a new RNA strand using the base pair rules

Transcription DNA Base pairs A-T G-C There is no thymine in RNA, a different nucleotide Uracil is used RNA Base pairs A-U G-C

Figure 10.7-1 Transcription and translation of codons (partial)

Transcription RNA polymerase recognizes part of the DNA strand and attaches at the promoter region

Transcription RNA synthesis begins after attachment

Transcription Using DNA as a template, RNA polymerase adds RNA nucleotides one at a time

Transcription Using DNA as a template, RNA polymerase adds RNA nucleotides one at a time If the DNA strand is: ATAGGC Then the RNA will be: UAUCCG U U A C G C A U A G C G DNA - A A T G C G T A T C G C

Transcription RNA synthesis ends when RNA polymerase reaches the terminator DNA sequence

Initiation Elongation Termination Direction of transcription RNA synthesis begins after RNA polymerase attaches to the promoter. Unused strand of DNA RNA polymerase Terminator DNA DNA of gene Newly formed RNA Template strand of DNA Promoter Elongation Direction of transcription Using the DNA as a template, RNA polymerase adds free RNA nucleotides one at a time. Free RNA nucleotide DNA strands reunite U A T C C A A T C G T A U G A U C C A A A T A G G T T A DNA strands separate Figure 10.9-3 Transcription of a gene (step 3) Newly made RNA Termination RNA synthesis ends when RNA polymerase reaches the terminator DNA sequence. Terminator DNA Completed RNA RNA polymerase detaches

Transcription and Translation DNA is transcribed into RNA RNA is translated into protein DNA NUCLEUS CYTOPLASM RNA Transcription Translation Protein Before leaving the nucleus, the RNA is processed

Transcription Addition of cap and tail Exon DNA Intron Transcription Addition of cap and tail Tail Introns removed Exons spliced together Cap Coding sequence RNA transcript with cap and tail mRNA Figure 10.10 The production of eukaryotic mRNA NUCLEUS CYTOPLASM

RNA processing A ‘cap’ and ‘tail’ are added – helps protect the RNA Introns (intervening sequences) are removed Exons (expressed sequences) are spliced together Exon DNA Intron

Transcription and Translation DNA is transcribed into RNA RNA is translated into protein DNA NUCLEUS CYTOPLASM RNA Transcription Translation Protein

Translation The genetic code is the amino acid translations of each of the nucleotide triplets. Three nucleotides specify one amino acid

Translation Sixty-one codons correspond to amino acids 64 Total Sixty-one codons correspond to amino acids AUG codes for methionine and signals the start of translation Three “stop” codons signal the end of translation

Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Figure 10.8b-1 Deciphering the genetic information in DNA (step 1)

Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Transcription RNA A U G A A G U U U U A G Figure 10.8b-2 Deciphering the genetic information in DNA (step 2)

Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Transcription RNA A U G A A G U U U U A G Figure 10.8b-3 Deciphering the genetic information in DNA (step 3) Start codon Stop codon Translation Polypeptide Met Lys Phe

Translation Types of RNA Messenger RNA – RNA that will be coded into protein (mRNA) Transfer RNA – RNA that is used in the decoding process (tRNA) Ribosomal RNA – part of the ribosome that puts the protein together (adds amino acids together) (rRNA)

Translation tRNA There are 61, for each of the codons Contains a section called the anticodon that base pairs with the codon on mRNA

Translation Ribosome A complex of rRNA and protein A small subunit and a large subunit Contains two sites for tRNA – A site and P site

Translation How does it actually work? Recall, mRNA was just transcribed in the nucleus and then processed before entering the cytoplasm DNA NUCLEUS CYTOPLASM RNA Transcription Translation Protein

Translation mRNA binds to a the small subunit of a ribosome a tRNA recognizes the start codon and binds

Translation The large ribosomal subunit binds to the small subunit The tRNA fits into the P site

Translation A new tRNA carrying an amino acid moves into the A site, amino acids are combined The tRNAs shift over This repeats until stop codon is reached

Amino acid Polypeptide Anticodon P site A site mRNA Codons 1 Codon recognition Figure 10.14-1 Polypeptide elongation (step 1)

Peptide bond formation Amino acid Polypeptide Anticodon P site A site mRNA Codons 1 Codon recognition Figure 10.14-2 Polypeptide elongation (step 2) 2 Peptide bond formation

Peptide bond formation Amino acid Polypeptide Anticodon P site A site mRNA Codons 1 Codon recognition Figure 10.14-3 Polypeptide elongation (step 3) New peptide bond 2 Peptide bond formation 3 Translocation

Peptide bond formation Amino acid Polypeptide Anticodon P site A site mRNA Codons 1 Codon recognition mRNA movement Stop codon Figure 10.14-4 Polypeptide elongation (step 4) New peptide bond 2 Peptide bond formation 3 Translocation

Try it DNA: T A C A A T C G T A C G (one strand) RNA: Amino Acid: A U G U U A G C A U G C Met – Leu – Ala – Cys

https://www.youtube.com/watch?v=h5mJbP23Buo