DNA and RNA

Replication Facts DNA has to be copied before a cell divides DNA is copied during the S or synthesis phase of interphase New cells will need identical DNA strands

Synthesis Phase (S phase) S phase during interphase of the cell cycle Nucleus of eukaryotes Mitosis -prophase -metaphase -anaphase -telophase G1 G2 S phase interphase DNA replication takes place in the S phase. copyright cmassengale

HOW IS DNA COPIED? The structure of DNA explains how it can be copied. Image from: http://evolution.berkeley.edu/evosite/evo101/images/dna_bases.gif HOW IS DNA COPIED? The structure of DNA explains how it can be copied. Each strand has all the info needed to construct the __________other half. If strands are separated, _____________ rules allow you to fill in the complementary bases. matching base-pairing

copyright cmassengale DNA Replication Begins at Origins of Replication Two strands open forming Replication Forks (Y-shaped region) New strands grow at the forks Replication Fork Parental DNA Molecule 3’ 5’ copyright cmassengale

Sites where strand separation and Original strand DNA polymerase New strand Growth DNA polymerase Growth Replication fork Replication fork Nitrogenous bases New strand Original strand Sites where strand separation and replication occur are called _____________ replication forks

copyright cmassengale DNA Replication As the 2 DNA strands open at the origin, Replication Bubbles form Prokaryotes (bacteria) have a single bubble Eukaryotic chromosomes have MANY bubbles Bubbles copyright cmassengale

copyright cmassengale DNA Replication Enzyme Helicase unwinds and separates the 2 DNA strands by breaking the weak hydrogen bonds Single-Strand Binding Proteins attach and keep the 2 DNA strands separated and untwisted copyright cmassengale

copyright cmassengale DNA Replication Enzyme Topoisomerase attaches to the 2 forks of the bubble to relieve stress on the DNA molecule as it separates Enzyme DNA Enzyme copyright cmassengale

copyright cmassengale DNA Replication Before new DNA strands can form, there must be RNA primers present to start the addition of new nucleotides Primase is the enzyme that synthesizes the RNA Primer DNA polymerase can then add the new nucleotides copyright cmassengale

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Direction of Replication DNA Replication DNA polymerase can only add nucleotides to the 3’ end of the DNA This causes the NEW strand to be built in a 5’ to 3’ direction RNA Primer DNA Polymerase Nucleotide 5’ 3’ Direction of Replication copyright cmassengale

Remember HOW the Carbons Are Numbered! O=P-O Phosphate Group N Nitrogenous base (A, G, C, or T) CH2 O C1 C4 C3 C2 5 Sugar (deoxyribose) copyright cmassengale

Remember the Strands are Antiparallel O 1 2 3 4 5 P O 1 2 3 4 5 G C T A copyright cmassengale

Synthesis of the New DNA Strands The Leading Strand is synthesized as a single strand from the point of origin toward the opening replication fork RNA Primer DNA Polymerase Nucleotides 3’ 5’ copyright cmassengale

Synthesis of the New DNA Strands The Lagging Strand is synthesized discontinuously against overall direction of replication This strand is made in MANY short segments It is replicated from the replication fork toward the origin RNA Primer Leading Strand DNA Polymerase 5’ 3’ Lagging Strand 5’ 3’ copyright cmassengale

Lagging Strand Segments Okazaki Fragments - series of short segments on the lagging strand Must be joined together by an enzyme Lagging Strand RNA Primer DNA Polymerase 3’ 5’ Okazaki Fragment copyright cmassengale

Joining of Okazaki Fragments The enzyme Ligase joins the Okazaki fragments together to make one strand Lagging Strand Okazaki Fragment 2 DNA ligase Okazaki Fragment 1 5’ 3’ copyright cmassengale

Replication of Strands Replication Fork Point of Origin copyright cmassengale

copyright cmassengale Proofreading New DNA DNA polymerase initially makes about 1 in 10,000 base pairing errors Enzymes proofread and correct these mistakes The new error rate for DNA that has been proofread is 1 in 1 billion base pairing errors copyright cmassengale

REPLICATION STEPS Enzymes “unzip” molecule by breaking _______________ that hold the strands together and unwind it. 2. _______________ joins nucleotides using original strand as template and ______________for errors. 3. Copying happens in ________ directions along the two strands & in __________ places at once. Hydrogen bonds DNA polymerase spell checks opposite multiple

Semiconservative Model of Replication Idea presented by Watson & Crick The two strands of the parental molecule separate, and each acts as a template for a new complementary strand New DNA consists of 1 PARENTAL (original) and 1 NEW strand of DNA DNA Template New DNA Parental DNA copyright cmassengale

copyright cmassengale DNA Damage & Repair Chemicals & ultraviolet radiation damage the DNA in our body cells Cells must continuously repair DAMAGED DNA Excision repair occurs when any of over 50 repair enzymes remove damaged parts of DNA DNA polymerase and DNA ligase replace and bond the new nucleotides together copyright cmassengale

copyright cmassengale Question: What would be the complementary DNA strand for the following DNA sequence? DNA 5’-CGTATG-3’ copyright cmassengale

copyright cmassengale Answer: DNA 5’-CGTATG-3’ DNA 3’-GCATAC-5’ copyright cmassengale

REPLICATION ANIMATION

RNA and PROTEIN SYNTHESIS © Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved

copyright cmassengale DNA DNA contains genes, sequences of nucleotide bases These Genes code for polypeptides (proteins) Proteins are used to build cells and do much of the work inside cells copyright cmassengale

copyright cmassengale Genes & Proteins Proteins are made of amino acids linked together by peptide bonds 20 different amino acids exist copyright cmassengale

copyright cmassengale Amino Acid Structure copyright cmassengale

copyright cmassengale Polypeptides Amino acid chains are called polypeptides copyright cmassengale

copyright cmassengale DNA Begins the Process DNA is found inside the nucleus Proteins, however, are made in the cytoplasm of cells by organelles called ribosomes Ribosomes may be free in the cytosol or attached to the surface of rough ER copyright cmassengale

copyright cmassengale Starting with DNA DNA ‘s code must be copied and taken to the cytosol In the cytoplasm, this code must be read so amino acids can be assembled to make polypeptides (proteins) This process is called PROTEIN SYNTHESIS copyright cmassengale

RNA is the BLUEPRINT of the Master Plan Roles of RNA and DNA DNA is the MASTER PLAN RNA is the BLUEPRINT of the Master Plan copyright cmassengale

copyright cmassengale RNA Differs from DNA RNA has a sugar ribose DNA has a sugar deoxyribose copyright cmassengale

copyright cmassengale Other Differences RNA contains the base uracil (U) DNA has thymine (T) RNA molecule is single-stranded DNA is double-stranded DNA copyright cmassengale

copyright cmassengale Structure of RNA Like DNA, RNA is a polymer of nucleotides. In an RNA nucleotide, the sugar ribose is attached to a phosphate molecule and to a base, either G, U, A, or C. Notice that in RNA, the base uracil replaces thymine as one of the pyrimidine bases. RNA is single-stranded, whereas DNA is double-stranded. copyright cmassengale

RNA- the Other Nucleic Acid NUCLEOTIDES Also made of ___________ Sugar is _______ instead of deoxyribose. RNA is _________ stranded Contains _________ instead of thymine. RIBOSE SINGLE URACIL http://images2.clinicaltools.com/images/gene/dna_versus_rna_reversed.jpg

3 KINDS OF RNA HELP WITH INFO TRANSFER FOR PROTEIN SYNTHESIS RIBOSOMAL _________________RNA (rRNA) Combines with proteins to form ribosomes _________________RNA (tRNA) transfers amino acids to the ribosomes where proteins are synthesized (Matches m-RNA codon to add correct amino acids during protein synthesis) _________________RNA (mRNA) copies DNA’s code (genetic information) carries code from DNA to ribosomes TRANSFER MESSENGER rRNA and t-RNA images from © Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved mRNA image from http://wps.prenhall.com/wps/media/tmp/labeling/1140654_dyn.gif

copyright cmassengale Messenger RNA Long Straight chain of Nucleotides Made in the Nucleus Copies DNA & leaves through nuclear pores Contains the Nitrogen Bases A, G, C, U ( no T ) copyright cmassengale

Messenger RNA (mRNA) Carries the information for a specific protein Made up of 500 to 1000 nucleotides long Sequence of 3 bases called codon AUG – methionine or start codon UAA, UAG, or UGA – stop codons #85

copyright cmassengale Ribosomal RNA (rRNA) rRNA is a single strand 100 to 3000 nucleotides long Globular in shape Made inside the nucleus of a cell Associates with proteins to form ribosomes Site of protein Synthesis copyright cmassengale

copyright cmassengale The Genetic Code A codon designates an amino acid An amino acid may have more than one codon There are 20 amino acids, but 64 possible codons Some codons tell the ribosome to stop translating copyright cmassengale

copyright cmassengale The Genetic Code Use the code by reading from the center to the outside Example: AUG codes for Methionine copyright cmassengale

Remember the Complementary Bases On DNA: A-T C-G On RNA: A-U copyright cmassengale

copyright cmassengale Transfer RNA (tRNA) Clover-leaf shape Single stranded molecule with attachment site at one end for an amino acid Opposite end has three nucleotide bases called the anticodon copyright cmassengale

copyright cmassengale Transfer RNA amino acid attachment site U A C anticodon copyright cmassengale

copyright cmassengale Codons and Anticodons The 3 bases of an anticodon are complementary to the 3 bases of a codon Example: Codon ACU Anticodon UGA UGA ACU copyright cmassengale

Transcription and Translation copyright cmassengale

Pathway to Making a Protein DNA mRNA tRNA (ribosomes) Protein copyright cmassengale

copyright cmassengale PROTEIN SYNTHESIS copyright cmassengale

copyright cmassengale Protein Synthesis The production or synthesis of polypeptide chains (proteins) Two phases: Transcription & Translation mRNA must be processed before it leaves the nucleus of eukaryotic cells copyright cmassengale

copyright cmassengale DNA  RNA  Protein Nuclear membrane Transcription RNA Processing Translation DNA Pre-mRNA mRNA Ribosome Protein Eukaryotic Cell copyright cmassengale

copyright cmassengale Transcription The process of copying the sequence of one strand of DNA, the template strand mRNA copies the template strand Requires the enzyme RNA Polymerase copyright cmassengale

Enzyme called _____________________ Adenine (DNA and RNA) Cystosine (DNA and RNA) Guanine(DNA and RNA) Thymine (DNA only) Uracil (RNA only) RNA polymerase DNA RNA Enzyme called _____________________ separates strands, then uses one strand as a template to assemble an RNA copy. RNA POLYMERASE

copyright cmassengale Template Strand copyright cmassengale

copyright cmassengale Question: What would be the complementary RNA strand for the following DNA sequence? DNA 5’-GCGTATG-3’ copyright cmassengale

copyright cmassengale Answer: DNA 5’-GCGTATG-3’ RNA 3’-CGCAUAC-5’ copyright cmassengale

copyright cmassengale Transcription During transcription, RNA polymerase binds to DNA and separates the DNA strands RNA Polymerase then uses one strand of DNA as a template to assemble nucleotides into RNA copyright cmassengale

copyright cmassengale Transcription Promoters are regions on DNA that show where RNA Polymerase must bind to begin the Transcription of RNA Called the TATA box Specific base sequences act as signals to stop Called the termination signal copyright cmassengale

copyright cmassengale RNA Polymerase copyright cmassengale

How does RNA POLYMERASE know where a gene starts and stops? Enzyme binds to places with specific DNA sequences called _______________. PROMOTERS tell _________________ where to start. Signals at the end of the gene code cause transcription to _____ . PROMOTERS RNA POLYMERASE stop http://images2.clinicaltools.com/images/gene/dna_versus_rna_reversed.jpg

copyright cmassengale mRNA Processing After the DNA is transcribed into RNA, editing must be done to the nucleotide chain to make the RNA functional Introns, non-functional segments of DNA are snipped out of the chain copyright cmassengale

copyright cmassengale mRNA Editing Exons, segments of DNA that code for proteins, are then rejoined by the enzyme ligase A guanine triphosphate cap is added to the 5” end of the newly copied mRNA A poly A tail is added to the 3’ end of the RNA The newly processed mRNA can then leave the nucleus copyright cmassengale

Result of Transcription New Transcript Tail CAP copyright cmassengale

copyright cmassengale mRNA Transcript mRNA leaves the nucleus through its pores and goes to the ribosomes copyright cmassengale

copyright cmassengale Translation Translation is the process of decoding the mRNA into a polypeptide chain Ribosomes read mRNA three bases or 1 codon at a time and construct the proteins copyright cmassengale

copyright cmassengale Transcription Transcription occurs when DNA acts as a template for mRNA synthesis. Translation occurs when the sequence of the mRNA codons determines the sequence of amino acids in a protein. Translation copyright cmassengale

copyright cmassengale Ribosomes Made of a large and small subunit Composed of rRNA (40%) and proteins (60%) Have two sites for tRNA attachment --- P and A copyright cmassengale

copyright cmassengale Step 1- Initiation mRNA transcript start codon AUG attaches to the small ribosomal subunit Small subunit attaches to large ribosomal subunit mRNA transcript copyright cmassengale

copyright cmassengale Ribosomes Large subunit P Site A Site mRNA A U G C Small subunit copyright cmassengale

copyright cmassengale Step 2 - Elongation As ribosome moves, two tRNA with their amino acids move into site A and P of the ribosome Peptide bonds join the amino acids copyright cmassengale

copyright cmassengale Initiation 2-tRNA G aa2 A U 1-tRNA U A C aa1 anticodon A U G C U A C U U C G A hydrogen bonds codon mRNA copyright cmassengale

copyright cmassengale Elongation 3-tRNA G A aa3 peptide bond aa1 aa2 1-tRNA 2-tRNA anticodon U A C G A U A U G C U A C U U C G A hydrogen bonds codon mRNA copyright cmassengale

copyright cmassengale aa1 peptide bond 3-tRNA G A aa3 aa2 1-tRNA U A C (leaves) 2-tRNA G A U A U G C U A C U U C G A mRNA Ribosomes move over one codon copyright cmassengale

copyright cmassengale peptide bonds 4-tRNA G C U aa4 aa1 aa2 aa3 2-tRNA 3-tRNA G A U G A A A U G C U A C U U C G A A C U mRNA copyright cmassengale

copyright cmassengale peptide bonds 4-tRNA G C U aa4 aa1 aa2 aa3 2-tRNA G A U (leaves) 3-tRNA G A A A U G C U A C U U C G A A C U mRNA Ribosomes move over one codon copyright cmassengale

copyright cmassengale peptide bonds U G A 5-tRNA aa5 aa1 aa2 aa4 aa3 3-tRNA 4-tRNA G A A G C U G C U A C U U C G A A C U mRNA copyright cmassengale

copyright cmassengale peptide bonds U G A 5-tRNA aa5 aa1 aa2 aa3 aa4 3-tRNA G A A 4-tRNA G C U G C U A C U U C G A A C U mRNA Ribosomes move over one codon copyright cmassengale

copyright cmassengale aa5 aa4 aa199 Termination aa3 primary structure of a protein aa200 aa2 aa1 terminator or stop codon 200-tRNA A C U C A U G U U U A G mRNA copyright cmassengale

End Product –The Protein! The end products of protein synthesis is a primary structure of a protein A sequence of amino acid bonded together by peptide bonds aa1 aa2 aa3 aa4 aa5 aa200 aa199 copyright cmassengale

copyright cmassengale Messenger RNA (mRNA) A U G C mRNA start codon codon 2 codon 3 codon 4 codon 5 codon 6 codon 7 codon 1 methionine glycine serine isoleucine alanine stop codon protein Primary structure of a protein aa1 aa2 aa3 aa4 aa5 aa6 peptide bonds copyright cmassengale

MASTER PLAN DNA stays safe in nucleus © Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved TRANSCRIPTION (DNA→ RNA) & PROCESSING takes place in nucleus TRANSLATION (RNA→ proteins) takes place on ribosomes in cytoplasm “Blueprints” of master plan are carried to building site http://www.home-improvement-resource.com/images/architect.jpg

RNA’s require EDITING before use Image by Riedell

WHY WASTE IT? Why spend energy making a large RNA and then throw parts away? May allow same gene to be used in different ways in different kinds of cells. May have a role in evolution… allows small changes in genes to have a big effect.

HOW CAN JUST 4 BASES GIVE DIRECTIONS TO MAKE 20 AMINO ACIDS? Message is read in groups of 3 = _________ UCGCACGGU UCG-CAC-GGU CODON Serine - Histidine - Glycine Codons represent different amino acids

AUG 64 possible codons Some amino acids have more than one codon.  The m-RNA Code Section 12-3 64 possible codons Some amino acids have more than one codon. START= _______ 3 codons for _____ AUG STOP

EACH tRNA carries only one kind of _____________ amino acid ANTICODON on tRNA matches up with ________ on mRNA CODON Images modified from © Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved

Figure 12–18 Translation Section 12-3

Figure 12–18 Translation (continued) Section 12-3

GENES & PROTEINS Proteins are the connection between the gene code in the DNA and how that gene is expressed. A gene that codes for an enzyme (protein) to make a pigment can control the color of a flower. A gene that codes for an enzyme (protein) adds carbohydrates to glycoproteins to produce your blood type. Enzymes catalyze and regulate chemical reactions so proteins build and operate all cell components.

REPLICATION DNA → DNA ____________ DNA → RNA ____________ RNA→ Protein ___________ TRANSCRIPTION TRANSLATION

Concept Map Section 12-3 can be also called which functions to from to to make up

Bring amino acids to ribosome Concept Map Section 12-3 RNA can be Messenger RNA Ribosomal RNA Transfer RNA also called which functions to also called which functions to also called which functions to mRNA Carry instructions rRNA Combine with proteins tRNA Bring amino acids to ribosome from to to make up DNA Ribosome Ribosomes

Let’s Practice! http://learn.genetics.utah.edu/content/begin/dna/transcribe/