Biology 189 Chapter 9 - Molecular Biology & DNA PDF

Chapter 9 Molecular Biology & DNA  Chapter 9 Outline  DNA: Structure explains function  DNA, RNA and proteins: Central Dogma of Biology  Transcription: From DNA to RNA  Translation: From RNA to protein ◦ The Genetic Code  Types of mutations  From gene to phenot...

Chapter 9 Molecular Biology & DNA  Chapter 9 Outline  DNA: Structure explains function  DNA, RNA and proteins: Central Dogma of Biology  Transcription: From DNA to RNA  Translation: From RNA to protein ◦ The Genetic Code  Types of mutations  From gene to phenotype: An overview What is DNA and how does it work? DNA in the Cell Each chromosome:  Is a single linear DNA molecule that is packed and supercoiled around histone proteins  Those structures are linked together like ‘beads on a string’ to form chromatin  Chromatin is wound and looped around itself to reduce the space taken up by a chromosome  The Structure of DNA  In the 1950s – Pauling, Wilkins, Franklin were working on observing molecular structure using x-ray crystallography DNA doesn’t look like what you think!  Watson & Crick used that information to model the structure of DNA as a double helix The Structure of DNA Nitrogenous bases (A, T, G, C) Nucleotide (=monomer unit)  The Structure of DNA They are side by side but The two strands of the run in opposite directions double helix are anti-parallel – like headlights and in orientation taillights in traffic!  The Structure of DNA  The two strands of DNA are complimentary to one another Bases pair in a ◦ Bases pair with complementary way each other in a A with T complementary G with C way such that AT and G C DNA Replication: When and how does DNA make more of itself?  When: DNA Replication  Recall: when a cell divides through mitosis, each daughter cell gets an identical copy of all chromosomes/DNA, made during S phase of Interphase Q: How is a double-helix of DNA used to make another exact duplicate of that DNA?  How: DNA Replication  The two strands of DNA are complimentary to one another Bases pair in a ◦ Bases pair with complementary way each other in a A with T complementary G with C way such that AT and G C  How: DNA Replication  The DNA molecule pulls apart using the enzyme DNA helicase and uses each strand as a template to make a new copy of the DNA molecule  The enzyme DNA polymerase is used to add new nucleotides (base + sugar-phosphate backbone) to build the molecule  Each new DNA molecule contains one old strand and one new strand of DNA  How: DNA Replication  This is known as semi-conservative replication  The two DNA copies will then have an identical sequence of bases and are divided equally into two daughter cells A DNA Two DNA molecule molecules How: DNA Replication Watch the video linked below to visualize the process of DNA replication  DNA Repair  While a new strand of DNA is being made, mistakes can happen but are proofread  If an error isn’t corrected, repairing can be used: ◦ Mismatch repair – incorrect base pair is removed, replaced with correct base ◦ Nucleotide excision repair – thymine dimers can result from UV exposure (T-T bonds, rather than T-A) – these are removed and repaired  Those with nucleotide excision repair gene flaws have extreme sunlight sensitivity  skin cancer  If errors are not corrected  mutation may result  How Does DNA Work?  Early studies suggest that DNA and its genes made enzymes – but how? ◦ Genes are made of DNA ◦ Genes are used to make RNA  There are several types of RNA (=messenger, transfer, ribosomal) ◦ RNA is used to make proteins This is called the Central Dogma of Molecular Biology DNA  RNA  Proteins Why are Proteins So Important?  Protein synthesis is one of a cell’s most energy- consuming metabolic processes  Proteins account for more mass than any other component of living organisms (except for water)  Proteins provide a wide variety of cell functions  The Central Dogma: DNA to RNA to Protein What are the processes that make this happen? The process of transcription The process of translation Watch for an overview of the steps of protein synthesis  What is RNA?  Both DNA and RNA are linear nucleotide polymers = nucleic acids  But RNA has several structural differences:  It is single-stranded (vs. double-stranded like DNA)  It has a ribose as a sugar (vs. deoxyribose)  It has the base uracil (U) instead of thymine (T)  The Central Dogma: DNA to RNA to Protein The genetic code is used as information from gene  protein in two steps: Transcription Process of making mRNA from DNA Occurs in the nucleus Translation Process of making proteins from mRNA Occurs on ribosomes in the cytoplasm  The RNA Players in Gene  Protein: Three Types of RNA  Messenger RNA (mRNA) ◦ Made from DNA during transcription – DNA is used as a template ◦ Contains a nucleic acid sequence that can be interpreted by the ribosomes to make proteins ◦ Includes U instead of T  Ribosomal RNA (rRNA) ◦ Used in translation – is what ribosomes are made of  Transfer RNA (tRNA) ◦ Used in translation to bring correct amino acids to ribosome to make proteins Transcription: Making mRNA from DNA  DNA is unwound to expose the DNA sequence (=gene) from which to make a protein. Then: ◦ Single-stranded mRNA is made is made ◦ RNA polymerase enzyme is used to build the new mRNA molecule ◦ Complementary base pairing rules are followed (G- C, A-U instead of A-T) to make this new mRNA Transcription: Making mRNA from DNA Of the two strands of DNA: --One functions as the (complimentary) template strand, used to make the new mRNA --The other strand is called the coding strand  Introns: Non-coding DNA  Introns are non-coding regions of genes that removed after transcription  The exons are connected to produce the mature mRNA that leaves the nucleus and will be used in translation  Transcription: A Recap DNA mRNA Translation: mRNA to Amino Acids How to get from an mRNA sequence to amino acids that will link to make proteins?  At the ribosome, mRNA is translated into the correct sequence of amino acids to build a protein ◦ Each group of 3 bases on mRNA is called a codon ◦ A codon represents the base sequence that corresponds to a particular amino acid  Translation: mRNA to Amino Acids  Amino acids are then added one at a time and bonded together in the sequence dictated by mRNA in order to make a protein  But how to get from codon to amino acid? ◦ The genetic code provides the rules to get from codon to amino acid – Is the same for all living things! The genetic code is like the Rosetta Stone: the codebreaker used to translate between languages (Hieroglyphics and Greek) Translation: mRNA to Amino Acids How to get from codon to amino acid?  There are 64 possible codons ◦ Codons are made of 3 bases, each with four possibilities per base position (A, U, G, C)  4 x 4 x 4 = 64  But, there are only 20 amino acids ◦ The code is redundant – there is more than one codon per amino acid ◦ So there is more than one way for each amino acid to be coded for  The Genetic Code While reading a sequence of mRNA:  The codon that initiates translation is AUG  Three codons have no amino acid ◦ Are called stop codons - UAA, UGA, UAG How to read a codon chart  The Genetic Code Let’s practice with codons  amino acids using the genetic code chart! Find: CCU AGG UCA UGA your understanding!  Translation: RNA to Protein  At the ribosome: Amino acid  Ribosome holds mRNA – begins at the start codon tRNA molecule  A tRNA molecules arrive at the ribosome, carrying the tRNA anticodon correct amino acid ◦ How does this tRNA know mRNA where to go? ◦ It has an anticodon that Ribosome recognizes the specific codon of mRNA  tRNA continues to build one Then the new protein (called amino acid at a time until the a polypeptide) is then stop codon is reached released from ribosome Translation: A Recap  From gene  protein: an overview Eukaryotic Genome & Gene Regulation Check what you know! Try the Amoeba Sisters interactive EdPuzzle quiz on protein synthesis - click on the image below to start! Complete this organizational table for the processes of transcription & translation Transcription Feature Translation Where does it occur? What nucleic acids are involved? What is the end product/ result?  What Are Mutations?  Mutations are changes that occur in the DNA sequence  This DNA sequence change can cause changes in mRNA sequence which can lead to incorrect proteins ◦ Even if the mRNA sequence changes, it might not result in a problem  This is due to the redundancy of the genetic code (one amino acid has more than one codon that represents it)  Types of Mutations  Substitution mutation: ◦ A single base change in DNA ◦ Can cause a change in a single amino acid ◦ May result in an incorrect protein, OR ◦ This change can be a silent mutation (=neutral)  Sickle Cell Disease: Substitution Mutation  Sickle cell disease results from a single-base mutation on DNA ◦ Results from a base pair substitution that causes one amino acid change ◦ This results in faulty hemoglobin protein that causes sickle-shaped RBCs  Types of Mutations  Frameshift mutation:  Occurs when a single base is added or deleted  Usually destroys the protein because it changes many amino acids ◦ Changes shape and function of protein  If this adds a stop codon: synthesis is halted, protein is truncated at that point Example of a Frameshift Mutation THE DOG ATE THE RAT Deleted base TH DOG ATE THE RAT THD OGA TET HER AT  Genetic Variation in Life  Individuals have slight differences in the sequence of nucleotides (the nitrogenous bases A, T, G, C) for a given gene ◦ This info can be used to distinguish/ID individuals  But, different species have greater differences between them than those seen within a species ◦ This also provides info about evolution and shared inheritance (more in Chapter 11!) From Gene to Phenotype: An Overview  Genes are inherited as DNA – the blueprint  DNA is transcribed into RNA  RNA is translated into protein  Proteins give the organism traits – a phenotype ◦ Mutations in DNA produce changes in traits Chapter 9 Review Questions  Self-Check Concept Quiz Which of the following does Cytosine pair with? A. Guanine B. Adenine C. A pyrimidine D. Thymine A  Self-Check Concept Quiz Which of the following statements best describes RNA? A. RNA does not leave the cell nucleus. B. RNA is a double-stranded nucleic acid polymer. C. RNA contains the base Uracil. D. RNA is a circular molecule. C  Self-Check Concept Quiz Which of the following statements is not correct regarding the genetic code? A. It is based on codons that are made of three bases. B. There are 64 possible codons. C. Amino acids can have more than one codon. D. Every codon has a corresponding amino acid. D  Self-Check Concept Quiz Which of the following statements correctly describes a process associated with protein synthesis? A. Transcription occurs in the cytoplasm and produces RNA. B. Transcription occurs in the nucleus and produces proteins. C. Translation occurs in the cytoplasm and produces proteins. D. Translation occurs in the nucleus and produces RNA. C  Self-Check Concept Quiz Which of the following statements describe a substitution mutation? (select all that apply): A. A part of the chromosome is missing B. One base is changed to another C. The structure of the protein may not be changed D. The entire sequence of amino acids is changed B, C  Short Answer Review Questions 1.) The DNA double helix is described as having an anti-parallel orientation. What does this mean? What is meant by the semi-conservative process of DNA replication? 2.) Be able to apply the genetic code table (as we did with the example in class and the slide here) to a DNA sequence in order to find the mRNA sequence, codons and resulting amino acids. 3.) Complete the comparison table (completed in class and on the slide here) for the processes of transcription and translation.  Short Answer Review Questions 4.) What is a mutation? What are the differences between substitution and frameshift mutations? What type of mutation is responsible for sickle cell disease? Explain how this mutation influences the function of the resulting protein.