Gene Expression & DNA Replication Notes PDF

# AAAAA Ch 4 ppt COMPLETE ## Overview of Gene Expression * During transcription, the base sequence in DNA is copied into a base sequence in mRNA. * During translation, tRNAs bring amino acids to ribosomes in an order determined by the sequence of codons in the mRNA. ## Ribosomes and Ribosomal RNA...

# AAAAA Ch 4 ppt COMPLETE ## Overview of Gene Expression * During transcription, the base sequence in DNA is copied into a base sequence in mRNA. * During translation, tRNAs bring amino acids to ribosomes in an order determined by the sequence of codons in the mRNA. ## Ribosomes and Ribosomal RNA * As ribosomes move along the mRNA, new tRNAs enter and the amino acids bond together, forming a protein. * Several ribosomes translate an mRNA at one time, forming a polyribosome ## Translation Requires Three Steps * During translation, codons on the mRNA base pair with anticodons on the tRNAs that are carrying specific amino acids. The order of the mRNA codons determines the sequence of amino acids in the protein being synthesized. * Translation is an orderly process that must produce a protein of a particular sequence. It involves three main steps: * initiation (requires energy) * elongation (requires energy) * termination (does not require energy) ## Initiation * Initiation involves assembly of components (initiation factors, small and large ribosomes, and mRNA), a start codon, AUG, on the mRNA, and amino acid methionine initiator tRNA. * A small ribosomal subunit binds to mRNA; an initiator tRNA pairs with the mRNA start codon AUG * The large ribosomal subunit completes the ribosome * Initiator tRNA occupies the P site. The A site is ready for the next tRNA. ## Elongation * Elongation is the protein synthesis step, when a polypeptide increases in length one amino acid at a time. Four steps are repeated until a codon that signals to stop is reached. 1. A tRNA-amino acid approaches the ribosome and binds at the A site. 2. Two tRNAs can be at a ribosome at one time; the anticodons are paired to the codons. 3. Peptide bond formation attaches the peptide chain to the newly arrived amino acid. 4. The ribosome moves forward; the "empty" tRNA exits from the E site; the next amino acid-tRNA complex is approaching the ribosome. ## Termination * Termination is the final step in protein synthesis. * A stop codon on the mRNA indicates where termination occurs * A release factor cleaves the new protein from the tRNA * Components for translation disassemble * The protein begins to fold into its proper shape. ## Replication at the Molecular Level 1. DNA helicase enzyme separates the DNA strands by breaking the hydrogen bonds between bases. 2. DNA polymerase enzyme catalyzes incorporation of new nucleotides by complementary base pairing. 3. DNA polymerase can only add nucleotides to one end of the growing chain. Therefore, replication is different for each strand. Leading strand synthesis follows the helicase enzyme. Lagging strand synthesis results in formation of Okazaki fragments. 4. DNA ligase connects the Okazaki fragments and seals any breaks in the sugar-phosphate backbone. ## Check Your Progress 1. Explain why DNA replication is said to be semiconservative? 2. Summarize the sequence of events that occur during DNA replication. 3. Describe the key enzymes involved in DNA replication. ## Messenger RNA * In eukaryotes, the primary mRNA is processed to mature RNA before it is exported from the nucleus to cytoplasm. * Introns of the mRNA are removed, and the remaining sections of DNA to be translated, called exons, are joined. * A cap is added to one end of the mRNA, and a poly-A tail is added to the other end of the mRNA. ## Translation * Translation is the second process in gene expression. It requires several enzymes and different types of RNA molecules that include mRNA, rRNA, and tRNA. * Translation relies on the genetic code to convert mRNA sequence to the amino acid sequence of a protein. The genetic code: * consists of triplets of RNA nucleotides called codons * has codons that code for amino acids * is degenerate and almost universal (suggesting it dates back to first organisms on Earth and a common evolutionary history) ## Transfer RNA * The transfer RNAs (tRNAs) bring amino acids for protein synthesis to the ribosomes. * Each tRNA is single-stranded and folds back on itself to form a boot-like shape. * One end has an amino acid. * The other end has an anticodon that is complementary to an mRNA codon. ## The Genetic Code * Although there are 64 different codons, there are only 40 different tRNA molecules. This is because the third nucleotide in some mRNA codons can vary, which is called the wobble effect. * For translation, the anticodons of tRNA-amino acid complexes pair with mRNA codons. * If the mRNA codon is CGG, what is the tRNA anticodon and amino acid attached to it? * Codon (mRNA): CGG * Anticodon (tRNA): GCC * Amino Acid (protein): Arginine ## Gene Expression relies on different forms of the nucleic acid RNA (ribonucleic acid). The most important are: * messenger RNA (mRNA) * transfer RNA (tRNA) * ribosomal RNA (rRNA) ## Processes of Gene Expression * **Transcription**: mRNA is synthesized from a DNA template (in eukaryotes it takes place in the nucleus) * **Translation**: Protein is synthesized from an mRNA template (in eukaryotes it takes place in the cytoplasm) * Genetic information lies in the sequence of DNA bases, which is transferred to the sequence of bases in mRNA. This is translated to an amino acid sequence of a protein, which determines the protein’s structure and function. Proteins determine the phenotype of an organism. ## Termination * Termination is the final step in protein synthesis. * A stop codon on the mRNA indicates where termination occurs. * A release factor cleaves the new protein from the tRNA. * Components for translation disassemble. * The protein begins to fold into its proper shape. ## Review of Gene Expression * A gene is expressed when a protein it codes for is made. It involves: * **Transcription**: * DNA serves as a template for mRNA synthesis. * Bases in mRNA are complementary to the DNA. * Each codon in mRNA is a triplet. * **In eukaryotes, the mRNA is processed and transported to the cytoplasm.** * **Translation**: * tRNAs with amino acids pair with mRNA codons until the protein is synthesized ## Review of Gene Expression * **Transcription**: * DNA in nucleus serves as a template for mRNA. * mRNA is processed before leaving the nucleus. * mRNA moves into cytoplasm and becomes associated with ribosomes. * tRNAs with anticodons carry amino acids to mRNA. * Anticodon-codon complementary base pairing occurs. * Polypeptide synthesis takes place one amino acid at a time. ## Causes of Mutations * Errors in replication are mistakes made while DNA is copied. These are rare (1 mistake per billion nucleotide pairs). * Mutagens are environmental factors, such as radiation, X rays, and some chemicals, that cause mutations. * Transposons are DNA sequences that move within and between chromosomes. Transposons can “jump” into another gene, causing a change in gene expression. ## Effect of Mutations on Protein Activity * Gene mutations can have a range of possible effects on protein activity, from no effect to complete inactivity or even lack of production at all. * A point mutation is a single nucleotide change. It can cause: * no change in amino acid sequence * a change in amino acid sequence that produces a protein that does not function properly * introduction of a stop codon, which shortens the protein ## Structure of DNA * DNA is a chain of nucleotides. * Each nucleotide consists of a phosphate group, a deoxyribose sugar, and a nitrogen-containing base. * There are four bases: * two purines, adenine (A) and guanine (G) * two pyrimidines, cytosine (C) and thymine (T) ## Structure of DNA * A DNA strand has a backbone of alternating phosphate and sugar molecules. * Two DNA strands twist about each other, forming a double helix. * Purines and pyrimidines on opposite strands form hydrogen bonds in complementary base pairing (A-T, G-C). ## DNA Replication * When cells divide, each new cell requires a copy of the DNA. * DNA replication: * Is the copying of one double helix into two identical double helices, which are also identical to the original. * Is semiconservative (each new double helix has one original strand and one newly synthesized strand). ## Review of Gene Expression (quick intro) * **Transcription**: * DNA in nucleus serves as a template for mRNA. * mRNA is processed before leaving the nucleus. * mRNA moves into cytoplasm and becomes associated with ribosomes. * tRNAs with anticodons carry amino acids to mRNA. * Anticodon-codon complementary base pairing occurs. * Polypeptide synthesis takes place one amino acid at a time. ## Transcription * A gene is a segment of DNA that acts as a template for RNA. * **Messenger RNA (mRNA)** is formed by transcription. * Transcription begins by RNA polymerase binding to a promoter on DNA. * RNA polymerase catalyzes incorporation of RNA nucleotides that are complementary to the DNA. * The mRNA formed has a sequence of bases that is complementary to the DNA strand that was the template for transcription. ## Transcription * During transcription, complementary RNA is made from a DNA template. * At the point of attachment of RNA polymerase, the DNA helix unwinds and unzips, and complementary RNA nucleotides are joined together. * After RNA polymerase has passed by, the DNA strands rejoin, and the mRNA transcript is released. ## The Polymerase Chain Reaction (PCR) * The polymerase chain reaction (PCR) is a way of making billions of copies of a segment of DNA in a test tube. PCR involves three steps that are repeated many times in cycles. * Denaturation: The DNA is heated to 95°C, and it becomes single-stranded. * Annealing: The temperature is lowered to 50-60°C, and primers are added that base pair to the DNA to be copied. * Extension: At 72°C, DNA polymerase used for PCR adds nucleotides to the ends of the primers. Eventually both DNA strands are copied and new double-stranded DNA forms. ## The Polymerase Chain Reaction * PCR is a chain reaction because the DNA is repeatedly copied. The amount of DNA doubles with each cycle. ## DNA Analysis * PCR has numerous applications, which includes identification of people based on their DNA fingerprint. * Short tandem repeat (STR) profiling identifies individuals according to how many repeats of a DNA sequence he or she has at a particular STR locus. ## Check Your Progress 1. Explain the roles of mRNA, RNA, and rRNA in gene expression. 2. Describe the movement of information from the nucleus to the formation of a functional protein. 3. Discuss why the genetic code is said to be degenerate. ## 4.4 Gene Mutations and Cancer * A gene mutation is a permanent change in DNA sequence. * Germ-line mutations occur in sex cells and can be passed on to future generations. * Somatic mutations occur in body cells and are not passed on to future generations. * Both types of mutations may lead to the development of cancer. ## Causes of Mutations * Errors in replication are mistakes made while DNA is copied. These are rare (1 mistake per billion nucleotide pairs). * Mutagens are environmental factors, such as radiation, X rays, and some chemicals, that cause mutations. * Transposons are DNA sequences that move within and between chromosomes. Transposons can “jump” into another gene, causing a change in gene expression. ## Recombinant DNA Technology * Gene cloning involves introducing a gene into a vector (often a plasmid) to produce recombinant DNA (rDNA). * A restriction enzyme cleaves the vector and the gene, which combine by base pairing between the “sticky ends”. ## Products of genetic engineering: * Gene Splicing allows scientists to remove or insert specific genes into hereditary material. * Steps: * A plasmid is removed from a bacterium. * The plasmid is broken at one point. * DNA molecules from a plant or animal cell are broken into fragments (a specific gene or genes) by restriction endonuclease. * The DNA fragment is spliced (glued back together) into the broken plasmid. The plasmid bow contains “RECOMBINANT DNA” (a gene or genes from another organism have been added to its own genes). * The plasmid is put into the bacterium. * The bacterium undergoes cell division many times, making copies of itself and copies of that recombinant DNA which will produce the desired result/product (insulin, growth hormone, insect hormones/pheromones...). ## Recombinant DNA Technology * DNA ligase is the enzyme that seals the gene and vector DNAs. * The rDNA is added to an organism such as bacteria, which makes many copies of the gene. ## Characteristics of Cancer Cells: * Cancer cells are genetically unstable. Tumor cells have multiple mutations and can have chromosomal changes. * Cancer cells do not correctly regulate the cell cycle. The rate of division and number of cells increases. * Cancer cells escape the signals for cell death. Normal cell signals for programmed cell death do not occur. * Cancer cells can survive and proliferate elsewhere in the body. Invasion of new tissues can occur (metastasis), which includes new blood vessel formation (angiogenesis). ## DNA Cloning * Genetic engineering involves altering the genome or genetic material of an organism. This often involves gene cloning, which is the production of copies of a gene. Gene cloning is done to: * study what biological functions a gene is associated with * produce large quantities of protein * produce transgenic organisms * help cure human diseases ## Recombinant DNA Technology * Gene cloning involves introducing a gene into a vector (often a plasmid) to produce recombinant DNA (rDNA). * A restriction enzyme cleaves the vector and the gene, which combine by base pairing between the "sticky ends". ## What is the sequence of bases that would normally be bonded to this section of the DNA molecule? - C-A-T-G-T-A-C ## Name the enzymes associated with DNA replication and state their function? - DNA helicase unzips the double helix. - DNA polymerase adds new nucleotides to the strand. - DNA ligase seals the gaps between Okazaki fragments. ## Explain why Okazaki fragments are formed during replication? - DNA Polymerase can only add nucleotides to the 3' end of a strand. Because DNA is antiparallel, one of the strands is synthesized in the direction opposite of the replication fork (away from the origin of replication) making synthesis discontinuous. This results in short fragments of DNA called Okazaki fragments. ## The mRNA codon A-U-C codes for the amino acid isoleucine. What is the base sequence of DNA molecule that is complementary to this codon? - T-A-G ## The mRNA codon AAA codes for leucine. What is the tRNA anticodon? - UUU ## Given the DNA sequence TACTTCAAACCG, what would most likely happen to the protein that it codes for if there was a change in the last three subunits on this strand so that the last 3 nitrogenous bases were CCC instead? The last three subunits on the strand would code for proline instead of glycine. The protein could have an altered conformation and function as a result. ## Given the DNA sequence TACTTCAAACCG, what would most likely happen to the protein that it codes for if there was a change in the last three subunits on this strand so that the last 3 nitrogenous bases were ATC instead? - The last three subunits on the strand would code for a stop codon instead of glycine. The protein would be incomplete and non-functional. ## If the anticodon on a tRNA is CAG, what is its associated amino acid that it brings to the ribosome? - Glutamine ## If the anticodon on a tRNA is UAC, what does this signal to the ribosome? - It signals that the tRNA carries the amino acid tyrosine. ## What would be the associated DNA code for the anticodon CAG? - GTC ## What would be the associated DNA code for the codon AAG? - CTT ## What is the codon associated with anticodon GAC? - CUG ## What is the amino acid associated with the anticodon UUU? - Phenylalanine ## How many amino acids are brought to the ribosome given the mRNA sequence GUCUCGUACGUA? - 4 amino acids ## What kind of bonds hold the amino acids together in the resulting protein? - Peptide bonds ## (a)What kind of bonds hold the nitrogenous bases together in a DNA? (b)How many bonds are between Adenine and Thymine and (c) How many bonds between Cytosine and Guanine? - (a) Hydrogen bonds - (b) Two bonds - (c) Three bonds ## What would happen to a protein if there were a mutation in a DNA code from GTA to ATC? - The amino acid would change from Glutamic Acid to Isoleucine. The effect of the mutation would depend on what position this mutation occurs in the protein, but it could have a significant effect on its structure and function. ## A tRNA molecule with the anticodon GAG would carry which amino acid? - Glutamic acid. ## A polypeptide chain with 10 amino acids is released from the ribosome after translation is terminated. How many nucleotides were on the mRNA that coded for this polypeptide? - 30, because each codon is 3 nucleotides long. ## How many peptide bonds are required for a protein that is 9 amino acids long? - 8, because it takes 8 peptide bonds to link 9 amino acids together. ## Chapter 4 Test Preparation **Goal #1 Students will understand the process of DNA replication. ** **Vocabulary to know**: complementary base pairing, DNA helicase, DNA polymerase, nucleotides, recombinant DNA, replication, semi-conservative replication **Learning Objectives**: Describe DNA replication: - describe the three steps in the semi-conservative replication of DNA: - "unzipping" (DNA helicase)- complementary base pairing (DNA polymerase)- joining of adjacent nucleotides (DNA ligase) and sealing of the Okasaki fragments - describe the purpose of DNA replication - identify the site of DNA replication within the cell - describe semi-conservative DNA replication **Learning Objective: Understand and describe Recombinant DNA** - define recombinant DNA, name the enzymes involved in the process and draw how recombinant DNA is made - describe a minimum of three uses for recombinant DNA **Goal #2 students will understand the process of protein synthesis.** **Vocabulary to know**: amino acid, anti-codon, codon, DNA sequence (genetic code), elongation, environmental mutagen, genetic disorder, initiation, messenger RNA (mRNA), mutation, polypeptide chain, ribosomes, termination, transcription, transfer RNA (tRNA), translation **Learning Objective:** Demonstrate an understanding of the process of protein synthesis: - identify the roles of DNA, messenger RNA (mRNA), transfer RNA (tRNA), and ribosomes in the processes of transcription and translation, including initiation, elongation, and termination - determine the sequence of amino acids coded for by a specific DNA sequence (genetic code), given a table of mRNA codons and explain how the code is degenerate and universal - identify the complementary nature of the mRNA codon and the tRNA anti-codon **Learning Objective:** Explain how mutations in DNA affect protein synthesis: - give examples of two environmental mutagens that can cause mutations in humans - use examples to explain how mutations in DNA change the sequence of amino acids in a polypeptide chain, and as a result may lead to genetic disorders (like sickle cell anemia) ==End of OCR==