Biology Ch. 17- Molecular Genetics 17.1 Isolating the Genetic Material

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1 Biology Ch. 17- Molecular Genetics 17.1 Isolating the Genetic Material Scientists who contributed to the development of our modern understanding of DNA and genomes: 1) Gregor Mendel early studies on genetics 2) Sutton and Boveri discovered the link between behavior of chromosomes during meiosis and Mendel s factors 3) Phoebus Levene isolated DNA and RNA and studied their properties 4) Griffith discovered the principle of transformation in bacteria (see fig 17.6, p. 570) transforming principle: genetic information that can be transferred. In 1928, Fred Griffith discovered that dead pathogenic (disease-causing) bacteria could pass on their pathogenic properties to live non-pathogenic bacteria Griffith died before discovering what the transforming factor was 5) MacLeod, McCarty, and Avery isolated the transforming factor in bacteria as DNA. This was the first evidence that DNA was the hereditary material (it was believed that protein was the hereditary material at the time) 6) Hershey and Chase finally demonstrated that DNA was the genetic material used radioactively labeled DNA and protein phages (viruses that attack bacteria). Infected bacteria with these phages and tracked whether it was the DNA or protein that entered the cell and caused the viruses to reproduce. Found that only the DNA entered the cell while the protein stayed outside. Therefore, DNA must be hereditary material. (see fig 17.8, p. 571) 7) Erwin Chargaff studies DNA structure. Found several things: the nucleotide composition of DNA varies from one species to another the nucleotide composition of DNA specimens taken from different animals of the same species is fairly constant in DNA, the amount of adenine is always equal to the amount of thymine and the amount of guanine is always equal to the amount of cytosine (Chargaff s rule) 8) Rosalind Franklin and Maurice Wilkins studied DNA structure found two distinct but regular repeating patterns in the structure of DNA also found that nitrogen bases must be located inside molecule because of how it reacts with water 9) James Watson and Francis Crick developed the current model of DNA structure

2 The Components of Nucleic Acids Nucleotide the monomers of nucleic acids. Each nucleotide is composed of a five-carbon sugar, a phosphate group and one of four nitrogen-containing bases DNA stands for deoxyribonucleic acid consists of long chains of individual nucleotides, each of which is composed of a five carbon sugar (deoxyribose), a phosphate group, and the nitrogen bases adenine, thymine, guanine, and cytosine. double-stranded (2 chains of nucleotides) RNA stands for ribonucleic acid consists of long chains of nucleotides, each of which contains a phosphate group, a five carbon sugar (ribose), and the nitrogen bases adenine, uracil, guanine, and cytosine single-stranded (1 chain of nucleotides) (see fig 17.4, p. 569) 17.2 The Structure of Nucleic Acids DNA The Double Helix (see fig and 17.13, pp ) Purines nitrogenous compounds that have a double-ring structure. The nucleotide bases adenine and guanine are derived from purines and always bind with pyrimidines in DNA Pyrimidines nitrogenous compounds that have a single-ring structure. The nucleotide bases thymine, uracil, and cytosine are derived from pyrimidines and always bind with purines in DNA If a DNA molecule was unwound, it would resemble a ladder. The sugar and phosphate groups would form the outside while the paired nitrogen bases would form the rungs. Complimentary base pairings pairing of bases between nucleic acid strands. The two strands of a DNA helix are complimentary with each other. Each purine base pairs with a pyrimidine base on the other side. A binds with T (2 hydrogen bonds) C binds with G (3 hydrogen bonds) Antiparallel describes the property by which the 5 to 3 phosphate bridges run in opposite directions on each DNA strand In essence, one DNA strand is upside down compared to the other one. This is necessary to allow the nitrogen bases to bind together correctly

3 Organization of Genetic Material Prokaryotic cells usually a single, double stranded DNA molecule nucleoid: area within prokaryotic cells where the DNA is found plasmid : small, self-replicating loop of DNA in a prokaryotic cell that is separate from the main chromosome and contains from one to a few genes. Plasmids often carry information that gives the cell resistance to certain antibiotics and heavy metals or the ability to break down unusual compounds Eukaryotic cells each human cell has about 2 m of DNA, yet it is packaged into a relatively small area histone: complex of small, very basic polypeptides that form the core of nucleosomes, around which DNA is wrapped nucleosome: the bead-like structural unit of chromosomes, composed of a short segment of DNA (about 200 base pairs) wrapped twice around a cluster of eight histone molecules. Genes and Genomes Gene a specific sequence of DNA that governs the expression of a particular trait and can be passed to an offspring Genome the sum of all the DNA in an organism s cells Exons the coding region of a eukaryotic gene. Each gene is composed of one or more exons Introns intervening non-coding sequences in a eukaryotic gene 17.3 DNA Replication The process of replication follows a semi-conservative model; when a molecule of DNA is copied, each new molecule contains one strand of parental DNA and one strand of new DNA Replication machine complex involving dozens of different enzymes and other proteins working together in the process of DNA replication Stages of Replication 1) Initiation (see fig 17.21, p. 583) replication starts at specific parts of a DNA molecule called replication origins (could be thousands at a time) involves several enzymes and steps

4 primer short strand of RNA that works as a starting point for the attachment of new nucleotides during DNA replication primase in DNA replication, an enzyme that forms a small RNA primer that is complimentary to the DNA sequence. helicases set of enzymes that cleave and unravel short segments of DNA just ahead of the replicating fork during DNA replication DNA polymerase during DNA replication, an enzyme that slips into the space between two strands, uses the parent strands as a template, and adds nucleotides to make complimentary strands replication fork during DNA replication, point at which the DNA helix is unwound and new strands develop 2) Elongation (see fig and 17.23, pp ) since the two strands are antiparallel, their replications occur differently leading strand in DNA replication, the strand that is replicated continuously in the 5 to 3 direction (in the same direction as the movement of the replication fork) lagging strand in DNA replication, the strand that is replicated by splicing together Okazaki fragments in the 5 to 3 direction (moving opposite to the replication fork) Okazaki fragments short-nucleotide fragments used during DNA replication on the lagging strand. They are made by DNA polymerase working in the direction opposite to the movement of the replication fork, after which they are spliced together. DNA ligase enzyme that splices together Okazaki fragments during DNA replication on the lagging strand. DNA ligase catalyses the formation of phosphate bonds between nucleotides. 3) Termination (see fig 17.24, p. 585) once the new strands are formed, the daughter DNA molecules rewind into helices automatically (no enzymes required) telomere specialized non-transcribed structure typically rich in G nucleotides, at the end of each chromosome. The use of telomeres protects us against the loss of genetic material during replication Proofreading and Correction DNA polymerase checks to see if base pairs are paired correctly. If there is a mistake, DNA polymerase will remove the incorrect base and insert the correct one.

5 17.4 Protein Synthesis and Gene Expression gene expression the transfer of genetic information from DNA to protein As described earlier, DNA is the genetic material in living things which gives the blueprint of how an organism develops. This blueprint, however, has to be put into a useful or structural form. In most living things, the main structural molecule is protein. Hence, DNA provides the blueprint for all the different proteins found in living organisms Examples of protein structures: 1) skeletal muscle tissue 4) enzymes 2) smooth muscle tissue 5) transporters in cell membranes 3) hormones However, DNA is not directly used to make protein. Instead, DNA is copied to RNA, and RNA is used to make protein. This leads us to the central dogma of gene expression, proposed by Francis Crick: DNA RNA protein The use of DNA to produce RNA is called transcription. The use of RNA to make protein is called translation. The Genetic Code Recall that in humans there are 20 amino acids (the basic units of proteins). However, there are only 4 different nucleotides. Therefore, if it only took 1 nucleotide to code for 1 amino acid only 4 amino acids could be produced. If 2 nucleotides in a row coded for 1 amino acid, you still could not code for all 20 amino acids (only 16 possible combinations). It takes combinations of 3 nucleotide sequences to code for 1 amino acid Codon the basic unit, or word, of the genetic code. It is a set of 3 adjacent nucleotides in DNA or mrna that codes for amino acid placement on polypeptides. (see table 17.2, p. 590) Characteristics of the genetic code more than one codon can code for an amino acid ex. UCA, UCU, UCG, and UCC all code for serine it is continuous (no spaces or overlap) universal code is almost the same in all living things Transcription (see fig 17.28, p. 591) The main job of transcription is to make a RNA copy of a small section of the organism s DNA (the particular gene needed to make a specific protein)

6 Messenger RNA (mrna) strand of RNA that carries genetic information from DNA to the protein synthesis machinery of the cell during transcription RNA polymerase main enzyme that catalyses the formation of mrna from a DNA template Sense strand strand of nucleotides containing the instructions that direct protein synthesis. It is located within a stretch of DNA that includes a gene Antisense strand strand of nucleotides that is complimentary to the sense strand (not transcribed) Steps in Transcription 1) Initiation RNA polymerase binds to a particular sequence of nucleotides in the sense strand RNA polymerase opens up the double helix and begins inserting complimentary nucleotides 2) Elongation proceeds in the 5 to 3 direction (no Okazaki fragments) as the polymerase molecule proceeds, the DNA helix reforms and the mrna molecule separates from the template DNA strand 3) Termination and processing the RNA polymerase proceeds until it reaches a signal to stop and the RNA polymerase and mrna completely separate from the DNA molecule a special sequence of nucleotides is added to the 5 and 3 ends introns are spliced out (removed), leaving only the exons the mrna is transported out of the nucleus. Translation (see fig 17.29, p. 593) Translation occurs outside the nucleus in eukaryotic cells, and involves several elements in order to occur. Transfer RNA (trna) RNA molecules that serve to link each codon along a mrna strand with its complimentary amino acid. Transfer RNA has an unusual structure. They have a cloverleaf shape (single-stranded), and contain an anticodon. Anticodon specialized base triplet located at one lobe of a trna molecule that recognizes its complimentary codon on an mrna codon. At the 3 end of a trna is an amino acid transport site. Ribosomes tiny two part structures found in the cell s cytoplasm and attaches to the rough endoplasmic reticulum that helps to put together proteins. They bring together the mrna strand, trna molecules carrying amino acids, and the enzymes involved in building proteins.

7 Ribosomal RNA (rrna) most common class of RNA molecules. During protein synthesis, these RNA molecules supply the site on the ribosome where the polypeptide is assembled. The Translation Cycle 1. mrna binds to an active ribosome in such a way to expose two adjacent codons. 2. The first trna molecule (carrying the amino acid methionine) binds to the codon AUG (start codon). 3. A second trna molecule carrying an amino acid arrives at the codon adjacent to the first trna. 4. Enzymes catalyze the formation of a peptide bond that joins the amino acid carried by the first trna to that carried by the second trna. At the same time, the polypeptide chain is transferred from the first trna to the second. 5. The ribosome moves a distance of one codon along the mrna strand. The first trna molecule detaches from the mrna and goes to pick up another amino acid. The second trna now holds a growing polypeptide chain. A third trna molecule arrives at the exposed codon next to the second trna and the cycle repeats. 6. When a stop codon is reached (UAG, UGA, UAA), the completed protein is released and the ribosome assembly comes apart. Regulating Gene Expression The rates of transcription and translation can be controlled to adjust to environmental conditions. For example, artic foxes have white fur in winter, but brown in warmer temperatures. Mutations Factors that affect transcription and translation in living cells: 1) changes in temp. or light 2) the presence or absence of nutrients in the environment 3) the presence of hormones in the body. Mutation in cellular reproduction, permanent change in the DNA molecule that can change the information of a gene, causing the gene to function improperly or not at all. Germ cell mutation permanent change in the genetic material in a reproductive cell of an organism. They can be passed on to offspring

8 Somatic cell mutation permanent change in the genetic material in a body cell. These mutations are not passed on to offspring. Types of mutations Point mutation chemical change that affects one or just a few nucleotides. Includes substitutions and frame-shift mutations. Chromosome mutation change in the number or structure of a chromosome. Includes nondisjunction, deletion, insertion, inversion, duplication, and translocation (see section 16.3 of notes) Point mutations: 1) substitution one or more nucleotides are substituted for a different nucleotide (see f ig 17.32, p. 597) i. silent mutation permanent change in the genetic material that has no effect on the metabolism of the cell ii. mis-sense mutation permanent change in the genetic material of a cell that results in slightly altered but still functional protein. iii. nonsense mutation permanent change in the genetic material of a cell that renders a gene unable to code for any functional polypeptide product 2) frame-shift mutation permanent change in the genetic material of a cell caused by the insertion or deletion of one or two nucleotides within a sequence of codons. Usually, a frame-shift causes a nonsense mutation (see fig 17.33, p. 597) transposons segments of DNA that move randomly throughout the cell s genome. Also called jumping genes. Discovered by Barbara McClintock. Causes of Mutations Spontaneous mutations occur naturally within cells Induced mutations caused by a mutagen introduced into the cell Mutagen substance or event that increases the rate of mutation in an organism. May be physical or chemical. Physical mutagen agent that forcibly breaks a nucleotide sequence and causes changes to one or both strands of a DNA molecule Ex. X-rays, UV radiation Chemical mutagen molecule that can enter the cell nucleus and induce a permanent change in the genetic material of a cell.

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