Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure enzymes control cell chemistry ( metabolism )

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1 Biology 1406 Exam 3 Notes Structure of DNA Ch. 10 Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure enzymes control cell chemistry ( metabolism ) Proteins - made of monomers called amino acids - polypeptide chain - many different proteins - each with unique shape and unique function - 20 different amino acids - basic chain with different R groups Levels of structure: primary - amino acid sequence secondary - regular coils and pleats tertiary - loops and bends in polypeptide quaternary - linking of polypeptides sequence final protein shape ( in chemical environment ) and shape determines function (good and bad examples) *What causes secondary, tertiary and quaternary levels? *A genetic mutation can change the function of a protein. How? *What is denaturation? What causes it? *How does it affect the function of a protein? Proteins have many functions determine structure and function of organisms : -enzymes - regulate and speed up chemical reactions - very specific (one enzyme for each reaction) - structural proteins - contractile proteins - antibodies, hormones - transport proteins - plasma membrane proteins (receptors, channels, markers, attachment) - transcription factors (regulate gene expression) Protein Synthesis The genetic code is a code to build proteins, determines amino acid sequence (primary structure) Chromosome - one very long DNA molecule with supporting (histone) proteins Gene - a section of the DNA molecule that codes for one polypeptide chain. A single chromosome contains thousands of genes. Locus - the particular location on a chromosome where a gene is located 8.11 Allele different forms of a gene due to mutations 9.3

2 Nucleic Acids Ch 10, types : Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA) DNA and RNA are polymers made of nucleotides Each nucleotide is made of: - a sugar (ribose in RNA, deoxyribose in DNA) - a phosphate (same in RNA and DNA) - a nitrogen base: - adenine, guanine, cytosine and thymine in DNA - adenine, guanine, cytosine and uracil in RNA (adenine and guanine are double C-N ring molecules) (cytosine, thymine and uracil are single C-N rings) Polymer is a long chain sugar phosphate backbone with nitrogen bases to the side - nucleotides can link in any sequence - sequence of nitrogen basis is information - sequence of nucleotides has a 3 and a 5 end - nucleotides added at 3 end only RNA is a single chain of nucleotides DNA is a double chain of nucleotides cross-linked by nitrogen bases ( double helix or twisted ladder ) -nitrogen bases always link a certain way: - adenine to thymine ( or uracil ) and guanine to cytosine *Why? Give 2 reasons based on the structure of these molecules. - nitrogen bases link by weak hydrogen bonds. *Why is this important? - each sugar-phosphate has 3 and 5 ends - cross-linked chains are antiparallel (opposite ends) *Why is it important that the polymer have distinct ends? *Describe three differences between DNA and RNA *What does the term complementary mean? *Why are nucleic acids said to have a sugar phosphate backbone if each nucleotide monomer is made of three parts?

3 DNA Replication: forming duplicate copies of DNA complex series of reactions directed by enzymes to uncoil helix, break hydrogen bonds between bases, join new nucleotides - possible because nitrogen bases are complementary Guanine Cytosine Adenine Thymine *Why is DNA important to living organisms? *Why is DNA replication important? - new polymer 5 3 (new nucleotides added at 3 end) - bubbles form as DNA is replicated 10.5 *What are these and why do they occur? *What is the function, or job, of DNA polymerase? *What is the function, or job, of DNA ligase? *What is the primary trait of DNA that makes replication possible? *Describe another trait of DNA that is important to this process. The genetic code: Chemical language of DNA into chemical language of proteins - plan to describe amino acid sequence in proteins - 4 nucleotides (nitrogen bases) in DNA - therefore 4 letter alphabet - 20 different amino acids make up all proteins - therefore 20 things to describe If 1 nitrogen base coded for 1 amino acid 4 possible 10.7 If 2 nitrogen bases coded for 1 amino acid 16 possible If 3 nitrogen bases coded for 1 amino acid 64 possible - 3 nucleotides in sequence code for 1 amino acid ( = codon or triplet code) - 64 codons - 20 amino acids, therefore several codons code for the same amino acid. - DNA code is redundant but not ambiguous - no punctuation between codons depends on starting point A T C G C C T A G C A A C T G C T T start and stop codons (mrna) : AUG = start here UAG, UAA, UGA = stop (5 3 ) - DNA and RNA constructed and translated codons are universal; they code for the same amino acid in all living organisms; suggests that all living organisms are from a common ancestor - Recombinant DNA possible because of this.

4 DNA mrna Protein transcription translation Transcription DNA mrna - messenger RNA (mrna) along DNA - only along sense strand of DNA (template strand or transcribed strand) - formed in nucleus, translated in ribosomes in the cytoplasm - complementary RNA nucleotides are assembled along DNA by RNA polymerase - RNA polymerase attaches at promoter and releases at terminator - the mrna is modified before it leaves the nucleus Examples: Translation - ( protein synthesis) occurs in ribosomes in the cytoplasm of the cell using mrna as a template Transfer RNA (trna) carries amino acid molecules to the ribosomes to be assembled into protein - trna has 2 specific binding sites: - anticodon nitrogen bases (1 of 64) - amino acid (1 of 20) Steps in protein synthesis: - begins at the 5 end of mrna - translation begins at first start codon (AUG) on mrna - trna molecule with anticodon that matches codon of mrna is placed in active site of ribosome - amino acid is bonded to amino acid chain and released from trna - proceeds one codon at a time until a stop codon (UAA, UAG, or UGA) is reached (these do not have a trna molecule)

5 Control of gene expression Ch 11 When, where and how much of protein determinesstructure and function of organism - only about 1.5 % of human DNA is translated ( 25,000 genes) - some used to make different types of RNA (mrna, trna, rrna, srna, mirna) - about 3 % of DNA used as switches (regulatory) to control gene expression -only some genes are expressed, others not ( turned off ) Ex.cell specialization, development, cell function under different conditions, sex determination 11.2 How can genes be turned on or off? prokaryotic - ex. lac operon in E. coli series of genes and promoter and operator promoter - RNA polymerase attaches operator - repressor attaches ( on/off switch ) regulatory gene translated to repressor protein eukaryotes (Protists, Fungi, Plants, Animals) - more complex Epigenetics is inheritance of traits transmitted by mechanisms other than nucleotide sequences DNA packing into chromosomes packed genes not expressed - methylation prevents transcription - --CH 3 to cytosine nucleotides Inactivation of X chromosome - one X permanently packed Why does this occur only in females? Example of this: Transcription factors transcription factors series of proteins that attach to enhancer area, allow RNA polymerase attachment to DNA for transcription - enhancers area of DNA for attachment of transcription factors - promoter area of DNA where RNA polymerase attaches RNA splicing - modified mrna in nucleus introns (noncoding sections) removed - exons linked in several alternate patterns - caps and tails added - smallrna (srna) and micro RNA (mirna) used to cut mrna Proteins modified (after translation) into active form or broken down 11.6

6 Homeotic genes homeotic genes master control genes called Hox genes - turn on sets of genes to produce body regions homeoboxes - part of gene that binds to protein to allow gene transcription - identical in many organisms worms to humans - very ancient, preserved through evolutionary time Cell signaling genes - important in body formation laying out body plan embryonic development depends on cell signaling Ex. thalidomide and cyclopamine *How is this connected to the cell cycle of cell division? The genetic tool kit maybe genes that control body development - very important in understanding evolutionary change Mutations random changes in DNA that are copied during replication - change the nitrogen base sequence - mutations within a gene produce alleles - can be base substitution ( point ) mutations or - base insertions or base deletions ( frame shift ) mutation *Which is most likely to cause the most severe change in the nucleotide sequence, a frame shift or a point mutation? Explain why. *What are the variations of a gene, which are caused by mutations, called? - mutations can cause larger changes - relocating genes within chromosomes, or breaking chromosomes, forming new chromosomes - gene duplication is important source of new genes - junk DNA thought to be genes that are no longer expressed and randomly duplicated sections ( 95% of our DNA)

7 Biology 1406 Exam 3 Review Why are proteins important to cells and organisms? What do they do? What are the monomers that form proteins? How many different monomers form the hundreds of thousands of polymers that make up organisms? How can so few monomers make so many polymers? How are amino acid sequence, protein shape and protein function related? What are the two types of nucleic acids and what monomers make up these molecules? Using the symbols D (=deoxyribose sugar), R (=ribose sugar), P (=phosphate) and A,C,G,T,U (=nitrogen bases) draw all of the possible nucleotides. List three differences between RNA and DNA. Using the symbols above draw a nine nucleotide section of DNA. Clearly indicate the location of the weaker hydrogen bonds and distinguish between the 5 and 3 ends. Describe two reasons why the nitrogen bases are complementary - always C to G and A to T or U. Specifically what information is stored in DNA? Define the terms chromosome and gene. Which is larger? What is an allele? What is a locus? What is DNA replication? What is produced by this process? What roles do the enzymes DNA polymerase and DNA ligase play in this process? Why is DNA replication important to living organisms? Describe two features of the DNA molecule that make this process possible. Compare the genetic code to a language. What are the letters are what are the words? What do these words describe? How are words distinguished from other words? How are sentences punctuated? What is the difference between the 3 and 5 ends and how is this used in the genetic code? Explain what is meant by the phrase the genetic code is redundant but never ambiguous. What is meant by the phrase the genetic code is universal. Why is this important to biologist? Describe the process of transcription. What is produced by this process? How does the sense strand (also called template or transcribed strand) of DNA differ from the nonsense strand? Which is the longer? If the nonsense strand is not transcribed what is its value? Is nature wasteful? What role does the enzyme RNA polymerase play in this process and what are promoters and terminators? Describe the process of translation. What is the product of this process? What cell organelle assembles protein? What molecule transports amino acids to the ribosome to be assembled? Describe the two binding sites of trna. Why is this important to the process of translation? Follow the steps in translating a six amino acid protein from start to finish. What does gene expression mean? What are genetic switches? What percent of our DNA might be switches? How is the Lac Operon system in bacteria regulated? What is epigenetics? List 5 ways gene expression is controlled in eukaryotes. What are homeotic genes? What do cell signaling genes do? How are homeotic genes and signaling genes important in evolutionary change? Define the term mutation. Distinguish between a point (base substitution) and a frame shift (base deletion or insertion) mutation. How are the resulting proteins affected by these mutations? What is the term for variations of a gene caused by mutations?

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