DNA and RNA structure

DNA Replication

Protein synthesis-Transcription and Translation

Transcription practice problems

Translation practice problems

Gene Expression and regulation

Mutations

Mutation practice problems

Biotechnology

Transformation and pre-lab instructions

1. DNA and RNA structure

   1. Describe the structures involved in passing hereditary information from one generation to the next

      1. DNA, and in some cases RNA, is the primary source of heritable information.

      2. Genetic information is transmitted from one generation to the next through DNA or RNA

         1. Generic information is stored in and passed to subsequent generations through DNA molecules, and in some cases, RNA molecules.

         2. Prokaryotic organisms typically have circular chromosomes, while eukaryotic organisms typically have multiple linear chromosomes.

      3. Prokaryotes and eukaryotes can contain plasmids, which are small extrachromosomal, double-stranded, circular DNA molecules.

   2. Describe the characteristics of DNA that allow it to be used as the hereditary material.

      1. DNA, and sometimes RNA, exhibits specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G)

         1. Purines (G and A) have double ring structure

         2. Pyrimidines (C, T, and U) have a single ring structure

2. Replication

   1. Describe the mechanisms by which genetic information is copied for transmission between generations.

      1. DNA replication ensures continuity of hereditary information:

         1. DNA is synthesized in the 5’ to 3’ direction

         2. Replication is a semiconservative process- one strand of DNA serves as the template for a new strand of complementary DNA.

         3. Helicase unwinds the DNA strands.

         4. Topoisomerases relaxes supercoiling in front of the replication fork.

         5. DNA polymerase requires RNA primers to initiate DNA synthesis.

         6. DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand.

         7. Ligase joins the fragments on the lagging strand.

            1. Do not need to know the steps or particular enzymes beyond DNA polymerase, ligase, RNA polymerase, helicase, and topoisomerase.

3. Transcription and RNA processing

   1. Describe the mechanisms by which genetic information flows from DNA to RNA to protein

      1. The sequence of RNA bases, together with the structure of the RNA molecule, determines RNA function:

         1. mRNA molecules carry information from DNA to the ribosome

         2. Distinct tRNA molecules bind specific amino acids and have anticodon sequences that base pair with the mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence

         3. rRNA molecules are functional building blocks of ribosomes.

      2. Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein.

      3. RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecules. This process is known as transcription.

      4. The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand. Selection of which DNA strand serves as the template strand depends on the gene being transcribed.

      5. The enzyme RNA polymerase synthesized mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction.

      6. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications:

         1. Addition of a poly-A tail

         2. Addition of a GTP cap

         3. Excision of introns and splicing and retention of exons.

         4. Excision of introns and splicing and retention of exons can generate versions of the resulting mRNA molecules, this is known as alternative splicing.

4. Translation

   1. Describe how the phenotype of an organism is determined by its genotype.

      1. Translation of the mRNA to generate a polypeptide occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the rough endoplasmic reticulum of eukaryotic cells.

      2. In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed.

      3. Translation involved energy and many sequential steps, including initiation, elongation, and termination.

         1. Do not need to know the details and names of enzymes and factors involved in each of these steps.

      4. The salient features of translation include:

         1. Translation is initiated when the rRNA in the ribosomes interacts with the mRNA at the start codon.

         2. The sequence of nucleotides on the mRNA is read in triplets called codons.

         3. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many AA are encoded by more than one codon.

         4. Nearly all living organisms use the same genetic code, which is evidence for the common ancestry of all living organisms.

         5. tRNA brings the correct AA to the correct place specified by the codon on the mRNA.

         6. The AA is transferred to the growing polypeptide chain.

         7. The process continues along the mRNA until a stop codon is reached.

         8. The process terminates by release of the newly synthesized polypeptide/protein.

            1. Do not need to know genetic code for specific AA.

      5. Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

         1. Do not need to know the steps or particular enzymes beyond DNA polymerase, ligase, RNA polymerase, helicase, and topoisomerase.

5. Regulation of gene expression

   1. Describe the types of interactions that regulate gene expression.

      1. Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.

      2. Epigenetic changes can affect gene expression through reversible modification of DNA or histones.

      3. The phenotype of a cell or organism is determined by the combination of genes that are expressed and the levels at which they are expresses:

         1. Observable cell differentiation results from the expression of genes for tissues specific proteins.

         2. Induction of transcription factors during development results in sequential gene expression.

   2. Explain how the location of regulatory sequences relates to their function.

      1. Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated:

         1. In prokaryotes, groups of genes called operons are transcribed in a single mRNA molecule. The lac operon is an example of an inducible system.

         2. In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression.

6. Gene expression and cell specialization

   1. Explain how the binding of transcription factors to promoter regions affects gene expression and/or the phenotype of the organism.

      1. Promoters are DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription.

      2. Negative regulatory molecules inhibit gene expression by binding to DNA and blocking transcription.

   2. Explain the connection between the regulation of gene expression and phenotypic differences in cells and organisms.

      1. Gene regulation results in differential gene expression and influences cell products and function.

      2. Certain small RNA molecules have roles in regulating gene expression.

7. Mutations

   1. Describe the various types of mutation.

      1. Changes in genotype can result in changes in phenotype:

         1. The function and amount of gene products determine the phenotype of organisms.

            1. The normal function of genes and gene products collectively comprises the normal function of organisms.

            2. Disruptions in genes and gene products cause new phenotypes.

      2. Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype. DNA mutation can be positive, negative, or neutral based on the effect or lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.

   2. Explain how changes in genotype may result in changes in phenotype.

      1. Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random mutations in the DNA:

         1. Whether a mutation is detrimental, beneficial, or neutral depends on the environmental context.

         2. Mutations are the primary source of genetic variation.

      2. Errors in mitosis or meiosis can result in changes in phenotype:

         1. Changes in chromosomal number often result in new phenotypes, including sterility caused by triploidy, and increased vigor of other polyploids.

         2. Changes in chromosome number often result in human disorders with developmental limitations, including Down syndrome/Trisomy 21 and Turner syndrome.

   3. Explain how alterations in DNA sequences contribute to variation that can be subject to natural selection.

      1. Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected for by environmental conditions:

         1. The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer of DNA), and transposition (movement of DNA segments within and between DNA molecules) increases variation.

         2. Related viruses can combine/recombine genetic information if they infect the same host cell.

         3. Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms.

8. Biotechnology

   1. Explain the use of genetic engineering techniques in analyzing or manipulating DNA.

      1. Genetic engineering techniques can be used to analyze and manipulate DNA and RNA:

         1. Electrophoresis separates molecules according to size and charge.

         2. During polymerase chain reaction (PCR), DNA fragments are amplified.

         3. Bacterial transformation introduces DNA into bacterial cells.

         4. DNA sequencing determines the order of nucleotides in a DNA molecule.

            1. Do not need to know the details of these processes, only conceptual understanding of the application of these techniques.