Chapter 10 & 11
Genetics
"The scientific study of heredity" Regulation of Genetic Expression: -Most genes are expressed at all times -Other genes are transcribed and translated when cells need them -Allows cell to conserve energy -Quorum sensing regulates production of some proteins; detection of secreted quorum-sensing molecules can signal bacteria to synthesize a certain protein -Regulation of polypeptide synthesis typically halts transcription and can stop translation directly -Genes encoding proteins of related functions are frequently transcribed under the control of a single promoter in prokaryotes, resulting in the formation of a polycistronic mRNA molecule that encodes multiple polypeptides.
Codons & Anticodons
*Codon* Sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule. *Anticodon* Sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA. Image: (a) After folding caused by intramolecular base pairing, a tRNA molecule has one end that contains the anticodon, which interacts with the mRNA codon, and the CCA amino acid binding end. (b) A space-filling model is helpful for visualizing the three-dimensional shape of tRNA. (c) Simplified models are useful when drawing complex processes such as protein synthesis
DNA Repair
*DNA Profreading* DNA polymerases have the ability to proofread, using 3' → 5' exonuclease activity. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base. *DNA Excision Repair* Damaged bases are cut out within a string of nucleotides, and replaced with DNA as directed by the undamaged template strand. This repair system is used to remove pyrimidine dimers formed by UV radiation as well as nucleotides modified by bulky chemical adducts. *Repair of Thymine Dimers* Photoreactivation repair, the PRE enzyme activated by blue light breaks the dimer, restoring the normal base pairing. Blue light can affect DNA because it is at the same end of the spectrum as UV radiation.
Nucleotide Bases
*DNA* -Adenine -Guanine -Cytosine -Thymine *RNA* -Uracil
DNA vs RNA
*Deoxyribonucleic Acid* -DNA replicates and stores genetic information. It is a blueprint for all genetic information contained within an organism -DNA consists of two strands, arranged in a double helix. These strands are made up of subunits called nucleotides. Each nucleotide contains a phosphate, a 5-carbon sugar molecule and a nitrogenous base. -DNA is a much longer polymer than RNA. A chromosome, for example, is a single, long DNA molecule, which would be several centimetres in length when unravelled. -The sugar in DNA is deoxyribose, which contains one less hydroxyl group than RNA's ribose. -Adenine and Thymine pair (A-T) Cytosine and Guanine pair (C-G) -DNA is found in the nucleus, with a small amount of DNA also present in mitochondria. -Due to its deoxyribose sugar, which contains one less oxygen-containing hydroxyl group, DNA is a more stable molecule than RNA, which is useful for a molecule which has the task of keeping genetic information safe. -DNA is vulnerable to damage by ultraviolet light. *Ribonucleic Acid* -RNA converts the genetic information contained within DNA to a format used to build proteins, and then moves it to ribosomal protein factories. -RNA only has one strand, but like DNA, is made up of nucleotides. RNA strands are shorter than DNA strands. RNA sometimes forms a secondary double helix structure, but only intermittently. -RNA molecules are variable in length, but much shorter than long DNA polymers. A large RNA molecule might only be a few thousand base pairs long. -RNA contains ribose sugar molecules, without the hydroxyl modifications of deoxyribose. -Adenine and Uracil pair (A-U) Cytosine and Guanine pair (C-G) -RNA forms in the nucleolus, and then moves to specialised regions of the cytoplasm depending on the type of RNA formed. -RNA, containing a ribose sugar, is more reactive than DNA and is not stable in alkaline conditions. RNA's larger helical grooves mean it is more easily subject to attack by enzymes. -RNA is more resistant to damage from UV light than DNA.
DNA Replication of Eukaryotes Vs. Prokaryotes
*Eukaryotes* -Uses four DNA polymerases -Thousands of replication origins -Shorter Okazaki fragments -Plant and animal cells methylate only cytosine bases -The linear nature of eukaryotic chromosomes necessitates telomeres to protect genes near the end of the chromosomes. Telomerase extends telomeres, preventing their degradation, in some cell types. -Eukaryotes typically have multiple linear chromosomes, each with multiple origins of replication. Overall, replication in eukaryotes is similar to that in prokaryotes. *Prokaryotes* -In bacteria, the initiation of replication occurs at the origin of replication, where supercoiled DNA is unwound by DNA gyrase, made single-stranded by helicase, and bound by single-stranded binding protein to maintain its single-stranded state. Primase synthesizes a short RNA primer, providing a free 3'-OH group to which DNA polymerase III can add DNA nucleotides.
Exon and Intron
*Exon* -A segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence. -Included in mRNA during transcription *Intron* -A segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes. -Gets left out of mRNA during transcription
Genotype vs. Phenotype
*Genotype* "Set of genes in the genome" -The genotype of a cell is the full collection of genes a cell contains. Not all genes are used to make proteins simultaneously. The phenotype is a cell's observable characteristics resulting from the proteins it is producing at a given time under specific environmental conditions. -The entire genetic content of a cell -A genotype is a complete heritable genetic identity; a unique genome that would be revealed by genome sequencing. However, the word genotype can also refer just to a particular gene or set of genes carried by an individual -The genetic constitution of an individual organism. -Collection of alleles -Genes code for proteins, or stable RNA molecules, each of which carries out a specific function in the cell. -Although the genotype that a cell possesses remains constant, expression of genes is dependent on environmental conditions. -Bacteria have the ability to change which σ factor of RNA polymerase they use in response to environmental conditions to quickly and globally change which regulons are transcribed. *Phenotype* "Physical features and functional traits of the organism" -A phenotype is the observable characteristics of a cell (or organism) at a given point in time and results from the complement of genes currently being used. -Physical expression of alleles -Set of observable characteristics of an individual resulting from the interaction of its genotype with the environment. -The composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior. --- -Genetic information determines physical characteristics -Genotype determines phenotype -Not all genes are active at all times -Phenotype is determined by the specific genes within a genotype that are expressed under specific conditions. Although multiple cells may have the same genotype, they may exhibit a wide range of phenotypes resulting from differences in patterns of gene expression in response to different environmental conditions.
DNA Repair Mechanisms
*Light Repair* DNA repair in cells previously exposed to UV light by a DNA repair enzyme that requires visible light *Dark Repair* Mechanism by which enzymes cut damaged DNA sections from a molecule, creating a gap that is repaired by DNA polymerase and DNA ligase. *Base-excision Repair* DNA repair that first excises modified bases and then replaces the entire nucleotide *Mismatch Repair* The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides. *SOS Response* a state of high-activity DNA repair, and is activated by bacteria that have been exposed to heavy doses of DNA-damaging agents. Their DNA is basically chopped to shreds, and the bacteria attempts to repair its genome at any cost; including inclusion of mutations due to error-prone nature of repair mechanisms.
What are the functions for the 3 main types of RNA involved in protein synthesis?
*Messenger RNA* -Serves as the intermediary between DNA and the synthesis of protein products during translation. -It is a copy of the information in a gene. -Carries the instructions from the nucleus to the cytoplasm. -Produced in the nucleus, as are all RNAs. *Ribosomal RNA* -A type of stable RNA that is a major componet of ribosomes. -Directs the translation of mRNA into proteins. -Ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes the formation of the peptide bonds between two aligned amino acids during protein synthesis. -Located in the cytoplasm of a cell, where ribosomes are found. -Prokaryotic (70S) and cytoplasmic eukaryotic (80S) ribosomes are each composed of a large subunit and a small subunit of differing sizes between the two groups. Each subunit is composed of rRNA and protein. Organelle ribosomes in eukaryotic cells resemble prokaryotic ribosomes. *Transfer RNA* -Small type of stable RNA that carries an amino acid to the corresponding site of protein synthesis in the ribosome. -Is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain being synthesized. -Located in the cellular cytoplasm. -Transfers amino acids to the ribosome that corresponds to each three-nucleotide codon of rRNA. The amino acids then can be joined together and processed to make polypeptides and proteins. -Some 60 to 90 species of tRNA exist in bacteria. Each tRNA has a three-nucleotide anticodon as well as a binding site for a cognate amino acid. All tRNAs with a specific anticodon will carry the same amino acid. (Although RNA is not used for long-term genetic information in cells, many viruses do use RNA as their genetic material.) -Viral genomes show extensive variation and may be composed of either RNA or DNA, and may be either double or single stranded.
Bacterial Mutants
*Mutants* -Descendants of a cell that does -not repair a mutation *Wild types* Cells normally found in nature *Methods to recognize mutants* -Positive selection -Negative (indirect) selection -Ames test -The Ames test, developed by Bruce Ames, is a method that uses bacteria for rapid, inexpensive screening of the carcinogenic potential of new chemical compounds. -The Ames test is an inexpensive method that uses auxotrophic bacteria to measure mutagenicity of a chemical compound. Mutagenicity is an indicator of carcinogenic potential (A carcinogen is a substance capable of causing cancer in living tissue). -The test measures the mutation rate associated with exposure to the compound, which, if elevated, may indicate that exposure to this compound is associated with greater cancer risk. -Through comparison of growth on the complete plate and lack of growth on media lacking specific nutrients, specific loss-of-function mutants called auxotrophs can be identified.
Prokaryotic Vs. Eukaryotic Transcription
*Prokaryotes* -Five types of RNA transcribed from DNA -RNA primers -mRNA -rRNA -tRNA -Regulatory RNA -Occur in nucleoid of prokaryotes -Three steps: --Initiation --Elongation --Termination *Eukaryotes* -RNA transcription occurs in the nucleus -Transcription also occurs in mitochondria and chloroplasts -Three types of nuclear RNA polymerases -Numerous transcription factors -mRNA is processed before translation -Capping -Polyadenylation -Eukaryotic primary transcripts are processed in several ways, including the addition of a 5' cap and a 3′-poly-A tail, as well as splicing, to generate a mature mRNA molecule that can be transported out of the nucleus and that is protected from degradation.
Discuss the similarities and differences in prokaryotic and eukaryotic genomes.
*Prokaryotic* -Circular DNA\ -Smaller genome -Have a single chromosome -Transcription in prokaryotes is performed by a single RNA polymerase, composed of a complex of four different subunits -Prokaryotic genomes typically code for only proteins -Usually single copy of circular genome -Often contain plasmids *Eukaryotic* -Linear DNA -Larger genome -Eukaryotes have genetic material is organized into membrane-bound nuclei -Eukaryotic transcription is performed by three different RNA polymerases, each with specific roles -In eukaryotic mRNA there is the occurence of splicing. This process removes intervening sequences (introns) from the primary transcript, and precisely assembles a set of exons which form the transcript that is translated. -Eurkaryotic genomes don't always code for proteins -Eukaryotic chromatin is coated with histones.
Chromosomes of Prokaryotes Vs. Eukaryotes.
*Prokaryotic* -Found in cytoplasm -Circular chromosome attached to the inside of the cell membrane -Single Chromosome plus plasmids -Made only of DNA -Copies its chromosome and divides immediately after *Eukaryotic* -Found in nucleus -Linear Chromosomes -Usually 10-50 chromosomes in somatic cells -Human body cells have 46 chromosomes -Made of chromatin, a nucleoprotein (DNA coiled around histone proteins) -Copies chromosomes, then the cell grows, then goes through mitosis to organize chromosomes in two equal groups
Purines and Pyrimidines
*Purines* A nitrogenous base that has a double-ring structure. -Adenine -Guanine *Pyrimidines* A nitrogenous base that has a single-ring structure -Thymine -Cytosine -Uracil
Explain how the terms redundant, degenerate, and unambiguous describe the genetic code.
*Redundant / Degenerate Genetic Code* -Refers to the fact that the genetic code contains more information than is needed to specify all 20 common amino acids. -Most amino acids are coded for by more than one codon -64 possible codons for 20 possible amino acids Degeneracy of codons is the redundancy of the genetic code *Unambiguous Genetic Code* Each codon encodes precisely one amino acid -i.e. AUG codes only for methionine
Replication vs. Transcription vs. Translation
*Replication* -The process of copying a double-stranded DNA molecule. DNA first spilts into two halves and both strands serve as templates for the reproduction of the opposite strand until it has duplicated itself into 2 new strands of DNA. *Transcription* "Synthesis of an RNA molecule from a DNA template" -Information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA), by the enzyme RNA polymerase. -The first part of the central dogma of molecular biology -(DNA safely and stably stores genetic material in the nuclei of cells as a reference, or template. Meanwhile, mRNA is comparable to a copy from a reference book because it carries the same information as DNA but is not used for long-term storage and can freely exit the nucleus. Although the mRNA contains the same information, it is not an identical copy of the DNA segment, because its sequence is complementary to the DNA template.) *Translation* "Polypeptides are synthesized from RNA" -The final step on the way from DNA to protein. -Process of protein biosynthesis wherein the genetic code carried by mRNA is decoded to produce the specific sequence of amino acids in a polypeptide chain.
Prokaryotic Vs. Eukaryotic Translation
*Translation* -In translation, polypeptides are synthesized using mRNA sequences and cellular machinery, including tRNAs that match mRNA codons to specific amino acids and ribosomes composed of RNA and proteins that catalyze the reaction. -Initiation of translation occurs when the small ribosomal subunit binds with initiation factors and an initiator tRNA at the start codon of an mRNA, followed by the binding to the initiation complex of the large ribosomal subunit. -In prokaryotes, transcription and translation may be coupled, with translation of an mRNA molecule beginning as soon as transcription allows enough mRNA exposure for the binding of a ribosome, prior to transcription termination. Transcription and translation are not coupled in eukaryotes because transcription occurs in the nucleus, whereas translation occurs in the cytoplasm or in association with the rough endoplasmic reticulum. Participants in translation: -Messenger RNA -Transfer RNA -Ribosomes and rRNA Three stages of translation: -Initiation -Elongation -Termination *Differences in Eukaryotes* -Initiation occurs when ribosomal subunit binds to 5′ guanine cap -First amino acid is methionine rather than f-methionine -Ribosomes can synthesize polypeptides into the cavity of the rough endoplasmic reticulum -Polypeptides often require one or more post-translational modifications to become biologically active.
How do vertical and horizontal gene transfer differ?
*Vertical Gene Transfer* Passing of genes to the next generation -Reproduction *Horizontal Gene Transfer* Transfer of genetic material between unrelated individuals -Donor cell contributes part of genome to recipient cell -Horizontal gene transfer is an important way for asexually reproducing organisms like prokaryotes to acquire new traits. -There are three mechanisms of horizontal gene transfer typically used by bacteria: transformation, transduction, and conjugation. *-Bacterial Conjugation* DNA is transferred between cells through a cytoplasmic bridge after a conjugation pilus draws the two cells close enough to form the bridge. Donor cell remains alive. Mediated by conjugation pili *-Transduction* a bacteriophage injects DNA that is a hybrid of viral DNA and DNA from a previously infected bacterial cell. *-Transformation* the cell takes up DNA directly from the environment. The DNA may remain separate as a plasmid or be incorporated into the host genome. -Transformation allows for competent cells to take up naked DNA, released from other cells on their death, into their cytoplasm, where it may recombine with the host genome.
Operons
-A unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis. An operon is like an on/off switch to save energy -Bacterial genes are often found in operons. Genes in an operon are transcribed as a group and have a single promoter. -Each operon contains regulatory DNA sequences, which act as binding sites for regulatory proteins that promote or inhibit transcription. -Regulatory proteins often bind to small molecules, which can make the protein active or inactive by changing its ability to bind DNA. -Some operons are inducible, meaning that they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule. *Prokaryotic Operons* -An operon consists of a promoter and a series of genes -Controlled by a regulatory element called an operator -Typically polycistronic (code for several polypeptides) *Prokaryotic Operons* -Inducible operons must be activated by inducers eg. Lactose operon -Repressible operons are transcribed continually until deactivated by repressors eg. Tryptophan operon *Inducible Operons* Usually off but can be stimulated when a specific molecule interacts with a regulator protein. *Repressible Operons* transcription is usually on, but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein. --- -Prokaryotic structural genes of related function are often organized into operons, all controlled by transcription from a single promoter. The regulatory region of an operon includes the promoter itself and the region surrounding the promoter to which transcription factors can bind to influence transcription. -Although some operons are constitutively expressed, most are subject to regulation through the use of transcription factors (repressors and activators). A repressor binds to an operator, a DNA sequence within the regulatory region between the RNA polymerase binding site in the promoter and first structural gene, thereby physically blocking transcription of these operons. An activator binds within the regulatory region of an operon, helping RNA polymerase bind to the promoter, thereby enhancing the transcription of this operon. An inducer influences transcription through interacting with a repressor or activator. -The trp operon is a classic example of a repressible operon. When tryptophan accumulates, tryptophan binds to a repressor, which then binds to the operator, preventing further transcription. -The lac operon is a classic example an inducible operon. When lactose is present in the cell, it is converted to allolactose. Allolactose acts as an inducer, binding to the repressor and preventing the repressor from binding to the operator. This allows transcription of the structural genes. -The lac operon is also subject to activation. When glucose levels are depleted, some cellular ATP is converted into cAMP, which binds to the catabolite activator protein (CAP). The cAMP-CAP complex activates transcription of the lac operon. When glucose levels are high, its presence prevents transcription of the lac operon and other operons by catabolite repression. -Small intracellular molecules called alarmones are made in response to various environmental stresses, allowing bacteria to control the transcription of a group of operons, called a regulon.
Meiosis
-Cell division that produces reproductive cells in sexually reproducing organisms -Where DNA recombination occurs
Story of DNA Replication
-In order for cells to be viable the have to have the ability to reproduce themselves. -A major part of that process is having the ability to replicate its DNA, which is done in a process called DNA replication -Key to replication is complementary structure of the two strands -Replication is semiconservative; new DNA composed of one original and one daughter strand -It is an anabolic polymerization process that requires monomers and energy 1) *Initiation: Replication Fork Formation* -Replication begins at the origin -DNA polymerase replicates DNA only 5′ to 3′ -Because strands are antiparallel, new strands are synthesized differently -Leading strand synthesized continuously -Lagging strand synthesized discontinuously -Bidirectional -Gyrases and topoisomerases remove supercoils in DNA -DNA is methylated: --Control of genetic expression --Initiation of DNA replication --Protection against viral infection --Repair of DNA Before DNA can be replicated, the double stranded molecule must be "unzipped" into two single strands. DNA helicase disrupts the hydrogen bonding between base pairs to separate the strands into a Y shape known as the replication fork. This area will be the template for replication to begin. DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies which side group is attached the DNA backbone. The 5' end has a phosphate (P) group attached, while the 3' end has a hydroxyl (OH) group attached. This directionality is important for replication as it only progresses in the 5' to 3' direction. However, the replication fork is bi-directional; one strand is oriented in the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two sides are therefore replicated with two different processes to accommodate the directional difference. 2) *Primer Binding* The leading strand is the simplest to replicate. Once the DNA strands have been separated, a short piece of RNA called a primer binds to the 3' end of the strand. The primer always binds as the starting point for replication. Primers are generated by the enzyme DNA primase. 3) *Elongation* Enzymes known as DNA polymerases are responsible creating the new strand by a process called elongation. Because replication proceeds in the 5' to 3' direction, the leading strand of DNA is synthesized continuously from a single primer. The lagging strand is synthesized discontinuously in short Okazaki fragments, each requiring its own primer. The RNA primers are removed and replaced with DNA nucleotides by bacterial DNA polymerase, and DNA ligase seals the gaps between these fragments. During the elongation stage of translation, a charged tRNA binds to mRNA in the A site of the ribosome; a peptide bond is catalyzed between the two adjacent amino acids, breaking the bond between the first amino acid and its tRNA; the ribosome moves one codon along the mRNA; and the first tRNA is moved from the P site of the ribosome to the E site and leaves the ribosomal complex. 4) *Termination* Once both the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with appropriate bases. Another exonuclease "proofreads" the newly formed DNA to check, remove and replace any errors. Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to 3′ direction. The ends of the parent strands consist of repeated DNA sequences called telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby chromosomes from fusing. A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA. Once completed, the parent strand and its complementary DNA strand coils into the familiar double helix shape. In the end, replication produces two DNA molecules, each with one strand from the parent molecule and one new strand.
Chromosomes
-The majority of genetic material is organized into chromosomes that contain the DNA that controls cellular activities. -Threadlike structures made of DNA molecules that contain the genes -Extrachromosomal DNA in eukaryotes includes the chromosomes found within organelles of prokaryotic origin (mitochondria and chloroplasts) that evolved by endosymbiosis. Some viruses may also maintain themselves extrachromosomally. -Extrachromosomal DNA in prokaryotes is commonly maintained as plasmids that encode a few nonessential genes that may be helpful under specific conditions. Plasmids can be spread through a bacterial community by horizontal gene transfer. -Prokaryotes are typically haploid, usually having a single circular chromosome found in the nucleoid. Eukaryotes are diploid; DNA is organized into multiple linear chromosomes found in the nucleus. -Supercoiling and DNA packaging using DNA binding proteins allows lengthy molecules to fit inside a cell. Eukaryotes and archaea use histone proteins, and bacteria use different proteins with similar function.
Replication Fork
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Mutagens
A chemical or physical agent that interacts with DNA and causes a mutation. -Mutagenic agents are frequently carcinogenic but not always. However, nearly all carcinogens are mutagenic. *Radiation* -Ionizing radiation: breaks -Nonionizing radiation: thymine dimers *Chemical Mutagens* -Nucleotide analogs: disrupt DNA and RNA replication -Nucleotide-altering chemicals: alter the structure of nucleotides resultinh in base-pair substitutions and missense mutations *Frameshift Mutagens* -Result in nonsense mutations -Intercalating agents- Ethidium bromide
DNA
A complex molecule containing the genetic information that makes up the chromosomes.
Lagging Strand
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.
Plastids
A group of membrane‐bound organelles commonly found in photosynthetic organisms and mainly responsible for the synthesis and storage of food.
What is a plasmid?
A plasmid is a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. -Rolling circle replication is a type of rapid unidirectional DNA synthesis of a circular DNA molecule used for the replication of some plasmids. -Small circular pieces of double-stranded DNA that can be exchanged between prokaryotes -Plasmids are much used in the laboratory manipulation of genes. -Conjugation is mediated by the F plasmid, which encodes a conjugation pilus that brings an F plasmid-containing F+ cell into contact with an F- cell. -Conjugation transfer of R plasmids is an important mechanism for the spread of antibiotic resistance in bacterial communities. -The rare integration of the F plasmid into the bacterial chromosome, generating an Hfr cell, allows for transfer of chromosomal DNA from the donor to the recipient. Additionally, imprecise excision of the F plasmid from the chromosome may generate an F' plasmid that may be transferred to a recipient by conjugation.
Mutation
A random error in gene replication that leads to a change -Change in the nucleotide base sequence of a genome -Rare event -Almost always deleterious -Rarely leads to a protein that improves ability of organism to survive Types of Mutations: *Point mutations* A point mutation or substitution is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a sequence of DNA or RNA. Point mutations have a variety of effects on the downstream protein product—consequences that are moderately predictable based upon the specifics of the mutation. *Frameshift mutations* A frameshift mutation is a genetic mutation caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame, resulting in a completely different translation from the original. --- -A mutation is a heritable change in DNA. A mutation may lead to a change in the amino-acid sequence of a protein, possibly affecting its function. -A point mutation affects a single base pair. A point mutation may cause a silent mutation if the mRNA codon codes for the same amino acid, a missense mutation if the mRNA codon codes for a different amino acid, or a nonsense mutation if the mRNA codon becomes a stop codon. -Missense mutations may retain function, depending on the chemistry of the new amino acid and its location in the protein. Nonsense mutations produce truncated and frequently nonfunctional proteins. -A frameshift mutation results from an insertion or deletion of a number of nucleotides that is not a multiple of three. The change in reading frame alters every amino acid after the point of the mutation and results in a nonfunctional protein. -Spontaneous mutations occur through DNA replication errors, whereas induced mutations occur through exposure to a mutagen. -Chemical mutagens include base analogs and chemicals that modify existing bases. In both cases, mutations are introduced after several rounds of DNA replication. -Ionizing radiation, such as X-rays and γ-rays, leads to breakage of the phosphodiester backbone of DNA and can also chemically modify bases to alter their base-pairing rules. -Nonionizing radiation like ultraviolet light may introduce pyrimidine (thymine) dimers, which, during DNA replication and transcription, may introduce frameshift or point mutations. -Pyrimidine dimers can also be repaired. In nucleotide excision repair (dark repair), enzymes recognize the distortion introduced by the pyrimidine dimer and replace the damaged strand with the correct bases, using the undamaged DNA strand as a template. Bacteria and other organisms may also use direct repair, in which the photolyase enzyme, in the presence of visible light, breaks apart the pyrimidines. -Cells have mechanisms to repair naturally occurring mutations. DNA polymerase has proofreading activity. Mismatch repair is a process to repair incorrectly incorporated bases after DNA replication has been completed.
What is a ribosome?
A structure upon which proteins are assembled
Chromosome
A threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
Nucleotides
Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases -Nucleotides are linked together by phosphodiester bonds between the 5ʹ phosphate group of one nucleotide and the 3ʹ hydroxyl group of another. A nucleic acid strand has a free phosphate group at the 5ʹ end and a free hydroxyl group at the 3ʹ end. -Nucleic acids are composed of nucleotides, each of which contains a pentose sugar, a phosphate group, and a nitrogenous base. Deoxyribonucleotides within DNA contain deoxyribose as the pentose sugar.
Mitosis
Cell division in which the nucleus divides into nuclei containing the same number of chromosomes
DNA complementarity
Complementary base pairing makes it possible to produce two identical strands by separating the parent molecule and using each strand as a template to build a new complementary strand Chargaff discovered that the amount of adenine is approximately equal to the amount of thymine in DNA, and that the amount of the guanine is approximately equal to cytosine. These relationships were later determined to be due to complementary base pairing.
Replication Enzymes
DNA replication would not occur without enzymes that catalyze various steps in the process. Enzymes that participate in the eukaryotic DNA replication process include: *DNA helicase* Unwinds and separates double stranded DNA as it moves along the DNA. It forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA. *DNA primase* A type of RNA polymerase that generates RNA primers. Primers are short RNA molecules that act as templates for the starting point of DNA replication. *DNA polymerases* Synthesize new DNA molecules by adding nucleotides to leading and lagging DNA strands. Can only add the the 3 prime end. -RNA polymerase synthesizes RNA, using the antisense strand of the DNA as template by adding complementary RNA nucleotides to the 3' end of the growing strand. -RNA polymerase binds to DNA at a sequence called a promoter during the initiation of transcription. -Unlike DNA polymerase, RNA polymerase does not require a 3'-OH group to add nucleotides, so a primer is not needed during initiation. *Topoisomerase or DNA Gyrase* Unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled. *Exonucleases* A group of enzymes that remove nucleotide bases from the end of a DNA chain. *DNA ligase* Joins DNA fragments together by forming phosphodiester bonds between nucleotides.
Structure of DNA
DNA serves two important cellular functions: It is the genetic material passed from parent to offspring and it serves as the information to direct and regulate the construction of the proteins necessary for the cell to perform all of its functions. -DNA or deoxyribonucleic acid is a type of molecule known as a nucleic acid. It consists of a 5-carbon deoxyribose sugar, a phosphate, and a nitrogenous base. Double-stranded DNA consists of two spiral nucleic acid chains that are twisted into a double helix shape. This twisting allows DNA to be more compact. In order to fit within the nucleus, DNA is packed into tightly coiled structures called chromatin. Chromatin condenses to form chromosomes during cell division. Prior to DNA replication, the chromatin loosens giving cell replication machinery access to the DNA strands. -DNA is composed of two complementary strands oriented antiparallel to each other with the phosphodiester backbones on the exterior of the molecule. The nitrogenous bases of each strand face each other and complementary bases hydrogen bond to each other, stabilizing the double helix. -Heat or chemicals can break the hydrogen bonds between complementary bases, denaturing DNA. Cooling or removing chemicals can lead to renaturation or reannealing of DNA by allowing hydrogen bonds to reform between complementary bases. -Consists of 2 polynucleotide chains or strands, wound around each other such that they resemble a twisted ladder, referred to as the double helix -The backbone of each of these strands is a repeating pattern of a 5-carbon sugar and a phosphate group. -The sugar present in the nucleotide is a deoxyribose, hence the name deoxyribonucleic acid (DNA). -In the double helix DNA structure, all four bases are confined to the inside of the double helix, held in place by hydrogen (H) bonds linking complimentary bases on the two strands. -The sugar-phosphate backbones of DNA are on the outside of the double helix. -Made up of molecules called nucleotides. -Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. -The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). -The order of these bases is what determines DNA's instructions, or genetic code. The genetic code is degenerate in that several mRNA codons code for the same amino acids. The genetic code is almost universal among living organisms. -Similar to the way the order of letters in the alphabet can be used to form a word, the order of nitrogen bases in a DNA sequence forms genes, which in the language of the cell, tells cells how to make proteins. -DNA is exceptionally long, in order to fit inside cells, DNA is coiled tightly to form structures we call chromosomes. -Each chromosome contains a single DNA molecule. -DNA stores the instructions needed to build and control the cell. This information is transmitted from parent to offspring through vertical gene transfer. -Humans have 23 pairs of chromosomes, which are found inside the cell's nucleus.
Alleles
Different versions of a gene
Structure of RNA
Function: 1) It assists the DNA and acts as a messenger between the DNA and the ribosomes. 2) Secondly it helps the ribosomes to choose the right amino acid which is required in building up of new proteins in the body. -There are three main types of RNA, all involved in protein synthesis. -RNA is typically single stranded and contains ribose as its pentose sugar and the pyrimidine uracil instead of thymine. An RNA strand can undergo significant intramolecular base pairing to take on a three-dimensional structure. -Adenine and uracil are considered as the major building blocks of RNA and both of them form base-pair with the help of 2 hydrogen bonds. -RNA resembles a hairpin structure and like the nucleotides in DNA, nucleosides are formed in this ribonucleic material(RNA). Nucleosides are nothing but the phosphate groups which sometimes also helps in the production of nucleotides in the DNA. -RNA is a single stranded polymer (long chain) made of ribonucleotides that are linked by phosphodiester bonds. -A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. -The subtle structural difference between the sugars gives DNA added stability, making DNA more suitable for storage of genetic information, whereas the relative instability of RNA makes it more suitable for its more short-term functions. -The RNA-specific pyrimidine uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA.
Genetic Recombination
Genetic Recombination is the regrouping of genes in an offspring that results in a genetic makeup that is different from that of the parents. *Crossing Over* Exchange of genetic material between homologous chromosomes during meiosis *Transformation* Process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria *Transduction* Donor DNA packaged in a bacteriophage infects the recipient bacterium. *Conjugation* In bacteria, the direct transfer of DNA between two cells that are temporarily joined.
DNA Redundancy
Genetic redundancy is a term typically used to describe situations where a given biochemical function is redundantly encoded by two or more genes. In these cases, mutations (or defects) in one of these genes will have a smaller effect on the fitness of the organism than expected from the genes' function.
Single Stranded Binding Proteins
Proteins that act as scaffolding, holding two DNA strands apart during replication
Okazaki fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
Termination
Termination: Release factors recognize stop codons, which modify ribosomes to activate ribozymes -Ribosome dissociates into Subunites -Polypeptides released at termination may function alone or together -Termination of replication in bacteria involves the resolution of circular DNA concatemers by topoisomerase IV to release the two copies of the circular chromosome. -Termination of translation occurs when the ribosome encounters a stop codon, which does not code for a tRNA. Release factors cause the polypeptide to be released, and the ribosomal complex dissociates. -Termination of transcription in bacteria occurs when the RNA polymerase encounters specific DNA sequences that lead to stalling of the polymerase. This results in release of RNA polymerase from the DNA template strand, freeing the RNA transcript.
Semiconservative Replication
The DNA replication process is semiconservative, which results in two DNA molecules, each having one parental strand of DNA and one newly synthesized strand.
Genome
The complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes
Chargaff's rules
The concentrations of adenine and thymine are always about the same and the concentrations of cytosine and guanine are always about the same A=T and C=G
5 prime to 3 prime
The direction in which DNA and RNA are synthesized If you have a 5 prime it has to match the 3 prime
Leading Strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
Antiparallel
The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.
What is gene expression?
The process by which DNA directs protein synthesis -There are additional points of regulation of gene expression in prokaryotes and eukaryotes. In eukaryotes, epigenetic regulation by chemical modification of DNA or histones, and regulation of RNA processing are two methods. -Gene expression is a tightly regulated process. -Gene expression in prokaryotes is largely regulated at the point of transcription. Gene expression in eukaryotes is additionally regulated post-transcriptionally.
Chromosomal Theory of Inheritance
The theory stating that hereditary traits are carried on chromosomes.
One gene - one enzyme hypothesis
The theory that each gene directly produces a single enzyme, which consequently affects an individual step in a metabolic pathway. In the 1940s, George Beadle and Edward Tatum used the mold Neurospora crassa to show that each protein's production was under the control of a single gene, demonstrating the "one gene-one enzyme" hypothesis.
The Central Dogma of Genetics
Theory that states that, in cells, information only flows from DNA to RNA to proteins -DNA is transcribed to RNA -RNA is translated to form polypeptides
Heredity
Transmission of traits from one generation to the next
Transpostion
Transposons - "Jumping genes" -A transposable genetic element that moves within a genome by means of a DNA intermediate. -Transposons are molecules of DNA with inverted repeats at their ends that also encode the enzyme transposase, allowing for their movement from one location in DNA to another. Although found in both prokaryotes and eukaryotes, transposons are clinically relevant in bacterial pathogens for the movement of virulence factors, including antibiotic resistance genes. -Segments of DNA that move from one location to another in the same or different molecule -Result is a kind of frameshift insertion (transpositions)
