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Genetics Test 2
| Term | Definition |
|---|---|
| Bacteria | Usually haploid, reproduce asexually, the majority of bacteria and viruses are not harmful to humans |
| What fraction of human deaths do bacteria and viruses account for? | 1/4 to 1/3 |
| Genetic Transfer | A segment of bacterial DNA is transferred from on bacterium to another |
| Bacteriophages | Viruses that infect bacteria |
| Conjugation | The transfer of DNA between two bacterium following direct cell-to-cell contact, discovered by Lederberg and Edward Tatum when studying E. coli |
| Auxotrophs | Can't synthesize a needed nutrient |
| Prototrophs | Make all their nutrients from basic components |
| Lederberg and Tatum's Experiment | Combined two auxotrophs and and prototroph was produced |
| Bernard's Discovery | Bacteria need direct contact for conjugation, discovered in an experiment using a U-tube and a very fine mesh |
| F Factor | Fertility factor, causes bacteria to conjugate, found on plasmid, F+ is the donor, F- is the recipient |
| Plasmid | General term for extra chromosomal DNA |
| Relaxisome | Cuts the F+ strand |
| Relaxase | Attaches to tDNA, reforms it in the recipient cell |
| Pilus | Structure connecting the cells |
| Cavali-Sforza Discovery | 1950s, discovered strains that transfer chromosomal genes, Hfr, used the F1 factor, made the first map of the bacterial chromosome with units in minutes |
| Hfr | High frequency of recombination |
| Episome | Segment of DNA that's a plasmid that can integrate into the chromosome |
| Bacterial Transduction | Transfer of DNA from one bacterium to another via bacteriophage, any piece of bacteria can be incorporated |
| Cotransduction | The packaging and transferring of two closely linked genes, can be used to determine the distance between genes |
| Bacterial Transformation | A bacterium will take up extracellular DNA released into the environment by a dead bacterium, discovered by Griffith in 1928 |
| Natural Transformation | Occurs with no outside help |
| Artificial Transformation | Happens in the lab |
| Competent Cells | Bacteria that are able to take up DNA, encode competence factors, calcium chloride and electricity can artificially make cells competent |
| Heteroduplex | Region of mismatch caused by sequence differences between two alleles |
| Horizontal Gene Transfer | Organisms can receive genes from other organisms without being the direct offspring, leads to antibiotic resistance and acquired virulence (the ability to cause disease) |
| Plaque | A clear area on an otherwise opaque lawn of bacteria, bacteriophages form them by killing bacteria |
| Complementation Experiments | Conducted by Benzer to determine where a mutation was from, rapid lysis, mutations are on different, complimentary genes |
| Genetic Variation | Differences between members of the same species, allelic variations commonly due to mutation |
| Cytogenetics | Field that involves the microscopic examination of chromosomes |
| 3 Main Features for Categorizing Chromosomes | Size, location of centromere, and bonding pattern (determined artificially) |
| Karyotype | A micrograph of all the chromosomes arranged in a standard fashion |
| G-Banding | Produced by Giesma stain, results in light and dark bands |
| Chromosome Arms | P is the long arm, Q is the short arm |
| Metacentric | The centromere is in the middle |
| Submetacentric | Centromere close to the middle but not exactly |
| Acrocentric | Chromosome closer to the top |
| Teleocentric | Centromere is all the way to one side |
| Changes in Chromosome Structure | Change in total amount (deletion, duplication) and Rearranged material (inversion, translocation) |
| Deletion | Occurs when a chromosome breaks and a fragment is lost, tends to lead to miscarriages |
| Terminal Deletion | Lose end gene, only one break |
| Interstitial Deletion | Lose middle gene, two breaks |
| Cri-du-Chat | Disorder caused by a deletion that the child survives, deletion on chromosome 5, child has physical and mental underdevelopment |
| Duplication | A segment of DNA is copied, normally pairs with deletion, occurs because of misalignment in homologous pairs during recombination, tends to be less harmful |
| Gene Family | Developed by duplication, two or more genes derived from the same ancestral gene |
| Paralogs | From the same species |
| Orthologs | From different species |
| Inversion | A segment of genes that has been flipped |
| Pericentric | Inversion includes the centromere, 50% chance of affected offspring |
| Paracentric | Inversion doesn't include the centromere, 100% chance of affected offspring |
| Breakpoint Effect | Inversion breaks in the middle of a gene |
| Position Effect | A gene is positioned in a way that affects its function |
| Translocation | A segment of chromosome is attached to another |
| Simple Translocation | One chromosome sends gene to another, always unbalanced |
| Reciprocal Translocation | Two non-homologous chromosomes exchange genetic material, can occur through chromosomal breakage and DNA repair or abnormal crossovers, balanced, generally nonharmful |
| Balanced | Amount of genetic material on each chromosome remains the same |
| Unbalanced | One chromosome has significantly more and one has less |
| Familial Down Syndrome | Unbalanced translocation, chromosomes 14 and 21 exchange and combine, inherited, Robertsonian translocation |
| Robertsonian Translocation | Break occurs in two non-homologous chromosomes, small bit is lost, big bit fuses to another chromosome |
| Euploidy | Variation in the number of sets of chromosomes, does not occur alive in humans but can occurs in animals like bees and ants and is very common in plants |
| Aneuploidy | Variation in the number of chromosomes in a set |
| Patau Syndrome | Trisomy 13, mental and physical defects, organ defects, and early death |
| Edward Syndrome | Trisomy 18, mental and physical defects, facial abnormalities, extreme muscle tone, early death |
| Down Syndrome | Trisomy 21, mental defects, abnormal build and muscle tone |
| Klinefelter Syndrome | XXY, sexual immaturity and breast swelling |
| Jacobs Syndrome | XYY, tall and thin |
| Triple X Syndrome | XXX, tall and thin, irregular periods |
| Turner Syndrome | X, short, sexual immaturity |
| Nondisjunction | Spindle fibers don't connect to sister chromatids properly, can occur during meiosis or mitosis |
| Molecular Genetics | The study of DNA structure and function at the molecular level |
| Criteria for Genetic Material | Contains information Transmits information Replicates itself Allows for variation |
| Griffith's Discovery | 1928, Transformation, combined dead smooth Streptoccocus pneumonia with an alive, rough variant and the genetic material from the smooth transformed the rough to be infectious |
| Avery, McCarty, and McLeod | 1940s, extracted macromolecules and combined them with the S strain and only DNA transformed, discovered transforming factor but there were still doubters |
| Hershey and Chase | 1952, used bacteriophages and radioactive markers in a blender experiment to determine without a doubt that DNA was the transforming factor |
| DNA Molecular Structure | Nucleotides form the repeating unit of nucleic acids Nucleotides are linked to form a linear strand Two strands interact to form a double helix Proteins influence how they fold |
| Nucleotides | Repeating structural unit of DNA and RNA, phosphate group, pentose sugar, and nitrogenous base, linked by phosphodiester bonds |
| Nucleoside | Base and sugar |
| Nucleotide | Phosphate and base and sugar |
| Watson and Crick | 1953, double helix of DNA, built on discoveries by Linus Pauling, Rosalind Franklin and Maurice Wilkins, and Erwin Chargoff |
| Linus Pauling | Helical model applied to protein |
| Rosalind Franklin | Discovered double strand using x-ray diffraction, Wilkins stole her data and gave it to Watson and Crick |
| Erwin Chargaff | Discovered adenine matched thymine and cytosine matched guanine (have equal percentages) Chargaff's Rule |
| Double Helix | Two strands twist together, 10 bases and 3.4 nm per turn, antiparallel strands, rotates to the right, major and minor grooves interact with protein |
| Z-Form DNA | Spirals the opposite way |
| Triple-Stranded Helix | Triplex, T binds to AT and C binds to CG |
| RNA Structure | One strand, ribose sugar, Uracil instead of thymine, bonds to itself to form unique structures |
| Ribozymes | RNA with catalytic function |
| Chromosomes | Structures that contain genetic material, made up of chromatin which is 50% DNA and 50% protein |
| Genome | All the genetic material in an organism, for bacteria that is a single circular chromosome and for eukaryotes it is one complete set of nuclear chromosome |
| Purpose of DNA Sequences | Synthesis of RNA and cellular protein, replication of chromosomes, proper segregation of chromosomes, compaction of chromosomes so they can fit in living cells |
| Bacterial Chromosomes | Single and circular, few million nucleotides in length, majority is protein encoding genes |
| Intergenic Regions | Non-transcribed DNA between adjacent genes |
| Nucleiod | Where the chromosome is found in bacterial cells, not a true nucleus, some cells might have multiple chromosomes when they are in the process of division |
| How much does the bacterial chromosome have to compact? | 1000x |
| Loop Domains | First level of bacterial chromosome compaction, formed with DNA binding proteins, compacts 10x smaller, number of loops vary based on the size of DNA |
| Super-coiling | Uses toperasisomerase, compacts 100x |
| Positive Supercoiling | Twists to the right |
| Negative Supercoiling | Twists to the left, what is found in cells |
| Effects of Negative Supercoiling | Opposite the coil of DNA, helps compact chromosome, creates tension that can be released by DNA separation |
| DNA Gyrase | (DNA Topoisomerase II) enzyme of supercoiling, aids in negative supercoiling, unique to bacteria |
| DNA Topoisomerase I | Enzyme of supercoiling, relaxes supercoiling |
| Exons | Protein encoding sequences, only about 2% of the human genome, amount varies based on the size of the gene |
| Introns | Non-coding intervening sequences, amount varies based on the size of the gene |
| Eukaryotic Chromosomes | Large, linear chromosomes that are usually diploid, large because they have a lot of repetitive DNA sequencing |
| Origins of Replication | Sites necessary to initiate DNA replication, Eukaryotes have several |
| Centromeres | Play a role in the segregation of sister chromatids |
| Telomeres | Specialized regions at the end of chromosomes, prevent chromosome translocation and shortening |
| Sequence Complexity | The number of times a particular base sequence appears in a genome |
| Unique or non-repetitive Sequencing | Base is found once or only a few time in a genome (41%) |
| Moderately Repetitive Sequencing | Base is found a few hundred or several thousand times (59%) |
| Highly Repetitive | Base is found tens of thousands to millions of times, relatively short, some sequences are interspersed throughout the gene, others are found in clusters |
| Breakdown of Genes | 2% encode protein 24% introns and enhancers 15% unique sequences Those make up unique sequencing 59% repetitive DNA |
| Eukaryote Compaction | Must compact 250,000x, DNA wraps around histones to form nucleosomes which are the repeating structure of chromatin |
| Nucleosome | "Beads on a string", DNA wraps around histone (10x compaction), super positively charged, histone is composed of 2 of each H2A, H2B, H3, and H4, H1 is the linker |
| 30 nm Fibers | histones are bound together, solenoid and zig-zag models |
| Solenoid Model | Nucleosomes are bound together in 3-deep bunches |
| Zig-Zag Model | Nucleosomes are bound together in a zig-zag, two deep |
| Nuclear Lamina | Fibers that line the inner nuclear membrane |
| Internal Matrix Proteins | Assist in forming loops |
| Loops Form | 30 nm fibers attach to the inner membrane of nucleus and form loops |
| Heterochromatin | Tightly compacted, almost inactive, used in cellular division |
| Euchromatin | Slightly less condensed, more active, used in non-dividing cells |
| M Phase | Level of compaction increases dramatically, cells become heterochromatic |
| DNA Replication | Process by which genetic material is copied, occurs very quickly and accurately |
| Daughter Strands | The two new strands formed in DNA replication |
| Parent Strands | The original strands of DNA used in replication |
| Semi-Conservative Process | Each new strand of DNA has one new strand and one old strand |
| Meselson and Stahl's Discovery | 1958, DNA replication is a semi-conservative process, labeled and traced the nitrogen atoms, saw a single strand after one round of replication and two bands after two rounds |
| Bacterial Replication | Only one origin of replication (oriC) and proceeds bidirectionally and forms two replication forks |
| GATC | Methylization sites that separate the template strand from the daughter strand |
| AT-Rich Regions | Break more easily because they have less hydrogen bonds |
| DnaA Box | Where helicase bonds and breaks the hydrogen bonds |
| DnaA Protein | Binds to the DnaA box to initiate replication |
| DnaC Proteins | Aids DnaA in attracting DnaB |
| Helicase (DnaB) | Separates double stranded DNA |
| Topoisomerase II (DNA gyrase) | Removes positive supercoiling |
| Single-Stranded Binding Proteins | Prevent DNA from reforming the double helix |
| Primase | Synthesizes short RNA primers, starts DNA polymerase III |
| DNA Polymerase III | Synthesizes DNA in leading and lagging strands, larger, cannot initiate synthesis and can only synthesize 5' to 3' |
| DNA Polymerase I | Removes RNA primers and fills in the gaps, single polypeptide |
| DNA Ligase | Links Okazaki fragments together |
| Tus | Binds to ter sequences and stops the replication |
| Leading Strand | Moves towards the replication fork, all one strand, 5' to 3' |
| Lagging Strand | Moves away from the replication fork, made in small fragments (Okazaki fragments), still 5' to 3' |
| DNA Polymerase I and III | Used in DNA replication |
| DNA Polymerase II, IV, and V | Repair damaged DNA |
| Primosome | Complex composed of DNA helicase and primase |
| Replisome | Complex of primosome and both DNA polymerase |
| Termination Sequeneces | Ter, occurs where the two replication forks meet, uses Tus protein to stop it |
| T1 | Stops counterclockwise forks |
| T2 | Stop clockwise forks |
| Catenanes | Two intertwined circular DNA molecules resulting from bacterial DNA replication, separated by topoisomerase |
| Mutagenesis | The creation of mutants |
| Temperature-Sensitive Mutants | Allowed to grow at certain temperatures but dies at others |
| Fidelity | How accurate synthesis is |
| Chemical Formation | Polymerase catalyzes the formation of covalent bonds between phosphate and sugar, lose two phosphate |
| DNA Pol is a Processive Enzyme | Remains attached to the template as it synthesizes the daughter strand, held on with a beta clump protein and a clamp hold stays on for 500,000 nucleotides at 750/sec |
| Why is the fidelity so high? | 1 mistake for every 1x10^8, Stability of base pairing Structure of DNA polymerase active site Proofreading function of DNA polymerase |
| Exonuclease Activity | Can remove and replace mistakes in the base sequence |
| Eukaryotic DNA Replication | multiple origins of replication Different DNA polymerases RNA Primers are removed differently Telomeres |
| Alpha Polymerase | Initiates DNA replication with primase |
| Epsilion Polymerase | Replicates the leading strand |
| Sigma Polymerase | Replicates the lagging strand |
| Gamma Polymerase | Replicates mitochondrial DNA |
| RNA Primer Removal (Eukaryote) | Uses flap endonuclease, RNA is pushed up and cut off in fragments |
| Telomeres | Shorten with age because it doesn't get replicated, telomerase keeps this from happening but it starts malfunctioning as you age |
| Senescent | Cells stop dividing |
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RoseGrace
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