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Biol 207 Midterm 1
Lecture 1-4, 11
| Term | Definition |
|---|---|
| Diploid | (2n) 2 copies of every chromosomes |
| Homologs | pair of similar but non-identical chromosomes, same gene order potentially different alleles |
| Haploid | (n) gametes, 1 copies of every chromosome |
| c-value | the amount of DNA measured in bp contained in a normal cell |
| n-value | number of chromosomes found in the haploid cell |
| Purpose of mitosis | to create genetically identical daughter cells |
| Mitosis | the separation of chromatids |
| Purpose of meiosis | to generate haploid gametes and generate genetic diversity |
| Meiosis I | reductional division & separation of homologs |
| Meiosis II | separation of sister chromatids and equational division, 4 meiotic products formed |
| Equational division | when n goes to 2 *n |
| Prophase I | chromosomes condense, crossing over occurs, synapsis occurs, spindle apparatus forms, nuclear envelope breaks down, chromatids attach to kinetochore MT's |
| Metaphase I | bivalents line up at metaphase plate and independent assortment begins |
| Anaphase I | dysjunction of homologs |
| Telophase I | two cells form by cytokinesis |
| Bivalents | pair of homologs |
| Karya | nucleus |
| Autosomes | non-sex determining chromosomes |
| chromosome | one molecule of DNA |
| Heterogametic | XY |
| Homogametic | XX |
| Metacentric | centromere at the middle of the chromosome (e.g. chromosome 1) |
| Acrocentric | centromere is asymmetrically placed (short arm (p) & long arm (q)) (e.g. chromosome 13) |
| Telocentric | centromere is right at the end of chromosome (none in humans, rare because it is unstable) |
| Submetacentric | centromere is just off the middle (e.g. chromosome 2) |
| Trypsin | giemsa stain (stain's DNA blue) - latches on to A-T rich regions |
| G-banding | to aid in visualizing chromosomes, the A-T rich regions will stain darker because it is heterochromatic (poor genes) |
| p | petite arm |
| q | long arm |
| Mutation | a permanent change in genetic material that can be either spontaneous or induced, and does not need to have a phenotypic effect |
| Recombination | system of establishing genetic variation that has been selected for |
| Base substitution transitions | single base pair change that swaps a pyrimidine for a pyrimidine or a purine for a purine at the same protein |
| Base pair transversion | single base pair changes that changes a pyrimidine for a purine, or vise versa. |
| Insertion/deletion (indel) | the insertion or delection of 3 or multiples of 3 nucleotides causes frameshift mutations |
| Silent mutation | base substitution transition that results in no change to the amino acid |
| Missense mutation | base pair substitution transition that results in the wrong amino acid |
| Nonsense mutation | base pair substitution transversion that results in no amino acid being encoded |
| wild-type | the reference strain |
| Frameshift mutation | shift the reading frame which therefore affects every codon downstream, and is caused by indels |
| Effective mutation rate | 1/10^6 base pairs |
| Fragile X disorder | most common form of inherited mental retardism. Individuals tend to have a smaller stature due to the effect of strand slippage in repeated DNA sequences |
| Huntington's disease | a disease caused by strand slippage in repeated sequences, particularily the trinucleotide repeat of CAG. The severity is linked to the number of repeats (more sepeats = more severe) |
| Depurination | loss of purine base of nucleotide |
| Deamination | when an amino acid is spontaneously removed and replaced with oxygen. This is very common and requires replication to stabilize the mutation |
| Oxidative damage | this is when a lesion is caused by a reactive oxygen species (ROS). ROS reacts with guanine to produce 8-oxo-dG. This results in carbon and oxygen double bond no longer participating in H bonds with cytosine, so 8-oxo-dG forms stable H bonds with A |
| ROS | reactive oxygen species that usually cause transversions |
| Tautomerization | isomers that are random and transient in aqueous reactive solution that cause transitions |
| Ames test | A very common test that takes a potential mutagen, expose it rat liver enzymes which will activate the mutagen in a biologically relative form, then expose it to His bacterial strain and observe growth. |
| Revertant | chemical is a mutagen |
| Base analogs (5-BU) | a chemical that looks like a base BUT causes incorrect base pairing |
| 5-Bromo-uracil | a chemotherapy drug that is a thymine analog that base pairs with G (and sometimes A) instead, causing transitions |
| Alkylating agents | add ethane groups or subgroups and causes transitions |
| Intercalating agents (proflavin) | a mutation that fits between stacked bases and cause distortions in double helix, which cause replication slippage and indels |
| UV damage | the most potent mutagen that causes the formation of thymidine dimers so when DNA polymerase comes to a dimer, it cannot read the base. During DNA replication, the lesion is filled with a variable number of adenines. It can be repaired by photolyase |
| Photolyase | an enzyme that cleaves to covalent bonds and repairs UV damage |
| Model organisms | used by scientists during experiments. Typically are rapidly reproducing, have lots of phenotypes, have certain universal traits, are small, and easy to work with |
| Mutagenesis screening | a very common process that looks for interesting phenotypes |
| RNA intererence (RNAi) | the introduction of a dsRNA molecule that triggers a targeted degradation of all the endogenous mRNA's. It mimicks a knock-down/deletion mutation |
| CRISPR/Cas9 | a gene editing tool that uses naturally occuring enzymes from the bacteria and alters the genome in a specific and targeted way |
| Somatic cell mutations | mutations that do not affect the transmission of genetic material to organismal progeny |
| Gene | a sequence of DNA that encodes a trait, also known as the unit of heredity |
| Operons | a set of coordinately controlled genes that are only in prokaryotes |
| Promoter | DNA sequence that indicates the start of a gene and is the site of RNA polymerase assembly |
| Upstream regulatory elements (URE) | controls regulation of genes. Some examples are enhancer elements, repressor elements, etc |
| Elements | another way to say DNA sequence |
| Major groove | more accessible to read DNA |
| Minor groove | less accessible to read DNA |
| MyoD | a positive regulator in eukaryotes that determines where a muscle is going to go. When it is bound to minor groove of DNA, it turns ON transcription |
| Lac I | a negative regulator in prokaryotes that binds protein to DNA to inhibit transcription. It is a repressor protein of Lac operon and it is heterotetramer. When it binds to DNA (operator sequence) it causes it to loop and inhibits Lac operon expression. |
| Lac operon | a set of structural genes that code for proteins to metabolize lactose |
| Heterotetramer | made of 4 proteins |
| Operons | occur in bacteria where a set of related genes are regulated together and are regulated at the operator |
| Lactose | disaccharide of glucose and galactose |
| Beta glactosidase | an enzyme that cleaves the disaccharide lactose to produce galactose and glucose which then ultimately enter glycolysis. |
| Allosteric shift | shape change |
| X-galactosidase | a substrate for Beta-gal that changes colour |
| Plasmid | an extra piece of DNA that can carry extra DNA and replicates separately from the genome and is ofund floating freely in the cytoplasm |
| Vectors | plasmids used for cloning |
| Lyse | to break |
| Restriction enzymes (RE) | Specific molecular scissors. Naturally occuring enzymes that evolved to destroy viral DNA. They recognize 4-6 base pair sequences and cut dsDNA |
| EcoR1 | an RE that cuts at a base pair palindromic sequence |
| Palindromic | same sequence on both strands, in terms of cutting dsDAN, it is staggered and leaves "sticky ends" |
| Gel electrophoresis | the separation of DNA based on size. The gel is made of agarose that polymerizes into a polymer-matrix and pulls DNA to the psotive end based on size. |
| Basic blot technique | to find a unique sequence in a mixture separated on a gel |
| Probe | a single stranded DNA sequence labelled with a fluor which anneals to complementary sequence |
| Fluor | fluorescent molecule |
| Southern blot | technique that looks for a specific DNA sequence on a gel and allows you to detect the presence of a sequence of interest |
| Northern blot | technique where you run a gel and use an ssDNA probe (without having to denature RNA) and it determines gene expression patterns |
| Western blot | technique that detects proteins on polyacrilamide gel |
| Restriction fragment length polymorphism (RFLP) | fancy term for dna fingerprinting where you use a highly polymorphic locus that does not have evolutionary pressures to identify individuals |
| Cloning | a technique where you replicate a piece of DNA in a foreign host (such as E. coli) and produce a lot of our gene of interest |
| Ligase | an enzyme that glues DNA fragments together |
| Mini prep | a plasmid extraction technique |
| Transformation | a technique where you introduce recombinant plasmid into E. coli |
| Multiple cloning site (MCS) | where many RE sites are clustered |
| ORI | the origin of replication. This bacterial sequence allows replication of vector in E. coli because bacteria recognizes it as its own |
| ampRgene | gene that confers antibiotic (ampicillin) resistance and allows for successful transformation because only the bacterio with the plasmid will survive |
| Selectable marker (LacZ) | selected for successful cloning |
| Successful transformation | bacteria that grows on ampicillin |
| Successful cloning | bacteria that grows on X-galactosidase |
| PCR product | a specific DNA sequence that was amplified by the polymerase chain reaction (PCR) from a mixture |
| cDNA | reversed transcribed mRNA, it represents a stable copy of expressed genes and processed mRNAs |
| cDNA library | set of bacteria that each contain a clone cDNA |
| Reverse transcriptase (RT) | a viral enzyme that reverses transcription and is used to make cDNA |
| Taq | acronym for thermus aquaticus. This is a thermsotable DNA polymerase that we use a lot and functions best at 72 degrees celsius |
Created by:
leahdemchuk
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