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Genetics Test 3
| Term | Definition |
|---|---|
| Genetic Code | 20 amino acids formed out of combos of 4 nucleotides, 64 combinations (redundancy) , 61 code for amino acids, 3 code for stop |
| Stop Codons | UGA, UAG, UAA |
| Coding Process | RNA-like template > mRNA > polypeptide |
| tRNA | Translates the mRNA into amino acid sequence using anticodons |
| What is primary structure of the amino acid sequence? | Polypeptides |
| 21st and 22nd Polypeptides | Stop codons code for these in some other organisms, means the genetic code is not universal |
| Transcription | DNA to mRNA, initiation, elongation, and termination |
| Transcription Initiation | Promoters signal RNA polymerase where to begin transcription, in prokaryotes, sigma factors help and in eukaryotes transcription factors help |
| Transcription Elongation | RNA polymerase catalyzes the synthesis of mRNA 5' to 3' |
| Transcription Termination | Terminator sequences tell RNA polymerase where to stop |
| Downstream | From the first letter on to the transcribed portion, positive numbers |
| Upstream | Moves towards the promoters, negative numbers |
| Prokaryotes | Transcription and Translation occur simultaneously |
| Eukaryotes | Transcription happens in the nucleus and translation happens in the cytoplasm, transcription > RNA processing > Translation |
| Hairpin loop | Made by the termination sequence, stops transcription |
| RNA Processing | Only in eukaryotes, 5' methylated Guanine cap and 3' poly-A tail, both work to increase RNA stability, modified by enzymes, RNA splicing |
| RNA Splicing | Removes introns that are found in the DNA but not in mature mRNA, removed by spliceosomes |
| Alternative Splicing | Different mRNAs can be produced by one transcript |
| Transplicing | Rare, multiple transcripts are used to form one mRNA |
| Translation | mRNA translated by tRNA to polypeptides |
| Codon | 3 base pair nucleotide sequence in mRNA |
| Anticodon | 3 base pair nucleotide sequence in tRNA |
| tRNA | Primary Structure: nucleotides Secondary Structure: attaches to amino acid at one end and anticodon at the other Amino acid and anticodon can be mismatched if treated chemically |
| Uncharged tRNA | tRNA with no amino acid attached |
| rRNA | Make up ribosomes, not translated just transcribed, bigger in eukaryotes |
| Ribosomes | Complex structures of rRNA and protein |
| Prokaryotic Ribosomes | 70s, 50s/30s, 16s nucleotides |
| Eukaryotic Ribosomes | 80s, 60s/40s, 18s nucleotides |
| Ribosome Structure | A (aminoacyl) site: where amino acid sits P site: where tRNA sits |
| Ribosome Process | Slides along mRNA A site > P site > E site (exit), Stops when stop codon brings in a release factor and causes it to disassemble |
| Regulation | Turning on or off, up or down, switch or dimmer, can occur at any point in the gene expression pathway (mostly at the very beginning of transcription) |
| Gene Regulation | The level of gene expression can vary under different conditions |
| Constitutive Genes | Nonregulated genes, constant levels of expression, normally encode proteins that are always required for survival |
| Benefit of Gene Regulation | Conserving energy and not making proteins that are not always necessary |
| Regulator Proteins | Repressors: bind to DNA and inhibit transcription (negative control) Activators: bind to DNA and increase transcription (positive control) |
| Small Effector Molecules | Bind to the repressor/activator, can aid or inhibit activators and repressors |
| Inducers | Aid activators in increasing transcription, work on inducible genes |
| Corepressors | Aid repressors in decreasing transcription, works on repressible genes |
| Inhibitors | Deactivate activators to decrease transcription, works on repressible genes |
| Operons | A group of genes that has a single promoter and is regulated as a unit |
| lac Operon | Processes lactose, three genes, E. coli is the example |
| Lactose | Milk sugar, disaccharide composed of galactose and glucose |
| lacZ | Encodes for beta-galactoside |
| lacY | Encodes for Lactose permease |
| lacA | Encodes for Galactoside transacetylase |
| Operators | Where activators and repressors bind, RNA polymerase binds here, repressors bind to the operator and stops transcription when lactose is not present |
| Complexities of lac operon | It is a continuum and it has three operator sites that bind in a loop to stop the RNA and it has Catabolite Activator Protein (CAP) |
| Catabolite Activator Protein (CAP) | Regulates in response to the presence or absence or glucose, allows for preferential use of glucose, functions in a global regulatory network |
| trp Operon | Involved in the synthesis of tryptophan, five genes |
| trpR | Encodes the trp repressor protein, made inactive unless corepressor (activated by the presence of tryptophan) binds to it and stops the creation of tryptophan |
| Attenuation (Cutting Short) | Transcription begins and is terminated before the entire mRNA sequence is made, uses translation to regulate transcription, leader sequence can regulate by shortening using the 3-4 loop which only forms under tryptophan levels |
| Catabolism Operons | Generally inducible |
| Anabolism Operons | Generally repressible |
| Translational Regulation | Regulatory proteins and anti-sense RNA |
| Translation Regulatory Proteins | Recognizes sequences in mRNA, inhibits translation, called translation repressors, binds next to or outside the Shine-Dalgarno sequence/start codon and prevents initiation |
| Antisense RNA | An RNA strand that is complementary to the mRNA is synthesized, prevents initiation |
| Posttranslational Regulation | Feedback inhibition and protein modification |
| Feedback Inhibition | Common mechanism, inhibits an enzyme that acts early in the pathway, changes the active site so it can no longer bind |
| Protein Modification | Some are irreversible: proteolyitc processing, attachment of prosthetic groups, sugars, and lipids Some are reversible: transiently affect protein function, add or remove a functional group |
| Riboswitches | Discovered in 2001, converts RNA between its two secondary confirmations through the binding of small molecules |
| Purpose of Riboswitches | Regulates 3 to 5% of bacterial genes, can regulate both transcription and translation, Gram negatives regulate at translation level and gram positives regulate at transcription level |
| How do eukaryotes benefit from gene regulation? | Respond to changes in the environment and respond to stress |
| What is gene regulation necessary for? | Accurate gene expression during various stages of development and differences among cell types |
| Transcription Factors | Proteins that influence the ability of RNA polymerase to transcribe a given gene, has sequences called control elements/regulatory elements/regulator sequences |
| General Transcription Factors | Required for the binding of RNA polymerase |
| Regulatory Transcription Factors | Serve to regulate the transcription of target genes |
| Activators | A regulatory protein that increases the rate of transcription (enhancer) |
| Repressor | A regulatory protein that decreases the rate of transcription (silencer) |
| Domains | Regions on transcription factor proteins that specific functions, one is for DNA binding and one is for binding to effector molecules |
| Motif | Subset of a domain, helix-turn-helix, recognition, zinc finger, and leucine zipper |
| Modulation Types | Binding a small effector molecule (hormone) Protein-protein interactions Covalent modification (phosphorylation) |
| Steroid Receptors | Regulatory transcription factors that respond to steroid hormones, hormones that bind to the transcription factor |
| Chromatin Remodeling | Dynamic changes in chromosome structure, ATP-dependent, carried out by diverse, multi=protein machines that change nucleosome positions, evict histones, and use histone variants to create special chromatin |
| Closed Confirmation | Heterochromatin, tightly packed, transcription is difficult/impossible |
| Open Confirmation | Euchromatin, loosely packed, transcription can occur |
| DNA Methylation | A change in chromatin structure that silences gene expression, carried out by DNA methyltranferase, present in some but not all eukaryotes, increases transcription |
| Unmethylated | No methylization |
| Hemimethylated | One strand is methylated, the other isn't |
| Fully Methylated | Both strands are methylated |
| Insulators | Wrap around DNA strands, limit regulation to a particular gene, some act as barriers and some block enhancers |
| ENCODE project | Encyclopedia of DNA Elements Consortium, isolate sequences in human RNA, identify transcription factor binding sites, map DNA methylation, identify histone modification, map DNase I cleavage sites |
| Epigenetics | The study of mechanisms that lead to changes in gene expression without changing the DNA sequence, reversible and heritable |
| Epigenetic Inheritance | Epigenetical changes passed from parent to offspring |
| Examples of Epigenetic Inheritance | DNA Methylation Chromatin Remodeling Covalent Histone Modification Localization of Histone Variants Feedback |
| Development | Series of stages where a fertilized egg becomes a mature adult, maintained by epigenetic mechanisms (genomic imprinting, x-chromosome inactivation, formation of specific cell types and tissues) |
| Environmental Agents | Commonly cause epigenetic changes, flowering plants, mice expressing the Agouti gene based on diet, toxins and cancer |
| Mice Experiment | Pregnant mice fed folic acid and vitamin B, increases DNA methylation and leads to darker fur |
| Toxins | Turn on oncogenes which cause cancer, down-regulate tumor repressors |
| Alternative Splicing | At RNA processing level, sometimes exons are removed and sometimes they are left in, means that multiple mature mRNAs can form from one RNA strand |
| RNA Stability | Varies considerably, can be modified through the length of the poly-A tail and destablizing elements |
| RNA i (interferences) | Discovered by Dr. Mello and Dr. Fire, double stranded RNA forms in the cell, RISC cuts it up and takes some antisense RNA to silence the gene, uses dicer, splicer |
| RNA Binding Proteins | Inhibit the ability of ribosomes to initiate transcription |
| Viruses | Nonliving particles with nucleic acids and genomes, have to infect cells to reproduce |
| Host Range | The number of species a particular virus can infect |
| Structure of Viruses | All have a nucleic acid genome (DNA or RNA) wrapped in a protein capsid, some have spike glycoproteins |
| Viral Envelope | Derived from plasma membrane of host cell, some viruses have it |
| Genome Composition | Can be DNA or RNA , single or double stranded, normally thousands of base pairs (which is small) |
| Helical | Long tube structure |
| Polyhedral | Multisided structure |
| Enveloped | Has a viral envelope |
| Bacteriophage | Spider-like shape with capsule containing viral genome |
| Viral Reproductive Cycle | Series of steps that results in the production of viruses, attachment, entry, integration, synthesis of viral components, viral assembly, release |
| Attachment | Virus attaches to the host cell |
| Entry | Virus/viral genome enters the cell |
| Integration/Excision | Does not occur in lytic cycle, viral genome integrates into the host genome |
| Synthesis of Viral Components | Viral proteins and DNA/RNA is formed by the host cell |
| Viral Assembly | Viral components assemble |
| Release | Viruses are released from the host |
| Latent | When viruses remain inactive and no new viruses are made, normally occurs during the lysogenic cycle |
| Lysogenic Cycle | Viral DNA is incorporated into host chromosomes as a prophage and may be latent for many cell divisions |
| Lytic Cycle | New virus particles are made |
| Temperate Phages | Can undergo both lytic and lysogenic cycles, phage lambda is an example |
| Emerging Viruses | Viruses that have risen recently and are more likely to cause infection than previous strains, Avian flu, COVID, Zika |
| Coronavirus | Enveloped, single-stranded RNA genome, helical nucleocapsid, named for the crown of sparks on the surface, seven different coronaviruses affect humans (SARS, MERS, and COVID-19 are fatal) |
| Bacteriophage | Virus that affects bacteria, lambda phage is a model |
| Lambda Phage | Linear in the virus, circular in the cell, genome is organized in operons based on function |
| CII Protein | Helps lambda transition between the lytic and lysogenic cycles, inhibits the lytic cycle, when conditions are favorable, the CII degrades and the virus switches from the lysogenic to the lytic cycle |
| HIV | Causes AIDS, infects T cells inhibiting immunity, RNA genome, has three unique enzymes: integrase, reverse transcriptase, and HIV protease |
| Integrase | Integrates into the host genome |
| Reverse Transcriptase | Makes DNA out of RNA |
| HIV Protease | Cuts out |
| HIV Progression | 1. HIV enters host cell 2. DNA transcribed from RNA> reverse transcriptase 3. Integrase cuts host chromosome, integrates viral DNA, becomes latent (provirus) 4. Viral components form 5. Virion assembles 6. HIV protease cuts and helps assemble it |
| Mutation | Heritable change in the genetic material sequence, creates allelic variation and helps species adapt, mutations are more often harmful than helpful |
| Chromosome Mutation | Changes in chromosome structure |
| Genome Mutation | Changes in chromosome number |
| Gene Mutations | Small changes in DNA that affect a single gene |
| Point Mutation | Change in a single base pair |
| Transition | Change of C or T to an A or G |
| Transversion | Change of a pyrimidine (C or T) to a purine (A or G), base substitution |
| Silent Mutation | A base substitution that does not result in a different amino acid |
| Missense Mutation | A base substitution that results in a different amino acid |
| Nonsense Mutation | A base substitution that results in a early stop codon |
| Frameshift | Addition/deletion of nonmultiple of three that changes the amino acid sequence |
| Reversion Mutations | One mutation undoes another to return the gene to its wild type |
| Intergeneic Reversion Mutation | Within the same gene |
| Intageneic Reversion Mutation | Happens in a different gene |
| Random Nature of Mutations | Mutations are random, experiment where identical colonies where treated and the ones with resistance had it before treatment |
| Spontaneous Mutations | Internal, results from abnormalities in normal cellular/biological processes (errors in DNA replication) |
| Induced Mutations | Result from changes outside the cell |
| Mutagens | Agents that alter the structure of DNA and cause mutations, can cause cancer, can affect offspring |
| Chemical Mutagens | Base modifiers, intercalating agents, and base analogues |
| Base Modifiers | Covalently modify base structure or disrupt pairing |
| Intercalating Agents | Directly interfer with replication |
| Base Analogues | Incorporate into DNA and disrupt structure |
| Physical Mutagens | Radiation can damage DNA, x-ray, gamma rays |
| Mutation Rate | The likelihood that a gene will be altered by a new mutation. 10^5 to 10^9 per generation, humans have 100-200 new mutations per generation |
| Mutation Frequency | The number of mutant genes divided by the number of genes in a population |
| Ames Test | Test for whether or not something is a mutagen |
| DNA Repair | Vital for the survival of all organisms 1. Detect structural irregularity 2. Abnormal DNA is removed 3. Normal DNA is synthesized |
| Genetic Recombination | Involves chromosomes breaking and rejoining to form new combinations, creates allelic variation |
| Homologous Recombination | Crossing over: occurs between homologous chromosomes, allelic variation Sister Chromatid Exchange (SCE): p roduces no allelic variation |
| Double Strand Break Mode | 1. Strand breaks 2. Degerdation and D-loop forms 3. Gap repair 50% recombinance |
| Site-Specific Recombination | 2 DNA segments (nonhomologous) align themselves at specific sites, used by viruses and mammals to produce antibodies |
| Transposition | Integration of small segments of DNA into the chromosome, called transposable elements (jumping genes) |
| Simple/Conservative Transposition | Cut and paste |
| Retrotransposition | Copy and paste, increases the number, limited to eukaryotes, alu is an example |
| LINEs | Long Interspersed Elements, 1000 to 10,000 bp, found a few thousand to several hundred times |
| SINEs | Short Interspersed Elements, less than 500 bp, alu is an example |
Created by:
RoseGrace
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