Test 1 Summary Material
Test 1 Summary Material Bio 300
Virginia Commonwealth University
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This 15 page Bundle was uploaded by Jewelle Williams on Sunday July 24, 2016. The Bundle belongs to Bio 300 at Virginia Commonwealth University taught by Dr Teshelle A. Ponteen Green in Summer 2016. Since its upload, it has received 53 views. For similar materials see Cellular and Molecular Biology in Biology at Virginia Commonwealth University.
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Date Created: 07/24/16
Bio 300 Study Guide Chapter 1-2,5-8 Chapter 1 Summary: Levels of Organization: o Organism Level: OrganismOrgan Systems Organs Tissues o Cellular Level: CellOrganelles Macromolecules Molecules Atoms Cell Theory- o All organisms are composed of one or more cells o Cells are the fundamental building blocks of life o All cells arise from preexisting cells What are cells? 3-D membrane bound structures that can create identical copies of themselves and have descended from a common ancestor o Many different types: neurons, paramecium, plant stems, bacteria o Small ~20 micrometers All cells have DNA and RNA of some sort o DNA/RNA long/short polymer chains of a sugar (deoxyribose/ribose), phosphate and nitrogenous base o Undergo Replication (DNA 2 DNA) Transcription (DNA RNA) and Translation (RNA Protien) Visualizing cells: o Naked eye: human eggs o Light Microscopy: use light to see most plant, animal and bacterial cells as well as some large membrane bound organelles Led to the discovery of cells and the start of cell biology Color Stains Can magnify to ~1000x Helped with developing the cell theory Fluorescence Microscopes- take advantage of the refractive index Laser light, single wave length, focus’ on a single layer Confocal Microscopy- to tag antibodies good for targeting specific genes o Electron microscopy: All the way down to the atomic level, small structures in the cell like ribosomes and lysosomes. Uses beams of electrons to illuminate the specimen, Black and white Transmission (TEM) to see internal structures Scanning (SEM) to see external 3-D shapes o Important parameters in microscopy: Magnification: the ratio of an objects image side to real sixe (ex 40x), 2. Resolution the clarity of the image, 3 Contrast the visible differences in brightness between parts of a sample Cellular processes: o Nutrition: Food needed for energy and building materials o Digestion glycolysismetabolism o Absorption of water nutrients ions and other materials o Biosynthesis- organizing organic substances activity o Excretion- removal of waste o Secretion- Hormones and neurotransmitters o Reproduction- nuclear division o Movement- cellular contractions kinetochore o Egestion- elimination of insoluble compounds and non-digestible particles Prokaryotes vs. Eukaryotes Eukaryotes: Both Prokaryotes, Bacteria/ Protests/fungi/plants/animals Archea Linear Cell Walls Circle DNA in nucleoid Compartmentalized!!! (complex DNA Non- segmented membrane bounded organelles) Nucleus Ribosomes No nucleus (Nucleoid) Cytoskeleton for more efficient Cytoplasm/ No cytoskeleton transport Cytosol single or multi-cellular (plants, Plasma Single celled animals, fungi) Membrane Sexual and Asexual Chromoso Asecual Reproduction mes Yeast is the most simple Archea and Bacteria eukaryote) Linear DNA (in nucleus) More Diverse More Complex Most diverse and numerous (Cocci, bacillus, spirillum) Vacuoles Complex Cell Wall Some don’t have cell walls Extremophiles (Archea) Many food sources (O2, H2 S, photosynthesis) Larger cells Organelles and their role in the “city” Organelle Function Plasma Membrane City Limits (regulates what goes in and out) Nucleus City Hall (controls cell activity using DNA) Nuclear Envelope Police force (protects the nucleus, reg. what goes in and out Ribosomes Factories (make protiens) 80-90% of activity Mitochondrion/Chloroplas Powerplant that makes ATP ts Lysosomes Recycling plants (contain enzymes to break things down) Golgi Apparatus Postal System- Packaging and transport (Cis face and trans face Rough ER Highways that make protiens and transport things Smooth ER Synthesizes lipids Peroxisomes ________ have H2O2 to destroy things produces free radicals that react with reactive O2 Cytosol Just the liquid gel fluid NO ORGANELLES Cytoplasm The organelles and the fluid Cytoskeleton Transport in the intermembrane system using microtubules,> intermediate filaments > actin Animal vs Plant Cells Animal Both Plants No cell wall Cytoplasm Chloroplast Heterotrophic (Cellular Ribosome Cellulose/Cell walls Respiration) Somatic and Gametic Cells DNA Autotrophic (photosynthesis) Cell membranes Only Somatic Mitochondrion DNA vs. RNA DNA Both RNA Thymine (C bound to Carbon/Phosphate Uracil H2C bound to H) Backbone the C Helix Nitrogen Bases Single strand Deoxyribose 5-Carbon Sugar Ribose (extra (hydrogen) hydroxyl) Replication A, C, G Translation More stable because Transcription Less stable because the H is more stable (Central Dogma of of the hydroxyl Biology) group Chapter Questions: 1.1A vacuum cannot reproduce, a potato and a person has all 1.2Different sizes, missing pieces, < bad. Better colors? 1.3You could use a flask with the __________ 1.4???? 1.5It helps with transport within the cell as well as specializing functions, protecting DNA and 1.6Light Electron Microscopy: Allows you to see small structures within the cell like the cristae inside the mitochondrion 1.7Because simple eukaryotic cells react similarly and are similar to our own cells studying brewers yeast allows us to see how things work on a simpler level 1.8Cytosol- just the gel like liquid without the organelles, Cytoplasm the liquid with the organelles, Mitochondrion- the power plant, Nucleus- city hall, Chloroplasts- power plant, Golgi Apparatus- packaging plant, Peroxisomes: H2O2 destruction, Plasma membrane- gate, Endoplasmic reticulum- _____________________, 1.9A False, B. True, C False, D True E False, F True, G. True H. True 1.10 , What makes up the Indomembrane system? o The RER, Golgi, Lysosomes, Nuclear envelope, Plasma membrane and vacuoles Methods of cell study: Reductionism (macro to micro) Chapter 2 Chemical Components of Cells 70% of our bodies are made of water. Out of the other 30% 26% is macromolecules Cells are made mainly of carbon complex’s like protiens sugars and nucleic acids o The “Big 4” = 96.5% of our carbon makeup 1. Oxygen 2. Carbon 3. Hydrogen 4. Nitrogen Cell operations stay within a VERY narrow pH Bonds: o Covalent: The strongest between 2 molecules who share electrons Nonpolar: equally shared electrons Molecular Marriage VERY STRONG require catalysts to break them Usually hydrophobic (lipids plastic, natural gas) Polar: unequally shared electrons Usually hydrophilic (DNA, RNA, Sugar, Salt etc.) o Ionic: The exchange of electrons resulting in charged ions who attract each other Molecular Cations are positive LEO Anions are negative GER o Non Covalent (ionic, hydrogen intermolecular forces): Weak bonds like intermolecular forces that determine viscosity and BP Molecular Dating o Hydrogen Bonds: Weakest bond out of covalent ionic and hydrogen (H and O, N, or F) o Bonds in macromolecules: Hydrogen bonds between nucleotide bases Phosphodiester (covalent) bonds in the phosphate backbone There are 3 bonds between C-G There are 2 bonds between A-T Polymerization involves covalent bonds!!! Macromolecules: o Fatty Acids Fats and membrane Lipids 2 distinctions a carboxyl group (-COOH- which becomes acidic in aqueous solutions) and a hydrocarbon chain Make up Lipids which are Amphipathic Hydrophobic (hydrocarbon chain) and hydrophilic (carboxyl group) Most biologically important are fats (glycerol + fatty acids) phospholipids and steroids Types of Fats: Saturated: carbon chains are “saturated” of full of hydrogens No double bonds o Solid at room temperature (butter) Unsaturated: Carbon chains have double bonds forcing a kink in the chain o Liquid at room temperature (Olive oil, “better for you”) Biological importance: Phospholipid bilayer (hydrophilic heads hydrophobic tails) made of glycerol 2 fatty acids and a Phophate group (part of the hydrophilic head) Triglycerides- 1 glycerol and 3 fatty acids with an ester bond holding them together Store 6x more energy than glucose Have Ester bonds and many others No real monomer!!! o Polymers: Synthesis of polymers involves condensation (-H2O) and breakdown requires hydrolysis (+H2O) to bind an OH- end of subunit to the H+ Have many conformations. They are stabilized into a specific shape via weak non-covalent interaction Binding of Macromolecules is specific which provides the basis for cellular functions. Non covalent interactions include: Vander walls (btwn polarized electron clouds) H-Bonds Ionic bonds Hydrophobic Exclusion Subunits (covalent bonds)macromolecules(non-covalent bonds)Macromolecule assembly (shape) Sugars Polysaccharides, starch, chitin, glycogen Pg. 70-71 Monosaccharides: (CH2O)n with n= 3, 4, 5, or 6 Orientations of -OH groups determine the sugar made from the monomer Isomers- have 2 mirror image forms D-form and L-form Disaccharides (sucrose, maltose) 2 monomers Oligosaccharides: 3-50 monomers Polysaccharides: 100-1000 monomers o Used for energy storage o Plants: Starch o Animals: Glycogen o Structural support: Cellulose (plants), fungi (chitin) Glycolytic Bonds Amino Acids Protiens (70-74) All amino acids have a carboxylic acid group (-COOH- COO-) They do all the things!!!! Make more protiens, structure, transport, degradation, enzymatic action etc. There are only 20 amino acids Amino acids form peptide bonds Have linear structures (until folded then they have a 3-D structure) Also have Isomers (2 mirror image forms) D-form and L- form o Folding is very specific. Some protiens are hydrophilic and some are hydrophobic. In an aqueous environment the 3-D shape will be effected by the hydrophic (inside) and hydrophilic (outside) qualities They have polarity and directionality Nucleotides Nucleic Acids Purines (A, G) and Pyrimidines (T, U, C), ATP (adenosine triphosphate), DNA, and RNA Nucleotides are made of a sugars, a nitrogenous base and a Phophate NucleoSIDES are made of just a nitrogenous base and a sugar Purines are larger than Pyrimidines Central Dogma: DNA codes for RNA and RNA makes DNA Phophodiester Bonds These molecules control gene expression (mainly DNA and RNA) Chapter 5 DNA and Chromosomes Scientists/Exspiriments/Discoverie: o 1869 Friedrich Meischer extracted “nuclein” from WBC’s o 1901 Kossel Isolated and described the organic compounds in DNA o 1910 Levene Tetra Nucleotide Theory o 1923 DNA was localized to chromosomes. Hereditary material? o Pneumococcus and Bacteriophage Esp. Asked: What is the molecule responsible for conveying hereditary characteristics? DNA What are the 4 biological molecules: Adenine, Thimine, Guanine and Cytosine o Griffith Exspirment: He injected mice with smooth and rough strains of streptococcus pneumonia. The mice with the rough (no-lipid), and heat killed s strains survived perfectly fine but the mice with the live s (lipid covered) strains died. So then he injected mice with the dead s and the live r strains and the mice still died because the r strain was able to use the dead s strains genetic material to form a lipid coating. o Avery, Macleod and McCarty Divided heat killed S-strains o Hershey and Chase (1952) Determined how bacteriophages infected bacteria by making the protiens in one and the DNA in one radioactive. By looking at the bacteria they found that the protein was just a transport system. o Chargaff’s Rule: %A=%T (2 bonds) and %G=%C (3 bonds) o Watson and Crick: Discovered the double helix using Rosalind Franklins pictures and Chargaff’s rule Nucleotides are the building blocks of DNA they are made of a Phosphate, a sugar, and a nucleotide base o Purines are larger and pyrimidines are smaller The phosphate backbones are covalently bonded DNA Packing: Chromosomes> loop chromatin fibers> nucleosomes> beads on a string> DNA o Levels: Chromosomes> bead on a string>nucleosomes> histones with DNA o Chromosomes: Bacteria: circular Eukaryotic: linear double stranded with large regions of “junk” non-coding DNA 23 pairs of chromosomes 22 pairs autosomal DNA 1 pair sex chromosomes Homologous (same) non-homologous (not a pair and XY) Karyotype lays all chromosomes out in order from largest to smallest in their homologous pairs abnormalities include Trisomy and monosomy FISH _________________________________________________________ karyotyping G-Banding (giemsa stain) binds to A-T rich areas allowing you to see translocation of genes In m-phase chromosomes are highly condensed compared to interphase interphase (long fine in loops and bands in specific sections of the nucleus) Heterochromatin – most highly condensed form of interphase chromatin o Gene poor and transcriptionally inactive 10% of interphase chromatin Euchromatin- less condensed chromatin o Transcriptionally active and gene rich Mitotic chromatin: Most compact form of chromatin centromere attaches to mitotic spindle, little to no transcription of genes o Condensin comes into the nucleus during interphase to condense the chromosomes even more by binding to chromosomes and forming radial loops Features of a Chromosomes: Centromere- allows the mitotic spindles to separate the identical chromosomes Telomere- where replication ends Replication origin- where replication occurs o Nucleosomes Made of histones, protiens and linker DNA Histone Octamers- 8 Protiens (H2A, H2B, H3 and H4) that are linked together and form the octamer Histone modifications: o The tails have different amino acids M, Ac, P, o Methylation- a form of gene silencing o Acetylation (Ac) and Phosphorylation- helps with gene expression H1 binds to the histone and the linker DNA to pack the nucleosomes more tightly (10-11nm30nm) What does that mean? Represses transcription o Chromatin Remodeling-complex’s- Use hydrolysis to change the position of DNA on nucleosomes They allow or deny access to the DNA promoters and they are inactive during mitosis o Gene silencing: Ex X-Inactivation in females. One X chromosome is chosen very early on and those traits are used while the other is passes on to offspring but not used for coding in that individual Chapter 6 DNA Replication Repair and Recombination Growth and development is dependent on DNA’s ability to store, retrieve and translate information correctly. Replication: o Uses a coding strand to replicate DNA o 99% accurate o Because the double helix is complementary base pairing each strand can serve as 5’3’ o Replication is semiconservative meaning 1 half of the parent strand is given to each of the daughter strands 1954 Melson and stahl figured out that DNA synthesis was semiconservative by growing bacteria in a nitrogen rich and normal nitrogen solution. Then they mixed the bacteria and observed that the DNA when centrifuged was between the light and the heavy nitrogen indicating the semiconservative nature of DNA) o Cell Cycles: G1 phase (7-9hrs check pt G1/S phase check point) repairs Dammage before DNA is copied S-phase (6-8 hrs, DNA replication, intra S phase check point), Slows DNA replication G2 Phase (4-5 hrs G2/M check point) repairs any errors prior to disjunction o Process: Read 3’5’ Replicated 5’3’ The Hydrogen bonds between A-T rich regions are broken first (bc A and T only have 2 H2 bonds) at points called the “Replication origins”. Prokaryotes only have one site of origin Each side of the loop at the replication origin is called a replication fork (2 fork/origin) DNA is replicated bidirectional with about 100 pairs /second in humans The leading strand is replicated continuously in the 5’3’ direction. However, since the other strand (lagging strand) is antiparallel it must be replicated discontinuously via okazaki fragments Okazaki Fragments: ~10bp are laid down by RNA polymerase (Primase) then they are replaced and ligated with DNA polymerase and ligase. Replisomes include: Helicase which unzips the DNA ahead of the DNA polymerase by breaking hydrogen bonds SSB (Single Strand binding) Protien prevents rebinding of nucleotides after helicase separates them by binding to the nucleotide until DNA polymerase comes in DNA polymerase which adds nucleotides 3’5’ on the polymerizing site and edits the strand on the editing site Topoisomerases (DNA gyrase)- creates nicks in one helix of the strand ahead of the DNA polymerase to prevent over winding of the DNA strand as the helicase unzips it then it is re-ligated so it can be read by DNA polymerase 1 Primase- puts on a “place holder” RNA primer to tell where to start replication. DNA polymerase kicks it off and it starts replication at that point Sliding Clamp promotes elongation keeps DNA polymerase attached to the DNA strands firmly. It is upstream of the replication. Ligase- Connects okazaki fragments and nicks in the helix caused by the DNA gyrase The Replisome catalyzes the replication process using the parental strand. Starting at the 3’ end, DNA polymerase catalyzes the addition of nucleotides to the __ end of the growing strand. Correcting Mistakes: Only ~10^7 pairs are messed up. Each strand is proofread by the Editing site of DNA polymerase Telemerase protects ends of DNA by adding another section of DNA information on the lagging strand by attaching an extended DNA sequence at the end of the chromosome. o Repair: Mutations are permanent changes in the DNA. They are often problematic (sickle cell anemia, germ cell mutations, cancer) Most mistakes are caught on the Editing site of polymerase however some mistakes are not caught. Mismatched Pair: When an improper pair is caught by polymerase there are 3 steps after recognition: 1 Excision of the incorrect base by nuclease, resynthesize of the correct bp by polymerase and ligation to fuse the strand by ligase this method corrects 99% or errors Other ways Dammage can occur Single-strand Break: Spontaneous break in one strand of DNA due to radiation alkylating or deamination Double-strand break: a break in both strands due to radiation mishaps in replication or chemicals that break the phosphate back bone. This can be repaired 2 ways: o Homologus Recombination Repair (HRR)- one strand of the damaged DNA invades the homologus chromosome to retrieve the lost data then it is used as the template strand to synthesize the complementary pair and it is ligated o Non-homologous End joining- “quick and Dirty” cleans the damaged ends and just sticks them back together. This often results in the loss of 1 or more base pairs. Depuination: the removal of a purine (A or G) resulting in the loss of an entire nucleotide pair if it is not caught Deamination- the loos of an ammine group due to oxidative drugs, hydrolic attack or uncontrolled methylation. Usually in C causing it to turn into U which binds with A instead of G causing several issues. UV-Dammage: can cause the bonds between 2 adjacent thimine nucleotides (thimine dimer) making replication very difficult or impossible o Apoptosis- programed cell death. Chapter 7 From DNA to Protien How Cells Read the Genome Transcription DNA RNA o Polyribosomes have multiple ribosomes on a given mRNA o Mistakes every 10^4 nucleotides o Types of RNA Messenger RNA- codes for protiens Ribosomal RNA- makes of the ribosomal structure and catalyzes protein synthesis microRNAs regulate gene expression by binding to mRNAs and reducing their stability and translation into their protein ~22 bp long over 400 types RISC RNA induced silencing complex transfer RNA carries amino acids to the ribosome to bound in a peptide snurps splicing RNAi (RNA interference)- double stranded DNA that destroys latent mRNA and itself siRNA Small interfering RNAs- destroy their complementary foreign RNA molecules o RNA polymerase starts the RNA chain without the use of primase and usually carries information for one gene RNA transcribes DNA with the use of transcription factors that regulate gene expression Transcription factors: Eukaryotic Cells: 3 Different types transcribe different genes in eukaryotic cells), Termination has a torpedo model protein involved in eukaryotic cells. Eukaryotes R M ty rRNA I mRNA II tRNA III Prokaryotes: Sigma factors with a pentameric core found in prokaryotic transcription help facilitate transcription in prokaryotes Rho dependent termination terminate transcription in prokaryotes o The promoter site tells RNA polymerase where to bind and the on the template strand, and the terminator site tells RNA polymerase where to stop coding Promoter sites have polarity to make sure the RNA polymerase binds in the proper direction on the strand Eukaryotic: The TATA (-10 nucleotides)/pribnow box helps RNA polymerase identify where to bind Other accessory protiens assemble upstream and downstream of the promoter to help transcription o mRNA is produced by RNA polymerase Eukaryotic n-RNA is processed as it is being translated: The pre-mRNA goes through Alternative splicing in which the introns are removed Spliceosomes and degraded and the exons are ligated together to form the m-RNA and exspress a specific gene. o Spliceosomes: Small nuclear RNA’s- recognize the spice site sequences Snurps U1 and U2 facilitate the lariat formation Lariat formation- where the adenine cutes the sugar backbone of the RNA 5’ slice site then binds covalently to the 5’ e not the 3’ oh group the free 3’ oh at the end of the exon binds to the next exon Capping: modifies the 5’ end of he RNA (the side transcribed first) by binding an atypical nucleotide (guanine) that has a methyl group that is attached to the RNA in an unusual way, serves as a point of recognition for the ribosome Polyadenylation: provides a “poly-A tail” made of a series of repeated Adenines mRNA lifetime varies depending on its function and the quantity of the protein necessary at a given time Post-transcriptional modifications provide a more stable mRNA strand and without them the mRNA wouldn’t be allowed out of the nucleus Translation: mRNAProtien o Translation of protiens is determined by the 3 base sequence on the mRNA called codons. It moves in a 5’ to 3’ direction AUG which codes for methionine is always the start codon The stop codons are UAA, UAG, and UGA There are 64 different codons that code for the 20 different amino acids Uses a template strand to for RNA (change all bases when The coding strand is the same with only U changed Charged tRNA has an amino acid and a positive charge. Uncharged tRNA has no amino acid and is uncharged. o The mRNA travels to a ribosome where a 3 step process produces a linear protien The mRNA binds to the ribosome at the A site and replication begins Ribosomes are protein building machines made of rRNA (2/3) and protiens (1/3). There are 2 parts: one large subunit that forms the peptide bond and one small subunit that matches tRNA to the codons of the mRNA o There are 3 sites the A (aminoacyl) site where the tRNA binds, P () site where peptide bonds are formed, and E (exit) site where the tRNA is degraded The P cite is activated by the stop codon to do hydrolysis to detach the last amino acid form the tRNA Reading Frames of RNA????? tRNA binds to the small subunit and the large subunit catalyzes a peptide bond between the amino acids on thee tRNA in the A (aminoacyl) site and the P (peptidyl) site. tRNA has codon and anti-codon sites that bind to amino acids (codon) and the small subunit of the ribosome (anti- codon) on the mRNA o Amino acids are bound to the 3’ end of the tRNA with aminoacyl tRNA synthetase. There are 20 tRNA synthetizes. All are charged with a high energy bond that links the amino acid to the polypeptide chain The initiator tRNA always carries methionine or a modified version of the same protein tRNA is read 35 but goes to 5’3 tRNA the sifts to the e (exit) site At the end of translation (when the stop codon is reached) release factors allow the protein to go free via hydrolysis on the p (peptidyl) site The protein goes on to be folded under the supervision of Molecular chaperone protiens or degraded’ Post-transcriptional modifications help with cell signaling o Folding of the peptide facilitated by molecular protiens so that the protein achieves the correct shape. Shape determines function!!!! o Ubiquitination- tagging protiens that are folded incorrectly with ubiquitin so that protease (a protein) will break into its component amino acids and be reused. o Phosphorylation- the addition of a Phophate o Glycosylation- the addition of a sugar Chapter 8 Gene Expression: All cells in a given organism have the same DNA. Differential protein Expression o Housekeeping protiens are found in all cells (RNA polymerase, DNA polymerase, ribosomal protiens etc.). Constitutive/basal gene expression requires these protiens o Specialized protiens help regulate gene expression and have a variation in size shape behavior and function in different cells Gene Expression: o Transcriptional control- most common. Controls how often a gene is transcribed Regulatory DNA sequences switch genes on and off they are about 10 bp long Eukaryotes: Protiens bind to the enhancers and form a loop by attaching to the mediator which is part of the Transcription complex HATs (Histone acetlyalses) help with gene expression HDACs (Histone Deacetylases) remove acetyls and promote gene suppression Regulatory protiens determine what type of cell it is and whether it can convert to a different type later or not. Prokaryotes Transcriptional Repressor protiens bind to the operator and prevent transcription Transcriptional Activators bind to the operator and promote transcription Operons in prokaryotes for gene regulation bind to the operator and prevent the production of a given protein Prokaryotes have about 100 regulatory DNA sequences Eukaryotes have about 1000 o RNA processing Control- controls how pre-mRNA is spliced o mRNA transport and localization control- decides what is exported and what isn’t o mRNA degradation Control-Regulates how quickly an mRNA is broken down o Translation control- deciding which mRNAs are turned into protiens o Protien degradation control- how quickly protiens are destroyed after being made o Protien activity control- whether the protein is active or inactive Protien degradation via the proteasome UTR (untranslated regions) regions that affect binding of regulators Alternative splicing and small regulatory RNAs Cells maintain their identity by: o Having a positive feedback loop that regulates transcription of its own genes o Methylation (gene silencing) o Propagation of chromatin structure through Epigenetic Inheritance which alters the gene expression but doesn’t affect nucleotide sequences
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