Final Study Guide Test 2 PDF

Mr. M Haylie Grace McLeod Study Guide Test 2 Due: Friday Oct. 4th @11:59 pm Chapter 5 Terms: 1. Capsid a. Composed of protein subunits (capsomeres) b. Protects nucleic acid & involved with attachment c. Aka a protein shell 2. Nucleocapsid a. An unit...

Mr. M Haylie Grace McLeod Study Guide Test 2 Due: Friday Oct. 4th @11:59 pm Chapter 5 Terms: 1. Capsid a. Composed of protein subunits (capsomeres) b. Protects nucleic acid & involved with attachment c. Aka a protein shell 2. Nucleocapsid a. An unit of viral structure, consisting of a capsid with the enclosed nucleic acid b. Nucleic acid + capsid 3. Virion a. Nucliec acid covered by protein (may also contain phospholipids covering the proteins) b. The complete, infective form of a virus outside a host cell, with a core of RNA or DNA & a capsid 4. Capsomere a. A subunit of the capsid, an outer covering of protein that protects the genetic material of a virus 5. Bacteriophage a. Infect bacteria 6. Viral specificity/tropism a. Deals with which cells/tissues a virus can grow in i. Requires proper host receptors ii. Can be a specific animal or a variety of animals iii. Includes specificity for specific tissues or cells of host 7. Envelope a. Capsid → some have an envelope i. Phospholipid bilayer with glycoprotein spikes that function in attachment to host cell  ii. Relevance: the envelope is destroyed by alcohol, thereby inactivating the virus 8. Naked virus a. Does not have an envelope i. Icosahedral= 20 side, each composed of an equilateral triangle 1. Ex. polio viruses ii. Helical= capsomeres helically arranged around nucleic acid strand 1. Ex. tobacco mosaic virus 9. Spikes a. A major structural proteins of severe acute respiratory syndrome-coronavirus 10. Provirus a. A virus genome that is integrated into the DNA of a host cell b. A form of a virus that is integrated into the genetic material of a host cell & by replicating with it can be transmitted from one cell generation to the next without causing lysis 11. Prophage a. a bacteriophage genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell Nucleic acid configurations: Nucleic acid is either DNA or RNA (can not be both) - DNA= double - RNA= single Primary ○ Secondary ○ Tertiary ○ Quaternary ○ Viral replication: Realize viruses are inactive except in living susceptible cells Lytic vs Lysogenic viruses 1. Lytic a. Takes over host → replicates → kills 2. Lysogenic a. Virus that takes DNA into the Host DNA → Host cell divides → remains hidden in host DNA Life cycle of temperate bacteriophage Those able of… Step 1 of lysogenic cycle a. Replicating and causing lysis b. Having their DNA integrated into host nucleic acid The Lysogenic Conversion Step 3 of lysogenic cycle 1. Lysogenic a. Bacteria obtain genetic material from virus enabling them to produce new toxins b. Becoming more pathogenic which causes disease i. Corynebacterium diphtheria: diphtheria ii. Streptococcus pyogenes: scarlet fever Compare & Contrast Animal virus life cycle vs Bacteriophage life cycle Compare ○ Both go through absorption, penetration, and replication Contrast Penetration 1. Prokaryote (bacteriophage) a. DNA injected into cell b. Protein capsid remains outside the bacteria 2. Eukaryote (animal virus) a. Whole virus engulfed by endocytosis  b. Membrane invaginates, bringing the virus into the cell c. Uncoating: viral nucleic acid released from capsid into cytoplasm of eukaryotic cell Summary of the info above ★ Bacteriophages inject DNA into the host cell, whereas animal viruses enter by endocytosis or membrane fusion Release 1. Prokaryotic: host cell lysis resulting in virion release 2. Eukaryotic a. Enveloped viruses bud from the host cell & take part of the cell membrane, which becomes the envelope of the virus. b. Nonenveloped viruses typically undergo lysis. RNA retroviruses What is the enzyme? ○ Reverse Transcriptase Allows RNA templates to be amplified in the same manner as DNA Synthesis of DNA from an RNA template Ex. HIV Importance of viral surface proteins 1. Protective covering 2. Allows for effective attachment to host cells Why viruses are considered living and nonliving Living 1. They have genes made from nucleic acids & a capsid made of smaller subunits called capsomeres 2. Can reproduce inside a host cell Nonliving 1. Not made out of cells, 2. Can't keep themselves in a stable state 3. Don't grow 4. Can't make their own energy How are viruses classified 1. Structure, size, & # capsomeres 2. NA type 3. Replication site 4. +/- envelope 5. Hosts and disease they cause Latent viral infections 1. Herpes virus 2. Chickenpox 3. Epstein-Barr virus 4. HIV Prions vs Viruses Infectious protein agents Lake a genome Do not contain nucleic acid Prions are Smaller than virus Prion-based diseases Cause chronic neurological diseases ○ Spongiform encephalitis ○ Kuru ○ Creutzfeldt-Jakob Disease- affect thinking and memory ○ Mad Cow disease Chapter 6 Terms: 1. Macronutrient Need lots of this for a diet -ex. proteins, carbohydrates, lipids, water (70% of cell mass) 2. Micronutrient a. Needed in small quantities in diet b. Ex vitamins and minerals 3. Essential nutrient a. Must have in diet or you get a nutrient deficiency  4. Organic vs. Inorganic compounds 5. Fastidious a. An organism that will only grow when specific nutrients are included 6. Facultative a. Can grow with or without oxygen b. Have catalase and SOD i. ex. E coli 7. Obligate a. Must have oxygen or it die b. Have catalase & SOD i. ex. Mycobacterium 8. Halophile a. Extremist b. Thrive and often require high salt concentrations in osmotic concentration 9. psychrophile a. Prefer the cold 10. Thermophile a. Can survive in heat i. Ex. Includes some eubacteria and archaebacteria 11. Acidophile a. Organisms that thrive in highly acidic pH environments 12. Neutrophil a. Type of white blood cells & thrives in a neutral pH 13. Alkaliphile a. Extremist and thrive in extremely alkaline pH environments like a ph of 10 or whateva 14. Mesophile a. An organism that grows best in moderate temperature, not too hot & not too cold. 15. Catalase a. An enzyme that breaks down hydrogen peroxide into water & oxygen, protecting cells from oxidative damage 16. Binary fission a. Type of asexual reproduction where a cell splits into two identical daughter cells The four groups of macromolecules Monomers vs Polymers Polymers Monomers Bonds Proteins Amino Acids Peptide Polysaccharides Monosaccharides=carbs Glycoside (oses) Lipids Fatty Acids + Glycerol Ester Nucleic Acids Nucleotides=sugar Phosphodiester Role in structure & function of bacterial cell Pages 1-4; starting a b. Types of macromolecules The four structures Primary: just AA sequence Secondary: how polypeptide chain twists due to H bonds Tertiary: overall 3-dimensional shape ○ Results in overall folding ○ Shape accounts for biological activity of protein Quaternary: 2 or more peptides connected together 1. Protein functions a. structural/fibrous: provide strength & shape to hold structures together b. Globular proteins: performs activities i. Enzymatic 1. Speeds up chemical reactions 2. Identify enzymes by suffix “ase” ii. Transport 1. Helps materials to enter/exit cells iii. Antibodies 1. Help fight infections Three components of nucleic acid A sugar A base A phosphate Nucleotides of DNA  a. 3 parts of a nucleotide 1. Phosphate group 2. Sugar: deoxyribose 3. Nitrogenous base pairs a. Adenine (A) b. Thymine (T) c. Guanine (G) d. Cytosine (C) Nucleotides of RNA a. Nucleotides building blocks 1. Phosphate 2. Sugar: ribose 3. Nitrogenous base pairs a. Adenine b. Uracil (instead of thymine) c. Guanine d. cytosine Components of ATP Nucleotide with 3 phosphates Releases chemical energy by breaking off a phosphate Very important with supplying energy for cellular needs Energy source term Phototroph: light → sunlight ○ Ex. plant Chemotroph: organic compounds, which have carbon & hydrogen → carbon ○ Ex. fungi/bacteria Lithotroph: inorganic compounds → electron ○ Ex. ammonia or Iron Carbon source term  Autotrophs: convert carbon dioxide into organic matter → make own food ○ Ex. plant Heterotrophs: require preformed organic matter and convert it to cellular materials → has to get food ○ Ex. human Bacteria based of temp preferences Three important temperatures a. minimum: below which no growth occurs b. optimum: fastest growth with maximum enzyme activity c. maximum: above which no growth occurs a. Psychrophiles: prefer the cold minimum: i. (-)20oC ii. Opt = 8oC iii. Max = 15oC b. Psychrotrophs/psychrotolerants: can tolerate warmth i. Grow between 0-30oC ii. Most likely responsible for food spoilage c. c. Mesophiles: thrives in moderate temperature -optimum loving human pathogens optimal i. Min = 10oC ii. Opt = 37oC iii. Max = 50oC d. Thermophiles (includes some eubacteria and archaebacteria) i. Min = 40oC ii. Opt = 55-75oC iii. Max = 70 or higher e. Extreme thermophiles i. Min 68oC ii. Opt = 122oC iii. Max = 130oC f. How do thermophiles survive the heat? i. Have heat stable proteins, ii. Archaebacteria: have heat stable ether linkages in their phospholipids Oxygen requirements  How different organisms deal with and/or use oxygen Include enzymes necessary for oxygen detoxification ALL OF PAGE 12 How does bacteria divide 1. Binary fission a. Asexual reproduction by a separation of the body into two new bodies Calculate population growth Subtract the initial population size from the final population size, then divide that difference by the initial population size & multiply by 100 to get the percentage growth rate Compare/Contrast the four phases of growth in a bacterial growth curve & the events that occur within each of the phases 1. Lag 2. Exponential 3. Stationary 4. Death a. Lag phase: dormant to active i. New is equal to Old 1. Hrs to days b. Exponential: is where is starts to multiple exponentially i. Undergoing binary fission ii. Doubles every generation period 1. 20 mins to days c. Stationary: balanced growth, does not go up or down  i. New is equal to dying d. Death: decline in population i. Cells are beginning to die Distinguish between an osmophile and a halophile They are both extremists & osmophiles that thrive in high solute concentrations ○ ex some fungi Halophiles are also extremists but they thrive and require high salt concentrations Chapter 8 Terms: 1. Genome a. All DNA in a cell can be formed as chromosomes & chromatin. b. Chromatin is unwound dna c. Chromosomes: condensed dna in wound up configuration 2. Gene a. The basic physical & functional unit of hereditary b. Made up of dna c. Act as instructions to make proteins 3. Chromosome a. Carry genetic information, specifically dna 4. Replication a. Purpose: to go from unduplicated chromosomes to duplicated chromosomes b. Process: semiconservative dna replication c. Semiconservative dna is that when dna replicates, each new double helix is made from the original strand. It’s being conservative!:) Semiconservative replication steps: 50% New & 50% Old… taking half old and adding half new a. Unwinding: i. Topoisomerase: unwinds the dna in the chromosome ii. Helicase: unwinds the double strand helix (each strand is a template to create a new strand) b. Leadings strand of replication: i. Dna polymerase III adds nucleotides to the template ii. creates a new strand in the direction of the original template c. Lagging strand  i. Dna can only be built in the 5’ to 3’ direction ii. The lagging strand makes the dna be 3’ to 5’ so it has to do this to fix it iii. Make small stretches in the dna strand as the helix unwinds 1. primase builds a small stretch of rna 2. Okazaki fragments due to DNA polymerase → Exonuclease removes the RNA primer from both strands → DNA ligase fixes the strands d. Transcription i. Making any rna from a dna template ii. (mrna, trna, rrna) Happens in the cytoplasm of prokaryotes & nucleus of eukaryotes e. Mechanism: i. A localized region of dna representing a gene is unwound ii. Rna polymerase uses one of the strands as a template 1. Connects rna nucleotides that are complementary to the strand 2. This creates a strand of rna f. Translation i. The process of protein synthesis ii. Occurs in cytoplasm of cells iii. You need mRNA & tRNA for protein synthesis The three RNA’s mRNA: ○ Codons: a group of 3 mrna nucleotides ○ Each codon represents an amino acid look at genetic code chart to determine proper AA (amino acids) Ribosomes connect AA together using peptide bonds tRNA: ○ Carries the AA thats encoded by the mrna ○ Attaches to that same mrna codon ○ The ribosomes connect the AA w peptide bonds ○ The process stops when it hits an end codon rRNA ○ Helps form ribosomes ○ Large or small & serve as ribosomal subunits for protein synthesis Anticodon ○ They are found on molecules on trna ○ They make sure the correct AA is added to a growing polypeptide during protein synthesis Nitrogenous base ○ Building blocks of dna & rna ○ Dna and rna contain genetic information that instructs cells on how to function & build structures in the body DNA replication Origin → helicase (unwinds/unzips) → primase (makes primer aka RNA) → DNA polymerase (builds strand by binding to primer/ proof reads) Be able to replicate a strand of DNA Be able to transcribe a strand of DNA Be able to translate a strand of mRNA The Central Dogma 1. It is the flow of biological information a. Dna makes dna(replication) b. Dna makes rna(transcription) c. Rna makes protein(translation) Importance of transcription & translation Transcribing and translating both focus on the process of converting information from one format to a slightly different one. Transcription is the process of replicating a gene’s dna into a messenger rna (mrna) molecule Translation uses the mrna molecule sequence to make a protein by converting the nucleotides into a sequence of amino acids. Differences between RNA & DNA 1. Strands a. DNA is double stranded forming a helix b. RNA is single stranded. 2. Sugar a. DNA is deoxyribose b. RNA contains ribose 3. Bases a. DNA= adenine, thymine, cytosine & guanine b. RNA= adenine, uracil, cytosine & guanine. List the three types of RNA directly involved in translation mRNA, rRNA, tRNA ○ Be able to explain their roles in the process ○ Explain the use of codons & anticodons. Codon  ○ A sequence of 3 nucleotides in mrna that determines the position of amino acids when a cell starts making proteins Anticodon ○ A sequence of three nucleotides in trna that binds to the corresponding codon & therefore designates a specific AA Eukaryotic vs Prokaryotic ribosomes 1. Eukaryotic a. 80S & are generally larger 2. Prokaryotic a. 70S & are smaller in size Describe three forms of horizontal gene transfer used by bacteria 1. Horizontal modes is when an organism gains dna & thereby gains new traits a. Conjugation= transfer between two bacteria using cell-cell contact i. Utilizes plasmids ii. Cells with plasmids form a conjugation pilus iii. Plasmids make copies of themselves iv. One of the copies enters a cell that lacks the plasmid b. Transformation= uptake of free genetic material from environment i. Naked strands of DNA picked up bacterial cells and these cells gain info from that c. Transduction= foreign genetic material via virus i. Involves viruses ii. The viruses are able to transport host dna from one host to another Vertical mode refers to sexual reproduction Asexual and sexual Test 2: Common Confusions 1. Aerotolerant anaerobes/facultative anaerobes Facultative-can grow with and without oxygen Aerotolerant- can grow with and without oxygen Differences: facultative anaerobes can utilize oxygen when present, while aerotolerant anaerobes simply tolerate its presence without using it 2. Growth calculations 3. Organic/inorganic compounds Organic compounds are chemical compounds that always contain carbon atoms, typically bonded with hydrogen, and are usually derived from living organisms, while inorganic compounds lack carbon atoms and are generally derived from non-living sources like minerals 4. Hetero/autotrophs Hetero:human, we take in oxygen release carbon dioxide/cellular materials that autotrophs take in, while they release the oxygen 5. Agar/buffers 6. Lag/log/stationary phase 7. Lytic/lysogenic cycles 8. Capsid/capsomeres 9. Transcription/translation 10.. DNA/RNA base pairing