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127 Cards in this Set
- Front
- Back
Energy ( E)
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Capacity to do work
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Prokaryotes utilize______ to do work
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Energy
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Chemical Energy
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Breaking bonds, & joining and linking elements through bonding.
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Metabolism
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Sum total, the complete collection of all the biochemical reactions required to produce the energy needed to survive.
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Survival involves:
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Reproduce, maintain, repair, function
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2 Major groups of metabolic reactions:
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Catabolism & Anabolism
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Metabolic pathways the 2 major groups are
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opposite
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Catabolism:
release E Degredation of a substance Process of oxidation involved- loss of electron which would result in a positive charge on the ion |
Anabolism
E is aquired, stored & used Synthesis of a substance Reduction is involved- gain of electron, which would result in a negative charge on an ion |
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ATP ( Adrenosine Triphosphate Production)
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Quantity that an organism produces
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ATP -------->ADP + P (----->E)
Catabolize- degrading, so it is ADP- "disulfide" Seperated a phosphate & E is released ADP-------->AMP+P (---->E) M-mono- one phosphate left & attached to a phosphate & releasing energy so the prokaryote can utilize E to complete the metabolic pathway. |
ATP <===> ADP + P (<---E)
Anabolism-Aquiring energy, adding phosphate to AMP, yielding ADP, aquiring E, phosphate added to ADP, yielding ATP. Utilizing the stored energy & synthesizing a substance for ATP. |
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Basic mechanism of an Enzyme
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Enzyme has an active site & there's a specific substrate for that active site on the enzyme. When a specific substrate fits the active site of a specific enzyme, it becomes a complex, yielding in end products.
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Characteristics of a Simple Enzyme "aka" Apoenzyme
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1) Is a protien
2) Is organic 3) It's a catalyst. 4)Speeds up biochemical reactions 5) Enzymes reycycle 6) (substrate/reactant)A+B (enzyme)---> C+D (end products) 7) A depletion or deletion of an enzyme will shut down a metabolic pathway. 8) "Lock & key Model" 9) ex. Substrate- lactose----> enzyme Lactase 10) The words of all enzymes end in -ase |
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Characterisitcs of Holoenzyme "aka" Conjugated enzyme
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APO (apoenzyme) + cofactor-----> Holoenzyme
Cofactor is non-protein |
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2 Types of Cofactors:
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1) APO+ ORGANIC-----> Holoenzyme
2) APO+ INORGANIC------> Holoenzyme |
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Organic cofactors are called
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Coenzymes
Ex. NAD ( Nicotinamide Adenine Dinucleotide NAD is derived from Niacine |
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Inorganic cofactors are called
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Metallic Ions
Ex. Iron |
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What 4 major factors influence enzomatic action?
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1. pH
2. Temperature 3. Substrate concentration: Constitutive- Always present in constant amounts. (Adding substrate doesn't increase the amount) Induced- present normally in trace amounts. (Adding substrate DOES increase amount.) 4. Inhibitors |
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2 Categories of Enzyme Inhibitors
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Competitive inhibition vs. Active site
& Non- Competitive inhibitor vs Allosteric Site |
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Competitive Inhibitor
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A substrate of similar structure can fit an active site an therefore, will compete with the specific subtrate. If it occupies the active site it will block normal metabolic pathways.
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Non- Competitive Inhibitor
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Non-Competitive vs. Allosteric Site
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Allosteric Site-
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Additional regulatory site on an enzyme.
If an enzyme has an allosteric site it is called an allosteric enzyme. |
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Allosteric Enzyme
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When an End Product (substrate) fits into the allosteric site, the enzyme can't bind with the substrate in the active site, resulting in feedback inhibition. The active site then becomes altered.
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Enzymes consume nutrients:
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Nutritional Patterns
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Phototroph
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organism that utilizes light energy to synthesize nutrients.
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Chemotroph
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derives energy from biochemical reactions and then utilizes it to synthesize nutrients.
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Autotroph
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Synthesizes its own food
ex. plants- photosynthesis |
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Heterotroph
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seeking pre-formed or pre-existing organic nutrients.
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Photoautotroph
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light energy and Co2 to synthesize it's nutrients.
Ex. Photosynthetic bacteria , plants & algae |
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Photoheterotroph
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uses light energy & organic C to synthisize it's nutrients.
Ex. Purple & non- sulfur bacteria |
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Chemoautotroph
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derive energy from chemical reactions and Co2 to synthesize nutrients.
Ex. Nitrobactor |
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Chemoheterotrophs
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derive energy from chenical reactions & organic C to synthesize nutrients.
Ex. Most bacteria & all animals |
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Energy Formation for Chemoheterotrophs
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Aerobic & Anaerobic Respiratio, and Fermentation
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Glycolysis "aka"
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Embden Meyerhof Parnas
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Glycolysis
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catabolize glucose to anabolize ATP.
occurs in cytoplasm |
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Glucokinase
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utilize an ATP.
Glucose-----> 2 Pyruvic Acid glucose yields 2 ATP--> 2 ADP--->2 NAD (coenzyme that picks up H ion and carry them all the way through the process)--->2 NADH (6 ATP)--->2 ADP--->2 ATP--->2 ADP--->2 ATP so 6 ATP + 2 ATP + 2 ADP= Net 8 ATP |
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2 Alternate Pathways for bacteria:
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PPP- Pentose Phosphate Pathway &
EDP- Enter-Doudoroff Pathway |
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PPP ( Pentose Phosphate Pathway) "aka"
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Hexose Monophosphate Shunt
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PPP Example
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PPP<-- Glycolysis--->Aerobic
/ Anaerobic Glycolysis and PPP occur simultaneously. Produces ATP. |
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EDP Example
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EDP PPP <---Glycolysis----> Aerobic
/ Anaerobic Does not occur with any other pathway or glycoysis. All on it's own. Utilized by SOME Gram Negative. Don't utilize glucose. |
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Example that uses PPP
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Escherichia coli
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Example that uses EDP
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Pseudomonas- It grows everywhere, and causes many things.
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Example of pathways
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EDP PPP<--- Glycolysis
/ \ Anaerobic Aerobic / \ Fermentation Kreb Cycle \ ETS |
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If it occurs under Anaerobic conditions.
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Oxygen was limited. Which causes Fermentation.
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Fermentation
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lack of oxygen
end products are Lactic Acid (animal)& Ethanol (plant) 2 Pyruvic Acid I (2 NAD) I (2 NADH) = 6ATP Lactic Acid & Ethanol |
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If it occurs under Aeobic Conditions
The Traditional Pathway |
Uses the Kreb Cycle
In the cytoplasm |
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Kreb cycle
Uses NAD & FAD ( not as successful)- coenzymes 1 FAD--> 2 ATP 1 NAD--> 3 ATP |
2 Pyruvic Acid
} 2 NAD } 2 NADH = 6ATP Acetyl Coa \ \_______Citric Acid 2 NAD-->2 NADH{ } 2 NAD--> 2 NADH= 6 ATP =6 ATP 2 FAD-->2 FADH { } 2 NAD--> 2 NADH= 6 ATP =4 ATP 2 ADT<---2 ADP = 2 ATP Total ATP= 30 |
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FAD
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Is part of the vitamin B complex, derived from Riboflavin
(Vitamins must be used to complete pathway.) |
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With Glycoysis =_8_ ATP
& With Kreb =__30__ATP Total ATP=_____ |
38 ATP
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ETS- Electron Transport System
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In the cell membrane, Cytochrome
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Equation of Aerobic Respiration:
Glucose and oxygenated environment in the process of carrying through with attaching phosphate groups that yields 6 molecules of CO2 and 6 molecules of water and finally 38 ATP. |
(Glucose)C6 H12 O6 + (oxygen) 6O2 + 38 ADP + 38P--->
(carbon dioxide) 6CO2 + 6H2O (water) + 38 ATP |
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Oxidative Phosphorylation Process
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occuring in an oxigenated environment with the accumulation of phosphates, creating ATP
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NADH
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moves into the membrane and carried into the membrane, shot out across the membrane with the use of a pump after transport.
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Proton pump
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fueled by ATP, Generates and shoots H ions across the membrane to re-enter the organism, exchanging H ions for Phosphates. Carrying Phosphates.
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Aeobic Pathway produces
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ATP, H2O, & CO2
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Genetics
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Discussing DNA
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Chromosomes
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Cellular structure that carries genes
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Gene
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A segment of DNA
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DNA
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sequence of nucleotides
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Genome 1995 science magazine
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Haemophilus influenzae
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Genotype
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Genetic composition in DNA ( not seen)
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Phenotype
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Physically expressed . ( can be seen; rods flagella)
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Synthesize protein
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DNA---> RNA---> Protein
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DNA
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Deoxyribose Nucleic Acid
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DNA
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is a polymer composed nucleotides- the monomers
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Polymers
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Carbos- polysaccharides
Lipids protein nucleic acid |
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monomers
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monosaccharides
glycerol & Fatty acids Amino acids nucleotides |
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nucleic acids are composed of nucleotides. What will change in the nucleotide?
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the base
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DNA Structure
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on one side are the deoxyribose sugar & phosphate group
the bonds in between are Hydrogen The other side are the bases: G-Guanine,C- Cytosine,A- Adenine,T- Thymine |
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Primes
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location on a structure- a poimt of attachment
3' prime & 5' prime |
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DNA have 4 bases divided into 2 groups:
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Adenine & Guanine- the Purines
Thymine & Cytosine- are the pyrimidine |
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RNA- Ribo Nucleic Acid
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RNA "DOES NOT" have a pyrimidine of Thymine, instead there is U- Uracil
single strand with sugar- ribo nucleic acid Uracil is in the base with RNA |
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Purine + pyrimidine= DNA structure
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A+T
A+U G+C |
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Complimentary Base Pairing
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A T C G
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DNA
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is anti-parrallel
base matches with base |
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DNA --(Transcription)--> mRNA---(Translation)--> Protein
To write To Read |
mRNA transcribes and carries message
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DNA Semiconservative Replication
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process that replicates using original DNA strand
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Replication Fork (Y)
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At the point where the DNA seperates & replicates
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Leading Strand
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continuous moving from 5' to 3'.
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Lagging Strand
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The lagging moves from 3' to 5' & completes connecting using enzymes
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Denature
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DNA unwinds & unzips. (Blue template)The original strand will be used to replicate more DNA. New strands will develope by more neucleotides arriving from the cytoplasm.
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Joining
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Old strand or parental strand with the new strand. New strand is called the daughter strand.
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DNA Polymerase
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Controlling enzyme, called an editor. Removing the primers, repairing, etc.
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Ligase
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In the lagging strand of DNA structure, will bind together the pieces of DNA called the okazaki fragments are linked together with enzyme ligase.
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Making more DNA at the point of the replication fork involving enzymes in certain directions.
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In the language of DNA
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DNA carries instructions for making protein. Protein is the polymer. the monomer is amino acid (aa).
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aa-(peptide bond)-aa-aa
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DNA carries instructions and must be written in RNA language to read and carried out by messenger RNA the message will be a nucleic acid to make that protein.
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Once translated in RNA, Amino acids will be collected in the exact order of request to create a specific protein.
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Condon
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RNA language is grouped into 3's (triplets) called
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We frame each codon for easier view.
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There are 64 Codons.
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There are 20 different types of amino acids
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RNA is formed in frame of a codon.
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AUG- For Start ( amino acid)
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Amino acid for stop- UAA,UAG, & UGA
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A codon is a representative for a word.
genetic code for amino acids. Creates a specific protein. |
examples
CAU-Histidine UUC-Phenylalanine CGC- Arginine |
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Transcription
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synthesized a complementary strand of RNA now called the message. From the instructions in DNA.
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Denature
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DNA seperated, used original template called the sense strand, RNA nucleotides from the cytoplasm come in and match up with the RNA bases, creating messenger RNA .Enzyme involved is RNA Polymerase( used to write the message in RNA language). In orde to read it is the process of translation which is looking at the genetic code chart and reading the message. Other RNA's involved in this process. To read it we use Transfer RNA (tRNA), that has a Reading mechanism called the anticodon.
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The message in a prokaryote is located
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in the nuclear region but with other RNA we are moving the message to.
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Ribosomes
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Composed of ribosomal RNA. Used in protein synthesis
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Translation
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Reading the message of RNA to synthesize a protein in the ribosome.
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Operon Model
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Traditional method of explaining transcription & translation. The environment can have a great effect upon gene expression many substances or compounds can be used.
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Differences between Prokaryotes & Eukaryotes
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Prokaryote- mRNA is not processed & Traslation of mRNA begins as it's being transcribed.
Eukaryote- The mRNA transcript is transported out of the nucleaus so that it can be translated in the cytoplasm. |
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LAC
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Lactose Operon Model
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Escherichia coli
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lactose metabolized by protein synthesis
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Representation of lactose
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Absence of lactose
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Induction of lactose
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presence of lactose
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Operon Off during-
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repression
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Operon On during-
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Induction
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LAC is an
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iducible model
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1st component: Regulator
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Gene that codes for repression or for repressor
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2nd component: Control Locus-
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a promoter
an operator- initiate transcription of the structural genes |
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3rd component: Structural Locus-
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3 enzymes act upon:
1. beta galactoseidase- catabolizing lactose 2. permease 3. transacetylase |
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Operon off is repression
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no lactose is present. Regulator- regulating gene.
operator structural gene 1- lactose is off |
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Operon on repressor
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active site- altered
lactose will alter active site & unlock it repressor no longer blocks, operator can proceed & lactose is metabolized |
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Possible mutations
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DNA(sense strand) T A C G G A G G G T T T
RNA A U G C C U C C C A A A |
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Mutation
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a permanent & inheritable change in the base sequence of DNA
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Point Mutation (base substitution)
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missense- amino acid substitution ( changes the protein)
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Nonsense
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involves a substitutive stop (stops the protein to continue)
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Frameshift mutation
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addition or loss of a base from codons. this can terminal or deadly
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Mutation can be either
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induced (planned)
or spontaneous (unexpected) |
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Examples of mutations
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MRSA
Methicillin- Med. to treat Staph. Staphylococcus aureus |
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3 Types of Transmissions or Mechanisms
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1. Conjugation- Bacterial sex. Cell to cell contact of 2 related species through a pilus. Plasmids (non-essential DNA) are transferred, resistance factors ( resistant to certain antibiotic) typically gram (-) rods. Donor & recipient are alive.
2.Transformation- transfer of naked DNA fragments. Dead or dying donor. Recipient is alive. |
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Transduction
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Involves bacteriophage (virus that attacks bacteria) Serves as a carrier of genetics. Both donor & recipient are alive.
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Recumbant DNA
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1971 opened/spliced out certain bacteria chromosomes & inserted other chromosomes.
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Transgenetics
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inducing foreign gene into bacteria called GEMS (Genetically Engineered Microbes) Can iduce with plants & animals
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Industrial developed insulin & growth hormones
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Use certain GEMs
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DNA or Parental running into 3' to 5' prime strand continuously synthesizes DNA til the end.
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True
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Aerobic respiration essay
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The equation for aerobic respiration
C6 H12 O6 + 6O2 + 38 ADP + 38 P ---> 6 CO2 + 6 H2O + 38 ATP |
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Aerobic essay contin.
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Glycolysis catabolizes glucose to anabolize ATP which occurs in cytoplasm. Glucose yields a total of 8 ATP. Coenzymes are used to pick up H ions and carry them all the way through the process. The end products are 2molecules of Pyruvic acid that then continue on through the aerobic pathway using the Krebs cycle that is still occurring in the cytoplasm. During the Krebs cycle, coenzymes, NAD Nicotinamide Adenine Dinucleotide which is derived from Niacin & FAD which is derived from riboflavin are used to produce 30 ATP. Now there is a total of 38 ATP. Moving now into the cell membrane the electron transport system occurs. The process of Oxidative Phosphorylation occurs. This is in an oxygenated environment with the accumulation of phosphates, to create ATP. NADH moves into the membrane and carried into the membrane, shot out across the membrane with the use of a pump after transport. The pump is known as a proton pump, fueled by ATP, Generates and shoots H ions across the membrane to re-enter the organism, exchanging H ions for Phosphates. Carrying Phosphates. So glucose and oxygenated environment goes through the process of carrying with it attaching phosphate groups that yield 6 molecules of co2 and 6 molecules of water and finally 38 ATP. There are alternate pathways. The anaerobic which lacks oxygen, goes through the process of fermentation which yields end products of Lactic acid and Ethanol. Two alternate pathways include the PPP, pentose phosphate pathway, which is utilized by Escherichia coli. Glycolysis and PPP occur simultaneously to produce ATP. EDP, Enter- Douordoff Pathway, which is utilized by Pseudomonas; does not occur with any other pathway. It’s all on its own and is used by some gram (-) bacteria. They typically don’t utilize glucose.
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Basic mechanism of an Enzyme
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Enzyme has an active site & there's a specific substrate for that active site on the enzyme. When a specific substrate fits the active site of a specific enzyme, it becomes a complex, yielding in end products. An Apoenzyme is also known as a simple enzyme. It is a protein and organic. It’s also a catalyst which speeds up biochemical reactions. A substrate and an enzyme yields end products, so enzymes recycle. A depletion or deletion of an enzyme will shut down a metabolic pathway. It is known for its lock & key model. Enzymes end in –ase. For example lactose will become lactase. If you add an APO with a cofactor it will yield holoenzymes also called conjugated enzyme. A cofactor is not a protein. There are two types of cofactors. Organic& inorganic. Organic cofactors are called coenzymes. An example would be NAD (Nicotinamide Adenine Dinucleotide), which is derived from Niacin. Inorganic cofactors are called Metallic Ions. An example would be iron. Four major factors that influence enzymatic action are pH, temperature, substrate concentration and inhibitors. Substrate concentrations are either constitutive meaning they are always present in constant amounts. Adding substrate doesn’t increase the amount. Or they are induced, meaning they are present normally in trace amounts. Adding substrate does increase amount. There are two categories of enzyme inhibitors; competitive inhibition vs. active site and non-competitive vs. allosteric site. Competitive inhibitor is where a substrate of similar structure can fit in the active site and therefore will compete with the specific substrate. If it occupies the active site it will block normal metabolic pathways. The allosteric site is an additional regulatory site on an enzyme. If an enzyme has an allosteric site it is call an allosteric enzyme. When an end product or substrate fits into the allosteric site, the enzyme can’t bind with the substrate in the active site, resulting in feedback inhibition. The active site then becomes altered. Enzymes consume nutrients. Phototrophs utilize light energy to synthesize nutrients. Chemotrophs derive energy from biochemical reactions to synthesize nutrients. Autotrophs synthesize their own food, such as plants. Heterotrophs seek pre-formed or per-existing organic nutrients. Photoautotrophs use light energy and carbon dioxide. An example is photosynthetic bacteria, plants & algae. Photoheterotrophs use light energy and organic carbon. An example is purple & non-sulfur bacteria. Chemoautotrophs derive energy from chemical reactions and carbon dioxide to synthesize nutrients, such as Nitrobactor. Chemoheterotrophs derive energy from chemical reactions & organic carbon to synthesize nutrients, which are most bacteria and all animals. Energy formation for chemoheterotrophs are aerobic, anaerobic, and fermentation.
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List and detail mechanisms of genetic transfer.
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1.Conjugation
Bacterial sex Cell to cell contact of 2 related species through a pilus. Plasmids (non-essential DNA) are transferred, resistance factors ( resistant to certain antibiotic) typically gram (-) rods. Donor & recipient are alive. 2. Transformation- transfer of naked DNA fragments . Dead or dying donor. Recipient is alive. 3. Transduction Involves bacteriophage (virus that attacks bacteria) Serves as a carrier of genetics. Both donor & recipient are alive. |