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127 Cards in this Set

  • Front
  • Back
Energy ( E)
Capacity to do work
Prokaryotes utilize______ to do work
Energy
Chemical Energy
Breaking bonds, & joining and linking elements through bonding.
Metabolism
Sum total, the complete collection of all the biochemical reactions required to produce the energy needed to survive.
Survival involves:
Reproduce, maintain, repair, function
2 Major groups of metabolic reactions:
Catabolism & Anabolism
Metabolic pathways the 2 major groups are
opposite
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
ATP ( Adrenosine Triphosphate Production)
Quantity that an organism produces
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.
Basic mechanism of an Enzyme
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.
Characteristics of a Simple Enzyme "aka" Apoenzyme
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
Characterisitcs of Holoenzyme "aka" Conjugated enzyme
APO (apoenzyme) + cofactor-----> Holoenzyme
Cofactor is non-protein
2 Types of Cofactors:
1) APO+ ORGANIC-----> Holoenzyme
2) APO+ INORGANIC------> Holoenzyme
Organic cofactors are called
Coenzymes
Ex. NAD ( Nicotinamide Adenine Dinucleotide
NAD is derived from Niacine
Inorganic cofactors are called
Metallic Ions
Ex. Iron
What 4 major factors influence enzomatic action?
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
2 Categories of Enzyme Inhibitors
Competitive inhibition vs. Active site
&
Non- Competitive inhibitor vs Allosteric Site
Competitive Inhibitor
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.
Non- Competitive Inhibitor
Non-Competitive vs. Allosteric Site
Allosteric Site-
Additional regulatory site on an enzyme.
If an enzyme has an allosteric site it is called an allosteric enzyme.
Allosteric Enzyme
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.
Enzymes consume nutrients:
Nutritional Patterns
Phototroph
organism that utilizes light energy to synthesize nutrients.
Chemotroph
derives energy from biochemical reactions and then utilizes it to synthesize nutrients.
Autotroph
Synthesizes its own food
ex. plants- photosynthesis
Heterotroph
seeking pre-formed or pre-existing organic nutrients.
Photoautotroph
light energy and Co2 to synthesize it's nutrients.
Ex. Photosynthetic bacteria , plants & algae
Photoheterotroph
uses light energy & organic C to synthisize it's nutrients.
Ex. Purple & non- sulfur bacteria
Chemoautotroph
derive energy from chemical reactions and Co2 to synthesize nutrients.
Ex. Nitrobactor
Chemoheterotrophs
derive energy from chenical reactions & organic C to synthesize nutrients.
Ex. Most bacteria & all animals
Energy Formation for Chemoheterotrophs
Aerobic & Anaerobic Respiratio, and Fermentation
Glycolysis "aka"
Embden Meyerhof Parnas
Glycolysis
catabolize glucose to anabolize ATP.
occurs in cytoplasm
Glucokinase
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
2 Alternate Pathways for bacteria:
PPP- Pentose Phosphate Pathway &

EDP- Enter-Doudoroff Pathway
PPP ( Pentose Phosphate Pathway) "aka"
Hexose Monophosphate Shunt
PPP Example
PPP<-- Glycolysis--->Aerobic
/
Anaerobic
Glycolysis and PPP occur simultaneously. Produces ATP.
EDP Example
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.
Example that uses PPP
Escherichia coli
Example that uses EDP
Pseudomonas- It grows everywhere, and causes many things.
Example of pathways
EDP PPP<--- Glycolysis
/ \
Anaerobic Aerobic
/ \
Fermentation Kreb Cycle
\
ETS
If it occurs under Anaerobic conditions.
Oxygen was limited. Which causes Fermentation.
Fermentation
lack of oxygen
end products are Lactic Acid (animal)& Ethanol (plant)
2 Pyruvic Acid
I (2 NAD)
I (2 NADH) = 6ATP
Lactic Acid & Ethanol
If it occurs under Aeobic Conditions
The Traditional Pathway
Uses the Kreb Cycle
In the cytoplasm
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
FAD
Is part of the vitamin B complex, derived from Riboflavin
(Vitamins must be used to complete pathway.)
With Glycoysis =_8_ ATP
&
With Kreb =__30__ATP
Total ATP=_____
38 ATP
ETS- Electron Transport System
In the cell membrane, Cytochrome
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
Oxidative Phosphorylation Process
occuring in an oxigenated environment with the accumulation of phosphates, creating ATP
NADH
moves into the membrane and carried into the membrane, shot out across the membrane with the use of a pump after transport.
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.
Aeobic Pathway produces
ATP, H2O, & CO2
Genetics
Discussing DNA
Chromosomes
Cellular structure that carries genes
Gene
A segment of DNA
DNA
sequence of nucleotides
Genome 1995 science magazine
Haemophilus influenzae
Genotype
Genetic composition in DNA ( not seen)
Phenotype
Physically expressed . ( can be seen; rods flagella)
Synthesize protein
DNA---> RNA---> Protein
DNA
Deoxyribose Nucleic Acid
DNA
is a polymer composed nucleotides- the monomers
Polymers
Carbos- polysaccharides
Lipids
protein
nucleic acid
monomers
monosaccharides
glycerol & Fatty acids
Amino acids
nucleotides
nucleic acids are composed of nucleotides. What will change in the nucleotide?
the base
DNA Structure
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
Primes
location on a structure- a poimt of attachment
3' prime & 5' prime
DNA have 4 bases divided into 2 groups:
Adenine & Guanine- the Purines
Thymine & Cytosine- are the pyrimidine
RNA- Ribo Nucleic Acid
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
Purine + pyrimidine= DNA structure
A+T
A+U
G+C
Complimentary Base Pairing
A T C G
| | | |
T A G C
| | | |
A U C G
DNA
is anti-parrallel
base matches with base
DNA --(Transcription)--> mRNA---(Translation)--> Protein
To write To Read
mRNA transcribes and carries message
DNA Semiconservative Replication
process that replicates using original DNA strand
Replication Fork (Y)
At the point where the DNA seperates & replicates
Leading Strand
continuous moving from 5' to 3'.
Lagging Strand
The lagging moves from 3' to 5' & completes connecting using enzymes
Denature
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.
Joining
Old strand or parental strand with the new strand. New strand is called the daughter strand.
DNA Polymerase
Controlling enzyme, called an editor. Removing the primers, repairing, etc.
Ligase
In the lagging strand of DNA structure, will bind together the pieces of DNA called the okazaki fragments are linked together with enzyme ligase.
Making more DNA at the point of the replication fork involving enzymes in certain directions.
In the language of DNA
DNA carries instructions for making protein. Protein is the polymer. the monomer is amino acid (aa).
aa-(peptide bond)-aa-aa
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.
Once translated in RNA, Amino acids will be collected in the exact order of request to create a specific protein.
Condon
RNA language is grouped into 3's (triplets) called
We frame each codon for easier view.
There are 64 Codons.
There are 20 different types of amino acids
RNA is formed in frame of a codon.
AUG- For Start ( amino acid)
Amino acid for stop- UAA,UAG, & UGA
A codon is a representative for a word.
genetic code for amino acids. Creates a specific protein.
examples
CAU-Histidine
UUC-Phenylalanine
CGC- Arginine
Transcription
synthesized a complementary strand of RNA now called the message. From the instructions in DNA.
Denature
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.
The message in a prokaryote is located
in the nuclear region but with other RNA we are moving the message to.
Ribosomes
Composed of ribosomal RNA. Used in protein synthesis
Translation
Reading the message of RNA to synthesize a protein in the ribosome.
Operon Model
Traditional method of explaining transcription & translation. The environment can have a great effect upon gene expression many substances or compounds can be used.
Differences between Prokaryotes & Eukaryotes
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.
LAC
Lactose Operon Model
Escherichia coli
lactose metabolized by protein synthesis
Representation of lactose
Absence of lactose
Induction of lactose
presence of lactose
Operon Off during-
repression
Operon On during-
Induction
LAC is an
iducible model
1st component: Regulator
Gene that codes for repression or for repressor
2nd component: Control Locus-
a promoter
an operator- initiate transcription of the structural genes
3rd component: Structural Locus-
3 enzymes act upon:
1. beta galactoseidase- catabolizing lactose
2. permease
3. transacetylase
Operon off is repression
no lactose is present. Regulator- regulating gene.
operator
structural gene 1- lactose is off
Operon on repressor
active site- altered
lactose will alter active site & unlock it
repressor no longer blocks, operator can proceed & lactose is metabolized
Possible mutations
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
Mutation
a permanent & inheritable change in the base sequence of DNA
Point Mutation (base substitution)
missense- amino acid substitution ( changes the protein)
Nonsense
involves a substitutive stop (stops the protein to continue)
Frameshift mutation
addition or loss of a base from codons. this can terminal or deadly
Mutation can be either
induced (planned)
or
spontaneous (unexpected)
Examples of mutations
MRSA
Methicillin- Med. to treat Staph.
Staphylococcus aureus
3 Types of Transmissions or Mechanisms
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.
Transduction
Involves bacteriophage (virus that attacks bacteria) Serves as a carrier of genetics. Both donor & recipient are alive.
Recumbant DNA
1971 opened/spliced out certain bacteria chromosomes & inserted other chromosomes.
Transgenetics
inducing foreign gene into bacteria called GEMS (Genetically Engineered Microbes) Can iduce with plants & animals
Industrial developed insulin & growth hormones
Use certain GEMs
DNA or Parental running into 3' to 5' prime strand continuously synthesizes DNA til the end.
True
Aerobic respiration essay
The equation for aerobic respiration
C6 H12 O6 + 6O2 + 38 ADP + 38 P ---> 6 CO2 + 6 H2O + 38 ATP
Aerobic essay contin.
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.
Basic mechanism of an Enzyme
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.
List and detail mechanisms of genetic transfer.
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.