Enzymes, DNA, and Metabolism 2

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What are enzymes made of?

Proteins or sometimes RNA

General funtion of enzymes?

Speed up chemical reactions, without being changed by the reaction.
They lower ACTIVATION ENERGY (energy required to get a reaction started)
+ This allows reactions to occur that normally would not occur under given conditions (temp, pressure)
+ Also allow reactios to occur in living cells taht would normally occun in vitro ( in a test tube)

Enzymes only catalyze energy RELEASING reactions....net reactions must be energy yielding.

What is an active site in general?

Portion where the substrate attaches and catylization reaction occurs.

What is a substrate molecule?

The molecule the enzyme acts on.

How does the enzyme interact with it's substrate molecule?

Binds and converts substrate into one or more products.

How does the shape of the enzyme's substrate molecule compare with the shape of the enzyme's active site?

They are complementary.

Enzyme reaction dehydration synthesis?

When larger molecules are synthesized brom buildingblocks by removing water.....eg proteins from amino acids. Always requires ATP

Enzyme reaction Hydrolysis?

When large molecules are split apart by adding water. Always spontaneous....no ATP needed.

Enzyme reaction Oxidation?

When a molecule loses electrons or H+ ions.

Enzyme reaction Reduction?

When a molecule gains electrons or hydrogens...eg photosynthesis CO2 reduced to glucose.

Nucleotide?

The two chains of a DNA helix are nucleotides.
They are composed of a nitrogenous base, deoxyrybose sugar, a single phosphate group.
They are Derived from Nucleosides.

Codon?

Is a three base nucleotide sequence that codes for an amino acid or a control signal........eg stop...start.

Gene?

Is a sequence of codons between a start and stop codon that codes fro a protein or RNA.

Operon?

A cluster of genes that operate as a unit.

Chromosome?

One DNA molecule.

Genome?

The sum total of all the chromosomal DNA in the cell.

What enzyme is primarily responsible for replicating DNA?

DNA polymerase.

Basic DNA replication?

) The enzyme DNA Helicase "unzips" the DNA double helix, breaking the hydrogen bonds that hold the nitrogen bases together.

2) Enzymes are added to the two separated strand portions so that the strands don't twist around and come back together. The two areas on either end of the DNA where the double helix separates are called replication forks.

3) DNA Polymerase glides along the exposed strands, adding complementary nucleotides to the existing ones. DNA Polymerase remains attached until all DNA has been copied and is signaled to detach.

4) When DNA Polymerase is done, two identical strands of DNA have been formed- each containing one old strand and one new strand. The nucleotide sequences in both DNA molecules are identical to each other and to the original DNA molecule.

Side note: In DNA replication, mutations can sometimes occur when the wrong nucleotide is added. DNA Polymerase can backtrack and remove the wrong nucleotide and add the right one. This makes it able to "proofread" its work.

Which enzyme transcribes DNA into mRNA>

RNA Polymerase

What is meant by template strand in DNA trnascription?

The strand of DNA copied during RNA transcription.

DNA transcription to mRNA?

1. DNA unwinds. (as we know that DNA have two strands, so the two strands are first unwind - double helix).

2. then, RNA polymerase (this is the enzymes) recognizes a specific base sequence (which it will recognize the beginning sequence so the transcription will start) in the DNA called a promoter (promoter is what is so-called the beginning sequence) and binds to it.

3. The promoter identifies the start of a gene, which strand is to be copied, and the direction that it is to be copied.

4. Complementary bases are assembled (U instead of T).

5. A termination code in the DNA indicates where transcription will stop (as just now is the beginning sequence to start the transcription now it will have a termination code to stop it) .

3 ways RNA differs from DNA?

1. RNA has robose; DNA had deoxyribose
2. DNA has thymine; RNA has uricile
3. DNA is in the nucleus, RNA is not.

Where is is mRNA translated into protein?

The ribosomes in the cytoplasm in bacteria and endoplasmic riticulum in eukaryotes.

What role does transfer RNA play in the translation process?

It translates mRNA into specific amino acid sequences to form proteins.

Which metabolic process uses CO2 and water to produce sugar and O2?

Photosynthesis

Which process produces CO2, H2O and ATP?

Cellular respiration

Which process nets 2 ATP along with producing molecules such as CO2 and alcohol?

Fermentation

Which process includes glycolysis?

Cellular respiration and fermentation

Which process utilizes a Kreb's cycle and electron transfer system?

Cellular respiration.

Which process includes a Calvin-Benson cycle?

Photosynthesis.

Core or Apoenzyme?

Is the largest component of an enzyme.
+ Made from protein and sometimes RNA
+ Contains the active site that interacts withthe enzyme's substrate
- the active sit makes each enzyme specific
- The induced fit molecule.

Coenzymes?

- Small, non-protein, organic molecules
- Synthesized from vitamins (the only vitamins we need are coenzymes.....ie C)
- AreSAre not specific to a given reaction, but ae able to only transfer one kind of small molecule...eg ....hydrogen or electrons or small function groups.
- Examples are NAD and NADP used during respiration and photosynthesis.

Cofactors?

- Are inorganic, eg metalic ions..most common copper and iron
- They adjust the shape of the active sites so they fit the substrate by binding to the active site.

Enzyme reaction phosphorylation?

When a phosphate is added to a molecule.
Photosynthetic- when cholrophyll is used in the conversion of ADP to ATP
Substrate - when a phosphorylated substrate donates its phosphate to ADP
Oxidative - When electrons from an oxidized substrate are used to convert ADP to ATP (involves electron transport system.

Endoenzymes?

Enzymes that do their job inside the cell (intracellular.....respiration ect..)

Exoenzymes?

Secreted to do their job outside the cell....digest food to small particles.

Constitutive>

Enzymes that are always produced ..........Strep F. produces Esculinase

Inducible Enzymes?

Enzymes that are produced in response to the presence of a particular substrate (only produced when needed)

Repressible enzymes?

Enzymes not produced when the product of the enzyme pathway is present.

Largest component of an enzyme?

Core or Apozyme.
+ made from protein or sometimes RNA
+ Contains the active site that interacts with the substrate molecule.
- Active site makes each enzyme specific
- The induced fit model

Coenzymes?

- Small NON-protein organic molecules.
- Synthesized by vitamins
- Are not specific to a given reaction, but are able to transfer onlu one kind of small molecule is..H+ or electrons or small function froups. The only vitamins we need are coenzymes.
- Examples are NAD and NADP used during cellular respiration and photosynthesis.

Cofactors?

- Inorganic ions eg. metallic ions, most commoly copper and iron
- Adjust the shape of the active site so they fit the substrate.

5 Enzyme reactions?

Dehydration Synthesis
Hydrolysis
Reduction
Oxidation
Phosphorylation

3 types of phosphorylation?

Photosynthetic- When a chlorophyll is used in the conversion of ADP to ATP
Substrate- When a phosphorylated substrate donates its phosphate to ADP
Oxidative- When electrons from an oxidized substrate are used to convert ADP to ATP (involves electron transport chain)

Endoenzymes?

Enzymes that do their job inside the cell.

Exoenzymes?

enzymes that are secreted to do their job outside the cell.

Constitutive enzymes?

Enzymes that are always produced Esculinase from Strep F.

Inducible enzymes?

Enzymes that are produced in response to the presence of a particular substrate (only produced when needed)

Repressible enzymes?

Enzymes that are not produced whent he product of the enzyme pathway is present.

4 things that affect enzyme activity?

- Anything that denatures protein
- Feedback inhibition
- Competitive inhibition
- Concentration of substrate

Feedback inhibition?

- occurs when the final roduct of an enzyme pathway blocks further enzyme activity.
- The product reacts witht the allosteric site (the enzyme associated with the first emzyme of a biosynthetic pathway)
+ The shape of the enzymes activity site is altered
+ Product production ceases.

Competitive inhibition?

- an inhibitior resembles the enzymes normal substrate and competes with the substrate for the activity site.
AZT and Acyclovir are nucleuside mimics that are used to inhibit the activity of reverse transcriptase AZT and DNA polymerase(acyclovir)
- Sulfa Drugs resemble and compete with PABA for a bacterial enzymes active sith. (PBA is normally converted to folic acid by microbial enzymes.)

How does the concentration of substrate infuence the efficiency of an enzyme?a

More substrate, the greater the enzyme activity will be, until all enzyme molecules are engaged.

DNA description?

two chains of nucleotides in a double helix.
Discovered by Rosalind Franklin, but stolen and presented by watson and Crick.
- Sides of ladder composed of deoxyribose molecules alternating with phosphate molecules.
- Rungs of the ladder consist of compimentary pairs of nitrogenous bases.
Adenine - Thymine
Guanine - cytosine
--- each base bound to compliment by a weak hydrogen bond.

Nucleotides?

Two compose one DNA strand.
Have three basc components.
- one of 4 nitrogenous bases (adanine and guanine)- purines.....(cytosine and thyamine) pyrimidines.
- A 5 carbon sugar deoxyribose
- A single phosphate group
....are derrived from nucleosides.

Nucleosides?

Smallest component of dna, and make up nucleotides.
- one of four nitrogenous bases attached to a molecule of deoxyribose
- when 3 phosphates area dded to a nucleoside by adenylate kinase, and a nucleoside triphosphate is created.
- A nucleotide is generated when two of the phosphates are lost as the triphosphate is attached to an elongating DNA molecule by DNA polymerase.

Codon?

A three base nucleotide sequence that codes foe an amino acid or a control signal.
- 64 different codons ATG- start TAA, TAG, TGA - stop.
- different organisms have a preference for different codons...there are multiple codons for each amino acid.
- multiple codons coding for the same amino acid reduces the risk of lethal mutation.

Gene?

A sequence of codons between start and stop codons that code for a protein or an RNA. Only 2% of codons code for proteins, the rest code for RNA.

Operon?

Cluster of genes that operate as a unit.....eg....genes for enzymes of the same biosynthetoc pathway (rare in eukarya)
Operon = gene+operon
2 kinds of operons...structural and regulatory
- A structural operon
+ includes a controlling site
- that regulates the expression of structural genes.
+ Composed of a PROMOTER site that serves as an attachment for RNA polymerase, and an operator site that serves as an attachment for a REPRESSOR protein
- A regulatory operon
+ includes a structural gene that codes foe a repressor protein
+ insludes a promoter site taht serves as an attachemetn for RNA polymerase (but no operator site.)

Ultraviolet radiation damage to DNA?

light with wavelengths 40-390nm found naturally in sunlight.
-causes redistribution of electrons and protons in Thymine and Cytosine, making them highly reactive.
- Bonding of adjacent thymines and or cytosines creates DIMERS..( wich distort the DNA...and interferes with DNA replicaiotn and transcription.

Ionizing Radiation?

Gamma Rays create hyperactive ions which react with nucleotides causing the release of bases and the breakage fo the DNA.....use in food industry irradiation.

What relaxes DNA supercoiling?

Topoisomerase in eukarya, DNA gyrase in prokarya
+ DNA Gyrase is not in eukarya, so we can target DNA gyrase with (Cipro) Ciprofloxacin and Naladixic acid.

Unwinding and unzipping of Helix?

Starts at a single "origin" in prokaryoes and unzips in both directions
Has multiple origins in eukarya
- catylized by DNA helicase in both cell types.

transctiption?

Each strand of DNA acts as a template foe the arrangement of complementary nucleotides (A-T and C-G)
- an RNA primer built by RNA polymerase is necessary to start the complementary strand.
- DNA POLYMERASE
+ takes over after the primer is built and catalyzes the addition of DNA nucleotides to the growing DNA molecule.
+ Archaea shas a unique DNA Polymerase that tolerates high temperatures used in PCR
- Replicatio is continuous on the 3' strand and discontinuous on the 5' strand, with fragments attaching with DNA ligase.
- Each new double strand twists into a double helix.

Polymerase Chain Reaction (PCR)?

Is a method fro rapidly generating identicals trands of DNA in the laboratory. Takes about 3 min 15 seconds.
- Heat DNA to 94C for 30 seconds causes the DNA to unwind and unzip.
- Cooling to 50C will allow primers to attach to 2 DNA strands.
-Raising temp to 72C for 2 min and providing DNA polymerase(from archaea) promotes the synthesis of complimentary DNA strands.
....used in forensics, disease identification, historic disease epidemic research.

AZT?

mimics Thymine nucleoside...inhibits the transcription of HIV RNA into HIV DNA....causes anemia and immunosupression.

Control of gene expression Inducible enzymes?

- Control catabolic (digestive) pathways.
- Example....Lactose Operon.
+ Structural genes code for enzymes that break down lactose.
+ Operator sire is normally blocked by a repressor protein derived from a regulatory operon.
+ In the presence of Lactose:
- Lactose is modified into and inducer of the lactose operon
- The inducer binds to the repressor protein, changind its shape so it has less affinity for the operator site.
- RNA polymerase can now attach to the promoter region and transcribes the structural genes into messenger RNA.
+ In the absence of Lactose, a repressor protein attaches tot he operator site and blocks the transcription f the structural genes that code for lactose digesting enzymes.
- RNA polymerase cannot attach tot he promoter site
- No lactose digesting enzymes are produced.

Control of Gene expression Repressible Enzymes?

Control anabolic (systhesis) pathways.
Example: Tryptophan operon.
- Includes the structural genes that code foe enzymes that synthesize the amino acid tryptophan.
- If tryptophan is absent..
+ the repressor protein is the wrong shape to blcok the operator site
+ RNA polymerase is able to transcribe the structural genes intomessenger RNA
+ Enzymes for Tryprophan synthesis are produces
+ tryptophan is produced
- If Tryptophan is present:
+ the tryptoophan forms a comples with the repressor protein
+ The tryptophan- repressor complex fits the site and blocks RNA polymerase
+ No transcription.

Protein synthesis nucleic acids?

DNA, Messenger RNA, Robosomal RNA, Transfer RNA
DNA - contains the code foe the kind, number and arrangement of amino acids in any given protein.
Messenger RNA-
- consists of a single chain o(half ladder) of nucleotides.
+ has the same bases as DNA except thymine is replaces by Uracile.
+ uses a sugar of ribose instead of deoxyribose
- Acts as a template during translation foe the arrngement of the amino acids in the newly forming protein.

Steps in protein synthesis?

DNA Transcription
Translation
- elongation
- Termination

How many classes of RNA phlymerase in Bacteria VS. Archaea and Eukarya?

1 class in Bacteria
3 classes in enkarya and archaea

Transcription?

Is messenger RNA Formation.
- DNA unwists to expose codons
- RNA polymerase attached to a promotor site of one the DNA strands
+ template strand
+ The strand from which M-RNA can be generated continously
- Complementary RNA nucleotides are attached sequentially until a "stop" codon is reached.
_ at this point, in Eukaryoes....the transcripts is processed via the removal of INTRONS.
- spliceosomes fold introns, remove them and splice remaining exons together.
- there are no introns to remove in prokarya and finished mRNA may represent more than one protein....because it is not processed, more than one ribosome 5-6 can be translating the same mRNA at the same time.
- Completed Mrna in eukaryotes is sent out to the cytoplasn where it will encounter 80s robosomes.

Polyribosome?

more than one ribosome may translate mRNA a the same time because there are no introns to process out like in Eukarya.

Introns?

Non coding sequences of nucleotides that must be removed before reamining exons can be spliced and translated by ribosomes.

Rifamycin?

Targets RNA polymerase to interfere with protein synthesis.
Binds to RNA polymerase to block transcription.....treats TB, Leprosy, meningitis,

Mutation definition?

changes in dna that result in genetic variation.

Induced mutation?

Mutations invove environmental mutagens such as viruses, uv radiation, and compounds foreign to the cell.

Spontaneous Mutation?

Involve DNA replication errors.

Point Mutations?

Base Substitution:
- When in a codon, one nucleotide is replaced with another with a different base.
- If new codon codes for teh same amino acid as the original, no change in the protein coded by the gene will occur.
- if the substitution results in a code for a different amino acid, the resultant protein may be defective, it one amino acid difference in sickel cell anemia.
- if th changein codon results in a "stop" signal, the resulting protein may be dramatically changed.

Frame Shift:
- are due to insertions or deletions of nucleotides
- can result in changing all the codons that folllow the insertion or deletion.

Mutation Rates?

- Are dependent upon DNA replication rate and the reliability of replication.
- Are dependent on exposure to radiation and other mutagens.
-Determines the evolutionary potential for cells, and gives fuel to natural selection.
- mutation rates in prokarya dn eukarya are equal, but there are so many bacteria replicating so much more quickly, compared to humans every 20 years, bacteria rates are tremendously higher.

Source of Genetic variation Transposon?

Genetic parysites...up to 45% of human genome is madeof transposons.
- A jumping gene that can jump between chromosomes or plasmids.
- Enters the host genome via the enzyme transposase generating Rocombinant DNA.

Recombinant DNA?

DNA generated from two or more sources.

Conjugation?

A mechanism used by prokaryotes to increase acces to beneficial mutations.
Involving plasmids:
- Transmitted via pili in G- cells
- Exchange of DNA through conjugation bridges in G+ cells.
Involving the Chromosome:
- the copy of a chromosome can begin the passage to s ascond cell via pili or conjugation bridge.
- The passage is usually interrupted and the chromosome breaks such that only a partial transfer occurs.
- Transferred chromosomal DNA can integrateitself into int othe new cell's genome, creating recombinant DNA.
+Conjugation can be accelerated when cells are exposed to environmental stress.

Transduction?

Mechanism in Prokarya to increase access to beneficial mutations.
- The transfer of genes from one bacterium to another via a virus.

Generalized transduction?

- The bacteria genome breaks into fragments and some of the newly forming viruses pick up a bacterial DNA fragment instead of viral DNA.
- Bacteria is then injected into another bacteria.

Specialized Transduction?

-Viral DNA is integrated into a bacterial genome at one specific site. (lysogenized)
- the virus excises itself along with the neighboring bacterial DNA. A restricted group of bacfterial genes are transferred to a new host cell, instead of a random fragment.

Transformation?

Prokaryotes....increases access to beneficial mutations.
Griffith 1928....rat experiment.
- Naked DNA can be taked up by bacteria and can recombine with the main bacterial genome.
- A bacteria must be competent in order to take up DNA
Competency:
- competencey can occur for a short time during the log phase.
- is facilitated by a competence factor that can be released itno the medium by the bacterial cells or displayed as a surface protein teh binds to DNA. A special protein for absorbing DNA from teh environment in bacteria.
- Low levels of oxygen and nutrients my stimulate the generation of a transport complex in the cell membrane.
- Cells can be made competent in the laboratory by suspending them in cold divalent ions and then heat shocking them to change the permeability of the cell membrane.

Lateral (Horizontal) Gene Transfer (LGT)?

- When genes are transfered to another existing cell, eg...from a bacterium to a neighboring bacterium.
- Conjugation, transduction, and transformation(transfection) all result in lateral gene transfer.
- About 80% of mocrobe genes have been laterally transferred at some point in their history.
-Bacterial speciation is driven by LGT rather than from mutations.

Requirements for geneic engineering?

A gene source:
- the gene must include start ans stop codons a controlling site.
- Gene production must not be toxic to the host cell.

A Vector:
- vector is the DNA into which the desired gene is spliced, so the gene can be inserted into a host cell ( host cells usually won't accpt a foreign gene all by itself.
- bacterial and yeast plasmids as well as viral DNA are often used.
+ must be able to replicate
+ must have a gene that allows selection of the DNA that is recombinant (eg...usually two genes for antibiotic resistance.)

A cell in which the recombinant can proliferate (clone).

Restricion endocucleases

An enzyme used in genetic engineering that:\
- binds DNA in the source and inthe vector and cut it in one or more paces at specific sites.
- It cuts the DNA so it has staggered ends and is used to prepare DNA so a foreign piece of genome can be spliced in.
DNA ligase binds the the gene and vector DNA together.

Introduction of recombinant DNA into host cell via vector?

- A viral genome can be used as a vector to carry and incorporate genes into bacterial or mammalian cells. (transduction)
- Transformation of bacterial cells and transfection of eukaryotic cells:
+ are the most common techniques foe delivering naked DNA to new hosts.
+ host cells need to be made competent.
_bacteria made competent through ELECROPORATIOn (exposing cells to pulses of electrical fields that open small pores in cell membranes.), or exposure to calcium salt solutions.
_ Eukarya animal cells can be:
+ Be induced to phagocytize DNA
+ Competent via electroporation
+ high velocity micro-projectile gun that shoots DNA into the cell.
Eukaryotic plant cell- can be transfected by the gram negative bacteria Agrobacterium tumefaciens, a plant pathogen.

Significance of Genetic Engineering?

Allows a population of organisms to rapidly acquire a new trait,
It takes generations to create a new GOOD trait via random mutations.

Genetically engineered human proteins that correct hereditary disease?

FactorVIII
Growth hormone and insulin
Gene for normal hemoglobin
genef ro normal chloride ion channels (cycstic fibrosis)
interlukin 2, for treatment of SCID (Bubble boy)
Drugs:
Alpha interferon
vaccines and enzymes like TPA tissue plasminogen activator.

Glycolysis?

- Is the breakdown of glucose to pyruvic acid.
- Fermentation and cellulaer respiration sart with glycolysis.
- Requires two ATP for activation energy. they donate two phosphates ot the glucose, two H+ are removed to make room for the phosphates (oxydation + phosphorlation.)
-Glucose splits into two 3 carbon glyceraldehyde 3 phsphate molecules.
- Two iorganic phosphates added.
- Two more hydrogens are released...one from each.
- Two NAD coenzymes are reduced to NADH.
- All 4 phosphates now removed from the 3-diphosphoglycerate and each phosphate is added to an ADP to form ATP

Products of Glycolsis?

A net of Two ATP
2 NADH +2 H+
2 molecules of pyruvic acid.

Fermentation?

- Does not involve an electron transport system to generate ATP
Can be acid fermentation or Alcohol fermentation.
- The net 2 ATP's generated during glycolysis are the 2 generated from fermentation.
- Depending on the type of bacteria, acids, alcohols, gases..(so2, H2, CH4 are generated.)
In- Sugar and 2 ATP
Out- 2 ATP and 2NADH + 2 H+ from Glycolysis (were not part of fermentation.)
Acid fermentation- Acid, CO2, H2, CH4
Alcohol Fermentation - Alcohol, + CO2

Acid Fermentation?

- Acid Fermentation:
+ The pyruvic acid receives hydrogens from NADH+ H+ generated during Glycolysis.
+ 2 pyruvic acid + 2 NADH +2H+ = 2 lactic acid 2 NAD+
In- 2 ATP 2 pyruvic acids
Out - Lactic Acid, CO2, H2, CH4 and 2 net ATP

Alcohol Fermentation?

- Pyruvic acid is broken down into two molecules of acetaldehyde and two molecules of carbon dioxide.
- The acetaldehyde receives the hydrogens from NADH+ H+ generated during glycolysis, and becomes ethanol.
In - 2 ATP and 2 Pyruvic acids

Aerobic Cellular Respiration?

Consists of Glycolysis, Kreb's cycle, and ETSa.
- Pyruvic acid from Glycolysis is first converted to acetic acid and c02, and then 2 molecule os acetyl-Co A and two NADH+H+

Then it procedes through Kreb cycle and ETS

Products of Aerobic Respiraton:
2 ATP
2 GTP
34 ATP from ETS

Electron Transport system?

Is used in Aerobic and a les complex version in Anaerobic respiration.

Kreb's cycle?

Kreb cycle- each acetyl-Co A that was converted from pyruvic acid, combines with a 4 carbon molecule and yields 6 NADH+6H+, 2 FADH2 and 2 GTP(ATP's)

Eukarya: Oxygenic photosynthesis plant and algae pigment and storage?

Chlorophyll b, stored in chloroplasts

Bacteria:Oxygenic photosynthesis Cyanobacteria pigment and storage?

Phyacobiliprotein, stored Thylacoids, not in (chloroplasts.)

Bacteria: Oxygenic photosynthesisProchlorophytes pigment and storage?

Chlorophyll b, stored in Thylacoids

Anoxygenic photosynthesis Bacteria: Pigment and storage?

Pigment: bacteriophyll, stored in Chlorosomes

Archaea photosynthesis: pigment and storage?

Pigment: bacteriorhodopsin, stored in cell membrane protein.

Anaerobic respiration?

-Included glycolysis and a krebs cycle.
- During ETS, an inorganic H+ acceptor other than O2 is used.
+ Nitrate Respiration, NO3 subs fro O2
+ Sulfate respiration SO4 subs for O2
+ Carbonate respiration CO3 subs for O2
- Approxamately 24 ATP generated from ETs due to shorter and less complex pathway.
+ Maximum ATP and GTP yiels form anaerobic resp:
- 2 ATP netted from glycolysis
- 2 GTP from Kreb's cycle
- About 24 ATP from the ETS
- Other final products include H2O, N2, S CH4

ATP is used for?

Aynthesis of DNA + RNA
Protein synthesis
cell wall synthesis
active transport
growth

Explain O2 as a toxin and microbial response?

All organisms exposed to oxygen produce toxic molecule superoxide, a free radical.
Obligate and facultative aerobes posess the enzyme superoxide dismutase which converts superoxide O2- to into hydrogen peroxide. H2O2 +O2
Aerobes also produce the enzyme catalase which converts toxic hydrogen peroxide ino H2O + O2
- Most anaerobes cannot produce superoxide dismutase or catalase so they die in the presence of O2.

Chemosynthesis?

- Used by chemoautotrophs.
+ no sunlight is required.
+ Chemicals are used as an energy source, and CO2 used as a carbon source.
+ a form of metabolism associated with Archaea and bacteria.

- Sulfur and sulfur compounds, hydrogen in rocks, and hydrogen gas are oxidized to generate elecrons and hydrogens which reduce carbon dioxide to sugar.
+ sulfur comoounds sxidized to------> CH2O sugar
+ Rocks oxidized ----> CH2O
+ Hydrogen gas ----->Ch2O
+ The only source of natural methane CH4.....are archea methanogens.

Archaea Photosynthesis?

Halophiles most ofen.
Pigment used: Bacretiorhodopsin
- It is antegran cell membrane protein.
- A proton H+ pump that changes shape when hit by light and pumps H+ across the cell membrane.
+Generates a diffusion gradient
+ ATP generated as H+ move back across the membrane through ATP SYNTHASE.
+ this is probably the evolutionary origin of the electron transport chain.
- There is no sugar or oxygen produced, just ATP because there is no further processes to get the ATP.

Oxygenic Photosynthesis?

- Occurs in Eukaryotes (plants and algae), cynaobacteria, prochlorophytes
CO2+H2O ---> CH2O + O2 + H2O

Consists of light Dependant and light independdent reactions.
Light dependent:
-Light absorption via pigments organized in photosystems.
-Cyclic photophosphorylation (photosystem 1)
-Non cyclic photophosphorylation (photosystem 2)
-Calvin-Benson Cycle sysnthesis of carbohydrates (carbon dioxide fixation.)

Oxygenic photosynthesis pigments?

Eukarya: use chlorophylls A and B and caretenoids in thylakoids of the chloroplasts membrane,
Prokarya:
- Cyanbacteria use phycobiliproteins associated with thylacoids as light absorbing pigment.
- Prochlorophytes use chlorophyl B as their light absorbing pigment in thylakoids.

Oxygenic photosynthesis Light absorption?

Each pigment absorbs a specific wavelength of light.
Ekectrons in pigment molecules are excited by the absorbed light energy and are elevated to a higher energy level.
- as electrons return to original energy level, they give off energy and a linger wavelength and heat. the wavelength tranfers through other pigment s until it hits a special pigment that is the only one that can give up an electron for use in photosynthesis. the electron is transfered to an acceptor molecule. (ie...quinone, ferrodoxine)

Oxygenic photosynthesis electron transfers: Cyclic photophosphorylation?

- the electron released from the chlorophyll or phycobiliprotein returns to its original photosystem (photosystem 1) via the electron transport system.
- ATP is generated.

Oxygenic photosynthesis: electron transfers: Noncyclic photophosphorylation?

pS 1 in- Light out: ATP
Ps 2 - in light, H2O, NADP+ Out: NADPH, O2(oxygenic)

- If electrons lost from photosystem 1 are pcked up by a molecule of NADP, the electrons released from the chlorophyll in Photoosystem 2 are used to replace the lost ones., and are delivered to photosystem 1 via an ETS that generates ATP.

-Photolysis of H20
-Generates O2
- involves the removal of electrons from the hydrogens in water
+ Electrons are used to replace the electrons kost from chlorophyll in photosystem 2
+ ATP generated via ETS
+ The H+ are used for the reduction of the NADP+ to NADPH

Products:
ATP, NADPH, O2...ATP and NADPH sent to calvin benson cycle.

Light independent reactions of photosynthesis, Calvin-Benson Cycle?

Process where carbohydrates are synthesized.
using carbon dioxide as the source of carbon.
Using the H+ carried by NADPHs (neneratede in light dependent reactions) as a soure of hydrogen and ATP as an energy source.
- involves fixing CO2 and reduction of CO2 to a carbohydrate. in both oxygenic and anoxygenic photosynthesis.
CO2 + 2NADPH + @H + 3ATP ---> CH2O + H2O

IN: (ATP, NADPH) from light dependent reactions. and CO2
Products:
Sugar--sent to fermentation or cellular respiration
H2O
RuBP

Anoxygenic photosynthesis?

-In green and purple sulfur bacteria.
CO2 + 2H2S ---> CH2O + 2S + H2O
Light absorbing pigment: Bacteriophyll
- is in chlorosomes.
- these bacteria have only photosystem 1 associated with cyclic photophosphorylation..
- Inorganic hydrogen other than water eg. H2S and H2 are used to supply replacement electrons lost form bacteriophyll when NADPH and NADH ae generated.
-H2S and H2 also provide hydrogens that reduce CO2
- O2 is NOT generated (non-oxygenic)

Generates:
ATP
NADPH or NADH sent to calvin benson cycle
May generate Sulfur
Sugar from calvin benson cycle sent to fermentation or cellular respiration.

Photosynthesis in Photohetertrophs?

Green and purple non-sulfur bacteria
Use organic acids as their source of carbon, hydrogens and replacement electrons.

Which include Glycolysis?

Fermentation, Anaerobic resp, Aerobic resp.

Amount of activation energy for each metabolic?

Fermentation 2 ATP, Anaerobic 2 ATP, Aerobic 2ATP

Which includes a Kreb cycle?

Anaerobic and Aerobic, not Fermentation.

Uses Electron Transport system?

Anaerobic and aerobic, not fermentation.

Metabolic net gain of ATP's?

Fermentation 2, Anaerobic resp 28, Aerobic resp 38

Metabolic products generated?

Fermentation: Acid, alcohol, CO2, H2, CH4
Anaerobic Resp: CO2, H2O, N2, S, CH4
Aerobic Resp: CO2, and H2O

Metabolic O2 requirements?

Fermentation: None
Anaerobic: None
Aerobic Resp: Yes, O2

Metabolic inorganic hydrogen acceptor?

Fermentation: none, Pyruvic acid and acetaldehyde
Anaerobic Resp: NO3, SO4,CO3
Aerobic Resp: O2

Microbe type in each systhesis type?

Archaea Photosynthesis: Archaea
Oxygenic Photosynthesis: Cyanobacteria, Prochlorophytes, Plants, Algae.
Anoxygenic Photosynthesis: Green and purple bacteria
Chemosynthesis: Bacteria and Archaea

Light absorbing pigments?

Archaea: Bacteriorhodopsin
Oxygenic: Chlorophyll A and B, phycobiliprotien
Anoxygenic: Bacteriochlorophyll
Chemosynthesis: None

Carbon source for sugar?

Archaea: None...just ATP generated
Oxygenic: CO2
Anoxygenic: CO2
Chemosynthesis: Co2

Pigment Location?

Archaea: membrane protein
Oxygenic: Chloroplasts in thylacoids.
Anoxygenic: Chlorosomes
Chemosynthesis: N/A

Source for replacememnt electrons in systhesis'?

Archaea: None
Oxygenic: H2O
Anoxygenic: H2 and H2S
Chemosynthesis: N/A

Hydrogen source for sugar?

Archaea: no sugar....only ATP generated
Oxygenic: H2O
Anoxygenic: H2 and H2S
Chemosynthesis: Sulfur compounds, H2, and rocks.

Inorganic molecules generated?

Archaea: None
Oxygenic: O2
Anoxygenic: Sulfur
Chemosynthesis: Methane

Oxygenic requirements?

Archaea: None
Oxygenic: None
Anoxygenic: None
Chemosynthesis: None

What custs plasmids or chromosomes and splices respectively?

Restriction endoneucleases cut, and Ligase splices.

What is DNA synthase associated with?

Archaea

DNA components form smallest to largest?

neucleoside ----> neucleoside triphosphate (via adenylate kynase)-----> Neucleotide (DNA polymerase)---->codon--->Gene---->Operon----->Chromosome (1 DNA molecule)-----> Genome

How much of DNA codes for protein?

2%....the rest codes for RNA

What blocks DNA gyrase?

Naladixic acid and profloxacin. Only Bacteric have DNA Gyrase, Eukarya have topoisomerase instead.

AZT?

Attacks reverse transcriptase, but is toxic because we have DNA polymerase.

Transduction VS Transfection?

Transduction is transfer of DNA in bacteria cell to cell via a virus, transfection is in Eukarya via a virus...ie....

Which drugs compete via Competitive inhibition?

AZT, Sulfa drugs

Examples of coenzymes?

NAD and NADP

Oxygen envoronment dismutase?

All organisms create superoxide, but only anaerobes make dismutase and catylase.

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