question

Catabolic Reactions

answer

Break things down, exergonic

question

Anabolic Reactions

answer

Synthesis Reactions --> making things
Endergonic reaction

question

Amphibolic Reactions

answer

Functions in both catabolic and anabolic, they tend to couple up

question

Difference between oxidation and reduction

answer

Oxidation is the loss of an electron and reduction is a gain of an electrion

question

Describe the 3 types of pathways:

answer

Linear- reactants to products with multiple intermediates
Branches- one intermediate can be used in more than one reaction and leads to multiple outcomes
Cyclic- starting compounds operate in a cycle. Generates an intermediate that is used to restart the cycle

question

The difference between a cofactor and a coenzyme

answer

coenzymes are bigger than cofactors. Co enzymes bind permanently while cofactors are normally temporary. Both promote the reaction in the same way. A reaction can have both a cofactor and a coenzyme.

question

Holoenzyme

answer

when an enzyme has all of its parts together

question

Apoenzyme

answer

an enzyme where a cofactor is necessary for completion

question

Oxidoreductase

answer

An enzyme that functions in oxidation-reduction reactions

question

Transferase

answer

An enzyme that transfers groups between molecules

question

Hydrolase

answer

an enzyme that breaks bond by hydrolysis

question

Lyase

answer

an enzyme that breaks bonds in a way other than hydrolysis

question

Isomerase

answer

an enzyme that functions in reactions involving isomerization- it makes the correct shape to fit

question

Ligase

answer

an enzyme that joins two molecules using ATP

question

The process of enzyme function

answer

Once the enzyme has its correct shape, it is able to bind the substrate and it makes the enzyme substrate complex. Once the substrate comes into the active site, a bond forms which makes it change shape. This is done by the bond strain. Enzymes are reusable.

question

Enzyme Kinetics

answer

Enzymes lower the activation energy of a reaction. This is because enzymes add bond strain. When the enzymes grab substrates, they start contorting the bonds to help them break.
They provide a site for positioning which makes it easier for atoms to collide
They are efficient- very quick and reusable

question

Describe the Lock and Key Model

answer

The enzyme is the lock and the substrates are like the keys. Only certain keys fit in certain locks, and this is how enzymes are specific

question

Describe the Induced Fit Model

answer

Active sites are generally the right shape and once the substrates enter the active site and the bond start forming, it takes into account the strain and the enzyme changed conformation to fit the substrate and kind of gives the substrate a hug around it

question

What are the environmental factors that influence enzyme activity?

answer

Temperature: If temp is too low, the atoms will move slower. If the temp is above optimum temp, the enzyme will denature which is a permanent change
pH: The optimal pH for most bacteria are about 6-7. Acidophiles and alkaophiles are exceptions
Ionic:
Concentrations: If there is more substrate than enzyme or vice versa, this is a limiting factor

question

Differences between competitive and non-competitive inhibition

answer

Competitive: the inhibitor binds to the active site
Non-competitive: the inhibitor binds to the allosteric site which changes the shape of the active site

Inhibitors can be both reversible and irreversible

question

Enzyme Regulation

answer

Reversible inhibition can regulate enzymes. Allosteric regulation is when an activator comes along and binds to the allosteric site to create the correct shape for a substrate. The energy from a phosphate is used to add an adenylyl group. This slows enzyme activity and is permanent until something removes it

question

Describe Feedback Inhibition

answer

Cells can use the product of a reaction to regulate the reaction itself. A substrate is used to make the products of the reaction, but as the concentration of the products increase, the products act as inhibitors for their production. This is non-competitive. The pathway shuts down until the quantity of the products decrease again.

question

Emben-Meyerhof Pathway Steps

answer

1: A phosphate is added to a glucose (uses ATP). This makes it glucose-6- phosphate which is unstable
2: Isomerization occurs and makes glucose-6-phosphate into fructose-6-phosphate. This is more stable
3: Another phosphate is added and makes fructose-6-phosphate into fructose-1,6-biphosphate. This uses ATP and destablizes the molecule. ATP is turned to ADP
4: Fructose 1-6-biphosphate becomes G3P and DHAP. This is because fructose is so unstable it rips itself apart
5: DHAP isomerizes to G3P. Now there are 2G3P, so every process is now being done twice.
6: G3P is oxidized and NAD+ is reduced. G3P becomes 1,3 bisphosglycerate and NAD+ becomes NADH
7: The phosphate is removed and ADP converts to ATP (substrate level phosphorlylation)
8: 3 phospholycerate becomes 2 phosphoglycerate due to isomerization
9: 2 phosphoglycerate becomes phosphoenol pyruvate (PEP) due to dehydration
10: The phosphate is removed and pyruvate is removed. The phosphate is pulled off to make this occur. ADP --> ATP

question

What is the product summary from glucose? (Emben Meyerhof)

answer

1 glucose uses 2 ATP and gains 4 ATP and 2NADH+. The net gain is 2 ATP and 2 NADH+

question

Entner Doudroff Pathway

answer

This pathway is used in place of glycolysis. The first four steps are the only steps that are different
1: Glucose converts to glucose-6-phosphate. ATP-->ADP
2: glucose-6-phosphate oxidizes into 6phosphogluconate. NAD+ is reduced to NADPH
3: G6P is dehydrated to KDPG
4: This splits into one molecule of G3P and one pyruvate

question

What is the product summary from glucose? (Enter doudroff)

answer

Less energy is produced here due to only having 1 G3P instead of 2. Only 1 ATP was put in and only 2 came out. This makes it less effective. EM and ED make the same amount of pyruvate (2). ED pathway makes 1 NADPH and 1 NADH while EM makes 2 NADH

question

Pentose Phosphate Pathway: Why is it important and steps

answer

PPP is amphibolic, makes sugar that can feed back into itself, it produces precursor metabolites, it makes G3P which can lead to making ATP, NADPH+ is produced
1: Glucose-6-phosphate is already phosphorylated and becomes 6-phosphogluconate by oxidation. NADP+ becomes NADPH
2: 6-phosphogluconate oxidizes and becomes ribulose 5-P. NADPH+ becomes NADPH

question

What is substrate level catabolism?

answer

It is an exergonic reaction and releases energy. It is coupled to make ATP. ADP + Phosphate = ATP

question

What is oxidative phosphorylation?

answer

There are 2 part: The ETC is oxidation reduction reactions that move through the chain. The proton motive force brings hydrogens in to make ATP

question

The Krebs Cycle (Info)

answer

The pyruvates are oxidized completely, so the carbons need to be removed. (3 carbons in pyruvate). It generates reducing power.

question

What occurs prior to entering the Krebs cycle

answer

Pyruvate cannot directly go into the KRebs cycle, but acetyl CoA can. This is the transition step. CoA is high energy and it binds with an ester bond. Pyruvate oxidizes to NAD+ becomes NADH. This happens twice per glucose. because of this, carbon is lost to the environment. This is considered the first decarboxylation because carbon went from 3 to 2.

question

The Krebs Cycle (Steps)

answer

1: The energy within the bond on Acetyl CoA powers this step. Oxaloacetate (4 carbon) is added to an acetyl group to get citrate. 4C + 2C = 6C
2: Citrate isomerizes to become isocitrate (6C)
3: Isocitrate is oxidized to become alpha-keytogluterate. This is the second decarboxylation to release co2. NAD+ reduces to NADH. 6C to 5C
4: alpha-keytogluterate is oxidized to becomes succinyl CoA. This is the third decarboxylation. NAD+ reduces to NADH. CoA was added (high energy). 5C to 4C
5: CoA is removed to make succinate. The energy is captures as GDP which is converted to GTP. ADP can then convert to ATP. 4C
6: Succinate is oxidized to create fumarate. FAD is reduced to FADH2. 4C
7: Fumerate is hydrated to create malate. 4C
8: Malate is oxidized to oxaloaxetate (regenerated) Electron lost from oxidation is added to NAD+ to make NADH. 4C

question

Product Summary for Krebs Cycle

answer

2NADH (transition step)
6NADH (Krebs Cycle)
2FADH2 (Krebs Cycle)
2GTP --> 2ATP (Krebs Cycle)

question

End result including glycolysis

answer

10 NADH+
4 ATP
2 FADH2

The net ATP gained is not the point, the 10 NADH+ and FADH2 leads to much higher yields.

question

What are the electron carrier molecules in the ETC?

answer

Flavoproteins: not contributing to the proton gradient but help with movement of electrons
Iron-Sulfer proteins- carries electrons
Quinones- can carry electrons and protons and only pass electrons
Cytochromes: iron of heme containing. Can carry electrons and export protons

question

The Electron Transport Chain

answer

NADH will go into the electron transport chain and go into Complex 1, NADH dehydrogenase. Next it will go into coenzyme Q (ubiquinone). Then complex 3 called cytochrome bc1, then cytochrome c, and then complex 4 called cytochrome aa3.

question

What is the difference between NADH's pathway, and FADH2's pathway in the ETC?

answer

FADH2 uses the same pathway, but it changes its entry molecule. It does not use complex 1, it used complex 2 (succinate dehydrogenase), which then joins back with coenzyme Q.

question

What type of proteins are the complex's in the ETC?

answer

Complex 1, 3, and 4 are integral proteins and act like a tunnel for protons to enter the cell. Complex 2 is a peripheral protein and cannot contribute to the proton gradient

question

What is the chemiosmotic hypothesis?

answer

The proton is going to go through ATP synthase which binds the protons as they come back in. In the ETC< the gradient of protons is more outside the cell than in so they want to come back in to equal out the gradient. The come back into the cell through ATP synthase and they grab them. This generates energy that begins to spin the synthase around which can be converted to stored potential energy. This kind of energy is used to put the phosphate back on the ADP to make ATP. In a perfect world, every NADH would yield 3 ATP but because protons are used in other processes besides oxidative phosphorylation this usually not the case

question

Why does NADH generate more ATP than FADH2 in the ETC?

answer

NADH uses more transmembrane proteins by starting with complex 1, while FADH2 begins with complex 2 which is a peripheral protein. NADH puts more protons in so it is responsible for more ATP production

question

What is the theoretical ATP yield from the ETC?

answer

4 of the 38 ATP are coming from substrate level phosphorylation and 34 of the 38 are coming from oxidative phosphorylation.

question

What do all respiratory chains have in common? (bacteria and eukaryotic)

answer

Presence of membrane associated e- carriers, arranged in order of increasing reduction potential
Alternating carriers: transmembrane, peripheral, transmembrane, peripheral
Generation of the proton motive force: H+ on the outside, OH- on the inside
Use of ATP synthase enzyme: very similar between bacteria and eukaryotic

question

What are the differences between bacteria and eukaryotic respiratory chains?

answer

Bacteria may have a greater variety of carriers based on how much oxygen is present
They can vary in their number of carriers
Bacteria respond to changing in growth conditions by altering their ETC
Bacteria ETC's may be branced with alternative e- transfer to different final e- acceptors

question

What is respiration using nitrate?

answer

Nitrate becomes nitrite through oxidation. Nitrite becomes nitric oxide. Nitric oxide becomes nitrous oxide when then coverts into dinitrogen. Complex 4 changes. It becomes nitrate reductase.

question

What is respiration using sulfate?

answer

When an anaerobe uses sulfate to recieve the final electron, it encouraged binding of protons to sulfate. The sulfate then becomes hydrogen sulfide which produces sulfuric acid. This has to be carefully controlled.

question

Why is nitrate better to use than sulfate?

answer

Nitrate is a large jump from NADH on reduction potenial while sulfate is a smaller jump, so nitrate will yield more ATP than sulfate.

question

What is fermentation?

answer

Fermentation occurs when organisms are unable to respire. Fermentation happens in the absence of oxygen. This could be due to a lack on the respiration pathway or due to a lack of the terminal acceptor on the ETC. For organisms that lack the ETC all together, the Krebs cycle is also missing because there is no need for NADH or NADH2. All ATP generation is coming from glycolysis when fermentation is being used.

question

How does fermentation work?

answer

A pyruvate is taken from glycolysis and is used, or an intermediate is used, to accept electrons from NADH. This movement of electrons from NADH to pyruvate or another chemical is crucial to the organism surviving. Fermentation allows the regeneration of NAD+ around the 6th step of glycolysis. Without NAD+ in the 6th step, oxidation would not occur. This regenerates glycolysis

question

What is the stickland reaction?

answer

It is an example of fermentation that can yield ATP. It involved fermenting amino acids alanine and glycine in a coupling of oxidation reduction reactions. Alanine is oxidized and is used to reduce NAD+ to NADH. This reduction of NAD+ is crucial because it is coupled to the process that produces Acetyl-P from glycine. Glycine oxidizes NADH to NAD+. Alanine and Glycine rely on one another for the NAD+ and NADH. Acetyl P is important because it makes ADP to ATP. Glycine is better at making ATP than Alanine. 2 ATP for glycine, 1 for alaine.

question

Characteristics of Bacterial Chromosomes

answer

Bacteria do not have formal histones. The grooves on the outside of the proteins allow the DNA to wrap around them which shortens it
DNA two strands shorten as the molecule twists
Bacteria tend to be more efficient at how they use genetic information
Bacterial DNA is not bound by a membrane but is still organized
Bacteria genome often is associate with the cytoplasmic membrane
Bacterial genomes are generally single closed circular pieces of DNA (euks are linear)
Bacteria contain extra DNA called plasmids
DNA is supercoiled

question

What are the bonds that hold DNA together?

answer

phosphodiester bonds

question

What is Chargaff's rule?

answer

A pairs to T and G pairs to C. When A and T pair, a double bond is formed, when G and C pair, a triple bond is formed.

question

What is DNA's orientation

answer

Antiparallel. 5' phosphate on the 5' carbon on the ribose sugar. On the other side, a hydroxyl group coming off the 3' carbon. To bind in the correct conformatio, it must bind 5' to 3' and its complement in the reverse order

question

What is DNA replication?

answer

It is when DNA is made from DNA, in an exact copy.

question

What is Theta replication?

answer

Theta replication begins at the origin and proceeds in a bidirectional process. Both sides move away from the origin at the same time until the process completes at the opposite site of the chromosome. It is completed at the termination site (ter)

question

What occurs in the initiation step of replication?

answer

Initiation begins at the OriC. This is a highly concerved sequence with two parts. One is called the 9-mer (or DnaA box or TTATACCACA). The other region is called the 13-mer and it is AT rich.
DNA must bind to the DNAA box in the OriC. The binding of the DnaA causes the helix to bend, which will allow the AT rich region of the 13-mer to break apart. With the helix open around the 13-mer, DnaC can chaperone the delivery of DnaB to the oriC. This achieves the open complex. With the helix open, it is important that the strands do not rebind each other. Single stranded proteins will come in and bind the two strands to keep them separated. This is the pre-priming complex. The next enzyme, primase, will add an RNA primer to get the process of replicatin started. DNA polymerase cannot start without a piece of a strand to hold on to. This is primases job (DnaG). The primer will be removed and replaced with DNA later on. This structure is primosome.

question

What is the structure of DNA polymerase?

answer

It exists as a dimer bound together at the gamma complex. In addition to holding the dimer together, gamma also loads the bta clamp onto the DNA. Extending from the gamma complex are flexible arms (tau). The tau arms connect the actual enzymatic part of the polymerase that will make DNA to the rest of the structure. The core enzyme will actually catalyze the addition of new nucleotides to a growing DNA strand

question

What are important proteins in elongation?

answer

Helicase
Topoisomerase: DNA gyrase relieves tension in DNA, breaks DNA strand and unwinds it
Primase
DNA ligase: forms phosphodiester bonds between the 3' strand and 5' strand

question

Characteristics of Bacterial Chromosomes

answer

Bacteria do not have formal histones. The grooves on the outside of the proteins allow the DNA to wrap around them which shortens it
DNA two strands shorten as the molecule twists
Bacteria tend to be more efficient at how they use genetic information
Bacterial DNA is not bound by a membrane but is still organized
Bacteria genome often is associate with the cytoplasmic membrane
Bacterial genomes are generally single closed circular pieces of DNA (euks are linear)
Bacteria contain extra DNA called plasmids
DNA is supercoiled

question

What is happening in the elongation step of DNA replication?

answer

The polymerase itself does not move, it pulls DNA through like a spool. For the leading strand, the same strand is constantly being pulled through. For the lagging strand, the DNA is looped out. When an Okazaki fragment hits the one before it, the enzyme is released and clamp is released soon after. Another clamp is waiting to reload the core enzyme to make another fragment in a different location.

question

How does the leading strand work?

answer

The polymerase is going from 3' to 5' and the DNA can continue copying.

question

How does the lagging strand work?

answer

As the leading strand progresses, he helix continues opening. Wherever the helix is open, it will lay down a primer and begin copying. Once that piece is done, the lagging strand will go where the helix is opening and copy until it runs out of room again (Okazaki). RNAase will break down the primer and Poli 1 will fill in the gaps. Pol1 replaces RNA with DNA. DNA polyermase 1 will take the 3' hydroxyl and the 5' phosphate and is going to link the phosphate to the carbon. This is the phosphodiester bond. Once the copying is done, there is a gap that is sealed by ligase.

question

What is happening in the termination step of DNA replication?

answer

Termination happens at the ter site. Thre are actually a lot of them opposite of the origin. They are bound by Tus. This bond halts replication machinery. Tus acts like a speed bump to slow down the polymerase. The polymerase has a proofreading ability that occurs in this step. If a mistake is read, the mismatch repair system fixes the mistake by going back a few base pairs.

question

What is rolling circle replication?

answer

This is the type of replication that plasma's use. This allows for multiple linear genomes to be copied that can cirularize. In a circular piece of DNA, the origin is cut and this is where it can start going. It will start adding on new pieces from 5' to 3'. As these new pieces are added on from copying, the old piece is pushed out and eventually the old strand can be bound by DNA polymerase and a compliment be made.

question

How do antibiotics affect DNA replication?

answer

There are large differences between human and bacterial replication, so this is positive when it comes to treating bacterial infections. Quinolones are used for this. Quinonles are synthetic so bacteria cannot become as resistant to them. Quinonles inhibit bacterial topoermase. This releases supercoiling so the coiling will becomes so tight it will break. There is a resistance because of a mutation in the gene DNA gyrase. This mutation relieves supercoiling.

question

Making RNA from DNA

answer

transcription

question

Making protein from RNA

answer

translation

question

What is a promoter?

answer

A promoter is used so the RNA polymerase knows where to start transcription. Each individual strand have have its own promoter. Promoters have two highly conserved regions. The -35 box and the pribnow box (-10). The -10 region is AT rich. The -35 region serves as recognition for RNA polymerase. The -10 is where it is going to actually bind.

question

What are the 4 protein subunits in RNA polymerase?

answer

Alpha, Beta, Beta Prime, Sigma

question

Why is sigma such an important subunit?

answer

Sigma is important because it is responsible for promoter recognition. Sigma is the portion of the enzyme that recognizes the -35 box. Bacteria can swap out either sigmas so they can control their genetic expression because promoters can differ.

question

How does binding of the RNA polymerase work in transcription?

answer

RNA polymerase is going to recognize the -35 box and then it is going to bind to the -10 (primnow box). This causes the helix to unwind (AT Rich). Once the helix is open, it is called the open complex. Once it's open, synthesis can begin. This reads from 3' to 5' so it is made 5' to 3'. Once RNA polymerase has started, the sigma drops off.

question

What is the difference between being rho dependent and rho independent?

answer

In rho independent, there is a secondary structure in mRNA called the step loop. No proteins are involved here. At the end of the message, there is a run of U's. When these get synthesized, the stem loop structure forms and the RNA polymerase becomes unstable. While RNA polymerase pauses, the U-rich sequence in the open complex is not able to hold the RNA-DNA hybrid together and termination occurs.
In Rho dependent termination, rho binds sequences called Rut in RNA. When rho binds Rut, it starts traveling along the RNA. When the polymerase hits the terminator, it will still form the stem-loop. While the polymerase pauses, rut catches us and causes the release.

question

What is translation?

answer

Translation is the change from nucleic acids to amino acids. The code is read in triple. Every 3 nucleotides in RNA is called a codon. Every codon will give an amino acid. There are 64 possible codons and 20 amino acids

question

What are the stop and start codons?

answer

Start: AUG (codes for methionine)
Stop: UGA, UAA, UAG

question

How to find protein from a strand of DNA

answer

You would match the DNA sequence to RNA. Find the start codon and do codon matching. The start codon establishes the reading frame. Find the stop codon and stop it. This cannot be done in reverse.

question

What is the structure of tRNA?

answer

It has a cloverleaf structure and has 4 arms. The right arm is called the Tyc arm. The left arm is the D arm. The bottom are is the anticodon loop. The anticodon is going to be complementary to the mRNA codon. This tRNA is going to be bringing the methionoine and needs to have complementary base pair to the mRNA codons.

question

How does the tRNA work?

answer

The CCA sequence at the top is where the amino acid will attach. All tRNA's end in CCA. An animoacytl-tRNA synthesis reaction recognizes the amino acid that needs to be put on the CCA. They use the consumption of ATP to get the energy to make a bond between amino acid and the tRNA.

question

What is the wobble?

answer

The 3rd nucleotide unit does not have to be complementary. 1 trna can recognize more than one codon. Ex: base pairing of one glycine tRNA with two codons due to wobble. CCG can pair with both GGC and GCG

question

How does the ribosome know there to start?

answer

The sgine delgarno sequence is used for ribosome bonding. This positions the ribosome at the right part of the message to start. these can be alternative start codons. Whenever methionine starts a message, it gets formulated. This means it gets a formal group put onto it.

question

What is the characteristics of bacterial ribosomes?

answer

They are 70S with 2 componants. A large subunit called the 30S, and a large subunit called the 50S. The small subunit has 16S RNA and the large has 2 subunits: 5S and 23S.

question

What are the sites of the 70S ribosome?

answer

The A site: where tRNA is coming in. A for acceptor and amino acids
The P site: connects amino acids into peptide bonds. P stands for peptidyl.
The E site: empty tRNA's leave here. E stands for exit.

question

What is the initiation step of translation?

answer

The small subunit is on the bottom, the small subunit is going to be carrying initiation factor 3. It prevents the small subunit from binding to the large subunit. IF3 insures that mRNA comes in on top of the small subunit. IF3 leaves, then tRNA is escorted by IF2. IF2 brings tRNA to the P site. IF1 helps in the act of binding the large subunit to the small

question

What is codon recognition?

answer

the tRNA is brought in and the anticodon will bind to the codon

question

What is transpeptidation?

answer

The p-site launches an attack on the A site. The peptide thats sitting in the a site attacks the A site and claims it with a peptide bond. Now the peptide is in the a site, there an empty rna in the p site.

question

What is translocation?

answer

Translocation is the fixing of transpeptidatin. What happens is that the ribosome will move forward one codon and then the ribosomes will shift to their correct positions. The helper that does this is called the EF-G. This happens over and over again until you hit a stop codon.

question

Describe termination of ribosomes

answer

The ribosome stalls at the nonsense codon and then falls off. There is no tRNA at the stop codon. When the ribosome stalls release factors come in and the peptide is cut off the last tRNA. it goes and matures the small subunit binds to if3 to start the process over again.

question

What is protein folding?

answer

Molecular chaperones aid in the folding of nascent polypeptides. There are also molecule chaperones that protect from thermal damage. They are required to properly fold a protein.

question

What is protein splicing?

answer

Bacteria have inteins and exteins. Inteins are between extiens and meed to be cut out and the exteins will be joined together. This is done before folding.

question

What is the antibotic that blocks transcription?

answer

Rifamycins: These bind and block rna polymerase and prevent elongation. They are bacterial killers and are useful in treating tuberculosis.

question

Aminoglycosides

answer

an antibiotic that targets translation. These prevent initiation. Used with beta lactam.

question

Tetracycline

answer

antibiotic that targets translation. blocks the attachment of tRNA to the ribosome. Broad spectrum. Bacteriostatic- slow growth or stop growth

question

Macrolides

answer

antibiotic that targets translation. blocks elongation. Blocks the exit hole and the pressure will bust the protein open. Broad spectrum

question

What is the difference between bacteria and eukaryotes when it comes to the 5' cap?

answer

Bacteria have the shine delgarno sequence and have no nucleus that it needs to leave, so a cap is not necessary

question

Why is it important for bacteria to have DNA that quickly degrades?

answer

This is important because the quick degredation of DNA make it easier for bacteria to respond to change.

question

Why dont bacteria need a poly-A-tail?

answer

bacteria translation begins before transcription even ends. This is why there is no tail. Once it comes off the polymerase, the ribosome is there to cover the end which provides protection.

Test 3- Chapters 10, 11, 13 Campbell – Flashcards

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