Micro Final 2

Question 1

Catabolic Reactions

Answer 1

Break things down, exergonic

Question 2

Anabolic Reactions

Answer 2

Synthesis Reactions –> making things

Endergonic reaction

Question 3

Amphibolic Reactions

Answer 3

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

Question 4

Difference between oxidation and reduction

Answer 4

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

Question 5

The difference between a cofactor and a coenzyme

Answer 5

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 6

Isomerase

Answer 6

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

Question 7

Ligase

Answer 7

an enzyme that joins two molecules using ATP

Question 8

The process of enzyme function

Answer 8

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 9

Enzyme Kinetics

Answer 9

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 are efficient- very quick and reusable

Question 10

Describe the Lock and Key Model

Answer 10

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 11

Describe the Induced Fit Model

Answer 11

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 12

What are the environmental factors that influence enzyme activity?

Answer 12

Temperature: If temp is low, the atoms will move slower. If the temp is high, 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 13

Differences between competitive and non-competitive inhibition

Answer 13

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 14

Describe Feedback Inhibition

Answer 14

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 15

What is substrate level catabolism?

Answer 15

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

Question 16

What is oxidative phosphorylation?

Answer 16

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

Question 17

The Krebs Cycle (Info)

Answer 17

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

Question 18

What occurs prior to entering the Krebs cycle

Answer 18

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 19

Entner Doudroff Pathway

Answer 19

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 20

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

Answer 20

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 21

Pentose Phosphate Pathway: Why is it important

Answer 21

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

Question 22

Product Summary for Krebs Cycle

Answer 22

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

Question 23

End result including glycolysis

Answer 23

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 24

What are the electron carrier molecules in the ETC?

Answer 24

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 25

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

Answer 25

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 26

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

Answer 26

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 27

What is the theoretical ATP yield from the ETC?

Answer 27

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

Question 28

What is the stickland reaction?

Answer 28

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.

Question 29

What is DNA’s orientation

Answer 29

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 30

What is DNA replication?

Answer 30

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

Question 31

What are important proteins in elongation?

Answer 31

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 32

What is a promoter?

Answer 32

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 33

What are the 4 protein subunits in RNA polymerase?

Answer 33

Alpha, Beta, Beta Prime, Sigma

Question 34

How does binding of the RNA polymerase work in transcription?

Answer 34

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 35

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

Answer 35

n 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 36

Stop and Start codons

Answer 36

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

Question 37

How does the ribosome know there to start?

Answer 37

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 38

What is the characteristics of bacterial ribosomes?

Answer 38

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.