Micro Final 2 Flashcards
Catabolic Reactions
Break things down, exergonic
Anabolic Reactions
Synthesis Reactions –> making things
Endergonic reaction
Amphibolic Reactions
Functions in both catabolic and anabolic, they tend to couple up
Difference between oxidation and reduction
Oxidation is the loss of an electron and reduction is a gain of an electrion
The difference between a cofactor and a coenzyme
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.
Isomerase
an enzyme that functions in reactions involving isomerization- it makes the correct shape to fit
Ligase
an enzyme that joins two molecules using ATP
The process of enzyme function
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.
Enzyme Kinetics
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
Describe the Lock and Key Model
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
Describe the Induced Fit Model
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
What are the environmental factors that influence enzyme activity?
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
Differences between competitive and non-competitive inhibition
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
Describe Feedback Inhibition
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.
What is substrate level catabolism?
It is an exergonic reaction and releases energy. It is coupled to make ATP. ADP + Phosphate = ATP
What is oxidative phosphorylation?
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
The Krebs Cycle (Info)
The pyruvates are oxidized completely, so the carbons need to be removed. (3 carbons in pyruvate). It generates reducing power.
What occurs prior to entering the Krebs cycle
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.
Entner Doudroff Pathway
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
What is the product summary from glucose? (Enter doudroff)
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
Pentose Phosphate Pathway: Why is it important
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
Product Summary for Krebs Cycle
2NADH (transition step)
6NADH (Krebs Cycle)
2FADH2 (Krebs Cycle)
2GTP –> 2ATP (Krebs Cycle)
End result including glycolysis
10 NADH+
4 ATP
2 FADH2
The net ATP gained is not the point, the 10 NADH+ and FADH2 leads to much higher yields.
What are the electron carrier molecules in the ETC?
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
What type of proteins are the complex’s in the ETC?
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
Why does NADH generate more ATP than FADH2 in the ETC?
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
What is the theoretical ATP yield from the ETC?
4 of the 38 ATP are coming from substrate level phosphorylation and 34 of the 38 are coming from oxidative phosphorylation.
What is the stickland reaction?
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.
What is DNA’s orientation
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
What is DNA replication?
It is when DNA is made from DNA, in an exact copy.
What are important proteins in elongation?
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
What is a promoter?
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.
What are the 4 protein subunits in RNA polymerase?
Alpha, Beta, Beta Prime, Sigma
How does binding of the RNA polymerase work in transcription?
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.
What is the difference between being rho dependent and rho independent?
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.
Stop and Start codons
Start: AUG (codes for methionine)
Stop: UGA, UAA, UAG
How does the ribosome know there to start?
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.
What is the characteristics of bacterial ribosomes?
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.
