Biochem 2 Flashcards
(122 cards)
- Pentose Phosphate Pathway (PPP)
- How many NADPH are produced per G6P molecule by the PPP?
- How many glutathione molecules are produced per G6P by the PPP?
NADPH:
For each G6P molecule:
-
two NADPH molecules are generated
- Both come from G6P converting to Ribulose 5-phosphate
Glutathione:
- The PPP does not DIRECTLY generate glutathione molecules.
- However, the NADPH generated in the PPP can be used to:
-
reduce the oxidized form of glutathione
- …to protect the cell from reactive oxygen species.
-
reduce the oxidized form of glutathione
- However, the NADPH generated in the PPP can be used to:
- To regenerate glutathione, the reaction is:
-
1 glutathione disulfide + NADPH → 2 glutathione + NADP+
- This means that for each G6P, four glutathiones are generated
- because two NADPHs are generated
- This means that for each G6P, four glutathiones are generated
-
1 glutathione disulfide + NADPH → 2 glutathione + NADP+
- Carbohydrate Metabolism
- Give a general definition for “Carbohydrate Metabolism”
- Also, define “Respiration” in this context
- General Definition:
- The sum (Σ)of all chemical reactions in the body
- Respiration:
- “the breakdown of macromolecules into smaller species to harvest energy in the form of ATP”
- Carbohydrate Metabolism
- Clarify the difference between aerobic and anaerobic respiration
- Which one do humans use? When would we use the other?
- What happens as a result of using the other?
- What does “Anaerobic respiration” typically refer to?
- Respiration is a process in which an inorganic compound serves as the ultimate electron acceptor
- …in order to generate ATP
- Aerobic respiration:
- uses oxygen as the final electron acceptor
- Anaerobic respiration:
- uses a molecule other than oxygen
- For question purposes, aerobic respiration involves all the reactions involved in:
- the citric acid cycle (CAC)
- electron transport chain (ETC)
- Humans use aerobic respiration to generate the vast majority of our ATP
However, we use anaerobic respiration in our muscles during exercise- which results in a buildup of lactic acid
- Anaerobic respiration will typically refer to fermentation:
- using glycolysis in the absence of oxygen
- or the lactic acid cycle in muscles
- Many bacteria and yeast use anaerobic respiration, including during fermentation

Feeder Pathways for GLY
-
FRUCTOSE Metabolism In the LIVER
-
Fructose⇒___⇒___+____⇒___
- Describe the 3 sequential rxns
-
Fructose⇒___⇒___+____⇒___
What step of Glycolysis does this funnel into?
LIVER:
-
Fructokinase converts:
- Fructose⇒Fructose-1P
-
Fructose-1-P ALDOLASE converts:
- Fructose-1P ⇒Glyceraldehyde 3-Phosphate (GAP) + DHAP
-
Triose Phosphate Isomerase converts:
- DHAP⇒ GAP
⇒5th step GLY
(Will get converted to 1,3 Bisphosphoglycerate by GAPDH)
- Principles of Bioenergetics
- ΔG=?
- What does each part represent?
- Here, how should you think of ΔG and ΔG°’?
- ΔG=?
-
ΔG = ΔG°’ + RTlnQ
- R =Universal Gas Law constant
- T=temperature
- Q=reaction quotient
- Think of ΔG°’ as:
- the fixed, unchangeable value
- ΔG°’ is fixed and predetermined for a given reaction at a given temperature
- It ONLY represents the reaction under all of those strictly standardized criteria
- the fixed, unchangeable value
- Think of ΔG as:
- the variable one
- ΔG can be measured anywhere, at any time during a reaction
- Pause the reaction at any precise moment of your choosing, subtract the sum of the free energy of the reactants present at that moment from the sum of the free energy of the products present at that moment
- The resulting value will be ΔG
- the variable one
- Organism-Level Regulation of Metabolism
- What does the Brain, Adipose Tissue, and Erythrocytes (RBC’s) use for fuel during well-fed states and during fasting states?
- Brain
- Glucose during well-fed state
- Glucose if fasting
- Ketones if prolonged fast or starvation
- Adipose Tissue
- Glucose in well-fed state
- Fatty acids during fasting
- Red Blood Cells
- Glucose in ALL states
- ALWAYS via ANAEROBIC glycolysis!!!
- aka FERMENTATION
- Glucose in ALL states
- Adenosine Triphosphate (ATP)
- Consumption of ATP
- Name the 3 ways ATP is consumed (that we need to know for MCAT)
- Consumption of ATP
- Hydrolysis
- Phosphoryl Group Transfers
- Phosphorylation using ATP
- Bioenergetics & Thermodynamics
- Describe the “Fundamental Thermodynamic Relation” that correlates enthalpy, entropy and Gibbs free energy.
- Draw a four quadrant chart showing all possible combinations for the signs of ΔS and ΔH for a reaction.
- For each scenario predict the sign of ΔG and whether or not the reaction will be spontaneous
- The fundamental thermodynamic=
- ΔG=ΔH-TΔS
-
Spontaneous if…
- ΔG is less than 0
-
Non-spontaneous if…
- ΔG is greater than 0
-
At equilibrium if…
- ΔG is = 0
- A reaction is favorable if…
- ΔH is negative and/or ΔS is positive.
- When ΔH is negative and ΔS is positive, the reaction will be spontaneous
- When ΔH is positive and ΔS is negative, the reaction will not be spontaneous
- ΔH is negative and/or ΔS is positive.
- In any other situation, the result will depend on the values of H and S

- Lipid Metabolism
- β-Oxidation of fatty acids
- In β-Oxidation, where on the FA are double bonds created?
- What happens if you come across a double bond that isnt in that position?
- What enzyme do you need to fix it?
- β-Oxidation of fatty acids
- Normal β-oxidation includes the creation of a double bond in the 2-3 position
- As successive rounds of oxidation occur, if a double bond ends up in this position, things may proceed as normal
- If double bond is in another position (like 3-4), β-oxidation cannot occur
-
Enoyl-CoA isomerase catalyzes the movement of double bonds to the 2-3 position
- Oxidation can again proceed
-
Enoyl-CoA isomerase catalyzes the movement of double bonds to the 2-3 position

- Carbohydrate Metabolism
- What is the difference between an obligate aerobe and a facultative aerobe?
- Between an obligate and a facultative ANAEROBE?
- Which one are you?
- “Obligate”
- implies that there is no other option, so obligate aerobes must use aerobic respiration and cannot survive without oxygen, while obligate anaerobes must use anaerobic respiration and cannot survive in the presence of oxygen.
- “Facultative”
- implies that the organism will use WHICHEVER RESPIRATION IS AVAILABLE
- So if oxygen is present, the organism will use aerobic respiration, and if oxygen is absent, the organism will use anaerobic respiration.
- Facultative anaerobes prefer anaerobic respiration but will use aerobic if needed.
- Facultative aerobes prefer aerobic respiration but will use anaerobic if needed
- ∴ HUMANS ARE “FACULTATIVE AEROBES”
- Bioenergetics & Thermodynamics
- Define “Bioenergetics”
- What is it analogous to?
- Bioenergetics
- The thermodynamics of biological systems
- is analogous to biochemistry being the “chemistry” of biological systems
- Anabolism of Fats & Carbohydrates
- Describe Non-Template Synthesis
- Why is the moniker “Non-Template” used to describe it?
- Describe Non-Template Synthesis
-
Non-Template Synthesis:
- Biosynthesis of lipids and polysaccharides (carbohydrates)
- The moniker “non-template” is used because the synthesis of fats and carbohydrates does not follow a template
- …as do protein and nucleic acid synthesis
- Regulation of Carbohydrate Metabolism
- Hormonal Control
-
GLUCONEOGENESIS:
- identify all molecules that:
- upregulate the process
- downregulate the given process.
- Specify the exact enzyme or step with which the regulatory molecule interacts
- identify all molecules that:
-
GLUCONEOGENESIS:
- Hormonal Control
- Gluconeogenesis is needed when energy levels are high and glucose levels are low
- the opposite of when glycolysis is needed.
- As such, the enzymes are regulated oppositely to those in glycolysis such that when one pathway is activated, the other is being actively inhibited, and vice versa.
-
Fructose 1,6-bisphosphatase
- inhibited by AMP
- stimulated by ATP
- exactly opposite of its glycolysis counterpart
- phosphofructokinase.
- Both:
- pyruvate carboxylase and
- phosphoenolpyruvate
- are inhibited by ADP
- These enzymes are the counterpart to pyruvate kinase in glycolysis
- Principles of Bioenergetics
- Describe the difference between ΔG, ΔG°, and ΔG°’
- What should you remember about the last two?
It is important to remember that a reaction is almost never going to be in these conditions!!!
- ΔG
- Free energy change at some present, non-standard set of conditions.
- ΔG°
- Free energy change at standard conditions:
- 25°C
- 1 atm
- [1M] of all species
- Free energy change at standard conditions:
- ΔG°’
- Free energy change at standard physiological conditions, pH = 7
- For the MCAT, think of ΔG° and ΔG°’ as essentially the same thing
- They both represent a standard state “from-the-textbook-table” value for Gibbs free energy calculated at a point where we have the exact same concentrations of all species, both products and reactants (i.e., Q = 1).
- Just remember that the prime (’) symbol means it is at physiological pH, too
Pentose Phosphate Pathway (PPP)
Describe the Oxidative Phase
- __–>__–>__–>__?
- Since the first 2 steps are UNfavorable, what EXERgonic reaction are they coupled to?
- What do NADPH and R5P each do in this phase?
OXIDATIVE PHASE:
Glucose-6-P ⇒
6-Phosphogluconate ⇒
Rib**ulose**-5-P ⇒
Ribose-5-P
The first two steps outlined above are both coupled to:
- the conversion of NADP+ to NADPH
NADPH is used to:
- REDUCE glutathione disulfide (GSSH) to glutathione (2GSH)
- Act as a COFACTOR for reductive biosynthesis
R5P
- is funneled into NT synthesis
Glycolysis
Aldolase catalyzes the breakdown of Fructose 1,6-bisphosphate (F1,6BP) into:
- one molecule of glyceraldehyde-3-phosphate (G3P)
- one molecule of dihydroxyacetone-phosphate (DHAP)
If the 2’ carbon of F1,6BP is radioactively labeled, aldolase is allowed to turnover a large number of molecules, and isomerase activity is blocked, how will the radio label be distributed?
- a) equally between F1,6BP and DHAP molecules
- b) only on F1,6BP molecules
- c) only on DHAP molecules
- All the radiolabeled molecules will be dihydroxyacetone phosphate (DHAP)
- This is because when fructose 1,6-bisphosphate is cleaved, it is cleaved the same way every time
- Carbons 1, 2, and 3 become:
- dihydroxyacetone phosphate (DHAP)
- Carbons 4, 5, and 6 become:
- Glyceraldehyde 3- phosphate (G3P)
- Carbons 1, 2, and 3 become:
- ∴ if carbon 2 is labeled, the labeled molecule will always be DHAP
- If the isomerase is active, some of the DHAP will be converted to GAP, so the label will be distributed between the two
- But without the isomerase, all labeled molecules will be DHAP

- Organism-Level Regulation of Metabolism
- Tissue-Specific Metabolism
- Different tissues use different ____ ____ preferentially
- What does the Liver prefer during well-fed & fasting states?
- Tissue-Specific Metabolism
- Different tissues use different fuel sources preferentially
- in the Liver:
- Glucose in well-fed state
- Fatty acids during fasting
- but NO ketones (lacks enzyme)
- Electron Transport Chain
- Using the NADH and FADH2 equivalents given,demonstrate for the complete oxidation of one glucose molecule:
- where each high energy molecule is created
- how they add up to 36 ATP per glucose
- HINT: Two common errors are
- not considering the “net” ATP from glycolysis
- ignoring the ATP required for the transport of NADH into the mitochondria
- Using the NADH and FADH2 equivalents given,demonstrate for the complete oxidation of one glucose molecule:
- The overall reaction for GLYCOLYSIS is
- glucose + 2 NAD+ + 2Pi + 2 ADP⇒2 pyruvate + 2ATP + 2NADH + 2H+
- The overall reaction for the CITRIC ACID CYCLE (including PDC) is:
- pyruvate + 4 NAD+ + FAD + GDP + Pi + 2 H20 ⇒3 CO2 + 4NADH + 4H+ + GTP + FADH2
- Keep in mind that you’ll need to DOUBLE the citric acid cycle equation
- because glycolysis results in TWO (!) pyruvates
- This means that from complete oxidation of one glucose, we get:
- (see attached)
- NADH = 3 ATP
- FADH2 = 2 ATP
- NADH from glycolysis = 2 ATP
- (because it costs 1 ATP to transport it in)
- Total, we have (2 x 2) + (8 x 3) + (2 x 2) + 4 = 36 ATPs

- Biochemical shuttles
- What are the 4 shuttles we need to know for the MCAT?
- Malate-Aspartate Shuttle
- Glycerol-3-Phosphate Shuttle
- Carnitite Shuttle
- Citrate-Acetyl-CoA Shuttle
- aka Tricarboxylate Transport System, “TTS”
- Lipid Metabolism
- β-Oxidation of fatty acids
- What happens in β-Oxidation when you have a conjugated double bond?
- What enzymes (2) are needed to continue β-Oxidation?
- What happens in β-Oxidation when you have a conjugated double bond?
- β-Oxidation of fatty acids

- β-Oxidation cannot proceed through conjugated DB’s
- Needs 2 enzymes:
-
2-4 dienoyl-CoA reductase
- converts 2 DB’s to 1 DB
-
Enoyl-CoA isomerase
- to move the DB’s to the 2-3 position
-
2-4 dienoyl-CoA reductase

- Lipid Metabolism
- β-Oxidation
- Draw a mechanism for the beta-oxidation of a fatty acid
- Indicate the point at which FADH2 and NADH are produced
- β-Oxidation

- Regulation of Carbohydrate Metabolism
- Hormonal Control
- Catecholamines (3)
- Describe the 3 types and what they do wrt metabolism
- Catecholamines (3)
- Hormonal Control
- Catecholamines are derived from tyrosine and have an amine side group
- 3 Types:
- Dopamine, Epinephrine, and Norepinephrine
- Dopamine
- is a CNS neurotransmitter
- Epinephrine (Adrenaline) and Norepinephrine (Noradrenaline)
- are the two metabolic hormones
- Catecholamines also have a “glucagon-like” effect (like Cortisol)
- …but should be thought of as causing a more rapid “mobilization” of energy stores
- which are necessary for the “fight or flight” response
- Fatty acids are mobilized for oxidation and glycogenolysis is increased
- Citric Acid Cycle
- Diagram
- Include:
- species that enter and exit the cycle
- including where they originated from and where they will go next
- species that enter and exit the cycle
- the starting substrate and final product of each step,
- when and where CO2 is produced
- changes to the carbon skeleton
- any points in the cycle where NAD+ , NADH, FAD, FADH2, ADP, GDP, ATP or GTP are either required or produced.
- Include:
- Diagram

- Regulation of Carbohydrate Metabolism
- Hormonal Control
-
GLYCOGENESIS
- identify all molecules that:
- upregulate the process
- downregulate the process
- Specify the exact enzyme or step with which the regulatory molecule interacts
-
GLYCOGENESIS
- Hormonal Control
- Glycogenesis, the synethesis of glygogen, is regulated oppositely to glycogenolysis.
- When glucagon and epinephrine are present in the bloodstream
- …the cAMP cascade is stimulated
- Protein kinase A phosphorylates glycogen synthase
- this phosphorylation inhibits the enzyme (instead of activating, as it does with glycogen phosphorylase)
- When the cAMP cascade is withdrawn, protein phosphorylase I will dephosphorylate glycogen synthase
- stimulating glycogen synthesis
- This way, the same stimulus will simultaneously shut down one pathway and turn on the other
































