Ch 13 Segway Lecture Flashcards
catabolism
breaks down food for energy and building blocks ex: glycolysis
anabolism
used energy and building blocks to make the molecules used for catabolism ex: photosynthesis
Where does the energy we consume come from and what is the general formula
Sun (Energy) + 6 CO2 + 6 H2O -> (C6H12O6)n + 6 O2
What molecules do most chemoheterotrophs use for energy?
reduced carbon
∆G°’
free energy change of reaction when all of its reactants and products are in their standard states: 25°C, 1 atm, and unit concentrations of 1M for reactants and products at a pH of 7. This never happens in biology, so a correction from ∆G°’ to actual ∆G must be made
∆G = (in terms of ∆G°’)
∆G = ∆G°’ + RT ln Keq
To make ( RT ln Keq ) negative (for reaction spontenuity) increase the concentration of the reactants or remove product to drive the reaction towards Keq
General charachteristics of metabolic pathways
- Individual pathways are irreversable: don’t waste energy on reactions that will revert back
- Catabolic and anabolic pathways must differ: for independent control of the two processes
- Every pathway has an early committed step
- All pathways are regualted
- Metabolic pathways in eukaryotes occur in different areas: glycolysis in cytosol and citric acid cycle in mitochondria
Why is the ATP to ADP conversion so energetically favourable?
Releif of charge repulsion between phosphate groups, resonance stabilisation of product (Pi), reionisation of ADP
Three easy ways to oxidise
loss of electrons, loss of hydrogen, gain of oxygen
Three easy ways to reduce
gain of electrions, gain of hydrogen, loss of oxygen
Transfer of electrions to O2 is exergonic or endergonic and why?
exergonic, oxygen has a very high standard reduction potential (wants to be reduced)
standard reduction potential
the affinity of a molecule to be reduced, greater is more likely to be reduced
list the oxidation states of carbon in biomolecules and give examples of each in order from most reduced to most oxidised
alkane > alcohol > ketone/aldehyde > carboxcylic acid > CO2
coenzyme
a low molecular weight organic compound which in cooperation with an enzyme, facilitates a reaction
coenzyme may appear to be a substrate and/or product. many coenzymes have a part of their structure that is derived from a vitamin
this is what makes vitamins a nutritional requirement, as the cell cannot biosynthesize an adequate amount for its own use
What is the difference between the types of reactions NAD+ and NADP
NAD+ is reduced to NADH during many oxidative reaction of catabolism
NADPH is oxidised to NADP in anabolic pathways
What happens to NAD+ during catabolism? What is the function of NAD+ in catabolism?
NAD+ is reduced to NADH during many oxidative reactions of catabolism.
NAD+ collects electrons released during catabolism.
NADH is a form of stored chemical energy: it can be oxidized in aerobic cells, this oxidation provides the energy for ADP + Pi –> ATP
H and electrons in a cell
H = e- + H+
• A hydrogen ion is a proton
• Water dissociates to H+ + OH-, so there are always lots of protons around free in the cell.
• Protons can exist free in the cell (recall pH), but electrons can’t.
• To move electrons, the cell uses electron carriers like NADH and FADH2
Where does reduced carbon factor into metabolism?
Reduced carbon (in carbohydrates, fats, or proteins) + O2 -> CO2 + H2O + Energy
Where are polymers broken down?
Polymers are broken down in the intestine. Only monomers are absorbed.
Where are monomers broken down?
Monomers are absorbed and broken down in the cells
What happens to individual biomolecules during catabolism?
Individual biomolecules are broken down by unique pathways into universal molecules (like acetyl-CoA) that can “feed into” a common energy producing pathway called the TCA cycle
exergonic reaction
Favorable reactions are exergonic and release free energy, represented by a negative ∆G
endergonic reaction
Nonspontaneous reactions that absorb free energy and has a positive ∆G are called endergonic
Favorable reactions are exergonic or endergonic? Is their ∆G positive or negative?
exergonic, -∆G
Unfavorable reactions are exergonic or endergonic? Is their ∆G positive or negative?
endergonic, +∆G
A reaction with +∆G is exergonic or endergonic? Spontaneous or nonspontaneous?
endergonic, nonspontaneous
A reaction with a -∆G is exergonic or endergonic? Spontaneous or nonspontaneous?
exergonic, spontaneous
What is true about a reverse reaction’s ∆G compared with the forward reaction?
It has the same magnitude but inverses the sign
NAD+ structure
Nicotinamide adenine dinucleotide, like all dinucleotides, consists of two nucleotides joined by a pair of bridging phosphate groups. The nucleotides consist of ribose rings, one with adenine attached to the first carbon atom (the 1’ position) and the other with nicotinamide at this position. The nicotinamide moiety can be attached in two orientations to this anomeric carbon atom. Because of these two possible structures, the compound exists as two diastereomers. It is the β-nicotinamide diastereomer of NAD+ that is found in organisms. These nucleotides are joined together by a bridge of two phosphate groups through the 5’ carbons
ln (natural log) of anything <1 is negative or positive
negative
What is one way biological systems can make a reaction with positive ∆G°’ spontaneous?
When products are quickly removed from the reaction by rapidly using them in a sequential reaction, making the second term in the equation for actual ∆G negative (products lower than reactants)
What is the structure of adenosine?
What is the structure of adenosine, and how does it relate to ATP?
What type of bond forms upon the conversion of adenosine to AMP?
phosphoester bond
What type of bond forms upon the conversion of AMP to ADP?
phosphoanhydride bond
what bond forms on upon the conversion of ADP to ATP?
phosphoanhydride bond
phosphoanhydride bond vs phosphoester bond vs phosphodiester bond and an example of where they are found
phosphoanhydride bond:
P-O-P, found linking the last two Pi groups in ATP
phosphoester bond:
C-O-P, found linking the first Pi group with adenosine in ATP
phosphodiester bond:
C-O-P-O-C, found along the DNA backbone linking nucleotides
NAD+: anabolism or catabolism energy carrier?
NAD+ collects electrons released during catabolism
How do coupled reactions work?
Using shared intermediates to take advantage of the free energy from an exergonic reaction to drive an endergonic reaction
NADPH: anabolism or catabolism?
NADPH is a stored form of reducing power, it is used to drive the reductive biosynthetic reaction of anabolic pathways
What is responsible (either directly or indirectly) for all work performed by a cell?
the flow of electrons in redox reactions
What is the general path of electrons through the cell?
Electrons move from electron rich molecules (food) to metabolic intermediates to electron carriers to oxygen
loss of hydrogen:
oxidation or reduction?
oxidation
loss of electrons:
oxidation or reduction?
oxidation
gain of oxygen:
oxidation or reduction?
oxidation
Can a reaction be either an oxidation reaction or a reduction rection?
No, they occur together, one species is being oxidised while another is reduced
gain of hydrogen:
oxidation or reduction?
reduction
gain of electrons:
oxidation or reduction?
reduction
loss of oxygen:
oxidation or reduction?
reduction
When NAD+ is converted to NADH, how many electrons are transferred? How many protons? Oxidation or reduction? Give an example of a reaction that would compliment this.
2 electrons (both stay with NADH), 2 protons (only one stays with NADH), reduction
what is the general rule for oxidation of carbon in an organic compound?
more C-O bonds means more oxidised
What is being reduced while carbon is being oxidised (the forward reaction shown)?
NAD+ + 2e- + 2H+ -> NADH + H+
explain the NAD+ to NADH conversion
RH2 + NAD+ -> NADH + H+ + R;
From the hydride electron pair, one electron is transferred to the positively charged nitrogen of the nicotinamide ring of NAD+, and the second hydrogen atom transferred to the C4 carbon atom opposite this nitrogen. The midpoint potential of the NAD+/NADH redox pair is −0.32 volts, which makes NADH a strong reducing agent. The reaction is easily reversible, when NADH reduces another molecule and is re-oxidized to NAD+. This means the coenzyme can continuously cycle between the NAD+ and NADH forms without being consumed.
what does NAD+ stand for?
Nicotinamide Adenine Dinucleotide
Why do molecules like NADH or FADH2 exist in cells the first place?
H = e- + H+
- A hydrogen ion is a proton, a hydrogen molecule is a proton+electron
- Water dissociates to H+ + OH-, so there are always lots of protons around free in the cell.
- Protons can exist free in the cell (recall pH), but electrons can’t.
- To move electrons, the cell uses electron carriers like NADH and FADH2
