BIOLOGY EXAM 3
• Metabolism: sum of chemical reactions to maintain an organism’s life
o Flow of electrons from one molecule to another – produces energy
o Catabolic pathways (catabolism): chemical pathways that release energy stored in
chemical bonds by breaking down complex molecules (ex: fats, carbs) into
simpler products (ex: carbon dioxide, H2O) via combustion
▪ Difference is released as energy --> energy comes from electrons (source)
▪ Fermentation pathways:
• Doesn’t require free oxygen (O2) --> compounds like food
molecules don’t completely oxidize, (break apart, loses electrons) -
-> doesn’t release a lot of energy (ATP)
• Body uses fermentation pathways if you don’t have oxygen
available and have been working muscles too hard, same with
cellular respiration but needs oxygen
• Using fermentation to break down glucose, it will produce 4 ATP
molecules (already investing 2, so net gain 2 ATP)
▪ Aerobic cellular respiration
• Requires oxygen which results in food molecules to completely
oxidizing and yielding a lot more energy
o Oxygen allows molecules to completely break chemical
bonds which releases energy
o Source of energy is electrons which are passed on from one
molecule to another to activate or raise their energy
• While breaking down with oxygen (cellular respiration), it
produces 40 ATP molecules
• Balanced equation: C6H12O6 (glucose) + 6O2 ---> 6CO2 + 6H2O
+ energy (ATP)
o This reaction takes place over dozens of chemical steps all
mediated by an enzyme
o Anabolic pathways: chemical pathways take simple starting materials, supply
energy (roll ball up hill) and create a more complex molecule
▪ Energy requiring pathways
▪ Opposite of catabolic pathways
o Remembering the difference: cats break, ants make
• ATP is closely related to nucleotide (nucleic acid)
o Nucleotide: nitrogen containing base, pentose sugar, and phosphate group
▪ AMP (adenosine monophosphate): adenine (nitrogen containing base),
hook it onto a pentose sugar (DNA=deoxyribose, RNA=ribose), and have
a phosphate group
o diagram
, o Third phosphate group of ATP is loosely attached because the phosphate groups
are very negatively charged-like things of the same charge do NOT like to bond
together
▪ The form for molecules to store energy to be used
o When the cell wants use ATP it will cleave off third phosphate to release energy
▪ ATP (more complicated) ---> ADP + Pi (less)
o Using energy will lead to it cell using a hydrolysis reaction-breaking molecule by
taking out H2O – loses electrons
▪ Opposite of condensation reaction: ADP + Pi ---> ATP
• Removing water to create the sites of bonds
o Third phosphate group constantly being attached and detached to store or release
energy
• Example of ATP being used to build a biomolecule
o Work = anything that requires energy
o Suppose (bound) X-Y from X+Y (free)
▪ Left has more energy because they are 2 simple bonded together
o Starting reagent X, then take ATP molecule (roll ball up hill), and enzyme will
transfer 3rd phosphate over to X
▪ Substrate level phosphorylation: transferring of a phosphate group from
one molecule to another to make energy
o Starting reagent Y, then take ATP molecule, and enzyme will transfer 3rd
phosphate over to Y (also uses substrate phosphate)
o Once a phosphate grp is transferred, it becomes an activated intermediate
▪ Activated intermediate: activated by phosphate group which increases
their energy
o Next, another enzyme will cleave the phosphate groups off (breaking bonds) of X
and Y which releases energy and allows X and Y to be bonded together
▪ X-Y + 2Pi
▪ Pi= phosphate group floating by itself, not connected to carbon
• Coenzymes help enzymes by gathering electrons and protons from broken chemical
bonds to reduce their energy before bonding to molecules like oxygen
o Done in multiple steps or else it will be unstable, bonding is very
reactive/explosive
o Oxygen is a very reactive molecule, causing cell damage so people take
antioxidants (dietary supplements) which scarf up oxygen radicals which cause
damage to cells
o NAD+ (nicotinamide adenine dinucleotide), physiological pH of the molecule has
a charge of 1+
▪ From vitamin D complex, niacin
▪ If you’ve been drinking alcohol, special molecules will produce alcohol
dehydrogenase (special enzyme)
• Alcohol: hydroxyl group
o Diagram of alcohol OH
, • Need to detoxify alcohol via alcohol dehydrogenase (substrate is
the alc) by taking out the hydrogens
• When hydrogen comes off, an electron does as well triggering
NAD+ to come in
o oxidized state - not carrying electrons
• Breaking apart 2 electrons (2 hydrogens), NAD+ gathers them up
as enzyme breaks the bond
o NAD+ 2e-, 2H+ (LEO) --> NADH, H+ (GER)
▪ LEO=lose electrons oxidize
▪ GER=gain electrons reduce
▪ H+ will be released into the cytosol
o FAD (flavin adenine dinucleotide), neutral
▪ FAD is from riboflavin in diet
▪ FAD (oxidized) --> FADH2 (reduced)
▪ FAD gathers up 2 electrons, 2 protons from broken chemical bonds
(broken by enzyme) and convert to FADH2
• Breaking of bonds are important because metabolism are flow of electrons (source of
energy)
o Break bonds, release electrons, coenzymes gather up electrons and protons from
these bonds which help enzymes do job of breaking bonds and prevents electrons
from wandering off
• Doesn't take place in one reaction step because it’s highly reactive, could blow
themselves up
• Coenzymes deliver electrons to the ETS
o Electron transport system: series of proteins built into various kinds of
membranes
▪ Built like a staircase
o Proteins have metal in the center of it has reoxygen potential and uses energy to
make ATP
o NAD+ (oxidized) ---> NADH, H+ (reduced) - carries two protons and electrons
o FAD (oxidized) ---> FADH2 (reduced)
o Coenzymes will drop off 2 electrons and 2 protons at the electron transport
system
▪ High energy electrons and protons will be handed off from one protein to
the next down the staircase (falls downhill) which reduces/lowers energy
level
• The energy transfer (lowering of energy) is used to make ATP
▪ Protons and electrons want to join with oxygen to make water
• ATP is attached to cytosol
o Oxidated phosphorylation: oxygen is necessary, used to stick a phosphate group
to ADP to make ATP
o Unlike substrate level phosphorylation - transfer of a phosphate group from one
molecule to another directly
• Metabolism: sum of chemical reactions to maintain an organism’s life
o Flow of electrons from one molecule to another – produces energy
o Catabolic pathways (catabolism): chemical pathways that release energy stored in
chemical bonds by breaking down complex molecules (ex: fats, carbs) into
simpler products (ex: carbon dioxide, H2O) via combustion
▪ Difference is released as energy --> energy comes from electrons (source)
▪ Fermentation pathways:
• Doesn’t require free oxygen (O2) --> compounds like food
molecules don’t completely oxidize, (break apart, loses electrons) -
-> doesn’t release a lot of energy (ATP)
• Body uses fermentation pathways if you don’t have oxygen
available and have been working muscles too hard, same with
cellular respiration but needs oxygen
• Using fermentation to break down glucose, it will produce 4 ATP
molecules (already investing 2, so net gain 2 ATP)
▪ Aerobic cellular respiration
• Requires oxygen which results in food molecules to completely
oxidizing and yielding a lot more energy
o Oxygen allows molecules to completely break chemical
bonds which releases energy
o Source of energy is electrons which are passed on from one
molecule to another to activate or raise their energy
• While breaking down with oxygen (cellular respiration), it
produces 40 ATP molecules
• Balanced equation: C6H12O6 (glucose) + 6O2 ---> 6CO2 + 6H2O
+ energy (ATP)
o This reaction takes place over dozens of chemical steps all
mediated by an enzyme
o Anabolic pathways: chemical pathways take simple starting materials, supply
energy (roll ball up hill) and create a more complex molecule
▪ Energy requiring pathways
▪ Opposite of catabolic pathways
o Remembering the difference: cats break, ants make
• ATP is closely related to nucleotide (nucleic acid)
o Nucleotide: nitrogen containing base, pentose sugar, and phosphate group
▪ AMP (adenosine monophosphate): adenine (nitrogen containing base),
hook it onto a pentose sugar (DNA=deoxyribose, RNA=ribose), and have
a phosphate group
o diagram
, o Third phosphate group of ATP is loosely attached because the phosphate groups
are very negatively charged-like things of the same charge do NOT like to bond
together
▪ The form for molecules to store energy to be used
o When the cell wants use ATP it will cleave off third phosphate to release energy
▪ ATP (more complicated) ---> ADP + Pi (less)
o Using energy will lead to it cell using a hydrolysis reaction-breaking molecule by
taking out H2O – loses electrons
▪ Opposite of condensation reaction: ADP + Pi ---> ATP
• Removing water to create the sites of bonds
o Third phosphate group constantly being attached and detached to store or release
energy
• Example of ATP being used to build a biomolecule
o Work = anything that requires energy
o Suppose (bound) X-Y from X+Y (free)
▪ Left has more energy because they are 2 simple bonded together
o Starting reagent X, then take ATP molecule (roll ball up hill), and enzyme will
transfer 3rd phosphate over to X
▪ Substrate level phosphorylation: transferring of a phosphate group from
one molecule to another to make energy
o Starting reagent Y, then take ATP molecule, and enzyme will transfer 3rd
phosphate over to Y (also uses substrate phosphate)
o Once a phosphate grp is transferred, it becomes an activated intermediate
▪ Activated intermediate: activated by phosphate group which increases
their energy
o Next, another enzyme will cleave the phosphate groups off (breaking bonds) of X
and Y which releases energy and allows X and Y to be bonded together
▪ X-Y + 2Pi
▪ Pi= phosphate group floating by itself, not connected to carbon
• Coenzymes help enzymes by gathering electrons and protons from broken chemical
bonds to reduce their energy before bonding to molecules like oxygen
o Done in multiple steps or else it will be unstable, bonding is very
reactive/explosive
o Oxygen is a very reactive molecule, causing cell damage so people take
antioxidants (dietary supplements) which scarf up oxygen radicals which cause
damage to cells
o NAD+ (nicotinamide adenine dinucleotide), physiological pH of the molecule has
a charge of 1+
▪ From vitamin D complex, niacin
▪ If you’ve been drinking alcohol, special molecules will produce alcohol
dehydrogenase (special enzyme)
• Alcohol: hydroxyl group
o Diagram of alcohol OH
, • Need to detoxify alcohol via alcohol dehydrogenase (substrate is
the alc) by taking out the hydrogens
• When hydrogen comes off, an electron does as well triggering
NAD+ to come in
o oxidized state - not carrying electrons
• Breaking apart 2 electrons (2 hydrogens), NAD+ gathers them up
as enzyme breaks the bond
o NAD+ 2e-, 2H+ (LEO) --> NADH, H+ (GER)
▪ LEO=lose electrons oxidize
▪ GER=gain electrons reduce
▪ H+ will be released into the cytosol
o FAD (flavin adenine dinucleotide), neutral
▪ FAD is from riboflavin in diet
▪ FAD (oxidized) --> FADH2 (reduced)
▪ FAD gathers up 2 electrons, 2 protons from broken chemical bonds
(broken by enzyme) and convert to FADH2
• Breaking of bonds are important because metabolism are flow of electrons (source of
energy)
o Break bonds, release electrons, coenzymes gather up electrons and protons from
these bonds which help enzymes do job of breaking bonds and prevents electrons
from wandering off
• Doesn't take place in one reaction step because it’s highly reactive, could blow
themselves up
• Coenzymes deliver electrons to the ETS
o Electron transport system: series of proteins built into various kinds of
membranes
▪ Built like a staircase
o Proteins have metal in the center of it has reoxygen potential and uses energy to
make ATP
o NAD+ (oxidized) ---> NADH, H+ (reduced) - carries two protons and electrons
o FAD (oxidized) ---> FADH2 (reduced)
o Coenzymes will drop off 2 electrons and 2 protons at the electron transport
system
▪ High energy electrons and protons will be handed off from one protein to
the next down the staircase (falls downhill) which reduces/lowers energy
level
• The energy transfer (lowering of energy) is used to make ATP
▪ Protons and electrons want to join with oxygen to make water
• ATP is attached to cytosol
o Oxidated phosphorylation: oxygen is necessary, used to stick a phosphate group
to ADP to make ATP
o Unlike substrate level phosphorylation - transfer of a phosphate group from one
molecule to another directly
