1. Metabolism & Enzymes

2. From food webs to the life of a cell
energy
energy
energy

3. Flow of energy through life
Life is built on chemical reactions
transforming energy from one form to another
organic molecules  ATP & organic molecules
sun
organic molecules  ATP & organic molecules
solar energy  ATP & organic molecules

4. The First Law of Thermodynamics
Energy cannot be created or destroyed, only transformed.
Living systems need to continually acquire and transform energy in order to remain alive. 
“Free energy”: The energy available in a system to do work.

5. The Second Law of Thermodynamics
Every time energy is transformed, the entropy (“disorder”) of the universe increases.
In order to increase/maintain their internal order, living systems must process more ordered forms of matter in to less ordered ones

6. Living Systems are “Open” Systems
Matter and energy move in to living systems from the environment. Living systems transform matter and energy and return it to the environment

7. Multi-Step Metabolism
To increase control, living systems produce free energy in multiple-step pathways, mediated by enzyme catalysts

8. That’s why they’re called anabolic steroids!
Metabolism
Chemical reactions of life
forming bonds between molecules
dehydration synthesis
synthesis
anabolic reactions
breaking bonds between molecules
hydrolysis
digestion
catabolic reactions
That’s why they’re called anabolic steroids!

9. Examples dehydration synthesis (synthesis) hydrolysis (digestion)
enzyme +
H2O
hydrolysis (digestion)
enzyme +
H2O

10. Examples dehydration synthesis (synthesis) hydrolysis (digestion)
enzyme
hydrolysis (digestion)
enzyme

11. Chemical reactions & energy
Some chemical reactions release energy
exergonic
digesting polymers
hydrolysis = catabolism
Some chemical reactions require input of energy
endergonic
building polymers
dehydration synthesis = anabolism
digesting molecules= LESS organization= lower energy state
building molecules= MORE organization= higher energy state

12. Endergonic vs. exergonic reactions
- energy released
- digestion
energy invested
synthesis
+G
-G
G = change in free energy = ability to do work

13. Energy & life Organisms require energy to live
where does that energy come from?
coupling exergonic reactions (releasing energy) with endergonic reactions (needing energy)
energy + +
digestion
synthesis
energy + +

14. Why don’t stable polymers spontaneously digest into their monomers?
What drives reactions?
If reactions are “downhill”, why don’t they just happen spontaneously?
because covalent bonds are stable bonds
Why don’t stable polymers spontaneously digest into their monomers?
starch

15. Activation energy
Breaking down large molecules requires an initial input of energy
activation energy
large biomolecules are stable
must absorb energy to break bonds
Need a spark to start a fire
energy
cellulose
CO2 + H2O + heat

16. Too much activation energy for life
amount of energy needed to destabilize the bonds of a molecule
moves the reaction over an “energy hill”
Not a match! That’s too much energy to expose living cells to!
glucose
2nd Law of thermodynamics
Universe tends to disorder
so why don’t proteins, carbohydrates & other biomolecules breakdown?
at temperatures typical of the cell, molecules don’t make it over the hump of activation energy
but, a cell must be metabolically active
heat would speed reactions, but… would denature proteins & kill cells

17. Reducing Activation energy
Catalysts
reducing the amount of energy to start a reaction
Pheeew… that takes a lot less energy!
uncatalyzed reaction
catalyzed reaction
NEW activation energy
reactant
product

18. Catalysts So what’s a cell got to do to reduce activation energy?
get help! … chemical help…
ENZYMES
Call in the ENZYMES! G

19. Enzymes Biological catalysts proteins (& RNA)
facilitate chemical reactions
increase rate of reaction without being consumed
reduce activation energy
don’t change free energy (G) released or required
required for most biological reactions
highly specific
thousands of different enzymes in cells
control reactions of life

20. Enzymes vocabulary substrate product active site active site products
reactant which binds to enzyme
enzyme-substrate complex: temporary association
product
end result of reaction
active site
enzyme’s catalytic site; substrate fits into active site
active site
products
substrate
enzyme

21. Properties of enzymes Reaction specific Not consumed in reaction
each enzyme works with a specific substrate
chemical fit between active site & substrate
H bonds & ionic bonds
Not consumed in reaction
single enzyme molecule can catalyze thousands or more reactions per second
enzymes unaffected by the reaction
Affected by cellular conditions
any condition that affects protein structure
temperature, pH, salinity

22. Naming conventions Enzymes named for reaction they catalyze
sucrase breaks down sucrose
proteases break down proteins
lipases break down lipids
DNA polymerase builds DNA
adds nucleotides to DNA strand
pepsin breaks down proteins (polypeptides)

23. In biology… Size doesn’t matter… Shape matters!
Lock and Key model
Simplistic model of enzyme action
substrate fits into 3-D structure of enzyme’ active site
H bonds between substrate & enzyme
like “key fits into lock”
In biology… Size doesn’t matter… Shape matters!

24. Induced fit model More accurate model of enzyme action
3-D structure of enzyme fits substrate
substrate binding cause enzyme to change shape leading to a tighter fit
“conformational change”
bring chemical groups in position to catalyze reaction

25. How does it work?
Variety of mechanisms to lower activation energy & speed up reaction
synthesis
active site orients substrates in correct position for reaction
enzyme brings substrate closer together
digestion
active site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules

26. Math Skills: Gibbs Free Energy
3.1: All living systems require constant input of free energy
Be able to use and interpret the Gibbs Free Energy Equation to determine if a particular process will occur spontaneously or non-spontaneously.
ΔG= change in free energy
(- = exergonic, + = endergonic) 
ΔH= change in enthalpy for the reaction
(- = exothermic, + = endothermic)
T = kelvin temperature
ΔS = change in entropy
(+ = entropy increase, - = entropy decrease)

27. Spontaneity
Spontaneous reactions continue once they are initiated. Non-spontaneous reactions require continual input of energy to continue.

28. Using the Equation
To use the equation, you’ll need to be given values.
Exothermic reactions that increase entropy are always spontaneous/exergonic
Endothermic reactions that decrease entropy are always non-spontaneous/endergonic.
Other reactions will be spontaneous or not depending on the temperature at which they occur.

29. Sample Problem
Determine which of the following reactions will occur spontaneously at a temperature of 298K, justify your answer mathematically:
Reaction 1:
A + B → AB
Δ H: KJ/mol
Δ S: KJ / K
Reaction 2:
BC→ B + C
Δ H: KJ/mol
Δ S: KJ/K

30. Got any Questions?!

31. Factors that Affect Enzymes

32. Factors Affecting Enzyme Function
Enzyme concentration
Substrate concentration
Temperature pH
Salinity
Activators
Inhibitors
Living with oxygen is dangerous. We rely on oxygen to power our cells, but oxygen is a reactive molecule that can cause serious problems if not carefully controlled. One of the dangers of oxygen is that it is easily converted into other reactive compounds. Inside our cells, electrons are continually shuttled from site to site by carrier molecules, such as carriers derived from riboflavin and niacin. If oxygen runs into one of these carrier molecules, the electron may be accidentally transferred to it. This converts oxygen into dangerous compounds such as superoxide radicals and hydrogen peroxide, which can attack the delicate sulfur atoms and metal ions in proteins. To make things even worse, free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules attack and mutate DNA. Fortunately, cells make a variety of antioxidant enzymes to fight the dangerous side-effects of life with oxygen. Two important players are superoxide dismutase, which converts superoxide radicals into hydrogen peroxide, and catalase, which converts hydrogen peroxide into water and oxygen gas. The importance of these enzymes is demonstrated by their prevalence, ranging from about 0.1% of the protein in an E. coli cell to upwards of a quarter of the protein in susceptible cell types. These many catalase molecules patrol the cell, counteracting the steady production of hydrogen peroxide and keeping it at a safe level. Catalases are some of the most efficient enzymes found in cells. Each catalase molecule can decompose millions of hydrogen peroxide molecules every second. The cow catalase shown here and our own catalases use an iron ion to assist in this speedy reaction. The enzyme is composed of four identical subunits, each with its own active site buried deep inside. The iron ion, shown in green, is gripped at the center of a disk-shaped heme group. Catalases, since they must fight against reactive molecules, are also unusually stable enzymes. Notice how the four chains interweave, locking the entire complex into the proper shape.
catalase

33. Enzyme concentration reaction rate enzyme concentration
What’s happening here?!
reaction rate
enzyme concentration

34. Factors affecting enzyme function
Enzyme concentration
as  enzyme =  reaction rate
more enzymes = more frequently collide with substrate
reaction rate levels off
substrate becomes limiting factor
not all enzyme molecules can find substrate
Why is it a good adaptation to organize the cell in organelles?
Sequester enzymes with their substrates!
enzyme concentration
reaction rate

35. Substrate concentration
What’s happening here?!
reaction rate
substrate concentration

36. Factors affecting enzyme function
Substrate concentration
as  substrate =  reaction rate
more substrate = more frequently collide with enzyme
reaction rate levels off
all enzymes have active site engaged
enzyme is saturated
maximum rate of reaction
Why is it a good adaptation to organize the cell in organelles?
Sequester enzymes with their substrates!
substrate concentration
reaction rate

37. Temperature
What’s happening here?!
37°
reaction rate
temperature

38. Factors affecting enzyme function
Temperature
Optimum T°
greatest number of molecular collisions
human enzymes = 35°- 40°C
body temp = 37°C
Heat: increase beyond optimum T°
increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate
H, ionic = weak bonds
denaturation = lose 3D shape (3° structure)
Cold: decrease T°
molecules move slower
decrease collisions between enzyme & substrate

39. Enzymes and temperature
Different enzymes function in different organisms in different environments
hot spring bacteria enzyme
human enzyme
37°C
70°C
reaction rate
temperature
(158°F)

40. How do ectotherms do it?
Enzymes work within narrow temperature ranges. Ectotherms, like snakes, do not use their metabolism extensively to regulate body temperature. Their body temperature is significantly influenced by environmental temperature. Desert reptiles can experience body temperature fluctuations of ~40°C (that’s a ~100°F span!).
What mechanism has evolved to allow their metabolic pathways to continue to function across that wide temperature span?

41. Metabolic Strategies
Ectothermy: Conform internal temperature to environmental temperature.
Endothermy: Regulate internal temperature within a narrow range.
Both strategies
have advantages and
tradeoffs.

42. Body Size Considerations
Smaller animals need to produce more energy per unit of mass due to increased radiation of heat into the environment.

43. Free Energy Considerations & Reproduction
Reproductive strategies are optimized for free energy considerations.
Ex. Seasonal Reproduction.

44. Insufficient Free Energy Production: Individuals
Insufficient free energy production by individuals will lead to disease and death.

45. Insufficient Free Energy Production: Populations
If the individuals in the population are unable to survive, the growth rate of the population will decline

46. Insufficient Free Energy Production: Ecosystems
If the populations in an ecosystem decline, the ecosystems will decrease in complexity

47. Math Skills: Coefficient Q10
3.1: All living systems require constant input
Be able to use and interpret the Coefficient Q10 equation:
t2 = higher temperature
t1 = lower temperature
k2= metabolic rate at higher temperature
k1= metabolic rate at lower temperature
Q10 = the factor by which the reaction rate increases when the temperature is raised by ten degrees of free energy

48. Q10 tells us how a particular process will be affected by a 10 degree change in temperature.
Most biological processes have a Q10 value between 2 and 3

49. Sample Problem
Data taken to determine the effect of temperature on the rate of respiration in a goldfish is given in the table below. Calculate the Q10 value for this data. (°C
Temperature (°C)
Heartbeats per minute 20 18 25 42

50. pH pepsin trypsin reaction rate pH 1 2 3 4 5 6 7 8 9 10 11 12 13 14
What’s happening here?!
pepsin
trypsin
pepsin
reaction rate
trypsin 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH

51. Factors affecting enzyme functionpH
changes in pH
adds or remove H+
disrupts bonds, disrupts 3D shape
disrupts attractions between charged amino acids
affect 2° & 3° structure
denatures protein
optimal pH?
most human enzymes = pH 6-8
depends on localized conditions
pepsin (stomach) = pH 2-3
trypsin (small intestines) = pH 8

52. Salinity
What’s happening here?!
reaction rate
salt concentration

53. Factors affecting enzyme function
Salt concentration
changes in salinity
adds or removes cations (+) & anions (–)
disrupts bonds, disrupts 3D shape
disrupts attractions between charged amino acids
affect 2° & 3° structure
denatures protein
enzymes intolerant of extreme salinity
Dead Sea is called dead for a reason!

54. Compounds which help enzymes
Fe in hemoglobin
Activators
cofactors
non-protein, small inorganic compounds & ions
Mg, K, Ca, Zn, Fe, Cu
bound within enzyme molecule
coenzymes
non-protein, organic molecules
bind temporarily or permanently to enzyme near active site
many vitamins
NAD (niacin; B3)
FAD (riboflavin; B2)
Coenzyme A
Hemoglobin is aided by Fe
Chlorophyll is aided by Mg
Mg in chlorophyll

55. Compounds which regulate enzymes
Inhibitors
molecules that reduce enzyme activity
competitive inhibition
noncompetitive inhibition
irreversible inhibition
feedback inhibition

56. Competitive Inhibitor
Inhibitor & substrate “compete” for active site
penicillin blocks enzyme bacteria use to build cell walls
disulfiram (Antabuse) treats chronic alcoholism
blocks enzyme that breaks down alcohol
severe hangover & vomiting 5-10 minutes after drinking
Overcome by increasing substrate concentration
saturate solution with substrate so it out-competes inhibitor for active site on enzyme
Ethanol is metabolized in the body by oxidation to acetaldehyde, which is in turn further oxidized to acetic acid by aldehyde oxidase enzymes. Normally, the second reaction is rapid so that acetaldehyde does not accumulate in the body.
A drug, disulfiram (Antabuse) inhibits the aldehyde oxidase which causes the accumulation of acetaldehyde with subsequent unpleasant side-effects of nausea and vomiting. This drug is sometimes used to help people overcome the drinking habit.
Methanol (wood alcohol) poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.

57. Non-Competitive Inhibitor
Inhibitor binds to site other than active site
allosteric inhibitor binds to allosteric site
causes enzyme to change shape
conformational change
active site is no longer functional binding site
keeps enzyme inactive
some anti-cancer drugs inhibit enzymes involved in DNA synthesis
stop DNA production
stop division of more cancer cells
cyanide poisoning irreversible inhibitor of Cytochrome C, an enzyme in cellular respiration
stops production of ATP
Basis of most chemotherapytreatments is enzyme inhibition. Many health disorders can be controlled, in principle, by inhibiting selected enzymes. Two examples include methotrexate and FdUMP, common anticancer drugs which inhibit enzymes involved in the synthesis of thymidine and hence DNA.
Since many enzymes contain sulfhydral (-SH), alcohol, or acid groups as part of their active sites, any chemical which can react with them acts as a noncompetitive inhibitor. Heavy metals such as silver (Ag+), mercury (Hg2+), lead ( Pb2+) have strong affinities for -SH groups.
Cyanide combines with the copper prosthetic groups of the enzyme cytochrome C oxidase, thus inhibiting respiration which causes an organism to run out of ATP (energy)
Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator.

58. Irreversible inhibition
Inhibitor permanently binds to enzyme
competitor
permanently binds to active site
allosteric
permanently binds to allosteric site
permanently changes shape of enzyme
nerve gas, sarin, many insecticides (malathion, parathion…)
cholinesterase inhibitors
doesn’t breakdown the neurotransmitter, acetylcholine
Another example of irreversible inhibition is provided by the nerve gas diisopropylfluorophosphate (DFP) designed for use in warfare. It combines with the amino acid serine (contains the –SH group) at the active site of the enzyme acetylcholinesterase. The enzyme deactivates the neurotransmitter acetylcholine.
Neurotransmitters are needed to continue the passage of nerve impulses from one neurone to another across the synapse. Once the impulse has been transmitted, acetylcholinesterase functions to deactivate the acetycholine almost immediately by breaking it down. If the enzyme is inhibited, acetylcholine accumulates and nerve impulses cannot be stopped, causing prolonged muscle contration. Paralysis occurs and death may result since the respiratory muscles are affected.
Some insecticides currently in use, including those known as organophosphates (e.g. parathion), have a similar effect on insects, and can also cause harm to nervous and muscular system of humans who are overexposed to them.

59. Allosteric regulation
Conformational changes by regulatory molecules
inhibitors
keeps enzyme in inactive form
activators
keeps enzyme in active form
Conformational changes
Allosteric regulation

60. Cooperativity Substrate acts as an activator
substrate causes conformational change in enzyme
induced fit
favors binding of substrate at 2nd site
makes enzyme more active & effective
hemoglobin
Hemoglobin
4 polypeptide chains
can bind 4 O2;
1st O2 binds
now easier for other 3 O2 to bind

61. Metabolic pathways A  B  C  D  E  F  G A  B  C  D  E  F  G
enzyme 1 
enzyme 3 
enzyme 2 
enzyme 
enzyme 4 
enzyme 5 
enzyme 6 
Chemical reactions of life are organized in pathways
divide chemical reaction into many small steps
artifact of evolution
 efficiency
intermediate branching points
 control = regulation

62. Whoa! All that going on in those little mitochondria!
Efficiency
Organized groups of enzymes
enzymes are embedded in membrane and arranged sequentially
Link endergonic & exergonic reactions
Whoa! All that going on in those little mitochondria!

63. allosteric inhibitor of enzyme 1
Feedback Inhibition
Regulation & coordination of production
product is used by next step in pathway
final product is inhibitor of earlier step
allosteric inhibitor of earlier enzyme
feedback inhibition
no unnecessary accumulation of product
A  B  C  D  E  F  G
enzyme 1 
enzyme 2 
enzyme 3 
enzyme 4 
enzyme 5 
enzyme 6  X
allosteric inhibitor of enzyme 1

64. Feedback inhibition Example
threonine
Feedback inhibition
Example
synthesis of amino acid, isoleucine from amino acid, threonine
isoleucine becomes the allosteric inhibitor of the first step in the pathway
as product accumulates it collides with enzyme more often than substrate does
isoleucine

65. Don’t be inhibited! Ask Questions!