1. Chapter 4
Cellular Metabolism

2. Nucleic Acids and Protein Synthesis

3. Introduction
Because enzymes regulate metabolic pathways that allow cells to survive, cells must have the information for producing these special proteins
Recall that proteins have several important functions in cells, including structure (keratin), transport (hemoglobin), defense (antibodies), etc

4. Genetic Information
DNA holds the genetic information which is passed from parents to their offspring
Offspring has a mix of the two parents’ DNA
This genetic information, DNA, instructs cells in the construction of proteins (great variety, each with a different function)
The portion of a DNA molecule that contains the genetic information for making one kind of protein is called a gene

5. Genetic Information cont.
All of the DNA in a cell constitutes the genome
Over the last decade, researchers have deciphered most of the human genome
The key to how DNA ,confined to the nucleus, can direct the synthesis of proteins, at ribosomes outside the nucleus, is in the structure of DNA and RNA molecules
i.e. the genetic code

6. Genetic Code Specified by sequence of nucleotides in DNA
Each triplet (three adjacent nucleotides) “codes” for an amino acid
Many triplets code for many amino acids, which are hooked together to form a polypeptide chain
RNA molecules facilitate the conversion of DNA triplets to an amino acid sequence

7. Nucleic Acid Structure
Both DNA and RNA share the same basic structure
Both are made up nucleotides, which consist of:
A 5-carbon sugar
Phosphate group
Nitrogen containing base
These Nitrogen containing bases pair up in specific ways

8. Basic structure of DNA and RNA

9. Base Pairs
Nucleotides will always for pairs with the same complimentary nucleotide
Complementary base pairs
DNA
A pairs with T
C pairs with G
RNA
A pairs with U

11. Deoxyribonucleic Acid: (DNA)
DNA is composed of nucleotides: a pentose sugar molecule (deoxyribose)
a nitrogen-containing base
a purine (double ring)
adenine (A) and guanine (G)
a pyrimidine (single ring)
cytosine (C) and thymine (T)
a phosphate group
The two strands are twisted into a double helix
Strands face opposing directions

12. Nucleotides (DNA and RNA)

13. DNA Structure

15. Ribonucleic Acid (RNA)
RNA (like DNA) is composed of nucleotides, each containing the following:
a pentose sugar molecule (ribose)
a nitrogen-containing base
purine:
adenine (A) and guanine (G)
pyrimidine:
cytosine (C) and uracil (U)
a phosphate group
Each RNA strand is made up of a backbone of ribose sugars alternating with phosphate groups.
Each ribose sugar is linked to either A, G, C, or U.

16. RNA cont.
Each RNA molecule consists of a single strand of nucleotides.
There are three types of RNA molecules which assist the cell in protein synthesis:
Messenger RNA (mRNA) carries the code for the protein to be synthesized, from the nucleus to the protein synthesizing machinery in the cytoplasm (i.e. ribosome).

17. RNA cont.
Transfer RNA (tRNA) carries the appropriate amino acid to the ribosome to be incorporated into the newly forming protein
Ribosomal RNA (rRNA) along with protein make up the protein synthesizing machinery, the ribosome

18. Protein Synthesis
Protein synthesis can be divided into two major steps, transcription and translation.
Transcription= The process of copying information from DNA to messenger RNA
Think of “transcribing (copying) from one nucleic acid to another”
Translation= The process of creating amino acid chains from messenger RNA
Think of “translating nucleic acid into protein”

19. Amino Acid chain (polypeptide)
Protein Synthesis
Nucleus:
Transcription
Cytoplasm:
Translation
DNA
mRNA
RNA polym-erase
mRNA
Amino Acid chain (polypeptide)
mRNA moves out of the nucleus
Ribosomes

20. Transcription
Transcription=is the process of copying the information from a DNA molecule, and putting it into the form of a messenger RNA (mRNA) molecule
One gene is read, containing the information for a specific protein
occurs in the nucleus of the cell
The DNA strands unwind and the H-bonds between the strands are broken

21. Transcription cont.
Only one of the exposed templates of the DNA molecule (i.e. the gene) is used to build the mRNA strand
Template strand= strand that the mRNA is made from
Coding strand= strand that is not used to make RNA
RNA polymerase (an enzyme) attaches to the template strand
Then positions and links RNA nucleotides into a strand

22. Transcription cont. The message (mRNA):
is complementary to the bases on the DNA strand
Matches up in the same was a bases in DNA match to each other
is in the form of a triple base code, represented by codons (i.e. AUG, CUA, ACG, GUU)
Each codon on mRNA codes for one amino acid in the protein to be synthesized

23. Transcription cont.
This code is redundant, meaning several codons can code for the same amino acid
Only 20 amino acids but many more possible combinations of codons
This is an advantage in a protection against mistakes in the next step, translation.
A mistake could be made in creating the mRNA, but the same amino acid may still be produced
The wrong one could result in a nom-functional protein

25. Transcription cont.

26. Translation
Translation =is the process by which the mRNA is "translated" into a protein.
occurs at ribosomes that are either free in the cytoplasm or are attached to ER (as RER).
can only start at the start codon AUG, which codes for methionine
Transfer RNA (tRNA) molecules assist in translation by bringing the appropriate amino acid for each codon to the ribosome.
Shape formed from hydrogen bonds

27. Translation cont.
The tRNA molecule has an anticodon which is complementary to the codon on the mRNA strand
Codon for Glycine = GGG
Anticodon on the tRNA =CCC
tRNA carries Glycine to the ribosome

28. Translation cont.
Two codons of mRNA are read in the ribosome at the same time.
The tRNA molecules deliver their amino acids to the ribosome, and a peptide bond is formed between adjacent amino acids.
The mRNA molecule is read codon by codon, with each corresponding amino acid being added to the chain of amino acids.
A protein is synthesized.

29. Translation cont.
The mRNA molecule is read until a stop codon (UAA, UAG, UGA) on the mRNA is reached:
The protein is released into the cytoplasm or RER
The mRNA molecule can be read again and again

32. DNA Replication

33. Introduction
DNA holds the genetic code which is passed from parents to their offspring.
Happens in the nucleus
During interphase (S phase) of the cell cycle, our DNA is replicated
so each new daughter cell is provided with an identical copy of this genetic material

35. Process of DNA Replication
DNA uncoils, and unzips (hydrogen bonds are broken between A:T and G:C)
The two strands separate
Necessary for enzymes to “read” the DNA
Each free nucleotide strand now serves as a template (a set of instructions) for building a new complementary DNA strand.
DNA nucleotides that are present in the nucleoplasm begin to match up with their complements on the templates.

37. Process of DNA Replication cont.
DNA polymerase (an enzyme) positions and links these nucleotides into a strand
This results in two identical DNA molecules, each consisting of one old and one newly assembled nucleotide strand.
This type of replication is called semi-conservative replication.

39. Changes in Genetic Information
If there is an error in the DNA code (i.e. in a gene), this is called a mutation.
Nature of Mutations
DNA replication errors
Proteins are altered
Usually repair enzymes prevent mutations

40. Effect of Mutations
One place mutations an occur is during DNA replication
There are several kinds of mutations that can effect the genetic code
Point mutations=single base pair change
Frame shift=insertion or deletion of a base
More dangerous
Mutations can also occur spontaneously
Mutagens=particular chemical substances
Mutations can effect the productions of proteins

42. Effects of Mutations Protein may not be made at all
When an enzyme is lacking from a metabolic pathway, childhood storage diseases (accumulation of A or B, etc) result.
This occurs in PKU, Tay-Sachs, and Niemin-Pick disease.
A protein may have altered function
In cystic fibrosis (altered chloride pump) & sickle-cell anemia (altered hemoglobin structure)
A protein may be produced in excess
In epilepsy where excess GABA leads to excess norepinephrine and dopamine

43. Metabolic Processes

44. Metabolic Processes
Metabolism = the sum of an organism's chemical reactions.
Each reaction is catalyzed by a specific enzyme
The reactions typically occur in pathways (i.e. in a sequence)
Reactions are divided into two major groups, anabolism and catabolism.
Products from one reaction can be the reactants for the next
New enzyme for each

45. Anabolic Reactions Anabolic Reactions = synthesis reactions:
Building complex molecules from simpler ones
(i.e. monomers into polymers)
Bonds are formed between monomers which now hold energy (= Endergonic reactions)
Water is removed between monomers to build the bond, termed Dehydration.
Used to make carbohydrate, lipid, and protein molecules

46. Anabolic Reactions cont.
energy 
C + D C---D
water
Example is to build a protein (polymer) from individual amino acids (monomers).

47. Catabolic Reactions Catabolic Reactions = decomposition reactions:
Breaking complex molecules into simpler ones
(i.e. polymers into monomers)
Bonds are broken between monomers releasing energy (= Exergonic reactions)
Water is used to break the bonds, termed Hydrolysis
Reverse of dehydration synthesis

48. Catabolic Reactions cont.
water 
A---B A + B
energy
Example is breaking a nucleic acid (polymer) into nucleotides (monomers)

51. Control of Metabolic Reactions

52. Enzymes
Enzymes are catalysts that increase the rate of a chemical (metabolic) reaction
Enzymes (most) are globular proteins
Enzymes are unchanged by the reaction they catalyze and can be recycled
Metabolic pathways involve several reactions in a row, with each reaction requiring a specific enzyme

53. Enzymes cont.
Enzymes are specific for the substance they act upon (called a substrate).
Only a specific region of the enzyme molecule actually binds the substrate. This region is called the Active Site.
The enzyme and substrate fit together like a "Lock and Key" through the active site on the enzyme.

56. Enzyme Reaction Rate Factors affecting the rate of chemical reactions:
Particle size: The smaller the particle, the faster the reaction will occur
Temperature: The higher the temperature, the faster the reaction will occur (up to a point).
Concentration: The greater number of particles in a given space, the faster the reaction.
Catalysts: Enzymes in biological systems.

57. Enzyme Names
Enzyme names are often derived from the substrate that they act upon (providing the root of enzyme name), and the enzyme names typically end in the suffix -ase:
The enzyme sucrase breaks down the substrate sucrose
A lipase breaks down a lipid
The enzyme DNA polymerase allows for DNA to be synthesized from DNA nucleotides

58. Cofactors and Coenzymes
The active site of an enzyme may not always be exposed (recall the 3-dimentional conformation of proteins)
A cofactor or coenzyme may be necessary to "activate" the enzyme so it can react with its substrate.
Cofactor = any substance that needs to be present in addition to an enzyme to catalyze a certain reaction
Coenzyme = organic molecule, non-protein

59. Factors that Alter Enzymes
Enzymes can become inactive or even denature in extreme conditions (review denaturation in chapter 2).
extreme temperatures
extreme pH values
harsh chemicals
radiation
electricity

60. Energy for Metabolic Reactions

61. Introduction Metabolic reactions require energy
The required amount of energy for a reaction to occur is the Activation Energy

62. Energy Energy is the capacity to do work.
Common forms include heat, light, sound, electrical energy, mechanical energy, and chemical energy.
Energy cannot be created or destroyed, but it changes forms
Law of Conservation of Energy
All metabolic reactions involve some form of energy

63. Release of Chemical Energy
Most metabolic reactions depend on chemical energy (opposed to other forms)
This form of energy is held within the chemical bonds that link atoms into molecules
When the bond breaks, chemical energy is released
This release of chemical energy is termed oxidation
The released chemical energy can then be used by the cell for anabolism

64. Release of Chemical Energy cont.
In cells, enzymes initiate oxidation by:
decreasing activation energy of a reaction
Less energy required to get it going
transferring energy to special energy-carrying molecules called coenzymes

65. Cellular Respiration

66. Introduction
CR is how animal cells use oxygen to release chemical energy from food to generate cellular energy (ATP)
The chemical reactions in CR must occur in a particular sequence, with each reaction being catalyzed by a different (specific) enzyme.

67. Introduction cont. There are three major series of reactions: Produces
1. glycolysis
2. citric acid cycle (Krebs)
3. electron transport chain
Produces
carbon dioxide
water
ATP (chemical energy)
heat

68. Introduction cont.
All organic molecules (carbohydrates, fats, and proteins) can be processed to release energy, but we will only study the steps of CR for the breakdown of glucose (C6H12O6)

69. Introduction cont.
Oxygen is required to receive the maximum energy possible per molecule of glucose and products of the reactions include water, CO2, and cellular energy (ATP)
Most of this energy is lost as heat.
Almost half of the energy is stored in a form the cell can use, as ATP
For every glucose molecule that enters CR usually 36 ATP are produced
however, up to 38 ATP can be generated

70. ATP Molecules
Adenosine Triphosphate (ATP) is the immediate source that drives cellular work
Structure of ATP:
adenine
ribose sugar
three phosphate groups
The triphosphate tail of ATP is unstable
The bonds between the phosphate groups can be broken by hydrolysis releasing chemical energy (EXERGONIC);
A molecule of inorganic phosphate (Pi) and ADP are the products of this REACTION
ATP Adenosine Diphosphate (ADP) Pi

72. ATP Molecules cont.
The inorganic phosphate from ATP can now be transferred to some other molecule which is now said to be "phosphorylated"
Phosphorylated=phosphate group added
ADP can be regenerated to ATP by the addition of a phosphate in a endergonic reaction
Adenosine Diphosphate (ADP) + Pi ATP
If ATP is synthesized by direct phosphate transfer the process is called substrate-level phosphorylation

74. Oxidation/Reduction Reactions (Redox)

75. Oxidation/Reduction Reactions
Many of the reactions in the breakdown of glucose involve the transfer of electrons (e-).
Reactions are called oxidation - reduction (or redox) reactions
Glucose is oxidized (loses e- and H), Oxygen is reduced (gains e- and H)

76. In a redox reaction:
the loss of electrons from a substance is called oxidation, while
the addition of electrons to a substance is called reduction.
In organic substances it is easy to follow redox reactions because you only have to watch H movement
because where one H goes, one electron goes

77. Oxidation/Reduction cont.
An electron transfer can also involve the transfer of a pair of hydrogen atoms (which possess two electrons), from one substance to another.
The H atoms (and electrons) are eventually transferred to oxygen
The transfer occurs in the final step of CR
In the meantime, the H atoms (with their electrons) are passed onto a coenzyme molecule [i.e. NAD+ (nicotinamide adenine dinucleotide) or FADH (flavin adenine dinucleotide)]
H:H + NAD NADH + H +
H:H + FADH FADH2 + H +
This is coenzyme reduction

78. Oxidation/Reduction cont.
In the final step of CR:
the electron transport chain
oxygen is the final electron acceptor (forming water)
NADH or FADH2 are oxidized
back to their original form
The energy released is used to synthesize ATP
The process of producing ATP indirectly through redox reactions is called oxidative phosphorylation

79. Glycolysis

80. Glycolysis series of ten reactions
breaks down glucose (6C) into 2 pyruvic acid molecules (3C)
occurs in cytosol
anaerobic phase of cellular respiration
No oxygen required
yields two ATP molecules per glucose

81. Glycolysis cont. Summarized by three main events
phosphorylation (of glucose)
splitting (of glucose)
production of NADH and ATP

82. Glycolysis cont. Event 1 - Phosphorylation
two phosphates added to glucose
requires ATP

83. Glycolysis cont. Event 2 – Splitting (cleavage)
6-carbon glucose split into two 3-carbon molecules

84. Glycolysis cont. Event 3 – Production of NADH and ATP
hydrogen atoms are released
hydrogen atoms bind to NAD+ to produce NADH
NADH delivers hydrogen atoms to electron transport chain if oxygen is available
ADP is phosphorylated to become ATP
two molecules of pyruvic acid are produced

85. Anaerobic Reactions If oxygen is not available
electron transport chain cannot accept new electrons from NADH
pyruvic acid is converted to lactic acid
glycolysis is inhibited
ATP production less than in aerobic reactions
Alcohol formation is also possible

86. Anabolic Reactions cont.
Lactic Acid Fermentation:
Pyruvate is converted to lactic acid, a waste product
occurs in many animal muscle cells;
serves as an alternate method of generating ATP when oxygen is scarce;
accumulation causes muscle soreness and fatigue.
Alcohol Fermentation:
Pyruvate is converted to ethanol
occurs in yeasts (brewing) and many bacteria.

87. Aerobic Reactions If oxygen is available –
pyruvic acid is used to produce acetyl CoA
citric acid cycle begins
electron transport chain functions
carbon dioxide and water are formed
36 molecules of ATP produced per glucose molecule

89. Citric Acid (Krebs) Cycle

90. Citric Acid (Krebs) Cycle
occurs in the mitochondrial matrix;
Acetyl CoA adds its 2 carbons to oxaloacetate (4C) forming citrate (6C)
2-CO2s are released during the series of steps where citrate (6C) is converted back to oxaloacetate (4C)
Energy yield is:
6 NADH per glucose
2 FADH2 per glucose
2 ATP per glucose
Substrate-level phosphorylation
involves many steps, each catalyzed by a different enzyme

91. Citric Acid Cycle
begins when acetyl CoA combines with oxaloacetic acid to produce citric acid

92. Citric Acid Cycle
citric acid is changed into oxaloacetic acid through a series of reactions

93. Citric Acid Cycle
cycle repeats as long as pyruvic acid and oxygen are available

94. Citric Acid Cycle for each citric acid molecule: one ATP is produced
eight hydrogen atoms are transferred to NAD+ and FAD
two CO2 produced

95. Electron Transport Chain (ETC)
NADH and FADH2 carry electrons to the ETC
ETC series of electron carriers located in cristae of mitochondria

96. Electron Transport Chain (ETC)
energy from electrons transferred to ATP synthase
ATP synthase catalyzes the phosphorylation of ADP to ATP

97. Electron Transport Chain (ETC)
water is formed
The final electron (and H) acceptor is oxygen which forms water

98. Overall ATP Yield From Glucose in CR:
4 ATP are generated directly:
2 from glycolysis
2 from Krebs
The remaining ATP is generated indirectly through coenzymes:
10 NADH are produced
2 from conversion
6 from Krebs
The yield from NADH is 30 ATP
2 FADH2 are produced in the Krebs Cycle
The yield from FADH2 is 4 ATP

99. Overall ATP Yield From Glucose in CR: cont.
The maximum net yield of ATP per glucose = 38 ATP
Most of the time it takes 2 ATP to move the 2 pyruvates into the mitochondrion, so normal ATP production is 36 ATP

102. Carbohydrate Storage

103. Carbohydrate Storage Catabolic Pathways Anabolic Pathways
Monosaccharides enter cells and are used in cellular respiration.
The cell can use the ATP generated for anabolic reactions.
Anabolic Pathways
Monosaccharides (when in excess) can be stored as:
glycogen
fat
amino acids

105. Metabolism of Lipids and Proteins

106. Metabolism of Lipids and Proteins
When liver glycogen stores are deplenished, fats and proteins can be metabolized to generate ATP.
All organic molecules enter CR at some point in the pathway.
Stored fats are the greatest reserve fuel in the body.
The metabolism of an 18-C lipid will yield 146 ATP by a process called Beta Oxidation, while the metabolism of 3 glucoses (18-C) will yield 108 ATP.