Chapter 4

Cellular Metabolism

Nucleic Acids and Protein Synthesis

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

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

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

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

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

Basic structure of DNA and RNA

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 – C pairs with G

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

Nucleotides (DNA and RNA)

DNA Structure

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.

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).

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

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”

Protein Synthesis Nucleus:

Transcription

DNA

mRNA

Cytoplasm:

Translation

mRNA moves out of the nucleus

mRNA

Amino Acid chain

(polypeptide)

RNA polym-erase

Ribosomes

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

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

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

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

Transcription cont.

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

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

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.

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

DNA Replication

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

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.

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.

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

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

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

Metabolic Processes

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

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

Anabolic Reactions cont.

energy

C + D C---D

water

• Example is to build a protein (polymer) from individual amino acids (monomers).

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

Catabolic Reactions cont.

water

A---B A + B

energy

• Example is breaking a nucleic acid (polymer) into nucleotides (monomers)

Control of Metabolic Reactions

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

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.

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.

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

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

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

Energy for Metabolic Reactions

Introduction

• Metabolic reactions require energy

• The required amount of energy for a reaction to occur is the Activation Energy

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

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

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

Cellular Respiration

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.

Introduction cont.

• There are three major series of reactions:1. glycolysis

2. citric acid cycle (Krebs)

3. electron transport chain

• Produces– carbon dioxide– water– ATP (chemical energy)– heat

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)

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

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

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

Oxidation/Reduction Reactions

(Redox)

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)

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

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

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

Glycolysis

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

Glycolysis cont.

• Summarized by three main events– phosphorylation (of glucose)– splitting (of glucose)– production of NADH and ATP

Glycolysis cont.

Event 1 - Phosphorylation– two phosphates

added to glucose– requires ATP

Glycolysis cont.

Event 2 – Splitting (cleavage)– 6-carbon glucose split

into two 3-carbon molecules

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

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

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.

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

Citric Acid (Krebs) Cycle

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

Citric Acid Cycle• begins when acetyl

CoA combines with oxaloacetic acid to produce citric acid

Citric Acid Cycle• citric acid is changed

into oxaloacetic acid through a series of reactions

Citric Acid Cycle• cycle repeats as long

as pyruvic acid and oxygen are available

Citric Acid Cycle• for each citric acid

molecule: – one ATP is produced– eight hydrogen atoms

are transferred to NAD+ and FAD

– two CO2 produced

Electron Transport Chain (ETC)

• NADH and FADH2 carry electrons to the ETC• ETC series of electron carriers located in cristae of

mitochondria

Electron Transport Chain (ETC)

• energy from electrons transferred to ATP synthase• ATP synthase catalyzes the phosphorylation of

ADP to ATP

Electron Transport Chain (ETC)

• water is formed• The final electron (and H) acceptor is oxygen

which forms water

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 glycolysis – 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

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

Carbohydrate Storage

Carbohydrate Storage

• Catabolic 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

Metabolism of Lipids and Proteins

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.