Transcript Chapter 4

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
Cytoplasm:
Translation
DNA
RNA polymerase
mRNA
mRNA
Ribosomes
Amino Acid
chain
(polypeptide)
mRNA moves
out of the
nucleus
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 semiconservative 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) & sicklecell 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.