Ch 4: Energy and Cellular
Metabolism

Energy as it relates to Biology

Chemical reactions

Enzymes and how they speed rxs

Metabolism and metabolic pathways
Catabolism (ATP production)
 Anabolism (Synthesis of biologically
important molecules)

Energy in Biological Systems
Review on your own!
Chemical Reactions
1.
Transfer energy
A + B
Substrates / reactants
2.
C + D
Products
or use energy to do work
Bioenergetics: Study of energy flow through
biol. systems
Reaction rate = speed of reaction
Activation Energy Starts Reaction
Fig 4-3
Reversible (most biol. rxs.) vs.
irreversible reactions
Endergonic vs. Exergonic Reactions
Coupling endergonic
Which kind?
and exergoinic rxs
Direct coupling vs.
indirect coupling
Enzymes are Proteins acting as
Biological Catalysts
4 important characteristics of enzymes
1.
 chemical reaction rate by lowering
activation energy
2.
are not changed themselves
3.
do not change nature of rx nor result
4.
are specific
Fig 4-8
Enzymes lower activation energy:
All chemical reactions in body
must be conducted at body
temp.!!
How do enzymes
lower activation
energy ?
Enzymes bind to reactant molecules and
bring them together in best position for rx.
Active Site:
Small region of the complex
3D structure is active (or
binding) site.
Enzymes bind to substrate
Old: Lock-and-key model / New: Induced-fit model
Fig 2-16
Enzyme-substrate interaction:
The old and the new model
Not in book
Naming of Enzymes
mostly suffix -ase
first part gives info on function
examples

Kinase

Phosphatase

Peptidase

Dehydrogenase
Isozymes = different models of same
enzyme (differ in 1 or few aa)
Catalize same reaction under
different conditions and in
different tissues/organs
Examples:
1.
2.
Amylase
LDH → importance in diagnostics
Review Table 4-3
Enzyme Activity
depends on
1.
proteolytic activation (for some)
2.
cofactors & coenzymes (for some)
3.
temperature
4.
pH
5.
other molecules interacting with enzyme
1) Proteolytic
Activation
Also
1. Pepsinogen
2. Trypsinogen
Pepsin
Trypsin
2) Cofactors & Coenzymes
structure:
___________ molecules
(e.g. ?)
function:
conformational change
of active site
structure:
Organic molecules (vitamin
derivatives, FADH2 ....)
function:
act as receptors & carriers
for atoms or functional
groups that are removed
from substrate
5) Molecules interacting with enzyme:
bind to enzyme away
from active site changing shape of active site for better or for
worse
Allosteric Modulators
Allosteric Activator
Fig 2-20
Allosteric Inhibitor
5) Molecules interacting with enzyme cont.
Competitive inhibitors:
reversible binding to
active site
block active site
Fig 2-19
Also possible: irreversible binding
via covalent bonds, e.g.:
• Penicillin
• Cyanide
Reversible Reactions follow the
Law of Mass Action
Fig 4-9
Three Major Types of Enzymatic
Reactions:
1.
Oxydation - Reduction reactions
(transfer of ?)
2.
Hydrolysis - Dehydration reactions
(breakdown & synthesis of ?)
3.
Addition-Subtraction-Exchange
reactions
?
Metabolism
Catabolism
Anabolism


Metabolism definition: ___________
Metabolic pathways = network of
linked reactions
Cells regulate metabolic pathways via
1. Control of enzyme concentration
2. Modulator production (allosteric
modulators, feedback inhibition, Fig 4-11)
3. Different enzymes for reversible rxs, Fig 412)
4.
Compartmentation of enzymes
5.
ATP / ADP ratio
Metabolic pathways: Network of
interconnected chemical reactions
Linear pathway
Intermediates
Circular pathway
Branched pathway
Special case:
= end product inhibition
Fig 4-11
Catabolic Pathways: ATP-Production
Amount of ATP produced reflects on
usefulness of metabolic pathways:
Aerobic pathways
Anaerobic pathways
Different
biomolecules
enter pathway at
different points
ATP = Energy Carrier of Cell (not very useful
for energy storage)
ATP Cycle
ATP : ADP ratio determines status of ATP synthesis reactions
Glycolysis

From 1 glucose to 2
pyruvate molecules

Main catabolic pathway of
cytoplasm

Does not require O2 
part of _________ and
____________ catabolism

Starts with
phosphorylation (“Before
doubling your money you first
have to invest!”)
Fig 4-13
Pyruvate has 2 Possible Fates
Anaerobic catabolism:
Pyruvate
lactate
Aerobic catabolism:
Pyruvate
Citric Acid Cycle
Citric Acid Cycle
Other names ?
Takes place in ?
Energy Produced:
1 ATP
3 NADH
1 FADH2
Fig. 4-16
Waste – 2 CO2
Energy Yield of Krebs Cycle
NADH
Compare to
Fig. 4-16
NADH
NADH
FADH2
Final step:
Electron Transport System

Chemiosmotic theory / oxydative phosphorylation

Transfers energy from NADH and FADH2 to ATP
(via e- donation and H+ transport)

Mechanism: Energy released by movement
of e- trough transport system is stored
temporarily in H+ gradient

NADH produces a maximum of 2.5 ATP
FADH2 produces a maximum of 1.5 ATP

1 ATP formed per 3H+ shuttled through ATP
Synthase
Fig 4-17
Cellular
Respiration
Maximum potential
yield for aerobic
glucose metabolism:
30-32 ATP
synthesized from
ADP
H2O is a byproduct
Synthetic Pathways
Anabolic rxs synthesize large biomolecules
Unit molecules
Macromolecules
nutrients &
energy required Polysaccharides
Lipids
DNA
Protein
Glycogen Synthesis
Made from glucose
Stored in all cells but especially in
 Liver (keeps 4h glycogen reserve for between meals)
 Skeletal Muscle  muscle contraction
Gluconeogenesis
Glycolysis in reverse
From glycerol, aa and lactate
All cells can make G-6-P, only liver
and Kidney can make glucose
Protein Synthesis
Proteins are the key to cell function →
necessary for all cell functions
Protein synthesis is under nuclear direction
 DNA specifies Proteins
?
DNA
mRNA
?
Protein
How can only 4 bases in DNA
encode > 20 different aa in protein?
1 letter word: 1 base = 1 aa  how many
possibilities?
2 letter word: 2 bases = 1 aa how many possibilities?
3 letter word: 3 bases = 1 aa  how many possibilities?
3 letter words =
base triplets or
codons
Redundancy of Genetic Code
1 start codon
(AUG =
Met)
3 stop codons
60 other
codons for
19 aa
Transcription
DNA is transcribed into
complementary mRNA
by
RNA Polymerase
+ nucleotides
+ Mg2+ ( = ?)
+?
Gene = elementary
unit of inheritance
Compare to Fig. 4-25
and review Fig 4-26
Translation
mRNA is translated into string of aa (= polypeptide)
2 important components ??
mRNA + ribosomes + tRNA meet in cytoplasm
Anticodon pairs with mRNA
codon  aa determined
Amino acids are linked via
______________ bond.
Fig 4-27
Post – Translational protein modifications:
Folding, cleavage, additions  glyco- , lipo- proteins
Protein Sorting
Due to signal/targeting sequence

No targeting sequence  protein stays in cytoplasm

Targeting sequence  protein destined for
translocation into organelles or for export from cell
For “export proteins”: Signal sequence
leads growing polypeptide chain across ER
membrane into ER lumen
Modifications in ER
Transition vesicles to
Compare to Fig 4-28
Golgi apparatus for further modifications
Transport vesicles to cell membrane
DNA Replication

Semiconservative

DNA
polymerase
Running problem:
Tay-Sachs Disease