Chemistry, Biochemistry, and Cell Physiology

CHAPTER
2
Chemistry,
Biochemistry, and Cell
Physiology
Part 2
PowerPoint® Lecture Slides prepared by

Stephen Gehnrich, Salisbury University
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Biochemistry
Metabolic pathways
 Series of reactions that convert subtrates to
products
 Catalyzed by enzymes
 Synthesis (anabolic)
 Degradative (catabolic)
 Metabolic pathways are linked by intermediates
 Metabolism – sum of metabolic pathways for the
synthesis and breakdown of molecules.

Enzymes
Catalysts that accelerate chemical reactions

 Enzymes have three properties
1. Active at low concentrations
2. Increase the rate of reactions but are not altered
3. Do not change the products
 Most are made of proteins
 Some are made of RNA (ribozymes)

Cofactors
 Nonprotein components of enzymes

 Many are loosely associated with enzymes
 Prosthetic group – cofactor covalently bonded into
the enzyme
 Coenzymes – organic cofactors usually derived
from vitamins
 Inorganic ion cofactors – copper, iron, magnesium,
zinc

Reaction Acceleration
 Enzymes accelerate reactions by reducing

activation energy (EA)
 Same substrate and product as uncatalyzed reaction
 Enzyme catalyzed reaction has a different
intermediate at the transition state
 S + E  ES  ES*  EP*  EP  E + P
 Active site – location in enzyme where substrate
binds
 Specific, 3-dimensional shape

Reaction Acceleration
Figure 2.12
Enzyme Kinetics
Conditions that influence the rate of enzymatic

reactions
 For example, changing the concentration of
substrate and product will affect reaction rates
Figure 2.13
Michaelis-Menten Rectangular Hyperbola
v = Vmax  [S] / ([S] + Km)

 v = initial velocity
 Vmax = maximum velocity
 Km = indicator of affinity of enzyme for the
substrate
Figure 2.14
Sigmoidal Relationships
 Homotropic enzymes – sigmoidal relationship

between v and [S]
 Cooperativity – enzymes show increased affinity
for S with increasing [S]
 Hill coefficient – degree of cooperativity (slope at
inflection)

Hyperbolic vs. Sigmoidal Relationships
Figure 2.13 and Figure 2.15

Environmental Effects
Enzyme activity is affected by temperature, pH,

salinity, and hydrostatic pressure
Enzymes are affected in different ways
 Changes in weak bonds alter three-dimensional
structure
 Changes in ionization state of amino acids within
the active site
 Changes in the ability of the enzyme to undergo
structural changes necessary for catalysis

Environmental Effects
Figure 2.16
Evolutionary Adaptation of Enzymes
Enzymes have evolved to meet physiological

conditions
Figure 2.17
Regulation of Enzyme Activity
Other molecules can affect enzyme kinetics

 Competitive inhibitors
 Block the active site
 Allosteric regulators
 Alter the three-dimensional shape of the enzyme
 Covalent modification
 Phosphorylation alters enzyme activity

Regulation of Enzyme Activity
Figure 2.18
Energy Storage
Cells store energy in two main forms

 Reducing energy
 High energy bonds

Reducing Energy
 Reducing equivalents – electrons bound to a carrier

 Example: NADH, NADPH, FADH2, FMNH2
 Oxidoreductases – enzymes that transfer reducing
equivalents between reduced (energy-rich) and oxidized
(energy-poor) molecules
 Example: lactate dehydrogensae
 NAD+ + lactate  NADH + H+ + pyruvate
 Redox status – reducing energy within a cell
 reduced form/oxidized form
 Example: [NADH/NAD+]

High Energy Bonds
Energy can be “stored” in covalent bonds

 Energy is released when bonds are broken
 ATP is the most common “high energy” molecule

High Energy Bonds
Figure 2.19
Biomolecules
Four main types

 Proteins
 Carbohydrates
 Lipids
 Nucleic acids

Proteins
 Contribute to cell structure and function

 Mediate all cellular processes
 Enzymes
 Have complex three-dimensional structure
 Protein structure is coded in DNA

Amino Acids
 Proteins are polymers of amino acids

 Amino acids – amino group (–NH2) and carboxylic
acid group (–COOH)
 Termed a-amino acids because –NH2 and –COOH
are located on the first (a) carbon
 Distinguished by side groups (R)
 Can be nonpolar (hydrophobic), polar-uncharged
(hydrophilic) and polar-charged (hydrophilic)

Protein Structure
Figure 2.20
Primary Structure
Linear sequence of amino acids joined by covalent

bond between the carboxyl and amino group
 Peptide bond

Secondary Structure
 Localized folding
 Linked by hydrogen bonds
 a-helix
 b-sheet
Figure 2.21
Tertiary Structure
Covalent bonds
 Disulfide bonds
Weak bonds
 van der Waals forces
 Ionic bonds
 Hydrogen bonds
Figure 2.22
Quaternary Structure
Protein made of multiple polypeptide chains

 Dimer – two subunits
 Homodimer – identical proteins
 Heterodimer – different proteins
 Trimer – three subunits
 Tetramer – four subunits

Protein Structure
Figure 2.20
Molecular Chaperones
Proteins function properly only when folded into

correct three-dimensional shape
 Some proteins fold spontaneously
 Some are helped by molecular chaperones
 Force protein into conformation that allows weak
bonds to form
 For example, heat shock proteins

Carbohydrates
 “Hydrates of carbon”
 Many hydroxyl (–OH) groups
 Glucose is the most common carbohydrate in
animal diets
 Energy metabolism
 Biosynthesis – precursor to many other
carbohydrates

Monosaccharides
 Used for energy and biosynthesis

 Small carbohydrates have three to seven carbons –
six is most common

Monosaccharides
Figure 2.23
Disaccharides
 Two monosaccharides connected by a covalent

bond
 Bond is broken during metabolism

Disaccharides
Figure 2.23
Carbohydrates + Other Macromolecules
Glycosylation – addition of carbohydrates to other

macromolecules
Alters function of the macromolecule
For example, glycolipids, glycoproteins
 Both are typically found in plasma membranes and
extracellular fluid

Complex Carbohydrates
 Polysaccharides
 Long chain of monosaccharides
 Energy storage
 Example: glycogen, starch
 Structural molecules
 chitin, hyaluronate, cellulose (in plants)

Complex Carbohydrates
Figure 2.25a
Glycogen Metabolism
Glycogen synthesis (glycogenesis)

Glycogen breakdown (glycogenolysis)
Figure 2.26
Glucose Metabolism
Glucose synthesis (gluconeogenesis)

 Uses reducing equivalents
 Requires energy
 2 pyruvate + 4ATP + 2GTP + 2NADH + 4H2O 
glucose + 4ADP + 2GDP + 6Pi + 2NAD+ + 2H+

Gluconeogenesis
Figure 2.27
Glucose Metabolism
Glucose breakdown (glycolysis)

 Produces reducing equivalents
 Releases energy
 Glucose + 2ADP + 2NAD+  2ATP + 2 pyruvate +
2NADH + 2H+
 Takes place in cytoplasm
 Does not require oxygen
 Produces intermediates for synthesis of various molecules
 Carbohydrates, nucleic acids, amino acids, and fatty acids

Glycolysis
Figure 2.28
Oxidation of Pyruvate in the Presence of O2
Glycolysis
 Converts carbohydrates to pyruvate within the
cytoplasm
 Lactate and amino acids can also be converted to
pyruvate
 Pyruvate is carried into the mitochondria
Pyruvate dehydrogenase (PDH)
 Pyruvate is oxidized by PDH to form acetyl CoA +
NADH

Oxidation of NADH in the Presence of O2
Glycolysis can only continue if NADH is

oxidized to NAD+
Two “redox shuttles” carry reducing equivalents
from cytoplasm into mitochondria
 a-glycerophosphate shuttle
 Malate-aspartate shuttle

Redox Shuttles
Figure 2.29
Oxidation of NADH in the Absence of O2
 NADH cannot be used by mitochondria when oxygen is not

present
 NADH is oxidized in the cytoplasm
 pyruvate + NADH + H+  lactate + NAD+
 Catalyzed by the enzyme lactate dehydrogenase (LDH)
 Other anaerobic pathways form less toxic end products and
more ATP than lactate (2 ATP)
 For example, succinate (4 ATP) and proprionate (6 ATP)

Oxidation of NADH in the Absence of O2
Figure 2.30
Lipids
 All are hydrophobic (do not dissolve in water)

 Carbon backbone
 Linear – aliphatic
 Ring – aromatic
 Examples: fatty acids, triglycerides, phospholipids,
steroids
 Lipids are used for energy metabolism, cell
structure, and signaling

Fatty Acids
 Chain of carbon atoms ending with a carboxyl

group
 Usually an even number of carbons
 Saturated
 No double bonds between carbons
 Unsaturated
 One or more double bonds between carbons

Fatty Acids
Figure 2.31
Fatty Acid Synthesis
Fatty acids are synthesized from Acetyl CoA

 Catalyzed by the enzyme fatty acid synthase (FAS)

Fatty Acid Oxidation (b-Oxidation)
Breakdown of fatty acids

 b-oxidation
 Takes place in mitochondria
 Results in formation of Acetyl CoA
 Acetyl CoA is oxidized

Fatty Acid Oxidation (b-Oxidation)
Figure 2.32
Ketones
 Some tissues cannot metabolize fatty acids, but

they can metabolize ketones
 For example, vertebrate brain, shark muscle
 Ketogenesis
 Fatty acids (acetyl CoA) are converted to ketones
 Ketolysis
 Ketones are broken down to acetyl CoA

Ketone Metabolism
Figure 2.33
Triglycerides
 Fatty acids esterified to a glycerol backbone

 For example, mono-,di-, tri-acylglycerol
 Fatty acids are stored as triglycerides
 Long-term storage of fatty acids
 Primary storage tissues: adipose and liver
(vertebrates), hepatopancreas (invertebrates)
 Lipases break the bond between fatty acid and
glycerol backbone (lipolysis)

Triglycerides
Figure 2.34
Triglyceride Synthesis or Lipogenesis
Figure 2.35
Phospholipids
 Dominate biological membranes

 Two classes of phospholipids in animal cells:
 Phosphoglycerides
 Constructed from diacylglycerol
 Polar group on third carbon
 Sphingolipids
 Sphingosine backbone
 Phospholipids are broken down by phospholipases

Phosphoglycerides
Figure 2.36a
Sphingolipids
Figure 2.36b
Steroids
 Four hydrocarbon rings

 Synthesis involves
many intermediates
Figure 2.37
Mitochondrial (Oxidative) Metabolism
Energy-yielding reactions that require oxygen

 Enzymes convert nutrients into metabolites
 Metabolites enter mitochondria
 Many metabolites are converted to acetyl CoA
 Acetyl CoA enters the tricarboxylic acid cycle (TCA cycle)
 Acetyl CoA is oxidized to form reducing equivalents
 Reducing equivalents are oxidized to release energy

Formation of acetyl CoA
Figure 2.38
Oxidative Metabolism
Acetyl CoA

Tricarboxylic acid (TCA) cycle
acetyl CoA  CO2 + reducing equivalent (NADH and
FADH2) and GTP

Electron transport system (ETS)
reducing equivalents are oxidized to release energy

Oxidative phosphorylation
ATP synthesis (phosphorylation)

Tricarboxylic Acid (TCA) Cycle
 Generates reducing equivalents within the

mitochondria
 Acetyl CoA + 3NAD+ + GDP + Pi + FAD  2CO2 +
3NADH + FADH2 + GTP
 Amphibolic pathway
 Some intermediates are broken down (catabolic)
 Some intermediates are used for syntheses (anabolic)

Tricarboxylic Acid (TCA) Cycle
Figure 2.39
Electron Transport System (ETS)
Electrons from NADH and FADH2 are transferred to

the ETS
 Found within the inner mitochondrial membrane
 Composed of four multisubunit proteins
(complexes I, II, III, IV) and two electron carriers
(ubiquinone and cytochrome c)
 Oxidation: 4e– + 4H+ + O2  2H2O
 Generates a proton gradient, heat, water, and
reactive oxygen species (ROS)

Electron Transport System (ETS)
Figure 2.40
ATP Synthesis
 Phosphorylation: ADP + Pi  ATP

 Proton motive force (Dp)
 pH gradient and the membrane potential (DY)
 F1F0ATPase uses energy in Dp to produce ATP
 There is no physical linkage between oxidation and
phosphorylation
 Two processes are functionally coupled through Dp

Phosphocreatine
 Alternative high-energy phosphate compound

 Creatine + ATP  ADP + phosphocreatine
 Creatine phosphokinase (CPK)
 Reaction is reversible so phosphocreatine can be
used to produce ATP when levels are low

Phosphocreatine
Figure 2.41
Integration of Metabolic Pathways
 Fluctuations in nutrient availability, energy

demand, and environmental conditions
 Reciprocal regulation avoids simultaneous
synthesis and degradation (futile cycles)
 Use of appropriate metabolic “fuel”
 Carbohydrate vs. lipid
 Energetic intermediates regulate balance between
anabolism and catabolism

Reciprocal Regulation
Figure 2.42
Respiratory Quotient
Type of fuel being used can be monitored by

measuring the RQ
 Respiratory quotient (RQ) = CO2 production/O2
consumption
 RQ – 0.7 for lipids, 1.0 for carbohydrates

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CHAPTER

PowerPoint® Lecture Slides prepared by

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Catalysts that accelerate chemical reactions

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Nonprotein components of enzymes

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Enzymes accelerate reactions by reducing

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Conditions that influence the rate of enzymatic

v = Vmax  [S] / ([S] + Km)

 Homotropic enzymes – sigmoidal relationship

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Figure 2.13 and Figure 2.15

Enzyme activity is affected by temperature, pH,

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Enzymes have evolved to meet physiological

Other molecules can affect enzyme kinetics

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cells store energy in two main forms

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Reducing equivalents – electrons bound to a carrier

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Energy can be “stored” in covalent bonds

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Four main types

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Contribute to cell structure and function

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Proteins are polymers of amino acids

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Linear sequence of amino acids joined by covalent

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Protein made of multiple polypeptide chains

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Proteins function properly only when folded into

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Used for energy and biosynthesis

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Two monosaccharides connected by a covalent

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Glycosylation – addition of carbohydrates to other

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Glycogen synthesis (glycogenesis)

Glucose synthesis (gluconeogenesis)

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Glucose breakdown (glycolysis)

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Glycolysis can only continue if NADH is

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 NADH cannot be used by mitochondria when oxygen is not

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 All are hydrophobic (do not dissolve in water)

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 Chain of carbon atoms ending with a carboxyl

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Fatty acids are synthesized from Acetyl CoA

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Breakdown of fatty acids