3 Chemisty Biochemistry and Cell Physiology

CHAPTER Chemistry and Physics of Life Cellular Processes & Physiological Systems
2 Physiological processes are based on cellular

function
Chemistry,
Biochemistry, and Cell
Cellular functions obey the laws of physics and
Physiology chemistry
Part 1
PowerPoint® Lecture Slides prepared by

Stephen Gehnrich, Salisbury University
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 2.1
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Thermodynamics Energy Energy Categories
Chemical reactions proceed according to the rules of Energy – ability to do work §  Radiant energy – transmitted from one object to
thermodynamics Energetics – energy transfer between systems another
§  The law of conservation of energy – energy can be §  Mechanical energy – movement of objects
converted from one form to another but the total §  Electrical energy – movement of charged particles
amount of energy is constant (i.e., you cannot Types of energy
§  Thermal energy – movement of molecules
“make” energy) §  Potential – trapped energy
§  Chemical energy – within chemical bonds
§  Entropy – the universe is becoming more chaotic §  Kinetic – energy of movement
§  Animals rely on all five types of energy, which are
interconvertible.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
1
Food Webs are Transfers of Energy Diffusion Gradients Electrochemical Gradients
Plants convert radiant energy into chemical energy Gradient – a difference between two points §  Gradients are a form of energy storage
by photosynthesis Diffusion – molecules disperse randomly in the §  Potential energy
Chemical energy is transferred from plants, to available space §  Organisms invest energy to delay diffusion
herbivores, to carnivores §  Gradients across membranes can be chemical,
electrical, or both (electrochemical)
Diffusion governs many biological processes
§  For example, membrane potential – electrical gradient
§  Diffusion leads to random distribution of molecules across a cell membrane
§  Diffusion of molecules is a source of energy
Electrochemical Gradients Thermal Energy Chemical Reactions and Thermal Energy
↑ Thermal energy → ↑ movement of molecules → ↑ Enthalpy – average thermal energy of a collection of

rate of chemical reactions molecules
Activation energy – energy required for a molecule to reach a
transition state
Most chemical reactions involve changes in thermal Transition state – intermediate structure between a substrate
energy and a product
§  Exothermic reactions – release heat Change in enthalpy (ΔH) = Hproducts – Hsubstrates
§  Endothermic reactions – absorb heat §  Exothermic: ΔH is negative
§  Endothermic: ΔH is positive
Figure 2.2
2
Temperature Influences Chemical Reactions Temperature Influences Chemical Reactions Chemical Bonds
Increasing temperature Most biologically available energy is stored in

§  Allows more molecules to reach activation energy chemical bonds
§  Increases the rate of the reaction Two main types of bonds
§  Increases the likelihood of endothermic reactions §  Covalent bonds (strong bonds) – atoms attached to
each other by sharing electrons
§  Noncovalent bonds (weak bonds) – molecules
organized into three-dimensional structures
Figure 2.3
Covalent Bonds Functional Groups Noncovalent Bonds (Weak Bonds)
§  Atoms with unpaired electrons can form covalent bonds §  Control macromolecule structure
§  That is, they share electrons with other atoms §  Arise between atoms with unequal distribution of electrons
§  Atoms with more than one unpaired electron can form
multiple covalent bonds
Four types
§  Chemical properties of the resultant molecule are influenced
§  van der Waals forces
by the bond angle
§  Hydrogen bonds
§  Bond energy – amount of energy needed to make or break
the bond §  Ionic bonds
§  Functional groups – combinations of atoms and bonds that §  Hydrophobic bonds
recur in biological molecules
Figure 2.4
3
van der Waals Interaction Hydrogen Bonds Hydrogen Bonds between Water Molecules
§  Transient dipole – polarity created by asymmetry Asymmetric sharing of electrons between two atoms
of electron distribution within an atom §  For example, organization of water molecules
§  van der Waals interaction – atom with transient §  Hydrogen (+) of one water molecule is attracted to
dipole affects the distribution of electrons in oxygen (–) of another
another atom
§  Effective only over a narrow range of distances
Figure 2.6
Ionic Bonds Hydrophobic Bonds Noncovalent Bonds (Weak Bonds)
§  Anion (–) – atom with too many electrons §  Aversion to water
§  Cation (+) – atom with too few electrons §  No significant dipoles (i.e., nonpolar)
§  Ionic bond – joining of anions and cations §  Electrons are equally shared
§  Example: salts, acids, and bases §  Cannot interact with polar molecules like water
§  For example, oil droplets in water – not attracted to
each other, but repelled by water
Figure 2.5
4
Weak Bonds are Sensitive to Temperature Water Solvents and Solutes
§  Weak bonds are sensitive to temperature because of §  Cells are primarily composed of water §  Solvent – most abundant molecule in a liquid
low bond energies §  Aquatic organisms live in water §  Solute – the other molecules in a liquid
§  Affects three-dimensional structure §  Cells of terrestrial animals are bathed in water §  Solution – solvents and solutes
§  Denature – molecules unfold due to high §  Many physiological processes arose to meet §  In biological systems the solvent is usually water
temperature challenges of the physical and chemical properties (i.e., aqueous solutions)
§  For example, protein, membranes, DNA of water
Properties of Water Surface Tension of Water Boiling and Freezing
§  Liquid water is a network of interconnected water Temperature changes the organization of water
molecules molecules
§  Water molecules are attracted to each other by §  High temperature – molecules possess enough
hydrogen bonds thermal energy to break the surface tension
§  Surface tension – the force due to attraction (i.e., boil)
between water molecules at the water–air interface §  Low temperature – stabilize molecules as a result
of additional hydrogen bonds (i.e., freeze)
Figure 2.7
5
Density of Water is Affected by Temperature Water is a Very Stable Liquid Many Solutes can Dissolve in Water
Temperature influences the density of water §  High melting point Solutes form hydrogen bonds with water molecules
§  Ice is less dense than liquid water §  High boiling point Hydration shell – solute surrounded by water
§  Ice has more hydrogen bonds, but molecules are held §  High heat of vaporization – amount of energy to molecules
further apart cause liquid water to boil
§  Ice floats in liquid water
§  Water is most dense at 4°C
§  Most deep waters are 4°C
§  Surface waters can be colder or warmer
Solutes Affect Properties of Water Solutes Move Through Water by Diffusion Solutes Create Osmotic Pressure
Colligative properties Direction of diffusion depends on the concentration Semipermeable membrane – allows some molecules
§  Reduce freezing point gradient to cross while restricting others
§  Increase Rate of diffusion (dQs/dt) depends on many factors Osmosis – the diffusion of water
§  Boiling point §  Size of concentration gradient (dC/dX) Osmotic pressure – force associated with the
§  Vapor pressure §  Size of molecule and hydration shell diffusion of water
§  Osmotic pressure §  Diffusion coefficient (Ds) Osmolarity – ability of solution to induce water to
§  Diffusion area (A) diffuse across a membrane
Depend on the number of solutes, not their size or
§  Fick equation: (dQs/dt) = Ds × A × (dC/dX) §  Determined by the concentration of dissolved
charge particles
6
Osmotic Pressure Osmotic Pressure Osmosis Across Cell Membranes
Comparing two solutions Tonicity – the affect of a solution on cell volume

§  Solution with higher osmolarity is hyperosmotic §  Cells shrink in hypertonic solution
§  Solution with lower osmolarity is hyposmotic §  Water leaves the cell by osmosis
§  If the osmolarities are the same, they are isosmotic §  Cells swell in hypotonic solution
§  Water diffuses from a hyposmotic solution to a §  Water enters the cell by osmosis
hyperosmotic solution §  Cell neither shrinks nor swells in isotonic solution
§  No net osmosis
Figure 2.8
Osmolarity vs. Tonicity pH and the Ionization of Water Neutrality
Dissociation of a water molecule into ions Neutrality: [H+] = [OH–] or pH = pOH

§  H:O:H → H:O:– + H+ §  Affected by temperature
pH = –log [H+] §  The amount of dissociation increases as temperature
increases
§  Brackets denote molar (M) concentration
§  pH at neutrality (pN) varies inversely with temperature
Pure water is pH 7 §  5°C: pN = 7.28
[H+] = 10–7 M §  25°C: pN = 7.00
§  45°C: pN = 6.72
–log 10–7 M = 7
Figure 2.9
7
Acids and Bases Alter the pH of Water Strength of Acids and Bases Temperature Affects Ionization State
Acids – release protons → ↓ pH pK increases as temperature decreases

§  HA ↔ H+ + A– (reaction goes to the right) Each ionizable group has a characteristic sensitivity
Bases – accept protons → ↑ pH to temperature
§  HA ↔ H+ + A– (reaction goes to the left) §  ΔpK / °C
Mass action ratio = ([H+] × [A–]) / [HA]
Equilibrium constant (Keq) – the mass action ratio at
equilibrium
§  pK = –log Keq
§  pK = pH – log ([A–] / [HA])
pK reflects the strength of acids or bases
Table 2.1
pH Affects Ionization State Buffers Limit Changes in pH Buffers Limit Changes in pH
§  Buffer – solute that dampens the effect of added

acid or base on the pH
§  Mixture of protonated and deprotonated molecules
§  Most buffers are weak acids
§  A buffer is effective only over a narrow range of
pH values
Figure 2.10 Figure 2.11

8
CHAPTER Biochemistry Enzymes
2 Metabolic pathways
§  Series of reactions that convert subtrates to
Catalysts that accelerate chemical reactions
§  Enzymes have three properties
Chemistry, products 1. Active at low concentrations
Biochemistry, and Cell §  Catalyzed by enzymes
2. Increase the rate of reactions but are not altered
Physiology §  Synthesis (anabolic)
Part 2 3. Do not change the products
§  Degradative (catabolic)
§  Most are made of proteins
§  Metabolic pathways are linked by intermediates
§  Some are made of RNA (ribozymes)
§  Metabolism – sum of metabolic pathways for the
synthesis and breakdown of molecules.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cofactors Reaction Acceleration Reaction Acceleration
§  Nonprotein components of enzymes §  Enzymes accelerate reactions by reducing

§  Many are loosely associated with enzymes activation energy (EA)
§  Same substrate and product as uncatalyzed reaction
§  Prosthetic group – cofactor covalently bonded into
the enzyme §  Enzyme catalyzed reaction has a different
intermediate at the transition state
§  Coenzymes – organic cofactors usually derived §  S + E ↔ ES ↔ ES* ↔ EP* ↔ EP ↔ E + P
from vitamins
§  Active site – location in enzyme where substrate
§  Inorganic ion cofactors – copper, iron, magnesium, binds
zinc §  Specific, 3-dimensional shape
Figure 2.12
1
Enzyme Kinetics Michaelis-Menten Rectangular Hyperbola Sigmoidal Relationships
Conditions that influence the rate of enzymatic v = Vmax × [S] / ([S] + Km) §  Homotropic enzymes – sigmoidal relationship
reactions §  v = initial velocity between v and [S]
§  For example, changing the concentration of §  Vmax = maximum velocity §  Cooperativity – enzymes show increased affinity
substrate and product will affect reaction rates for S with increasing [S]
§  Km = indicator of affinity of enzyme for the
substrate §  Hill coefficient – degree of cooperativity (slope at
inflection)

Hyperbolic vs. Sigmoidal Relationships Environmental Effects 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
Figure 2.13 and Figure 2.15 Figure 2.16

2
Evolutionary Adaptation of Enzymes Regulation of Enzyme Activity Regulation of Enzyme Activity
Enzymes have evolved to meet physiological Other molecules can affect enzyme kinetics
conditions §  Competitive inhibitors
§  Block the active site
§  Allosteric regulators
§  Alter the three-dimensional shape of the enzyme
§  Covalent modification
§  Phosphorylation alters enzyme activity

Energy Storage Reducing Energy High Energy Bonds
Cells store energy in two main forms §  Reducing equivalents – electrons bound to a carrier Energy can be “stored” in covalent bonds
§  Example: NADH, NADPH, FADH2, FMNH2
§  Reducing energy §  Energy is released when bonds are broken
§  Oxidoreductases – enzymes that transfer reducing
§  High energy bonds equivalents between reduced (energy-rich) and oxidized §  ATP is the most common “high energy” molecule
(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+]
3
High Energy Bonds Biomolecules Proteins
Four main types §  Contribute to cell structure and function

§  Proteins §  Mediate all cellular processes
§  Carbohydrates §  Enzymes
§  Lipids §  Have complex three-dimensional structure
§  Nucleic acids §  Protein structure is coded in DNA
Figure 2.19
Amino Acids Protein Structure Primary Structure
§  Proteins are polymers of amino acids Linear sequence of amino acids joined by covalent
§  Amino acids – amino group (–NH2) and carboxylic bond between the carboxyl and amino group
acid group (–COOH) §  Peptide bond
§  Termed α-amino acids because –NH2 and –COOH
are located on the first (α) carbon
§  Distinguished by side groups (R)
§  Can be nonpolar (hydrophobic), polar-uncharged
(hydrophilic) and polar-charged (hydrophilic)
Figure 2.20
4
Secondary Structure Tertiary Structure Quaternary Structure
§  Localized folding Covalent bonds Protein made of multiple polypeptide chains
§  Linked by hydrogen bonds §  Disulfide bonds §  Dimer – two subunits
§  α-helix Weak bonds §  Homodimer – identical proteins
§  β-sheet §  Heterodimer – different proteins
§  van der Waals forces
§  Ionic bonds §  Trimer – three subunits
§  Hydrogen bonds §  Tetramer – four subunits

Protein Structure Molecular Chaperones Carbohydrates
Proteins function properly only when folded into §  “Hydrates of carbon”
correct three-dimensional shape §  Many hydroxyl (–OH) groups
§  Some proteins fold spontaneously §  Glucose is the most common carbohydrate in
§  Some are helped by molecular chaperones animal diets
§  Force protein into conformation that allows weak §  Energy metabolism
bonds to form §  Biosynthesis – precursor to many other
§  For example, heat shock proteins carbohydrates
Figure 2.20
5
Monosaccharides Monosaccharides Disaccharides
§  Used for energy and biosynthesis §  Two monosaccharides connected by a covalent
§  Small carbohydrates have three to seven carbons – bond
six is most common §  Bond is broken during metabolism
Figure 2.23
Disaccharides Carbohydrates + Other Macromolecules Complex Carbohydrates
Glycosylation – addition of carbohydrates to other §  Polysaccharides

macromolecules §  Long chain of monosaccharides
Alters function of the macromolecule §  Energy storage
§  Example: glycogen, starch
For example, glycolipids, glycoproteins
§  Structural molecules
§  Both are typically found in plasma membranes and §  chitin, hyaluronate, cellulose (in plants)
extracellular fluid
Figure 2.23
6
Complex Carbohydrates Glycogen Metabolism Glucose Metabolism
Glycogen synthesis (glycogenesis) Glucose synthesis (gluconeogenesis)

Glycogen breakdown (glycogenolysis) §  Uses reducing equivalents
§  Requires energy
§  2 pyruvate + 4ATP + 2GTP + 2NADH + 4H2O à
glucose + 4ADP + 2GDP + 6Pi + 2NAD+ + 2H+
Figure 2.25a Figure 2.26

Gluconeogenesis Glucose Metabolism Glycolysis
Glucose breakdown (glycolysis)

§  Produces reducing equivalents
§  Releases energy
§  Glucose + 2ADP + 2NAD+ à 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

7
Oxidation of Pyruvate in the Presence of O2 Oxidation of NADH in the Presence of O2 Redox Shuttles
Glycolysis Glycolysis can only continue if NADH is

§  Converts carbohydrates to pyruvate within the oxidized to NAD+
cytoplasm
Two “redox shuttles” carry reducing equivalents
§  Lactate and amino acids can also be converted to
from cytoplasm into mitochondria
pyruvate
§  Pyruvate is carried into the mitochondria §  α-glycerophosphate shuttle
Pyruvate dehydrogenase (PDH) §  Malate-aspartate shuttle
§  Pyruvate is oxidized by PDH to form acetyl CoA +
NADH
Figure 2.29
Oxidation of NADH in the Absence of O2 Oxidation of NADH in the Absence of O2 Lipids
§  NADH cannot be used by mitochondria when oxygen is not §  All are hydrophobic (do not dissolve in water)
present
§  Carbon backbone
§  NADH is oxidized in the cytoplasm
§  Linear – aliphatic
§  pyruvate + NADH + H+ à lactate + NAD+
§  Catalyzed by the enzyme lactate dehydrogenase (LDH) §  Ring – aromatic
§  Other anaerobic pathways form less toxic end products and §  Examples: fatty acids, triglycerides, phospholipids,
more ATP than lactate (2 ATP) steroids
§  For example, succinate (4 ATP) and proprionate (6 ATP) §  Lipids are used for energy metabolism, cell
structure, and signaling
Figure 2.30
8
Fatty Acids Fatty Acids Fatty Acid Synthesis
§  Chain of carbon atoms ending with a carboxyl Fatty acids are synthesized from Acetyl CoA
group §  Catalyzed by the enzyme fatty acid synthase (FAS)
§  Usually an even number of carbons
§  Saturated
§  No double bonds between carbons
§  Unsaturated
§  One or more double bonds between carbons
Figure 2.31
Fatty Acid Oxidation (β-Oxidation) Fatty Acid Oxidation (β-Oxidation) Ketones
Breakdown of fatty acids §  Some tissues cannot metabolize fatty acids, but
§  β-oxidation they can metabolize ketones
§  For example, vertebrate brain, shark muscle
§  Takes place in mitochondria
§  Results in formation of Acetyl CoA §  Ketogenesis
§  Fatty acids (acetyl CoA) are converted to ketones
§  Acetyl CoA is oxidized
§  Ketolysis
§  Ketones are broken down to acetyl CoA
Figure 2.32
9
Ketone Metabolism Triglycerides 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)

Triglyceride Synthesis or Lipogenesis Phospholipids Phosphoglycerides
§  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
Figure 2.35 Figure 2.36a

10
Sphingolipids Steroids Mitochondrial (Oxidative) Metabolism
§  Four hydrocarbon rings Energy-yielding reactions that require oxygen

§  Synthesis involves §  Enzymes convert nutrients into metabolites
many intermediates §  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
Figure 2.36b Figure 2.37

Formation of acetyl CoA Oxidative Metabolism Tricarboxylic Acid (TCA) Cycle
Acetyl CoA §  Generates reducing equivalents within the

↓ mitochondria
Tricarboxylic acid (TCA) cycle §  Acetyl CoA + 3NAD+ + GDP + Pi + FAD à 2CO2 +
acetyl CoA à CO2 + reducing equivalent (NADH and 3NADH + FADH2 + GTP
FADH2) and GTP
§  Amphibolic pathway
↓
§  Some intermediates are broken down (catabolic)
Electron transport system (ETS)
§  Some intermediates are used for syntheses (anabolic)
reducing equivalents are oxidized to release energy
↓
Oxidative phosphorylation
ATP synthesis (phosphorylation)
Figure 2.38
11
Tricarboxylic Acid (TCA) Cycle Electron Transport System (ETS) 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 à 2H2O
§  Generates a proton gradient, heat, water, and
reactive oxygen species (ROS)

ATP Synthesis Phosphocreatine Phosphocreatine
§  Phosphorylation: ADP + Pi à ATP §  Alternative high-energy phosphate compound

§  Proton motive force (Δp) §  Creatine + ATP ↔ ADP + phosphocreatine
§  pH gradient and the membrane potential (ΔΨ) §  Creatine phosphokinase (CPK)
§  F1F0ATPase uses energy in Δp to produce ATP §  Reaction is reversible so phosphocreatine can be
§  There is no physical linkage between oxidation and used to produce ATP when levels are low
phosphorylation
§  Two processes are functionally coupled through Δp
Figure 2.41
12
Integration of Metabolic Pathways Reciprocal Regulation Respiratory Quotient
§  Fluctuations in nutrient availability, energy Type of fuel being used can be monitored by
demand, and environmental conditions measuring the RQ
§  Reciprocal regulation avoids simultaneous §  Respiratory quotient (RQ) = CO2 production/O2
synthesis and degradation (futile cycles) consumption
§  Use of appropriate metabolic “fuel” §  RQ – 0.7 for lipids, 1.0 for carbohydrates
§  Carbohydrate vs. lipid
§  Energetic intermediates regulate balance between
anabolism and catabolism
Figure 2.42
13
CHAPTER Cellular Membranes Membrane Structure
2 Two main roles

§  Isolate cells from the environment
Chemistry,
§  Control of intracellular conditions
Biochemistry, and Cell
Physiology §  Organize intracellular pathways into subcellular
Part 3 compartments

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 2.43
Lipid Profile Membrane Properties of Cholesterol Membrane Heterogeneity
§  Lipid bi-layer More PE and PS phosphoglycerides in inner leaflet

§  Phospholipids
More PC phosphoglycerides in the outer leaflet
§  Primarily phosphoglycerides
§  Other lipids Glycolipids only in the outer leaflet
§  Sphingolipids Lipid rafts
§  Alter electrical properties
§  Enriched in glycolipids and cholesterol
§  Glycolipids
§  Communication between cells §  More rigid and thicker
§  Cholesterol
§  Increase fluidity while decreasing permeability
Figure 2.44
1
Membrane Heterogeneity Membrane Fluidity Temperature and Membrane Fluidity
§  Environmental conditions affect membrane fluidity

§  For example, low temperature increases van der Waals
forces between lipids and restricts movement
§  Homeoviscous adaptation
§  Cell keeps membrane fluidity constant by altering the
lipid profile

Membrane Proteins Membrane Proteins Membrane Transport
§  Can be more than half of the membrane mass §  Cells must transport molecules across membranes
§  Structural and regulatory functions §  Three main types of transport:
§  Two main types §  Passive diffusion
§  Integral membrane proteins §  Facilitated diffusion
§  Tightly bound to the membrane §  Active transport
§  Embedded in bilayer or spanning the entire membrane Distinguished by direction of transport, nature of the
§  Peripheral membrane proteins carriers, and the role of energy
§  Weaker association with the lipid bilayer
Figure 2.47
2
Membrane Transport Passive Diffusion Facilitated Diffusion
§  Lipid-soluble molecules §  Hydrophilic molecules

§  No specific transporters are needed §  Protein transporter is needed
§  Molecules cross lipid bilayer §  No energy is needed
§  No energy is needed §  Depends on concentration gradient
§  Depends on concentration gradient §  High concentration à low concentration
§  High concentration à low concentration §  Steeper gradient results in faster rates
§  Steeper gradient results in faster rates
Figure 2.48
Facilitated Diffusion Ion Channels Active Transport
Three main types of protein carriers: §  Protein transporter is needed

§  Ion channels §  Energy is required
§  Small pores for specific ions
§  Molecules can be moved from low to high
§  Open and close in response to cellular conditions
§  “Gated” channels concentration
§  Porins
§  Like ion channels, but for larger molecules
§  Permeases
§  Function more like an enzyme
§  Carries molecule across membrane
Figure 2.49
3
Active Transport Primary Active Transport Secondary Active Transport
Two main types of active transport §  Hydrolysis of ATP provides energy §  Use energy in electrochemical gradient of one
§  Primary active transport §  Transporters are ATPases molecule to drive another molecule against its
§  Direct use of an exergonic reaction §  Three types gradient
§  P-type §  Antiport or exchanger carrier: molecules move in
§  Secondary active transport
§  Pump specific ions (e.g., Na+, K+, Ca2+)
opposite directions
§  Couples the movement of one molecule to the
§  F-type and V-type §  Symport or cotransporter carrier: molecules move in
movement of a second molecule
the same direction
§  Pump H+
§  Distinguished by the source of energy
§  ABC type
§  Carry large organic molecules (e.g., toxins)
Electrical Gradients Membrane Potential (Vm) Equilibrium Potential (Eion)
§  All transport processes affect chemical gradients §  Difference in charge inside and outside the cell Each ion has its own equilibrium potential
§  Some transport processes affect electrical gradients membrane §  Ion concentration gradient
§  Electroneutral carriers §  Concentration gradients formed by active transport
§  Ion diffuses down its concentration gradient
§  Transport uncharged molecules or exchange an equal §  Two main functions
number of particles with the same charge §  Eion is the Vm at which the ion is at electrochemical
§  Provide energy for membrane transport equilibrium
§  Electrogenic carriers
§  Changes in membrane potential used by cells in cell-
§  Transfer a charge §  Depends upon the size of the concentration gradient
to-cell signaling
§  For example, Na+/K+ATPase à exchanges 3Na+ for §  Eion can be calculated using the Nernst equation
2K+ §  Assumes electrochemical equilibrium
4
Equilibrium Potential (Eion) Membrane Potential (Vm) Changes in Membrane Potential (Vm)
§  Cell membranes are not at equilibrium Changes in membrane permeability cause changes in
§  Varying permeability membrane potential
§  Multiple ion gradients §  Depolarization
§  Goldman equation §  Cell becomes more positive on the inside
§  Accounts for permeability and multiple ions §  For example, if Na+ ions enter
§  Vm is most dependent upon Na+, K+, and Cl– §  Hyperpolarization
§  Na+/K+ ATPase maintains Na+ and K+ gradients §  Cell becomes more negative on the inside
across membrane §  For example, if K+ ions leave
Figure 2.50
Depolarization and Hyperpolarization Cellular Structures Mitochondria
§  Eukaryotic cells share many common cellular §  Produce most of the cell’s ATP
compartments §  Intricate network of internal membranes
§  Large surface area
§  Compartmentalization allows for regulation of
§  Mitochondrial reticulum
specific processes
§  Network of interconnected mitochondria
§  Mitochondrial DNA (mtDNA)
§  Some mitochondrial proteins
§  Required for mitochondrial biogenesis
§  Most genes for mitochondrial proteins are in the nucleus
Figure 2.51
5
Mitochondria Cytoskeleton Functions of the Cytoskeleton
Network of protein-based fibers §  Maintains cell structure

§  Microfilaments §  External cell shape
§  Flexible chains of actin
§  Organization of intracellular membranes
§  Microtubules
§  Tubes of tubulin §  Cellular processes
§  Intermediate filaments §  Movement
§  Composed of many types of monomers §  Motor proteins
Maintains cell structure §  Signal transduction
§  External cell shape
§  Organization of intracellular membranes
Cellular processes
For example, movement, signal transmission
Figure 2.52
Cytoskeleton Endoplasmic Reticulum and Golgi Apparatus Intracellular Traffic
§  Membranous organelles

§  Proteins are made on the ER
§  Proteins are modified and packaged into vesicles by the
Golgi apparatus
§  Vesicles carry proteins between compartments
§  Vesicles are carried throughout the cell by motor proteins
moving on cytoskeletal tracks
§  Contents of vesicles can be released from the cell via exocytosis
§  Extracellular substances can be taken into the cell via
endocytosis
Figure 2.23a,b Figure 2.54

6
Extracellular Matrix Extracellular Matrix Extracellular Matrix
§  Gel-like “cement” between cells Molecules of the extracellular matrix

§  Cell membranes are bonded to the matrix §  Proteins
§  Insect exoskeleton, vertebrate skeleton, and mollusc §  Glycoproteins
shells are modified extracellular matrices
§  Glycosaminoglycans
§  Molecules of the matrix are synthesized within the
§  Proteoglycans
cells and secreted by exocytosis
Figure 2.55
Extracellular Matrix Extracellular Matrix Physiological Genetics and Genomics
Cells can break down the extracellular matrix with Physiological diversity resides in genes
matrix metalloproteinases §  How genes differ between species
Cells can move through tissues by controlling the §  How genes are regulated in individual cells
production and breakdown of the matrix Homeostatic regulation depends upon having
§  For example, blood vessel growth and penetration §  the right protein,
§  in the proper place,
§  at the proper time,
§  with the appropriate activity
Figure 2.56
7
Nucleic Acids Nucleic Acids DNA
Two types: §  DNA and RNA are polymers of nucleotides §  Double-stranded α-helix
§  DNA – deoxyribonucleic acid §  linked by phosphodiester bonds §  Two strands of nucleotides linked by hydrogen bonds
§  Genetic blueprint §  Complementary strands
§  Nucleotide
§  Genes in nucleus §  Antiparallel
§  Nitrogenous base
§  RNA – ribonucleic acid §  Nucleotides can form bonds with only one other
§  Cytosine, Adenine, Guanine,Thymine (DNA only), Uracil
§  Read and interpret DNA to make protein nucleotide
(RNA only)
§  Three main forms §  A + T: two hydrogen bonds
§  Transfer RNA (tRNA)
§  Sugar
§  Deoxyribose (DNA), ribose (RNA) §  G + C: three hydrogen bonds
§  Ribosomal RNA (rRNA)
§  Messenger RNA (mRNA) §  Phosphate
Structure of DNA Histones DNA Organization
§  Mammalian DNA is several meters long §  Genome

§  Entire collection of DNA within a cell
§  DNA is compressed by DNA-binding proteins
(histones) §  Chromosome
§  Separate segments of DNA
§  DNA in this form is referred to as chromatin
§  Genes
§  Advantages of compression by histones §  DNA sequence within a chromosome
§  Large amounts of DNA fit into small volumes §  Used to produce RNA
§  Reduces damage caused by radiation and chemicals §  Exons
§  Must be uncompressed for DNA and RNA §  Segments of DNA that encode RNA
synthesis §  Introns
§  Interspersed DNA sections between exons
Figure 2.57
8
DNA Organization Genome Size Transcription
Synthesis of messenger RNA (mRNA)

§  DNA is wrapped by histones
§  Must be unwrapped to allow transcription
§  Transcription regulators form regulatory complexes
at promoter
§  Region of the gene where transcription begins
§  mRNA synthesis begins

Transcription Mature mRNA Protein Synthesis (Translation)
§  Primary mRNA transcript §  Ribosomes

§  Exons – sequences that will code for the protein §  Made of rRNA and proteins
§  Introns – noncoding sequences
§  Bound to endoplasmic reticulum
§  Introns are removed and exons are spliced together
§  Catalyze the formation of peptide bonds between
§  mRNA is polyadenylated
amino acids
§  200+ adenosines are added to the 3´ end
§  poly A+ tail §  Transfer RNA (tRNA)
§  mRNA is exported from the nucleus to the cytoplasm §  Carry the amino acids that bind to a codon (three
§  mRNA is ultimately degraded by nucleases (RNases) nucleotides on mRNA)
Figure 2.60
9
Protein Degradation Protein Isoforms Origins of Protein Isoforms
§  Proteins may have structural changes that result in §  Variations in protein structure
dysfunction §  Genetic rearrangements
§  Structural changes recruit enzymes that mark the §  Alternative splicing of exons
protein with a small protein called ubiquitin §  Alleles
§  Ubitquitin-labeled protein is then bound by a large §  Gene duplications
enzyme complex called a proteasome §  Subsequent mutation of some copies
§  Enzymes degrade the protein to amino acids
Figure 2.61
Genome Duplication
Figure 2.62
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CHAPTER Chemistry and Physics of Life Cellular Processes & Physiological Systems

2 Physiological processes are based on cellular

PowerPoint® Lecture Slides prepared by

Thermodynamics Energy Energy Categories

Electrochemical Gradients Thermal Energy Chemical Reactions and Thermal Energy

↑ Thermal energy → ↑ movement of molecules → ↑ Enthalpy – average thermal energy of a collection of

Increasing temperature Most biologically available energy is stored in

Covalent Bonds Functional Groups Noncovalent Bonds (Weak Bonds)

Ionic Bonds Hydrophobic Bonds Noncovalent Bonds (Weak Bonds)

Properties of Water Surface Tension of Water Boiling and Freezing

Comparing two solutions Tonicity – the affect of a solution on cell volume

Osmolarity vs. Tonicity pH and the Ionization of Water Neutrality

Dissociation of a water molecule into ions Neutrality: [H+] = [OH–] or pH = pOH

Acids – release protons → ↓ pH pK increases as temperature decreases

pH Affects Ionization State Buffers Limit Changes in pH Buffers Limit Changes in pH

§ Buffer – solute that dampens the effect of added

Figure 2.10 Figure 2.11

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

Cofactors Reaction Acceleration Reaction Acceleration

§ Nonprotein components of enzymes § Enzymes accelerate reactions by reducing

Figure 2.13 Figure 2.14

Hyperbolic vs. Sigmoidal Relationships Environmental Effects Environmental Effects

Enzyme activity is affected by temperature, pH,

Figure 2.13 and Figure 2.15 Figure 2.16

Figure 2.17 Figure 2.18

Energy Storage Reducing Energy High Energy Bonds

Four main types § Contribute to cell structure and function

Amino Acids Protein Structure Primary Structure

Figure 2.21 Figure 2.22

Protein Structure Molecular Chaperones Carbohydrates

Disaccharides Carbohydrates + Other Macromolecules Complex Carbohydrates

Glycosylation – addition of carbohydrates to other § Polysaccharides

Glycogen synthesis (glycogenesis) Glucose synthesis (gluconeogenesis)

Figure 2.25a Figure 2.26

Gluconeogenesis Glucose Metabolism Glycolysis

Glucose breakdown (glycolysis)

Figure 2.27 Figure 2.28

Glycolysis Glycolysis can only continue if NADH is

Oxidation of NADH in the Absence of O2 Oxidation of NADH in the Absence of O2 Lipids

Fatty Acid Oxidation (β-Oxidation) Fatty Acid Oxidation (β-Oxidation) Ketones

§ Fatty acids esterified to a glycerol backbone

Figure 2.33 Figure 2.34

Triglyceride Synthesis or Lipogenesis Phospholipids Phosphoglycerides

§ Dominate biological membranes

Figure 2.35 Figure 2.36a

§ Four hydrocarbon rings Energy-yielding reactions that require oxygen

Figure 2.36b Figure 2.37

Formation of acetyl CoA Oxidative Metabolism Tricarboxylic Acid (TCA) Cycle

Acetyl CoA § Generates reducing equivalents within the

Electrons from NADH and FADH2 are transferred to

Figure 2.39 Figure 2.40

ATP Synthesis Phosphocreatine Phosphocreatine

§ Phosphorylation: ADP + Pi à ATP § Alternative high-energy phosphate compound

2 Two main roles

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Lipid Profile Membrane Properties of Cholesterol Membrane Heterogeneity

§ Lipid bi-layer More PE and PS phosphoglycerides in inner leaflet

§ Environmental conditions affect membrane fluidity

Figure 12.45 Figure 2.46

Membrane Proteins Membrane Proteins Membrane Transport

§ Lipid-soluble molecules § Hydrophilic molecules

Facilitated Diffusion Ion Channels Active Transport

Three main types of protein carriers: § Protein transporter is needed

Electrical Gradients Membrane Potential (Vm) Equilibrium Potential (Eion)

§  Buffer – solute that dampens the effect of added

§  Nonprotein components of enzymes §  Enzymes accelerate reactions by reducing

Four main types §  Contribute to cell structure and function

Glycosylation – addition of carbohydrates to other §  Polysaccharides

§  Fatty acids esterified to a glycerol backbone

§  Dominate biological membranes

§  Four hydrocarbon rings Energy-yielding reactions that require oxygen

Acetyl CoA §  Generates reducing equivalents within the

§  Phosphorylation: ADP + Pi à ATP §  Alternative high-energy phosphate compound

§  Lipid bi-layer More PE and PS phosphoglycerides in inner leaflet

§  Environmental conditions affect membrane fluidity

§  Lipid-soluble molecules §  Hydrophilic molecules

Three main types of protein carriers: §  Protein transporter is needed

Network of protein-based fibers §  Maintains cell structure

§  Membranous organelles

§  Gel-like “cement” between cells Molecules of the extracellular matrix

§  Mammalian DNA is several meters long §  Genome

§  Primary mRNA transcript §  Ribosomes