Marieb Chapter 2 Part B: Chemistry Comes Alive Student version.
-
Upload
milton-holt -
Category
Documents
-
view
226 -
download
0
Transcript of Marieb Chapter 2 Part B: Chemistry Comes Alive Student version.
Marieb Chapter 2 Part B: Chemistry Comes Alive
Student version
© 2013 Pearson Education, Inc.
Biochemistry
• Study of chemical composition and reactions of living matter
• All chemicals are either organic or inorganic
© 2013 Pearson Education, Inc.
Classes of Compounds
• Inorganic compounds• • Do not contain carbon (exception is CO2)
• Organic compounds•
• Contain carbon, are usually large, and atoms are covalently bonded
• Both equally essential for life
© 2013 Pearson Education, Inc.
Water in Living Organisms
• Most abundant inorganic compound – 60%–80% volume of living cells
• Most important inorganic compound– Due to water’s properties– Let’s discuss this!
© 2013 Pearson Education, Inc.
Properties of Water
• High heat capacity– Absorbs and releases heat with little
temperature change– Prevents sudden changes in temperature
• High heat of vaporization– Evaporation requires large amounts of heat– Useful cooling mechanism
© 2013 Pearson Education, Inc.
Properties of Water
• Acts as a polar solvent– Dissolves and dissociates ionic substances– Forms layers around large charged
molecules, e.g., proteins (colloid formation)– Body’s major transport medium– Most biological molecules are happy in it
(uhm, dissolve!)
© 2013 Pearson Education, Inc.
Water molecule
δ+
δ+
δ–
Ions insolution
Saltcrystal
Figure 2.12 Dissociation of salt in water.
© 2013 Pearson Education, Inc.
Properties of Water
• Formed or used in some chemical reactions– Necessary part of hydrolysis and dehydration
synthesis reactions
• Used as cushioning– Protects certain organs from physical trauma,
e.g., cerebrospinal fluid
© 2013 Pearson Education, Inc.
What Are Salts?
•
– Ions ( ) conduct electrical currents in solution– Ions play specialized roles in body functions
– Ionic balance vital for homeostasis
• Contain cations other than H+ and anions other than OH–
• Common electrolytes found in the body– sodium, chloride, carbonate, potassium, calcium,
phosphates
© 2013 Pearson Education, Inc.
Acids and Bases
• Both form electrolytes–
• Acids are– Release H+ (a bare proton) in solution– HCl H+ + Cl–
• Bases are– Take up H+ from solution or release OH- into solution
• NaOH Na+ + OH–
– OH– accepts an available proton (H+) to form water– OH– + H+ H2O
© 2013 Pearson Education, Inc.
Some Important Acids and Bases in Body
• Important acids– HCl, HC2H3O2 (acetic acid), and H2CO3
• Important bases – Bicarbonate ion (HCO3–) and ammonia (NH3)
© 2013 Pearson Education, Inc.
pH: Acid-base Concentration
• Relative free [H+] of a solution measured in a special way
• As free [H+] increases, acidity increases• [OH–] decreases as [H+] increases
• pH decreases
• As free [H+] decreases, alkalinity increases• [OH–] increases as [H+] decreases
• pH increases
© 2013 Pearson Education, Inc.
pH: Acid-base Concentration
• pH = negative logarithm of [H+] in moles per liter
• pH scale ranges from 0–14
• Because pH scale is logarithmic (like the Richter Scale)– A pH 5 solution is 10 times more acidic than a
pH 6 solution
© 2013 Pearson Education, Inc.
pH: Expression Of Acid-base Concentration• Acidic solutions
[H+], pH – Acidic pH:
• Neutral solutions– Equal numbers of H+ and OH–
– All neutral solutions are pH – Pure water is pH neutral
• pH of pure water = pH 7: [H+] = 10–7 m
• Alkaline (basic) solutions [H+], pH– Alkaline pH:
© 2013 Pearson Education, Inc.
Concentration(moles/liter)
[OH−] [H+] pH
100
10−1
10−2
10−3
10−4
10−5
10−6
10−7
10−8
10−9
10−10
10−11
10−12
10−13
10−14
10−14
10−13
10−12
10−11
10−10
10−9
10−8
10−7
10−6
10−5
10−4
10−3
10−2
10−1
100
1
2
3
4
5
6
7
8
9
10
11
12
13
14
1M Hydrochloricacid (pH=0)
Lemon juice; gastricjuice (pH=2)
Wine (pH=2.5–3.5)
Black coffee (pH=5)
Milk (pH=6.3–6.6)
Blood (pH=7.4)
Egg white (pH=8)
Household bleach(pH=9.5)
Household ammonia(pH=10.5–11.5)
Oven cleaner, lye(pH=13.5)
1M Sodiumhydroxide (pH=14)
Examples
Incr
easi
ng
ly a
cid
ic
Neutral
Incr
easi
ng
ly b
asi
c
0
Figure 2.13 The pH scale and pH values of representative substances.
pH Paper
Strong and Weak Acids and Bases
strong weak
© 2013 Pearson Education, Inc.
Acid-base Homeostasis
• A pH change interferes with cell function and may damage living tissue
• Even a slight change in pH can be fatal
• What are the extremes of pH of the blood?• Lowest = Highest =
• pH is regulated by kidneys, lungs, and chemical buffers (observe in Lab Expt. 2)
© 2013 Pearson Education, Inc.
Buffers
• Acidity reflects only free H+ in solution• Buffers resist abrupt and large swings in pH
– Release hydrogen ions if pH rises– Bind hydrogen ions if pH falls
• Carbonic acid-bicarbonate system (important buffer system of blood):
Buffers
• H2CO3 H+ + HCO3-
• All three present in solution.
• What happens if we add H+?
-
• What happens if we add OH-?
-
Where Do We Find Buffers?
© 2013 Pearson Education, Inc.
Organic Compounds
• Molecules that contain – Except CO2 and CO, which are considered
inorganic
• Carbon always shares electrons; never gains or loses them
• Carbon forms four covalent bonds with other elements
• Unique to living systems• Carbohydrates, lipids, proteins, and
nucleic acids
© 2013 Pearson Education, Inc.
Organic Compounds
• Many are(ex.= glycogen, DNA, proteins)
– Chains of similar units called(I call them the “building blocks”)
• Polymers are synthesized by dehydration synthesis ( )
• Polymers are broken down by hydrolysis reactions ( )
© 2013 Pearson Education, Inc.
Dehydration synthesis
Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation.
Monomer 1
Hydrolysis
Monomers linked by covalent bond
Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other.
Example reactions
Dehydration synthesis of sucrose and its breakdown by hydrolysis
+
Glucose Fructose
Water isreleased
Water isconsumed
Sucrose
Monomer 2
Monomer 1 Monomer 2
Monomers linked by covalent bond
+
+
Figure 2.14 Dehydration Synthesis and Hydrolysis.
© 2013 Pearson Education, Inc.
Carbohydrates
• Sugars and starches
• Come in monomers and polymers
• Contain C, H, and O [formula =(CH20)n]
• Three classes– Monosaccharides – one sugar– Disaccharides – two sugars covalently
bonded– Polysaccharides – many sugars covalently
bonded
© 2013 Pearson Education, Inc.
Carbohydrates
• Functions of carbohydrates
– Major source of cellular fuel (e.g., glucose)
– Structural molecules
© 2013 Pearson Education, Inc.
Monosaccharides
• Simple sugars • These are the monomers of carbohydrates• Important monosaccharides
– Pentose sugars• Ribose and deoxyribose (in DNA and RNA)
– Hexose sugars• Glucose (blood sugar)
© 2013 Pearson Education, Inc.
Monosaccharides
Monomers of carbohydratesExampleHexose sugars (the hexoses shown here are isomers)
ExamplePentose sugars
Glucose Fructose Galactose Deoxyribose Ribose
Figure 2.15a
Simple carbohydrate molecules important to the body.
© 2013 Pearson Education, Inc.
Disaccharides
• Double sugars (two covalently linked monomers)
• Also called simple carbohydrates
• Too large to pass through cell membranes
• Important disaccharides– Sucrose, maltose, lactose– We have enzymes to break these down
© 2013 Pearson Education, Inc.
Disaccharides
Consist of two linked monosaccharidesExampleSucrose, maltose, and lactose(these disaccharides are isomers)
FructoseGlucose GlucoseGlucose GlucoseGalactose
Sucrose Maltose Lactose
Figure 2.15b
Simple carbohydrate molecules important to the body.
© 2013 Pearson Education, Inc.
Polysaccharides
• Polymers of monosaccharides
• Complex sugars
• Important polysaccharides– Plant starch– Animal starch (glycogen) – Cellulose (woody plants)
© 2013 Pearson Education, Inc.
PLAYPLAY Animation: Polysaccharides
Polysaccharides
Long chains (polymers) of linked monosaccharidesExampleThis polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose units.
Glycogen
Figure 2.15c Carbohydrate molecules important to the body.
© 2013 Pearson Education, Inc.
Animation: Fats
Lipids
• Contain C, H, O (less than in carbohydrates), and sometimes P
• Insoluble in water
• Main types:– – – –
PLAYPLAY
© 2013 Pearson Education, Inc.
Neutral Fats or Triglycerides
• Called fats when solid (lard, butter)
• Oils when liquid (canola oil)
• Composed of three fatty acids covalently bonded to a glycerol molecule
• Main functions– Energy storage– Insulation– Protection
© 2013 Pearson Education, Inc.
Triglyceride formation
Three fatty acid chains are bound to glycerol by dehydration synthesis.
Glycerol 3 fatty acid chainsTriglyceride, or neutral fat
3 watermolecules
+ +
Figure 2.16a Lipids.
Dehydration Synthesis
© 2013 Pearson Education, Inc.
Saturation of Fatty Acids
• Saturated fatty acids– Single covalent bonds between C atoms
• Maximum number of H atoms
– Solid animal fats, e.g., butter
and lard
Saturation of Fatty Acids
• Unsaturated fatty acids– One or more double bonds between C atoms
• Reduced number of H atoms
– Plant oils, e.g., olive oil–
Saturation of Fatty Acids
Saturation of Fatty Acids
• Trans fats – modified oils –
• Omega-3 fatty acids –
Saturation of Fatty Acids
Types Of Fat
© 2013 Pearson Education, Inc.
Phospholipids
• Modified triglycerides: – Glycerol + two fatty acids and a phosphorus
(P) - containing group
• “Head” and “tail” regions have different properties
• Important in cell membrane structure
© 2013 Pearson Education, Inc.
“Typical” structure of a phospholipid molecule
Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.
ExamplePhosphatidylcholine
Nonpolar “tails”(schematic
phospholipid)
Polar “head”
Phosphorus-containinggroup
(polar “head”)
Glycerolbackbone 2 fatty acid chains
(nonpolar “tails”)
Figure 2.16b Lipids.
© 2013 Pearson Education, Inc.
Steroids
• Steroids—interlocking four-ring structure
• Cholesterol, vitamin D, steroid hormones, and bile salts
• Most important steroid–
• Important in cell membranes, vitamin D synthesis, steroid hormones, and bile salts
© 2013 Pearson Education, Inc.
Simplified structure of a steroidFour interlocking hydrocarbon rings
form a steroid.ExampleCholesterol (cholesterol is thebasis for all steroids formed in the body)
Figure 2.16c Lipids.
Anabolic Steroids
© 2013 Pearson Education, Inc.
Eicosanoids
• Many different ones
• Derived from a fatty acid (arachidonic acid) in cell membranes
• Most important eicosanoid– Prostaglandins
• Role in blood clotting, control of blood pressure, inflammation, and labor contractions
© 2013 Pearson Education, Inc.
Other Lipids in the Body
• Fat-soluble vitamins– Vitamins A, D, E, and K
• Lipoproteins– Transport fats in the blood (LDL, HDL)
© 2013 Pearson Education, Inc.
Proteins
• Contain C, H, O, N, and sometimes S and P• Proteins are polymers • Amino acids (20 types) are the monomers in
proteins– Joined by covalent bonds called peptide bonds– Contain amine group and acid group– Can act as either acid or base– All identical except for “R group” (in green on figure)
© 2013 Pearson Education, Inc.
Generalizedstructure of allamino acids.
Glycineis the simplestamino acid.
Aspartic acid(an acidic aminoacid) has an acidgroup (—COOH)in the R group.
Lysine(a basic aminoacid) has an aminegroup (—NH2) inthe R group.
Cysteine(a basic amino acid)has a sulfhydryl (—SH)group in the R group,which suggests thatthis amino acid is likelyto participate in intramolecular bonding.
Aminegroup
Acid group
Figure 2.17 Amino acid structures.
© 2013 Pearson Education, Inc.
Amino acid
Dehydration synthesis:The acid group of one aminoacid is bonded to the aminegroup of the next, with lossof a water molecule.
Hydrolysis: Peptide bondslinking amino acids togetherare broken when water isadded to the bond.
Dipeptide
Peptidebond
Amino acid
+
Figure 2.18 Amino acids are linked together by peptide bonds.
© 2013 Pearson Education, Inc.
Primary structure:The sequence of amino acids formsthe polypeptide chain.
Amino acid Amino acid Amino acid Amino acid Amino acid
Figure 2.19a Levels of protein structure.
© 2013 Pearson Education, Inc.
Secondarystructure:The primary chainforms spirals(α-helices) andsheets (β-sheets).
α-Helix: The primary chain is coiledto form a spiral structure, which isstabilized by hydrogen bonds.
β-Sheet: The primary chain “zig-zags”back and forth forming a “pleated”sheet. Adjacent strands are heldtogether by hydrogen bonds.
Figure 2.19b Levels of protein structure.
© 2013 Pearson Education, Inc.
Tertiary structure:Superimposed on secondary structure.α-Helices and/or β-sheets are folded upto form a compact globular moleculeheld together by intramolecular bonds.
Tertiary structure ofprealbumin (transthyretin),a protein that transportsthe thyroid hormonethyroxine in blood andcerebrospinal fluid.
Figure 2.19c Levels of protein structure.
© 2013 Pearson Education, Inc.
Quaternary structure:Two or more polypeptide chains,each with its own tertiary structure,combine to form a functionalprotein.
Quaternary structure of a functional prealbuminmolecule. Two identicalprealbumin subunits joinhead to tail to form thedimer.
Figure 2.19d Levels of protein structure.
© 2013 Pearson Education, Inc.
Fibrous and Globular Proteins
• (structural) proteins– – Most have tertiary or quaternary structure (3-D)– Provide mechanical support and strength– Examples:
© 2013 Pearson Education, Inc.
Fibrous and Globular Proteins
• (functional) proteins – Compact, spherical, water-soluble and
sensitive to environmental changes– Tertiary or quaternary structure (3-D)– Specific functional regions (active sites) – Examples:
Fibrous and Globular Proteins
© 2013 Pearson Education, Inc.
Protein Denaturation
• Denaturation– Globular proteins unfold and lose functional,
3-D shape• activity destroyed
– Can be cause by decreased pH, increased ions, or increased temperature
• Usually reversible if normal conditions restored
• Irreversible if changes are extreme– e.g., cooking meat
Protein Denaturation
© 2013 Pearson Education, Inc.
Enzymes
– Globular proteins that act as biological catalysts
• Regulate and increase speed of chemical reactions
– Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!)
© 2013 Pearson Education, Inc.
WITHOUT ENZYME WITH ENZYME
Activationenergy required
Less activationenergy required
ReactantsReactants
En
erg
y
En
erg
yProgress of reactionProgress of reaction
Product Product
Figure 2.20 Enzymes lower the activation energy
required for a reaction.
© 2013 Pearson Education, Inc.
Characteristics of Enzymes
• Some functional enzymes consist of two parts – Protein portion
– Cofactor (metal ion) or coenzyme (organic molecule often a vitamin)
• Enzymes are specific– Act on specific substrate
• Usually end in the suffix “- ”
• Often named for the reaction they catalyze– Hydrolases, oxidases
–
Enzyme Action
© 2013 Pearson Education, Inc.
Figure 2.21 Mechanism of enzyme action.
Substrates (S)e.g., amino acids
Active site
Energy isabsorbed;bond is formed.
Water isreleased.
Product (P)e.g., dipeptide
Peptidebond
Enzyme-substratecomplex (E-S)
Enzyme (E)
The enzyme releasesthe product of thereaction.
Substrates bind at active site, temporarily forming an enzyme-substrate complex.
The E-S complex undergoes internal rearrangements that form the product.
+
1 2
3
Slide 1
Enzyme (E)
Enzyme Action
Enzyme Action
Enzyme Action
Enzyme Reactants
Reactantsapproach enzyme
Reactantsbind to enzyme
Enzymechanges shape
Productsare released
Product
© 2013 Pearson Education, Inc.
Nucleic Acids
• Deoxyribonucleic acid ( ) and ribonucleic acid ( )– Largest molecules in the body
• Contain C, O, H, N, and P
• Polymers– Monomer = nucleotide
• a• a• a
Figure 2.23
Adenine (A)
Phosphate
Deoxyribose
Thymine (T) Cytosine (C) Guanine (G)
Nucleotides - The Building Blocks of DNA and RNA
© 2013 Pearson Education, Inc.
Deoxyribonucleic Acid (DNA)
• Utilizes four nitrogen bases: – Purines: Adenine (A), Guanine (G) – Pyrimidines: Cytosine (C), and Thymine (T)– Base-pair rule – each base pairs with its
complementary base • A always pairs with T; G always pairs with C
• Double-stranded helical molecule (double helix) in the cell nucleus
• Pentose sugar is deoxyribose• Provides instructions for protein synthesis• Replicates before cell division ensuring genetic
continuity
© 2013 Pearson Education, Inc.
PhosphateSugar:
DeoxyriboseBase:
Adenine (A) Thymine (T) Sugar Phosphate
Adenine nucleotide Thymine nucleotide
Hydrogenbond
Deoxyribosesugar
PhosphateSugar-phosphatebackbone
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
Figure 2.22 Structure of DNA.
Base pair
Phosphate
Sugar
Nucleotide
© 2013 Pearson Education, Inc.
Ribonucleic Acid (RNA)
• Four bases: – Adenine (A), Guanine (G), Cytosine (C), and
Uracil (U)
• Pentose sugar is ribose• Single-stranded molecule mostly active
outside the nucleus• Three varieties of RNA carry out the DNA
orders for protein synthesis– Messenger RNA (mRNA), transfer RNA
(tRNA), and ribosomal RNA (rRNA)
Phosphate
Ribose
Uracil
© 2013 Pearson Education, Inc.
ATP Carries Energy
Structure and function of adenosine triphosphate (ATP)Nucleotide – adenosine triphosphate
Universal energy source
Bonds between phosphate groups contain potential energy
Breaking the bonds releases energyATP → ADP + P + energy
© 2013 Pearson Education, Inc.
High-energy phosphatebonds can be hydrolyzedto release energy.
Adenine
Ribose
Phosphate groups
Adenosine
Adenosine monophosphate (AMP)
Adenosine triphosphate (ATP)
Adenosine diphosphate (ADP)
Figure 2.23 Structure of ATP (adenosine triphosphate).
© 2013 Pearson Education, Inc.
Function of ATP
• Phosphorylation – Phosphates are enzymatically transferred to
and energize other molecules – Such “primed” molecules perform cellular
work (life processes) using the phosphate bond energy
© 2013 Pearson Education, Inc.
Solute
Membraneprotein
+
Transport work: ATP phosphorylates transport proteins, activating them to transport solutes (ions, for example) across cell membranes.
Relaxed smoothmuscle cell
Contracted smoothmuscle cell
+
Mechanical work: ATP phosphorylates contractile pro-teins in muscle cells so the cells can shorten.
+
Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions.
Figure 2.24 Three examples of cellular work driven by energy from ATP.