Chemistry Comes...

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prepared by

Karen Dunbar Kareiva

Ivy Tech Community College© Annie Leibovitz/Contact Press Images

Chapter 2 Part B

Chemistry

Comes Alive

© 2017 Pearson Education, Inc.

Part 2 – Biochemistry

• Biochemistry is the study of chemical

composition and reactions of living matter

• All chemicals either organic or inorganic

– Inorganic compounds

• Water, salts, and many acids and bases

• Do not contain carbon

– Organic compounds

• Carbohydrates, fats, proteins, and nucleic acids

• Contain carbon, are usually large, and are covalently

bonded

• Both equally essential for life


2.6 Inorganic Compounds

Water

• Most abundant inorganic compound

– Accounts for 60%–80% of the volume of living

cells

• Most important inorganic compound because of

its properties

– High heat capacity

– High heat of vaporization

– Polar solvent properties

– Reactivity

– Cushioning© 2017 Pearson Education, Inc.

Water

• High heat capacity

– Ability to absorb and release heat with little

temperature change

– Prevents sudden changes in temperature

• High heat of vaporization

– Evaporation requires large amounts of heat

– Useful cooling mechanism


Water (cont.)

• Polar solvent properties

– Dissolves and dissociates ionic substances

– Forms hydration (water) layers around large

charged molecules

• Example: proteins

– Body’s major transport medium


Figure 2.12 Dissociation of salt in water.


d+

d+

d−

Water molecule

H

H

O

Na+

Na+

Cl− Cl−

Ions in

solutionSalt

crystal

Water (cont.)

• Reactivity

– Necessary part of hydrolysis and dehydration

synthesis reactions

• Cushioning

– Protects certain organs from physical trauma

• Example: cerebrospinal fluid cushions nervous system

organs


Salts

• Salts are ionic compounds that dissociate into

separate ions in water

– Separate into cations (positively charged

molecules) and anions (negatively charged)

• Not including H+ and OH– ions


Salts (cont.)

• Salts (cont.)

– All ions are called electrolytes because they

can conduct electrical currents in solution

– Ions play specialized roles in body functions

• Example: sodium, potassium, calcium, and iron

– Ionic balance is vital for homeostasis

– Common salts in body

• NaCl, CaCO3, KCl, calcium phosphates


Clinical – Homeostatic Imbalance 2.1

• Ionic balance is vital for homeostasis

• Kidneys play a big role in maintaining proper balance of electrolytes

• If electrolyte balance is disrupted, virtually all organ systems cease to function


Acids and Bases

• Acids and bases are both electrolytes

– Ionize and dissociate in water

• Acids

– Are proton donors: they release hydrogen

ions (H+), bare protons (have no electrons) in

solution

• Example: HCl → H+ + Cl–

– Important acids

• HCl (hydrochloric acid), HC2H3O2 (acetic acid,

abbreviated HAc), and H2CO3 (carbonic acid)


Acids and Bases (cont.)

• Bases

– Are proton acceptors: they pick up H+ ions in

solution

• Example: NaOH → Na+ + OH–

– When a base dissolves in solution, it releases a

hydroxyl ion (OH –)

– Important bases

• Bicarbonate ion (HCO3–) and ammonia (NH3)



• pH: Acid-base concentration

– pH scale is measurement of concentration of

hydrogen ions [H+] in a solution

– The more hydrogen ions in a solution, the more

acidic that solution is

– pH is negative logarithm of [H+] in moles per liter

that ranges from 0–14

– pH scale is logarithmic, so each pH unit

represents a 10-fold difference

• Example: a pH 5 solution is 10 times more acidic than

a pH 6 solution



• pH: Acid-base concentration (cont.)

– Acidic solutions have high [H+] but low pH

• Acidic pH range is 0–6.99

– Neutral solutions have equal numbers of H+ and

OH– ions

• All neutral solutions are pH 7

• Pure water is pH neutral

– pH of pure water = pH 7: [H+] = 10–7 m

– Alkaline (basic) solutions have low [H+] but high

pH

• Alkaline pH range is 7.01–14


Figure 2.13 The pH scale and pH values of representative substances.


Concentration (moles/liter)

[OH−] [H+] pH Examples

Neutral

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

Inc

rea

sin

gly

ac

idic

Inc

rea

sin

gly

ba

sic

1M Sodium

hydroxide (pH=14)

Oven cleaner, lye

(pH=13.5)

Household ammonia

(pH=10.5–11.5)

Household bleach

(pH=9.5)

Egg white (pH=8)

Blood (pH=7.4)

Milk (pH=6.3–6.6)

Black coffee (pH=5)

Wine (pH=2.5–3.5)

Lemon juice; gastric

juice (pH=2)

1M Hydrochloric

acid (pH=0)

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

10−14 100

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


• Neutralization

– Neutralization reaction: acids and bases are

mixed together

• Displacement reactions occur, forming water and a

salt

NaOH + HCl → NaCl + H2O



• Buffers

– Acidity involves only free H+ in solution, not H+

bound to anions

– Buffers resist abrupt and large swings in pH• Can release hydrogen ions if pH rises

• Can bind hydrogen ions if pH falls

– Convert strong acids or bases (completely

dissociated) into weak ones (slightly dissociated)

• Carbonic acid–bicarbonate system (important buffer

system of blood):


2.7 Organic Compounds: Synthesis and

Hydrolysis

• Organic molecules contain carbon

– Exceptions: CO2 and CO, which are inorganic

• Carbon is electroneutral

– Shares electrons; never gains or loses them

– Forms four covalent bonds with other elements

– Carbon is unique to living systems

• Major organic compounds: carbohydrates,

lipids, proteins, and nucleic acids


2.7 Organic Compounds: Synthesis and

Hydrolysis

• Many are polymers

– Chains of similar units called monomers

(building blocks)

• Synthesized by dehydration synthesis

• Broken down by hydrolysis reactions


Figure 2.14 Dehydration synthesis and hydrolysis.


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.

Monomers are released by the addition of a water molecule,

adding OH to one monomer and H to the other.

Hydrolysis

Monomer

1

Monomer

2

Monomers linked by covalent bond

H2O

H2O

Monomer

1

Monomer

2

Monomers linked by covalent bond

Example reactions

Dehydration synthesis of sucrose and its breakdown by hydrolysis

H2O

H2O

Glucose Fructose Sucrose

Water is

released

Water is

consumed

2.8 Carbohydrates

• Carbohydrates include sugars and starches

• Contain C, H, and O

– Hydrogen and oxygen are in 2:1 ratio

• Three classes

– Monosaccharides: one single sugar

• Monomers: smallest unit of carbohydrate

– Disaccharides: two sugars

– Polysaccharides: many sugars

• Polymers are made up of monomers of

monosaccharides


2.8 Carbohydrates

• Monosaccharides

– Simple sugars containing three to seven carbon

atoms

– (CH2O)n: general formula

• n = number of carbon atoms

– Monomers of carbohydrates

– Important monosaccharides

• Pentose sugars

– Ribose and deoxyribose

• Hexose sugars

– Glucose (blood sugar)


Figure 2.15a Carbohydrate molecules important to the body.


Glucose Fructose Galactose Deoxyribose Ribose

Monosaccharides

Monomers of carbohydrates

Example

Hexose sugars (the hexoses shown here are isomers)

Example

Pentose sugars

Carbohydrates (cont.)

• Disaccharides

– Double sugars

– Too large to pass through cell membranes

– Important disaccharides

• Sucrose, maltose, lactose

– Formed by dehydration synthesis of two

monosaccharides

• glucose + fructose → sucrose + water


Figure 2.15b Carbohydrate molecules important to the body.


Glucose Fructose Glucose Glucose Glucose

Maltose Lactose

Galactose

Sucrose

Disaccharides

Consist of two linked monosaccharides

Example

Sucrose, maltose, and lactose (these disaccharides are isomers)

Carbohydrates (cont.)

• Polysaccharides

– Polymers of monosaccharides

• Formed by dehydration synthesis of many monomers

– Important polysaccharides

• Starch: carbohydrate storage form used by plants

• Glycogen: carbohydrate storage form used by animals

– Not very soluble


Figure 2.15c Carbohydrate molecules important to the body.


*Notice that in Figure 2.15 the carbon (C) atoms present at the angles of the carbohydrate ring

structures are not illustrated and in Figure 2.15c only the oxygen atoms and one CH2 group

are shown. The illustrations at right give an example of this shorthand style: The full structure of

glucose is on the left and the shorthand structure on the right. This style is used for nearly all

organic ringlike structures illustrated in this chapter.

Glycogen

This polysaccharide is a simplified representation of

glycogen, a polysaccharide formed from glucose molecules.

Polysaccharides

Long chains (polymers) of linked monosaccharidesExample

2.9 Lipids

• Contain C, H, O, but less than in carbohydrates,

and sometimes contain P

• Insoluble in water

• Main types:

– Triglycerides or neutral fats

– Phospholipids

– Steroids

– Eicosanoids


Animation – Fats


Lipids (cont.)

• Triglycerides or neutral fats

– Called fats when solid and oils when liquid

– Composed of three fatty acids bonded to a

glycerol molecule

– Main functions

• Energy storage

• Insulation

• Protection


Lipids (cont.)

• Triglycerides can be constructed of:

– Saturated fatty acids

• All carbons are linked via single covalent bonds,

resulting in a molecule with the maximum number of H

atoms (saturated with H)

• Solid at room temperature (Example: animal fats,

butter)


Lipids (cont.)

– Unsaturated fatty acids

• One or more carbons are linked via double bonds,

resulting in reduced H atoms (unsaturated)

• Liquid at room temperature (Example: plant oils, such

as olive oil)

• Trans fats – modified oils; unhealthy

• Omega-3 fatty acids – “heart healthy”


Figure 2.16a Lipids.


Triglyceride formation

Three fatty acid chains are bound to glycerol by dehydration synthesis.

Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water

molecules

3H2O

Lipids (cont.)

• Phospholipids

– Modified triglycerides

• Glycerol and two fatty acids plus a phosphorus-

containing group

– “Head” and “tail” regions have different

properties

• Head is a polar region and is attracted to water

• Tails are nonpolar and are repelled by water

– Important in cell membrane structure


Figure 2.16b Lipids.


“Typical” structure of a phospholipid molecule

Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.

Example

Phosphatidylcholine

Polar “head”

2 fatty acid chains

(nonpolar “tail”)Glycerol

backbone

Phosphorus-containing

group (polar “head”)

Nonpolar “tail”

(schematic phospholipid)

Lipids (cont.)

• Steroids

– Consist of four interlocking ring structures

– Common steroids: cholesterol, vitamin D, steroid

hormones, and bile salts

– Most important steroid is cholesterol

• Is building block for vitamin D, steroid synthesis, and

bile salt synthesis

• Important in cell plasma membrane structure


Figure 2.16c Lipids.


Example

Cholesterol (cholesterol is the basis for all steroids

formed in the body)

Simplified structure of a steroid

Four interlocking hydrocarbon rings form a steroid.

Lipids (cont.)

• Eicosanoids

– Many different ones

– Derived from a fatty acid (arachidonic acid)

found in cell membranes

– Most important eicosanoids are prostaglandins

• Play a role in blood clotting, control of blood pressure,

inflammation, and labor contractions


2.10 Proteins

• Comprise 20–30% of cell mass

• Have most varied functions of any molecules

– Structural, chemical (enzymes), contraction

(muscles)

• Contain C, H, O, N, and sometimes S and P

• Polymers of amino acid monomers held

together by peptide bonds

• Shape and function due to four structural

levels


Amino Acids and Peptide Bonds

• All proteins are made from 20 types of amino

acids

– Joined by covalent bonds called peptide bonds

– Contain both an amine group and acid group

– Can act as either acid or base

– Differ by which of 20 different “R groups” is

present


Unnumbered Figure 2.2_page47


Amine

groupAcid

group

Figure 2.17 Amino acids are linked together by peptide bonds.


Amine

group

Acid

group

Amino acid Amino acid

Dehydration synthesis:

The acid group of one amino

acid is bonded to the amine

group of the next, with loss of

a water molecule.

Hydrolysis: Peptide bonds

linking amino acids together

are broken when water is

added to the bond.

H2O

H2O

Peptide

bond

Dipeptide

Structural Levels of Proteins

• Four levels of protein structure determine shape

and function

1. Primary: linear sequence of amino acids (order)

2. Secondary: how primary amino acids interact

with each other

• Alpha () helix coils resemble a spring

• Beta () pleated sheets resemble accordion ribbons

3. Tertiary: how secondary structures interact

4. Quaternary: how 2 or more different

polypeptides interact with each other


Figure 2.18a Levels of protein structure.


Amino acid Amino acid Amino acid Amino acid Amino acid

H

H

C C C C CN NH

H

H

H

H

H

H

H OOO

C C C C CN N N

R R

O RRR O

Primary structure

The sequence of

amino acids forms the

polypeptide chain.

Figure 2.18b Levels of protein structure.


Secondary structure

The primary chain forms

spirals (-helices) and

sheets (-sheets).

-Sheet: The primary chain

“zig-zags,” forming a “pleated”

sheet. Adjacent strands are held

together by hydrogen bonds.

-Helix: The primary chain is coiled

to form a spiral structure, which is

stabilized by hydrogen bonds.

Figure 2.18c Levels of protein structure.


Tertiary structure

Superimposed on secondary

structure. -Helices and/or -sheets

are folded up to form a compact

globular molecule held together by

intramolecular bonds.

Tertiary structure of transthyretin,

a protein that transports the thyroid

hormone thyroxine in blood and

cerebrospinal fluid.

Figure 2.18d Levels of protein structure.


Quaternary structure

Quaternary structure of a

functional transthyretin molecule.

Four identical transthyretin

subunits join to form a complex

protein.

Two or more polypeptide

chains, each with its own

tertiary structure, combine

to form a functional protein.

Animation – Introduction to Protein Structure


Fibrous and Globular Proteins

• Shapes of proteins fall into one of two

categories: fibrous or globular

1. Fibrous (structural) proteins

• Strandlike, water-insoluble, and stable

• Most have tertiary or quaternary structure (3-D)

• Provide mechanical support and tensile strength

• Examples: keratin, elastin, collagen (single most

abundant protein in body), and certain contractile

fibers


Fibrous and Globular Proteins (cont.)

2. Globular (functional) proteins

• Compact, spherical, water-soluble, and sensitive to

environmental changes

• Tertiary or quaternary structure (3-D)

• Specific functional regions (active sites)

• Examples: antibodies, hormones, molecular

chaperones, and enzymes


Protein Denaturation

• Denaturation: globular proteins unfold and lose

their functional 3-D shape

– Fibrous proteins are more stable

– Active sites become deactivated

• Can be caused by decreased pH (increased

acidity) or increased temperature

• Usually reversible if normal conditions restored

• Irreversible if changes are extreme

– Example: cannot undo cooking an egg


Enzymes and Enzyme Activity

• Enzymes: globular proteins that act as

biological catalysts

– Catalysts regulate and increase speed of

chemical reactions without getting used up in the

process

– Lower the energy needed to initiate a chemical

reaction

• Leads to an increase in the speed of a reaction

• Allows for millions of reactions per minute!


Enzymes and Enzyme Activity (cont.)

• Characteristics of enzymes

– Most functional enzymes, referred to as

holoenzymes, consist of two parts

• Apoenzyme (protein portion)

• Cofactor (metal ion) or coenzyme (organic molecule,

often a vitamin)

– Enzymes are specific

• Act on a very specific substrate

– Names usually end in –ase and are often named

for the reaction they catalyze

• Example: hydrolases, oxidases


Enzymes and Enzyme Activity (cont.)

• Enzyme action

– Enzymes lower activation energy, which is the

energy needed to initiate a chemical reaction

• Enzymes “prime” the reaction

– Enzymes allow chemical reactions to proceed

quickly at body temperatures

– Three steps are involved in enzyme action:

1. Substrate binds to enzyme’s active site, temporarily

forming enzyme-substrate complex

2. Complex undergoes rearrangement of substrate,

resulting in final product

3. Product is released from enzyme© 2017 Pearson Education, Inc.

Figure 2.19 Enzymes lower the activation energy required for a reaction.


Reactants

Product

Reactants

Product

Progress of reaction Progress of reaction

WITHOUT ENZYME WITH ENZYME

Less activation

energy required

Activation

energy

required

En

erg

y

En

erg

y

Figure 2.20 Mechanism of enzyme action.


Substrates (S)

e.g., amino acids

Energy is

absorbed;

bond is

formed.

Water is

released.

H2O

Peptide

bond

Product (P)

e.g., dipeptide

Enzyme (E)

Enzyme-substrate

complex (E-S)

Enzyme (E)

Active site

Substrates bind at

active site, temporarily

forming an enzyme-

substrate complex.

1 The E-S complex

undergoes internal

rearrangements that

form the product.

2

The enzyme

releases the

product of the

reaction.

3

Slide 1



Substrates (S)

e.g., amino acids

Enzyme (E)

Enzyme-substrate

complex (E-S)

Active site

Substrates bind at


forming an enzyme-

substrate complex.

1

Slide 2



Substrates (S)

e.g., amino acids

Energy is

absorbed;

bond is

formed.

Water is

released.

H2O

Enzyme (E)

Enzyme-substrate

complex (E-S)

Active site

Substrates bind at


forming an enzyme-

substrate complex.

1 The E-S complex

undergoes internal

rearrangements that

form the product.

2

Slide 3



Substrates (S)

e.g., amino acids

Energy is

absorbed;

bond is

formed.

Water is

released.

H2O

Peptide

bond

Product (P)

e.g., dipeptide

Enzyme (E)

Enzyme-substrate

complex (E-S)

Enzyme (E)

Active site

Substrates bind at


forming an enzyme-

substrate complex.

1 The E-S complex

undergoes internal

rearrangements that

form the product.

2

The enzyme

releases the

product of the

reaction.

3

Slide 4

2.11 Nucleic Acids

• Nucleic acids, composed of C, H, O, N, and P,

are the largest molecules in the body

• Nucleic acid polymers are made up of

monomers called nucleotides

– Composed of nitrogen base, a pentose sugar,

and a phosphate group

• Two major classes:

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)


2.11 Nucleic Acids

• DNA holds the genetic blueprint for the

synthesis of all proteins

– Double-stranded helical molecule (double helix)

located in cell nucleus

– Nucleotides contain a deoxyribose sugar,

phosphate group, and one of four nitrogen

bases:

• Purines: adenine (A), guanine (G)

• Pyrimidines: cytosine (C) and thymine (T)


2.11 Nucleic Acids

• DNA holds the genetic blueprint for the

synthesis of all proteins (cont.)

– Bonding of nitrogen base from strand to opposite

strand is very specific

• Follows complementary base-pairing rules:

– A always pairs with T

– G always pairs with C


Figure 2.21 Structure of DNA.


Phosphate

Adenine nucleotide Thymine nucleotide

Phosphate PhosphateSugarThymine (T)

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

P

P

A

A

G

A

T

T

T

C

G C

G C

A

A

G

G

A

Hydrogen

bond

Sugar-

phosphate

backbone

Deoxyribose

sugar

Sugar:

Deoxyribose

Base:

Adenine (A)

2.11 Nucleic Acids

• RNA links DNA to protein synthesis and is

slightly different from DNA

– Single-stranded linear molecule is active mostly

outside nucleus

– Contains a ribose sugar (not deoxyribose)

– Thymine is replaced with uracil

– Three varieties of RNA carry out the DNA orders

for protein synthesis

• Messenger RNA (mRNA), transfer RNA (tRNA), and

ribosomal RNA (rRNA)


Animation – DNA and RNA


2.12 ATP

• Chemical energy released when glucose is

broken down is captured in ATP (adenosine

triphosphate)

• ATP directly powers chemical reactions in cells

– Offers immediate, usable energy needed by

body cells

• Structure of ATP

– Adenine-containing RNA nucleotide with two

additional phosphate groups


Figure 2.22 Structure of ATP (adenosine triphosphate).


Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

Adenosine monophosphate (AMP)

Adenosine

Adenine

Ribose

Phosphate groups

P PP

High-energy phosphate

bonds can be hydrolyzed

to release energy.

2.12 ATP

• Terminal phosphate group of ATP can be

transferred to other compounds that can use

energy stored in phosphate bond to do work

– Loss of phosphate group converts ATP to ADP

– Loss of second phosphate group converts ADP

to AMP


Unnumbered Figure 2.3_page55


H2O

H2O

ATP ADP energyPi+ +

Figure 2.23 Three examples of cellular work driven by energy from ATP.


ATP

ATP

ATPADP

ADP

ADP

Pi

+

+

+

PiP

Pi

Pi

PiP

A B

Membrane

protein

Transport work: ATP phosphorylates transport

proteins, activating them to transport solutes

(ions, for example) across cell membranes.

Mechanical work: ATP phosphorylates

contractile proteins in muscle cells so the

cells can contract (shorten).

Chemical work: ATP phosphorylates key

reactants, providing energy to drive

energy-absorbing chemical reactions.

Relaxed smooth

muscle cell

Contracted smooth

muscle cell

Solute

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