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Chapter 2: The Chemical Level of Organization. Introduction to Chemistry. Matter is made up of atoms Atoms join together to form chemicals with different characteristics Chemical characteristics determine physiology at the molecular and cellular level. Atomic Particles. Proton :

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introduction to chemistry
Introduction to Chemistry
  • Matter is made up of atoms
  • Atoms join together to form chemicals with different characteristics
  • Chemical characteristics determine physiology at the molecular and cellular level
atomic particles
Atomic Particles
  • Proton:
    • positive, 1 mass unit
  • Neutron:
    • neutral, 1 mass unit
  • Electron:
    • negative, low mass
particles and mass
Particles and Mass
  • Atomic number:
    • number of protons
  • Mass number:
    • number of protons plus neutrons
  • Atomic weight:
    • exact mass of all particles (daltons)
isotopes

Electron

shell

n

p+

e

p+

e

e

n

+

n

p

(c) Hydrogen-3,

tritium

Hydrogen-1

(electron-shell model)

(b) Hydrogen-2

deuterium

Isotopes
  • 2 or more elements with equal numbers of protons but different numbers of neutrons
molecules and compounds
Molecules and Compounds
  • Molecules:
    • atoms joined by strong bonds
  • Compounds:
    • atoms joined by strong or weak bonds
chemical bonds
Chemical Bonds
  • Ionic bonds:
    • attraction between cations (+) and anions (-)
  • Covalent bonds:
    • strong electron bonds
    • Non polar covalent bonds: equal sharing of electrons
    • Polar covalent bonds: unequal sharing of electrons
  • Hydrogen bonds:
    • weak polar bonds
ionic bonds
Ionic Bonds

Are atoms with positive or negative charge

Figure 2–3a

covalent bond
Formed between atoms that share electrons

Electron-Shell Model and

Structural Formula

Molecule

Hydrogen

(H2)

H–H

Oxygen

(O2)

O=O

Carbon

Dioxide

(CO2)

O=C=O

Nitric

Oxide

(NO)

N=O

Covalent Bond

Free Radicals:

Ion or molecule that

contain unpaired

electrons in the outermost

shell.

- Extremely Reactive

-Typically enter into

destructive reactions

-Damage/destroy vital

compounds

hydrogen bonds
Hydrogen Bonds
  • Attractive force between polar covalent molecules
  • Weak force that holds molecules together
  • Hydrogen bonds between H2O molecules cause surface tension

Figure 2–6

slide13

How is it possible for two samples of hydrogen to contain the same number of atoms, yet have different weights?

A.One sample has more bonds.

B. One sample contains fewer electrons, decreasing weight.

C. One sample contains more of hydrogen’s heavier isotope(s).

D. One sample includes more protons, increasing weight.

slide14

Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why?

A. Neon has 8 electrons in its valence shell, oxygen has only 6.

B. Neon cannot undergo bonding due to its polarity.

C. Neon is exergonic.

D. Neon’s molecular weight is too low to allow bonding.

slide15

Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why?

A. Neon has 8 electrons in its valence shell, oxygen has only 6.

B. Neon cannot undergo bonding due to its polarity.

C. Neon is exergonic.

D. Neon’s molecular weight is too low to allow bonding.

slide16

Which kind of bond holds atoms in a water molecule together? What attracts water molecules to one another?

A. polar covalent bonds; hydrogen bonds

B. ionic bonds; charge interactions

C. hydrogen bonds; charge interactions

D. covalent bonds; hydrogen bonds

energy
Energy
  • Energy:
    • the capacity to do work
  • Work:
    • a change in mass or distance
forms of energy
Forms of Energy
  • Kinetic energy:
    • energy of motion
  • Potential energy:
    • stored energy
  • Chemical energy:
    • potential energy stored in chemical bonds

When energy is exchanged, heat is produced

- cells cannot capture it or use it for work

break down build up
Break Down, Build Up
  • Decomposition reaction(catabolism):

AB A + B

  • Synthesis reaction(anabolism):

A + B AB

  • Exchange reaction(reversible):

AB + CD AD + CB

If Water is Involved:

  • Hydrolysis:

A—B—C—D—E + H2O A—B—C—H + HO—D—E

  • Dehydration synthesis(condensation):

A—B—C—H + HO—D—E A—B—C—D—E + H2O

key concept
KEY CONCEPT
  • Reversible reactions seek equilibrium, balancing opposing reaction rates
  • Add or remove reactants:
    • reaction rates adjust to reach a new equilibrium
activation energy
Activation Energy
  • Chemical reactions in cells cannot start without help
  • Activation energy gets a reaction started

Figure 2–7

materials in reactions
Materials in Reactions
  • Reactants:
    • materials going into a reaction
  • Products:
    • materials coming out of a reaction
  • Enzymes:
    • proteins that lower the activation energy of a reaction
energy in energy out
Energy In, Energy Out
  • Exergonic reactions:
    • produce more energy than they use
    • Heat will be the by-product
  • Endergonic reactions:
    • use more energy than they produce
  • Most chemical reactions that sustain life cannot occur unless the right enzymes are present
slide26

In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy.

How would you classify this reaction?

A. endergonic

B. exergonic

C. decomposition

D.B and C

slide27

In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy.

How would you classify this reaction?

A. endergonic

B. exergonic

C. decomposition

D.B and C

slide28

Why are enzymes needed in our cells?

A. to promote chemical reactions

B. for chemical reactions to proceed

under conditions compatible with

life

C. to lower activation energy

requirements

D. all of the above

organic and inorganic molecules
Organic and Inorganic Molecules
  • Organic:
    • molecules based on carbon and hydrogen
  • Inorganic:
    • molecules not based on carbon and hydrogen
essential molecules
Essential Molecules
  • Nutrients:
    • essential molecules obtained from food
  • Metabolites:
    • molecules made or broken down in the body
properties of water
Properties of Water
  • Solubility:
    • water’s ability to dissolve a solute in a solvent to make a solution
  • Reactivity:
    • most body chemistry uses or occurs in water
  • High heat capacity:
    • water’s ability to absorb and retain heat
  • Lubrication:
    • to moisten and reduce friction

Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids

aqueous solutions
Aqueous Solutions

Polar water molecules form hydration

spheres around ions and small polar molecules

to keep them in solution

Figure 2–8

electrolytes
Electrolytes
  • Inorganic ions: conduct electricity in solution
  • Electrolyte imbalance seriously disturbs vital body functions
molecules and water
Molecules and Water
  • Hydrophilic:
    • hydro = water, philos = loving
    • reacts with water
  • Hydrophobic:
    • phobos = fear
    • does not react with water
solutions
Solutions
  • Suspension:
    • a solution in which particles settle (sediment)
  • Concentration:
    • the amount of solute in a solvent (mol/L, mg/mL)
ph neutral acid or base
pH: Neutral, Acid, or Base?
  • pH:
    • the concentration of hydrogen ions (H+) in a solution
  • Neutral pH:
    • a balance of H+ and OH—
    • pure water = 7.0
  • Acid(acidic): pH lower than 7.0
    • high H+ concentration, low OH— concentration
  • Base(basic): pH higher than 7.0
    • low H+ concentration, high OH— concentration
ph scale
pH Scale
  • Has an inverse relationship with H+ concentration:
    • more H+ ions mean lower pH, less H+ ions mean higher pH

Figure 2–9

key concept41
KEY CONCEPT
  • pH of body fluids measures free H+ ions in solution
  • Excess H+ ions (low pH): Acidosis
    • damages cells and tissues
    • alters proteins
    • interferes with normal physiological functions
  • Excess OH— ions (high pH): Alkalosis
    • Uncontrollable and sustained skeletal muscle contractions
controlling ph
Controlling pH
  • Salts:
    • positive or negative ions in solution
    • contain no H+ or OH— (NaCl)
  • Buffers:
    • weak acid/salt compounds
    • neutralizes either strong acid or strong base
slide43

Why does a solution of table salt conduct electricity, but a sugar solution does not?

A.Electrical conductivity requires ions.

B. Sugar forms a colloid, salt forms a suspension.

C. Electricity is absorbed by glucose molecules.

D. Table salt is hydrophobic, sugar is hydrophilic.

slide44

How does an antacid help decrease stomach discomfort?

A.by reducing buffering capacity of the stomach

B. by decreasing pH of stomach contents

C. by reacting a weak acid with a stronger one

D. by neutralizing acid using a weak base

functional groups of organic compounds
Functional Groups of Organic Compounds
  • Molecular groups which allow molecules to interact with other molecules

Table 2–4

carbohydrates
Carbohydrates
  • Consist of C:H:O in 1:2:1 ratio

1. Monosaccharides:

    • simple sugars with 3 to 7 carbon atoms (glucose)
      • Glucose: important metabolic fuel

2. Disaccharides:

    • 2 simple sugars condensed by dehydration synthesis (sucrose)
simple sugars
Simple Sugars
  • Structural Formula:
  • Straight-chain form
  • Ring from
  • 3-D
  • Isomers: Glucose vs. Fructose:
  • - Same chemical formula
  • but different shape

Figure 2–10

polysaccharides
Polysaccharides
  • Chains of many simple sugars (glycogen)
  • Formation:
    • Dehydration synthesis
  • Breakdown:
    • Hydrolysis synthesis

Glycogen: made and stored in muscle cells

Figure 2–12

carbohydrate functions
Carbohydrate Functions

Polysaccharides

Glycogen: made and stored in muscle cells

Cellulose: structural component of plants

-Ruminant Animals: Cattle, sheep, and deer

Table 2–5

slide51

The Ruminant Stomach

Ruminant stomach is polygastric: four compartments

-Rumen -Reticulum

-Abomasum -Omasum

rumen
Rumen
  • Occupies 80% of the stomach
  • Muscular Pillar
    • Contract to mix feed
  • Digest starch and fibers
    • Microbes produce VFA’s
  • Lined with Papillae
  • pH of 5.8-7.0
    • Provide a suitable environment for bacteria and protozoa
key concept53
KEY CONCEPT
  • Carbohydrates are quick energy sources and components of membranes
  • Lipids have many functions, including membrane structure and energy storage
    • Provides 2x more energy then carbohydrates
lipids
Lipids
  • Mainly hydrophobic molecules such as fats, oils, and waxes
  • Made mostly of carbon and hydrogen atoms (1:2), and some oxygen
    • Less oxygen then carbon
classes of lipids
Classes of Lipids
  • Fatty acids
  • Eicosanoids
  • Glycerides
  • Steroids
  • Phospholipids and glycolipids
fatty acids
Carboxyl group -COOH

Hydrophilic

Hydrocarbon tail:

Hydrophobic

Longer tail = lower solubility

Saturated vs. Unsaturated

Saturated: solid at room temp.

Cause solid plaques in arteries

Unsaturated: liquid at room temp.

Healthier

Fatty Acids

Figure 2–13

eicosanoids
Eicosanoids
  • Used for cellular communication
  • Never burned for energy

1. Leukotrienes:

    • active in immune system
    • Used by cells to signal injury

2. Prostaglandins: local hormones

    • Used for cell-to-cell signaling to coordinate events
steroids
Steroids
  • 4 carbon ring with attached carbon chains
  • Not burned for energy

Figure 2–16

types of steroids
Types of Steroids
  • Cholesterol:
    • cell membrane formation and maintenance, cell division, and osmotic stability
  • Estrogens and testosterone:
    • Regulation of sexual function
  • Corticosteroids and calcitrol:
    • Tissue metabolism and mineral balance
  • Bile salts:
    • Processing of dietary fats
glycerides
Glycerides
  • Glycerides: are the fatty acids attached to a glycerol molecule
  • Triglyceride: are the 3 fatty-acid tails, fat storage molecule
  • Fat Deposits are Important
  • Energy Storage
  • Insulation
  • Mechanical Protection
    • -Knees and Eye Sockets

Figure 2–15

phospholipids vs glycolipids combination lipids
Phospholipids Vs. GlycolipidsCombination Lipids

Cell Membranes are Composed of these lipids

Hydrophilic

Diglyceride

Hydrophobic

Figure 2–17a, b

phospholipids vs glycolipids combination lipids62
Phospholipids Vs. GlycolipidsCombination Lipids

Spontaneous formation of Micelle

Figure 2–17c

5 lipid types
5 Lipid Types

Table 2–6

slide64

A food contains organic molecules with the elements C, H, and O in a ratio of 1:2:1. What class of compounds do these molecules belong to, and what are their major functions in the body?

A.lipids; energy source

B. proteins; support and movement

C. nucleic acids; determining inherited characteristics

D. carbohydrates; energy source

slide65

When two monosaccharides undergo a dehydration synthesis reaction, which type of molecule is formed?

A.polypeptide

B. disaccharide

C. eichosanoid

D. polysaccharide

slide66

Which kind of lipid would be found in a sample of fatty tissue taken from beneath the skin?

A.eichosanoid

B. steroid

C. triglyceride

D. phospholipid

slide67

Which lipids would you find in human cell membranes?

A.cholesterol

B. glycolipids

C. phospholipids

D. all of the above

protein structure
Protein Structure
  • Proteins arethe most abundant and important organic molecules
  • Basic elements:
    • carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)
  • Basic building blocks:
    • 20 amino acids
protein functions
Protein Functions
  • 7 major protein functions:
    • support: structural proteins
    • movement: contractile proteins
    • transport: transport proteins
    • buffering: regulation of pH
    • metabolic regulation: enzymes
    • coordination and control: hormones
    • defense: antibodies
proteins
Proteins
  • Proteins:
    • control anatomical structure and physiological function
    • determine cell shape and tissue properties
    • perform almost all cell functions
amino acid structure
central carbon

hydrogen

amino group (—NH2)

carboxylic acid group (—COOH)

variable side chain or R group

Amino Acid Structure

Figure 2-18

peptide bond
A dehydration synthesis between:

amino group of 1

amino acid

and the carboxylic acid group of another amino acid

producing a peptide

Peptide Bond
primary structure
Primary Structure
  • Polypeptide:
    • Linear sequence of amino acids
      • How many amino acids were bound together
      • What order they are bound

Figure 2–20a

secondary structure
Secondary Structure
  • Hydrogen bonds form spirals or pleats

Figure 2–20b

tertiary structure
Tertiary Structure
  • Secondary structure folds into a unique shape
  • Global coiling or folding due to R group interaction

Figure 2–20c

quaternary structure
Quaternary Structure
  • Final protein shape:
    • several tertiary structures together
  • Fibrous proteins:
    • - structural sheets
  • Globular proteins:
    • - soluble spheres
    • with active functions

Figure 2–20d

shape and function
Shape and Function
  • Protein function is based on shape
  • Shape is based on sequence of amino acids
  • Denaturation:
    • loss of shape and function due to heat or pH
enzymes
Enzymes
  • Enzymes are catalysts:
    • proteins that lower the activation energy of a chemical reaction
    • are not changed or used up in the reaction
how enzymes work
How Enzymes Work

Substrates: reactants in enzymatic reactions

Active site: location on an enzyme that fits a

particular substrate

Figure 2–21

enzyme helpers
Enzyme Helpers
  • Cofactor:
    • an ion or molecule that binds to an enzyme before substrates can bind
  • Coenzyme:
    • nonprotein organic cofactors (vitamins)
  • Isozymes:
    • 2 enzymes that can catalyze the same reaction
enzyme characteristics
Enzyme Characteristics
  • Specificity:
    • one enzyme catalyzes one reaction
  • Saturation limits:
    • an enzyme’s maximum work rate
  • Regulation:
    • the ability to turn off and on
conjugated protein
Conjugated Protein
  • Glycoproteins:
    • large protein + small carbohydrate
      • includes enzymes, antibodies, hormones, and mucus production
  • Proteoglycans:
    • large polysaccharides + polypeptides
      • promote viscosity
slide83

Proteins are chains of which small organic molecules?

A.saccharides

B. fatty acids

C. amino acids

D. nucleic acids

slide84

Which level of protein structure would be affected by an agent that breaks hydrogen bonds?

A.the primary level of protein structure

B. the secondary level of protein structure

C. the tertiary level of protein structure

D. the protein structure would NOT be affected by this agent

slide85

Why does boiling a protein affect its structural and functional properties?

A.Heat denatures the protein, causing unfolding.

B. Heat causes the formation of additional quaternary structure.

C. Heating rearranges the primary structure of the protein.

D. Heat alters the radical groups on the amino acids.

slide86

Why does boiling a protein affect its structural and functional properties?

A.Heat denatures the protein, causing unfolding.

B. Heat causes the formation of additional quaternary structure.

C. Heating rearranges the primary structure of the protein.

D. Heat alters the radical groups on the amino acids.

slide87

How might a change in an enzyme’s active site affect its functions?

A.increased activity due to a better fit with the substrate

B. decreased activity due to a poor substrate fit

C. inhibited activity due to no substrate fit

D. all of the above

nucleic acids
NucleicAcids
  • C, H, O, N, and P
  • Large organic molecules, found in the nucleus, which store and process information at the molecular level
  • DNA – deoxyribonucleic acid
  • RNA – ribonucleic acid
dna and rna
DNA and RNA

DNA

  • Determines inherited characteristics
  • Directs protein synthesis
  • Controls enzyme production
  • Controls metabolism

RNA

  • Codes intermediate steps in protein synthesis
key concept90
KEYCONCEPT
  • DNA in the cell nucleus contains the information needed to construct all of the proteins in the body
nucleotides
Nucleotides
  • Are the building blocks of DNA
  • Have 3 molecular parts:
    • sugar (deoxyribose)
    • phosphate group
    • nitrogenous base (A, G, T, C)
the bases
The Bases

Figure 2–22b, c

complementary bases
Complementary Bases
  • Purines pair with pyrimidines:
      • DNA:
        • adenine (A) and thymine (T)
        • cytosine (C) and guanine (G)
      • RNA:
        • uracil (U) replaces thymine (T)
rna and dna
RNA and DNA
  • RNA:
    • a single strand
  • DNA:
    • a double helix joined at bases by hydrogen bonds
protein synthesis three forms of rna
Protein Synthesis:Three forms of RNA
  • messenger RNA (mRNA)
    • Protein blueprint or instructions
  • transfer RNA (tRNA)
    • Carry amino acids to the place where proteins are being synthesized
  • ribosomal RNA (rRNA)
    • Forms the site of protein synthesis in the cell
      • Factory = ribosomes
high energy compounds adp and atp
High-Energy Compounds:ADP and ATP

- Assembled using RNA Nucleotides

- Bonds are broken easily by cells to release energy as needed

  • During digestion and cellular respiration:
    • energy from food is transferred to high energy compounds for quick and easy access.
adp to atp phosphorylation
ADP to ATP:Phosphorylation

ADP vs. ATP:

  • adenosine diphosphate(ADP):
    • 2 phosphate groups (di = 2)
  • adenosine triphosphate(ATP):
    • 3 phosphate groups (tri = 3)

Adding a phosphate group to ADP with a high-energy bound to form the high-energy compound ATP

  • ATPase:
    • the enzyme that catalyzes phophorylation
the energy molecule
The Energy Molecule
  • Chemical energy stored in phosphate bonds

Figure 2–24

slide99

A large organic molecule composed of the sugar ribose, nitrogenous bases, and phosphate groups is which kind of nucleic acid?

A.DNA

B. ATP

C. tRNA

D. RNA

slide100

What molecule is produced by the phosphorylation of ADP?

A.ATPase

B. ATP

C. Adenosine Diphosphate

D. Uridine Triphosphate

summary
SUMMARY
  • Atoms, molecules, and chemical bonds control cellular physiology
  • Metabolism and energy work within the cell
  • Importance of organic and inorganic nutrients and metabolites
summary103
SUMMARY
  • Role of water and solubility in metabolism and cell structure
  • Chemistry of acids and bases, pH and buffers
  • Structure and function of carbohydrates, lipids, proteins, and nucleic acids