Chapter 2

Chemistry of Life

Mader, Sylvia S. Human Biology. 13th Edition. McGraw-Hill, 2014.

Points to ponder

• How are living things organized from atoms to molecules?

• What is pH and how is it important to living organisms?• What are the four macromolecules found in living

organisms?• What are the structure (subunits) and function of these 4

macromolecules?• How are proteins organized and how is their shape

important to their function?• How are DNA similar and how are they different?

Building blocks from large to small

• Matter is anything that has weight and takes up space

• Elements are the basic building blocks of matter that cannot be broken down by chemical means

• Atoms are the smallest units of an element that retain the element’s physical and chemical properties. These bond together to form molecules

• 90% of the human body is composed of 4 elements– Carbon, nitrogen, oxygen, and hydrogen

2.1 From atoms to molecules

Atoms• Atom symbol • Atomic mass

– Quantity of matter– Protons & Neutrons

• = 1 mass unit

– Electrons• = 0 mass units

• Atomic number– # of protons– When electrically neutral:

• # protons = # electrons

2.1 From atoms to molecules

Subatomic particles of atoms

• Neutrons have a neutral charge

• Protons are positively charged

• Neutrons and protons make up the nucleus

• Electrons are electrically charged and orbit around the nucleus

2.1 From atoms to molecules

Isotopes

• 2 or more elements with equal numbers of protons but different numbers of neutrons

Electron shell

p+ p+

p+n

n

n

e e e

(a) Hydrogen-1(electron-shell model)

(b) Hydrogen-2 deuterium

(c) Hydrogen-3, tritium

Isotopes• Radioactive isotopes

– Unstable isotopes break down/decay and release energy in the form of rays and subatomic particles

• Low Levels of Radiation– Useful in dating old objects,

imaging body organs and tissues through x-rays and killing cancer cells

• High Levels of Radiation– Harmful by damaging cells and

DNA and/or causing cancer

2.1 From atoms to molecules

Radiation therapy• Radiation therapy works by damaging the DNA of cells. • The damage is caused by a photon, electron, proton, neutron,

or ion beam directly or indirectly ionizing the atoms which make up the DNA chain.

• Cells have mechanisms for repairing DNA damage, breaking the DNA on both strands proves to be the most significant technique in modifying cell characteristics.

• Cancer cells generally are undifferentiated and stem cell-like, they reproduce more, and have a diminished ability to repair sub-lethal damage compared to most healthy differentiated cells.

• The DNA damage is inherited through cell division, accumulating damage to the cancer cells, causing them to die or reproduce more slowly.

Molecules:

• Are made of atoms that are bonded together

• Can be made of the same atom or different atoms

• If atoms are different = compound

2.1 From atoms to molecules

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

Figure 2–3a

- Atoms donate or take on electrons- Results in a stable outer shell- Occurs between particles that are charged (ions)

Covalent bonds:• Atoms in this type of bond share electrons• Results in a stable outer shell

2.1 From atoms to molecules

Covalent Bond

Hydrogen(H2)

Oxygen(O2)

CarbonDioxide

(CO2)

NitricOxide(NO)

MoleculeElectron-Shell Model and

Structural Formula

H–H

O=O

N=O

O=C=O

Free Radicals:Ion or molecule that contain unpaired electrons in the outermost shell. - Extremely Reactive -Typically enter into destructive reactions -Damage/destroy vital compounds

What are the properties of water?1. Liquid at room temperature due to hydrogen bonds2. Liquid water does not change temperature quickly

– Good temperature buffer since it absorbs heat3. High heat of vaporization

– Prevents body from overheating4. Frozen water is less dense than liquid water

– Ice acts as an insulator to prevent water below from freezing

5. Molecules of water cling together– Allow dissolved and suspended molecules to be evenly

distributed throughout a system• Example: Blood is 92% water and transports oxygen and nutrients to the body organs and removes wastes and CO2

6. A solvent for polar (charged) molecules – facilitates chemical reactions

7. Makes up 60-70% of the total body weight

What bond holds water molecules together?

• Hydrogen bonds occur between a hydrogen in a covalent bond anda negatively charged atom

• These are relatively weak bonds

2.2 Water and living things

Acids and bases

• Acids are substances that dissociate and release hydrogen (H+) atoms

• Bases are substances that take up hydrogen atoms or release

hydroxide (OH-) ions

2.2 Water and living things

What is the pH scale?

• A measure of hydrogen ion concentration

• Working scale is between 0 and 14 – 7 = neutral pH

• A pH below 7 is acidic

• A pH above 7 is basic

• The concentration of ions between each whole number is a factor of 10

2.2 Water and living things

pH Scale

Figure 2–9

• Has an inverse relationship with H+ concentration: – more H+ ions mean lower pH, less H+ ions

mean higher pH

Looking at the pH scale2.2 Water and living things

pH Scale• 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

• Buffers prevent pH changes:– Chemicals or combinations of chemicals that take up

excess H+ or OH-

– Example: In blood H+ + HCO3- H2CO3

OH- + H2CO3 HCO3- + H2O

Organic and Inorganic Molecules

• Organic: – molecules based on carbon and hydrogen

• Inorganic: – molecules not based on carbon and hydrogen

What organic molecules are found in living organisms?

• 1. Carbohydrates

• 2. Lipids

• 3. Proteins

• 4. Nucleic acids

2.3 Molecules of life

Making and breaking down organic molecules

• Dehydration reaction – the removal of water that allows subunits to link together into larger molecules

• Hydrolysis reaction – the addition of water that breaks larger molecules into their subunits

2.3 Molecules of life

How do we build and break down organic molecules?

2.3 Molecules of life

1. What are carbohydrates?

• Made of subunits called monosaccharides

• Made of C, H and O in which the H and O atoms are in a 2:1 ratio

• Function as short and long-term energy storage

• Found as simple and complex forms

2.4 Carbohydrates

What are simple carbohydrates?

• Monosaccharide – 1 carbon ring as found in glucose

• Disaccharide – 2 carbon rings asfound in maltose– 2 glucose molecules

2.4 Carbohydrates

What are complex carbohydrates?

• Polysaccharides made of many carbon rings

• Glycogen is the storage form of glucose in animals– Insulin promotes the

storage of glucose as glycogen

• Starch is the storage form of glucose in plants

2.4 Carbohydrates

Carbohydrate Functions

Table 2–5

PolysaccharidesGlycogen: made and stored in muscle cellsCellulose: structural component of plants -Ruminant Animals: Cattle, sheep, and deerCattle, sheep, and deer

The Ruminant StomachRuminant stomach is polygastric: four compartments

-Rumen -Reticulum

-Abomasum -Omasum

RumenOccupies 80% of the stomach

Muscular PillarContract to mix feed

Digest starch and fibersMicrobes produce VFA’s

Lined with Papillae

pH of 5.8-7.0Provide a suitable environment for bacteria and protozoa

2. What are lipids?

• Molecules that do not dissolve in water

• Used as energy molecules

• Found in cell membranes

• Found as fats and oils, phospholipids and steroids

2.5 Lipids

How are fats and oils different?

• Fats• Usually animal origin• Solid at room temperature• Function as long-term energy storage, insulation from

heat loss and cushion for organs

• Oils• Usually plant origin• Liquid at room temperature

2.5 Lipids

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 resulting in cardiovascular disease• Butter

– Unsaturated: liquid at room temp.• Healthier• Cooking oils and margarines

• Trans-Fatty Acids: semi-solid– Partially hydrogenated

Figure 2–13

The structure of a Fat Molecule

• A glycerol molecule and 3 fatty acid tails• Fat molecule = triglyceride

2.5 Lipids

Phospholipids and GlycolipidsCombination Lipids

Figure 2–17a, b

Diglyceride

Cell Membranes are Composed of these lipids

Hydrophilic

Hydrophobic

Phospholipids Vs. GlycolipidsCombination Lipids

Figure 2–17c

Understanding fats when reading a nutrition label

• Recommendation for total amount of fat for a 2,000 calorie diet is 65g

• Be sure to know how many servings there are

• A % DV of 5% or less is low and 20% or more is high

• Try to stay away from trans fats

• Would you eat the food on the right? Why or why not?

2.5 Lipids

What are steroids?

• A lipid

• Structure is four fused carbon rings

• Examples are cholesterol and sex hormones

2.5 Lipids

3. Protein

• Proteins are the 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

• 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: – control anatomical structure and physiological

function– determine cell shape and tissue properties– perform almost all cell functions

Amino Acid Structure

1. central carbon

2. hydrogen

3. amino group (—NH2)

4. carboxylic acid group (—COOH)

5. variable side chain or R group

Figure 2-18

What do amino acids look like?2.6 Proteins

Peptide Bond

• A dehydration synthesis between:– amino group of 1

amino acid– and the carboxylic acid

group of another amino acid

– producing a peptide

What are the four levels of protein organization?

• Primary – linear order of amino acids

• Secondary – localized folding into pleated sheets and helices

• Tertiary – the 3-D shape of the entire protein in space

• Quaternary – combination of more than one polypeptide

• All proteins have primary, secondary and tertiary structure, while only a few have quaternary structure

2.6 Proteins

Figure 2–20a

Primary Structure

• Polypeptide:– Linear sequence of amino acids

• How many amino acids were bound together• What order they are bound

Secondary Structure

Figure 2–20b

• Hydrogen bonds form spirals or pleats

Figure 2–20c

Tertiary Structure

• Secondary structure folds into a unique shape

• Global coiling or folding due to R group interaction

Quaternary Structure

Figure 2–20d

• Final protein shape: – several tertiary structures together

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

4. What are nucleic acids?

• Made of nucleotide subunits

• Function in the cell to make proteins

• Includes DNA and RNA – DNA deoxyribonucleic acid– RNA ribonucleic acid

2.7 Nucleic acids

DNA and RNA

DNA• Determines inherited characteristics• Directs protein synthesis• Controls enzyme production• Controls metabolismRNA• Codes intermediate steps in protein

synthesis

KEY CONCEPT

• DNA in the cell nucleus contains the information needed to construct all of the proteins in the body

Nucleotides

• Are the building blocks of DNA

• Have 3 molecular parts: – sugar (deoxyribose)– phosphate group– nitrogenous base (A, G, T, C)

What are the 3 parts of a nucleotide?

2.7 Nucleic acids

The Bases

Figure 2–22b, c

RNA and DNA

• RNA: – a single strand

• DNA: – a double helix joined at bases by hydrogen

bonds

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

Summary of DNA and RNA structural differences?

• DNA– Sugar is deoxyribose– Bases include A, T, C

and G– Double stranded

• RNA– Sugar is ribose– Bases include A, U, C

and G– Single stranded

2.7 Nucleic acids

Figure 2–24

ATP: An Energy Carrier

Adenosine triphosphate (ATP): – Adenine + ribose + 3 phosphate groups (tri=3)

• Chemical energy stored in phosphate bonds

Summary of the macromolecules