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CHAPTER 2: The Chemistry
of Life
BIO 121
Chemistry is relevant…
(even if we don’t like it)
All people (and things) are made up of matter
Matter
Elements
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Everything is made up of matter…
• Matter? What’s the matter wit you?
– Anything that takes up space and has mass
• Many different forms of matter:
–
–
–
–
Rocks
Metals
Oils
Gases
Atoms Make Up All Matter
This dog, the water, and the air are all forms of matter. Section 2.1
Dog: © Photodisc/Getty Images RF
Atoms Make Up All Matter
Matter is any material that takes up space. Section 2.1
Dog: © Photodisc/Getty Images RF
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Atoms Make Up All Matter
The matter that makes up every object consists of one or more elements. Section 2.1
Dog: © Photodisc/Getty Images RF
Atoms Make Up All Matter
An element is a substance that cannot be broken down by chemical means into other substances. Section 2.1
Dog: © Photodisc/Getty Images RF
Atoms Make Up All Matter
The periodic table lists all of the known elements. Section 2.1
Figure 2.1
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Atoms Make Up All Matter
This abbreviated periodic table shows some of the most important elements in life. Section 2.1
Figure 2.1
Atoms Make Up All Matter
In a complete periodic table (like the one in Appendix D), each box contains four pieces of information: Section 2.1
Figure 2.1
Atoms Make Up All Matter
(1) The element’s full name. Section 2.1
Figure 2.1
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Atoms Make Up All Matter
(2) The element’s one‐letter symbol, like those in this abbreviated periodic table. Section 2.1
Figure 2.1
Atoms Make Up All Matter
(3) and (4): The element’s atomic number and atomic weight. To understand these, we first need to learn about protons, neutrons, and electrons. Section 2.1
Figure 2.1
Elements
• Fundamental substance
• Can’t be broken down into a simpler
substance
• Examples include – Carbon, Oxygen,
Hydrogen, Calcium, Gold, Iron, Silver
Image Source:http://education.jlab.org/qa/pen_number.html
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Atoms Make Up All Matter
This is an atom, the smallest piece of an element that retains the characteristics of the element. Section 2.1
Figure 2.2
Atoms Make Up All Matter
An atom is composed of three smaller particles: protons, neutrons, and electrons. Section 2.1
Figure 2.2
Atoms Make Up All Matter
Protons and neutrons are close together in the nucleus, which is the center of the atom. Section 2.1
Figure 2.2
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Atoms Make Up All Matter
Electrons surround the nucleus. They are very small and move very fast. Section 2.1
Figure 2.2
Atoms Make Up All Matter
Protons are positively charged, neutrons are neutral, and electrons are negatively charged. Section 2.1
Table 2.1
Atoms Make Up All Matter
An element’s atomic number indicates how many protons are in each atom of that element. Section 2.1
Figure 2.1
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Atoms Make Up All Matter
An atom’s mass number is the total number of protons and neutrons in its nucleus. The mass number of the atom shown below is 12.
Section 2.1
Figure 2.2
Atoms Make Up All Matter
The number of neutrons may vary among atoms of the same element. An isotope is any of these different forms of an element. Section 2.1
Figure 2.3
Atoms Make Up All Matter
Each isotope of an element therefore has a different mass number. Carbon isotopes have mass numbers of 12, 13, and 14. Section 2.1
Figure 2.3
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Atoms Make Up All Matter
An element’s atomic weight is the average mass of all isotopes of that element. Section 2.1
Figure 2.1
Atoms Make Up All Matter
Carbon’s atomic weight is close to 12, even though some carbon isotopes have an atomic mass of 13 and 14. This low atomic weight means that most carbon isotopes have an atomic mass of 12.
Section 2.1
Figure 2.1
Question #1
The atomic mass of nitrogen is very near 14, indicating that most nitrogen atoms have a mass number of 14. How many neutrons does the average nitrogen atom have?
A. 0
B. 7
C. 8
D. 14
E. Not enough information to determine. 9
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Answer
The atomic mass of nitrogen is very near 14, indicating that most nitrogen atoms have a mass number of 14. How many neutrons does the average nitrogen atom have?
A. 0
B. 7
C. 8
D. 14
E. Not enough information to determine. Flower: © Doug Sherman/Geofile/RF
Chemical Bonds Link Atoms
Atoms are organized into molecules. O
H
Each of these water molecules is a composite of two hydrogen atoms and one oxygen atom. H
O
H
H
Section 2.2
Molecules
• Two or more atoms held together by a bond
• Bonds are made between atoms by electron
interaction
• Types of bonds
– Covalent
– Ionic
– Hydrogen
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Chemical Bonds Link Atoms
Electrons determine bonding. The number and distribution of electrons around an atom determines whether atoms react with one another. Section 2.2
Figure 2.4
Chemical Bonds Link Atoms
Electrons exist in energy shells of various distances from the atom’s nucleus. The shell farthest from the nucleus is important for bonding.
Section 2.2
Figure 2.4
Chemical Bonds Link Atoms
Within each energy shell, electrons are arranged in pairs. Unpaired electrons form bonds with other atoms. Section 2.2
Figure 2.4
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Chemical Bonds Link Atoms
Atoms are most stable when their outer shells have no vacancies. Bonding with other atoms fills the vacancies. Section 2.2
Figure 2.4
Chemical Bonds Link Atoms
For example, carbon has four vacancies in its outer shell. Hydrogen has one vacancy. Section 2.2
Figure 2.7
Chemical Bonds Link Atoms
When four hydrogen atoms share their electrons with one carbon atom, all five atoms fill their outer energy shells. Section 2.2
Figure 2.7
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Chemical Bonds Link Atoms
The result is a methane molecule. Notice how the outer shells of the atoms overlap to form this molecule. Section 2.2
Figure 2.7
Chemical Bonds Link Atoms
When atoms share electrons, as in this methane molecule, covalent bonds are formed. Section 2.2
Figure 2.7
Chemical Bonds Link Atoms
Some covalent bonds, called double bonds, share four electrons between atoms. Section 2.2
Figure 2.8
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Chemical Bonds Link Atoms
Water forms by a similar process to methane. Water is held together by single covalent bonds. Each bond has two electrons. Section 2.2
Figure 2.7
Chemical Bonds Link Atoms
In methane, all atoms equally share electrons. In water, the oxygen atom pulls the electrons more strongly than the hydrogen atoms. Section 2.2
Chemical Bonds Link Atoms
Electronegativity is a measure of an atom’s ability to attract electrons. Section 2.2
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Water is a polar molecule
• Oxygen is more electronegative than hydrogen – shared electrons are pulled more toward oxygen
• Results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens
Chemical Bonds Link Atoms
Look at a periodic table to determine the relative electronegativity of two elements. Section 2.2
Figure 2.5
Chemical Bonds Link Atoms
The carbon and hydrogen atoms that make up methane have similar electronegativities. Neither pulls electrons much more strongly than the other. Section 2.2
Figure 2.5
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Chemical Bonds Link Atoms
Methane is therefore held together by nonpolar covalent bonds. Section 2.2
Figure 2.5
Chemical Bonds Link Atoms
The oxygen and hydrogen atoms of a water molecule have very different electronegativities. Oxygen attracts electrons more strongly than hydrogen. Section 2.2
Figure 2.5
Chemical Bonds Link Atoms
Since electrons spend more time near oxygen, the oxygen atom has a slightly negative charge. The hydrogen atoms have a slight positive charge. Section 2.2
Figure 2.9
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Chemical Bonds Link Atoms
The charge difference between oxygen and hydrogen in water gives the bonds polarity. A water molecule is held together by polar covalent bonds. Section 2.2
Figure 2.9
Chemical Bonds Link Atoms
The polarity of water molecules results in another bond type, called the hydrogen bond.
Section 2.2
Figure 2.9
Water © McGraw-Hill Education/Jacques Cornell Photographer
Chemical Bonds Link Atoms
The slight positive charge on the hydrogen atom of one water molecule attracts the slight negative charge on the oxygen of an adjacent water molecule. The result is a hydrogen bond. Section 2.2
Water © McGraw-Hill Education/Jacques Cornell Photographer
Figure 2.10
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Chemical Bonds Link Atoms
Hydrogen bonds give water unique properties, and they are important in protein and DNA structure. We will return to these ideas later in the lecture. Section 2.2
Water © McGraw-Hill Education/Jacques Cornell Photographer
Figure 2.10
Chemical Bonds Link Atoms
Some atoms have such different electronegativities that one atom completely pulls an electron from the other.
Section 2.2
Figure 2.5
Chemical Bonds Link Atoms
The atom that loses an electron is positively charged; the atom that gains an electron is negatively charged. This charge difference attracts the atoms to each other, forming an ionic bond.
Section 2.2
Figure 2.6
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Chemical Bonds Link Atoms
Notice that even in an ionic bond, both atoms achieve full outer energy shells. Section 2.2
Figure 2.6
Chemical Bonds Link Atoms
In summary, you can use electronegativity to make predictions about bonding. Section 2.2
Chemical Bonds Link Atoms
Two elements with similar electronegativities will likely form nonpolar covalent bonds.
Section 2.2
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Chemical Bonds Link Atoms
Two elements with moderately different electronegativities will likely form nonpolar covalent bonds.
Section 2.2
Chemical Bonds Link Atoms
Two elements with very different electronegativities will likely form ionic bonds.
Section 2.2
Question #2
Nitrogen has three vacancies in its outer electron shell. What type of bond might nitrogen form with hydrogen? How many hydrogen atoms would one nitrogen atom bind? (You might need to reference the electronegativity scale in Fig. 2.6.) A. ionic bond; 1 hydrogen atom
B. ionic bond; 3 hydrogen atoms
C. covalent bond; 1 hydrogen atom
D. covalent bond; 3 hydrogen atoms
E. hydrogen bond; 1 hydrogen atom
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ANSWER
Nitrogen has three vacancies in its outer electron shell. What type of bond might nitrogen form with hydrogen? How many hydrogen atoms would one nitrogen atom bind? (You might need to reference the electronegativity scale in Fig. 2.6.) A. ionic bond; 1 hydrogen atom
B. ionic bond; 3 hydrogen atoms
C. covalent bond; 1 hydrogen atom
D. covalent bond; 3 hydrogen atoms
E. hydrogen bond; 1 hydrogen atom
Flower: © Doug Sherman/Geofile/RF
Water Has Many Unique Properties
The hydrogen bonds that hold water molecules together give water unique properties. Section 2.3
Water Has Many Unique Properties
Water is cohesive
Cohesion is the tendency of water molecules to stick to one another. Section 2.3
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The molecule that supports all of life!
• Water!
• Required for all life
• Molecules of water participate in many chemical reactions necessary for life
• Most cells are surrounded by water, and are about 70‐
95% made of water
• ¾ of Earth is covered in water (ice, liquid and gas forms)
Water, what we know so far?
• 2 hydrogen’s, 1 oxygen
• Polar
• Forms hydrogen bonds with other water molecules
• 4 major properties of water that are important to life
Water Has Many Unique Properties
Water is cohesive
Cohesion between molecules on the surface of liquid water give it high surface tension.
Section 2.3
Water strider © Herman Eisenbeiss/Science Source
Figure 2.10
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Water Has Many Unique Properties
Water is adhesive
Water molecules also form hydrogen bonds with other molecules, a property called cohesion.
Section 2.3
Figure 2.11
Beach: © Getty Images/flickr RF
Water Has Many Unique Properties
Water is cohesive and adhesive
Together, cohesion and adhesion allow water molecules to “climb” from a tree’s roots to its highest leaves. Section 2.3
Figure 2.11
Beach: © Getty Images/flickr RF
Water Has Many Unique Properties
Water is a good solvent
Water dissolves hydrophilic (“water‐loving”) solutes.
‐ Polar solutes
‐ Ions
Section 2.3
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Water Has Many Unique Properties
Water is a good solvent
The polarity of water molecules helps water dissolve ions.
Section 2.3
Figure 2.12
Water Has Many Unique Properties
Water is a good solvent
The slight negative charge on water attracts positive charges (Na+). The slight positive charge on water attracts negative charges (Cl‐). Section 2.3
Figure 2.12
Water Has Many Unique Properties
Water is a good solvent
Water does not dissolve hydrophobic (“water‐fearing”) solutes.
‐ Nonpolar molecules, such as fats
Section 2.3
Butter: © D. Hurst/Alamy RF
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Water Has Many Unique Properties
Other characteristics of water
Water regulates temperature.
‐ Hydrogen bonds make water resist changes in temperature.
‐ Coastal regions have milder temperatures than landlocked regions.
‐ Sweating cools the body. Section 2.3
Water Has Many Unique Properties
Other characteristics of water
Water expands when it freezes.
‐ Ice is less dense than liquid water. ‐ Aquatic life survives the winter. Section 2.3
Figure 2.13
Water Has Many Unique Properties
Other characteristics of water
Water participates in chemical reactions. ‐ Photosynthesis
‐ Respiration
Section 2.3
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Question #3
Which property contributes to the high surface tension of water? A. hydrogen bonding
B. polar covalent bonds
C. cohesion
D. polar covalent bonds and cohesion
E. All of the choices are correct. ANSWER
Which property contributes to the high surface tension of water? A. hydrogen bonding
B. polar covalent bonds
C. cohesion
D. polar covalent bonds and cohesion
E. All of the choices are correct. Flower: © Doug Sherman/Geofile/RF
Organisms Balance Acids and Bases
The pH scale is based on the amount of H+ in a solution. Section 2.4
Figure 2.14
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Organisms Balance Acids and Bases
Acidic solutions have a low pH and a high H+ concentration.
Section 2.4
Figure 2.14
Organisms Balance Acids and Bases
Basic solutions have a high pH and a low H+ concentration. Bases have more OH‐ ions than H+ ions.
Section 2.4
Figure 2.14
Organisms Balance Acids and Bases
If an organism strays too far from its optimal pH, it could die. Buffer solutions help maintain a constant pH by consuming or releasing H+.
Section 2.4
Figure 2.14
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Question #4
Of the following, the most acidic solution is one with a(n): A. H+ concentration of 10‐2.
B. pH of 12.
C. H+ concentration of 10‐14.
D. higher OH‐ concentration than H+
concentration.
E. pH of 3.
ANSWER
Of the following, the most acidic solution is one with a(n): A. H+ concentration of 10‐2.
B. pH of 12.
C. H+ concentration of 10‐14.
D. higher OH‐ concentration than H+
concentration.
E. pH of 3.
Organic Molecules: Overview
H
H
C
H
An organic molecule contains both carbon and hydrogen. Methane is a simple organic molecule. H
Methane
Section 2.5
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Organic Molecules: Overview
H
H
C
H
H
Many organic molecules are categorized into four main types: ‐ Carbohydrates
‐ Proteins
‐ Nucleic acids
‐ Lipids
Methane
Section 2.5
Organic Molecules: Overview
Carbohydrates
Carbohydrates, proteins, and fats are common in our diets.
Proteins
Fats
Section 2.5
Proteins: © Comstock/Jupiter Images RF; Fried Chicken: © Burke/Triolo/Brand X Pictures RF
Organic Molecules: Overview
A monomer is a single unit of a carbohydrate, protein, or nucleic acid. Monomers join to form polymers. Section 2.5
Figure 2.31
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Organic Molecules: Overview
During dehydration synthesis, an enzyme binds two monomers, releasing a water molecule. Section 2.5
Figure 2.16
Organic Molecules: Overview
Hydrolysis is the reverse reaction of dehydration synthesis; it breaks polymers into monomers.
Section 2.5
Figure 2.16
Organic Molecules: Carbohydrates
Carbohydrates include simple sugars and polysaccharides. Monosaccharides are the monomers of carbohydrates.
Section 2.5
Figure 2.17
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Organic Molecules: Carbohydrates
Dehydration synthesis binds two monosaccharides, forming a disaccharide. Hydrolysis separates disaccharides into monosaccharides. Section 2.5
Figure 2.17
Organic Molecules: Carbohydrates
Polysaccharides are long chains of carbohydrates. Cellulose: structure
Starch: energy
Glycogen: energy
Section 2.5
Cellulose: © Dr. Dennis Kunkel; Starch: © Gary Gaugler/Visuals Unlimited; Glycogen: © Marshall Sklar/Science Source
Figure 2.17
Organic Molecules: Proteins
Proteins have more variable structures and functions than any of the other organic molecules. Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.20
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Organic Molecules: Proteins
The monomers of proteins are amino acids. All amino acids have the same general structure. Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.18
Organic Molecules: Proteins
The R group of amino acids is variable.
Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.18
Organic Molecules: Proteins
Dehydration synthesis binds two amino acids, forming a dipeptide. Hydrolysis separates dipeptides into amino acids. Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.18
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Organic Molecules: Proteins
The function of a protein depends on its shape. Protein structure is described on the next two slides.
Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.21
Organic Molecules: Proteins
Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.19
Organic Molecules: Proteins
Section 2.5
Proteins: © Comstock/Jupiter Images RF
Figure 2.19
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Organic Molecules: Nucleic Acids
Nucleic acids include DNA and RNA. These molecules contain genetic information. Section 2.5
Figure 2.23
Organic Molecules: Nucleic Acids
The monomers of nucleic acids are nucleotides.
Section 2.5
Figure 2.22
Organic Molecules: Nucleic Acids
There are five types of nucleotides. DNA and RNA both incorporate adenine, cytosine, and guanine into their strands. Only DNA uses thymine. Only RNA uses uracil.
Section 2.5
Figure 2.22
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Organic Molecules: Nucleic Acids
Dehydration synthesis links two nucleotides. Hydrolysis separates nucleotides. Section 2.5
Figure 2.22
Organic Molecules: Lipids
Lipids are hydrophobic and energy‐rich. This class of organic molecules includes triglycerides (fats) and sterols. Fried chicken: © Burke/Triolo/Brand X Pictures RF;
Butter: © D. Hurst/Alamy RF
Section 2.5
Figures 2.24, 2.26
Organic Molecules: Lipids
Unlike carbohydrates, proteins, and nucleic acids, lipids are not built from chains of monomers. Fried chicken: © Burke/Triolo/Brand X Pictures RF;
Butter: © D. Hurst/Alamy RF
Section 2.5
Figures 2.24, 2.26
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Organic Molecules: Lipids
Dehydration synthesis links three fatty acids to a glycerol molecule, forming a triglyceride. Hydrolysis separates fatty acids from glycerol. Fried chicken: © Burke/Triolo/Brand X Pictures RF;
Butter: © D. Hurst/Alamy RF
Section 2.5
Figures 2.24, 2.26
Organic Molecules: Lipids
All carbons of a saturated fatty acid are bonded to four other atoms. Saturated fat
Section 2.5
Fried chicken: © Burke/Triolo/Brand X Pictures (RF); Butter: © D. Hurst/Alamy (RF)
.
Figure 2.24
Organic Molecules: Lipids
An unsaturated fatty acid contains at least one double bond, so at least two carbons are only bonded to three other atoms.
Saturated fat
Section 2.5
Unsaturated fat
Fried chicken: © Burke/Triolo/Brand X Pictures (RF); Butter: © D. Hurst/Alamy (RF)
Figure 2.24
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Organic Molecules: Lipids
Double bonds create “kinks” in the fatty acids that prevent them from packing close together. Unsaturated fats like oils are therefore liquids. Section 2.5
Fried chicken: © Burke/Triolo/Brand X Pictures (RF); Butter: © D. Hurst/Alamy (RF)
Figure 2.24
Organic Molecules: Lipids
Trans fats have double bonds, like unsaturated fats, but remain straight. They therefore are solid at room temperature. Section 2.5
Fried chicken: © Burke/Triolo/Brand X Pictures RF; Butter: © D. Hurst/Alamy RF
Figure 2.25
Organic Molecules: Lipids
Sterols are also important lipid molecules. Cholesterol is in animal cell membranes; also, several hormones are derived from cholesterol. Section 2.5
Fried chicken: © Burke/Triolo/Brand X Pictures RF
Figure 2.28
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Question #5
Which monomer is incorrectly paired? A. protein: monopeptide
B. carbohydrate: monosaccharide
C. nucleic acid: nucleotide
D. lipid: no monomer
ANSWER
Which monomer is incorrectly paired? A. protein: monopeptide
B. carbohydrate: monosaccharide
C. nucleic acid: nucleotide
D. lipid: no monomer
Flower: © Doug Sherman/Geofile/RF
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