Chemistry of Life

1
Chapter 2

• Chemistry of Life

2
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?

3
Building blocks from large to small
2.1 From atoms to molecules

• 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 elements 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

4
Atoms
2.1 From atoms to molecules

• 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

5
Subatomic particles of atoms
2.1 From atoms to molecules

• 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

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Isotopes

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

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Isotopes
2.1 From atoms to molecules

• 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

8
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.

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Molecules
2.1 From atoms to molecules

• Are made of atoms that are bonded together
• Can be made of the same atom or different atoms
• If atoms are different compound

10
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

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Ionic Bonds
- Atoms donate or take on electrons - Results
in a stable outer shell - Occurs between
particles that are charged (ions)
Figure 23a
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Covalent bonds
2.1 From atoms to molecules

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

13
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
14
What are the properties of water?

• 1. Liquid at room temperature due to hydrogen
  bonds
• 2. Liquid water does not change temperature
  quickly
• Good temperature buffer since it absorbs heat
• 3. High heat of vaporization
• Prevents body from overheating
• 4. 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

15
What bond holds water molecules together?
2.2 Water and living things

• Hydrogen bonds occur between a hydrogen in a
  covalent bond anda negatively charged atom
• These are relatively weak bonds

16
Acids and bases
2.2 Water and living things

• Acids are substances that dissociate and release
  hydrogen (H) atoms
• Bases are substances that take up hydrogen atoms
  or release
• hydroxide (OH-) ions

17
What is the pH scale?
2.2 Water and living things

• 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

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pH Scale

• Has an inverse relationship with H
  concentration
• more H ions mean lower pH, less H ions mean
  higher pH

Figure 29
19
Looking at the pH scale
2.2 Water and living things
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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

21
Organic and Inorganic Molecules

• Organic
• molecules based on carbon and hydrogen
• Inorganic
• molecules not based on carbon and hydrogen

22
What organic molecules are found in living
organisms?
2.3 Molecules of life

• 1. Carbohydrates
• 2. Lipids
• 3. Proteins
• 4. Nucleic acids

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Making and breaking down organic molecules
2.3 Molecules of life

• 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

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How do we build and break down organic molecules?
2.3 Molecules of life
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1. What are carbohydrates?
2.4 Carbohydrates

• Made of subunits called monosaccharides
• Made of C, H and O in which the H and O atoms are
  in a 21 ratio
• Function as short and long-term energy storage
• Found as simple and complex forms

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What are simple carbohydrates?
2.4 Carbohydrates

• Monosaccharide 1 carbon ring as found in
  glucose
• Disaccharide 2 carbon rings asfound in maltose
• 2 glucose molecules

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What are complex carbohydrates?
2.4 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

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Carbohydrate Functions
Polysaccharides Glycogen made
and stored in muscle cells Cellulose structural
component of plants -Ruminant Animals
Cattle, sheep, and deer
Table 25
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The Ruminant Stomach
Ruminant stomach is polygastric four
compartments -Rumen
-Reticulum -Abomasum
-Omasum
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Rumen

• Occupies 80 of the stomach
• Muscular Pillar
• Contract to mix feed
• Digest starch and fibers
• Microbes produce VFAs
• Lined with Papillae
• pH of 5.8-7.0
• Provide a suitable environment for bacteria and
  protozoa

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2. What are lipids?
2.5 Lipids

• Molecules that do not dissolve in water
• Used as energy molecules
• Found in cell membranes
• Found as fats and oils, phospholipids and steroids

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How are fats and oils different?
2.5 Lipids

• 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

33
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 213
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The structure of a Fat Molecule
2.5 Lipids

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

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Phospholipids and GlycolipidsCombination Lipids
Cell Membranes are Composed of these lipids
Hydrophilic
Diglyceride
Hydrophobic
Figure 217a, b
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Phospholipids Vs. GlycolipidsCombination Lipids
Figure 217c
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Understanding fats when reading a nutrition label
2.5 Lipids

• 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?

38
What are steroids?
2.5 Lipids

• A lipid
• Structure is four fused carbon rings
• Examples are cholesterol and sex hormones

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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

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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

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Proteins

• Proteins
• control anatomical structure and physiological
  function
• determine cell shape and tissue properties
• perform almost all cell functions

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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
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What do amino acids look like?
2.6 Proteins
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Peptide Bond

• A dehydration synthesis between
• amino group of 1
• amino acid
• and the carboxylic acid group of another amino
  acid
• producing a peptide

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What are the four levels of protein organization?
2.6 Proteins

• 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

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Primary Structure

• Polypeptide
• Linear sequence of amino acids
• How many amino acids were bound together
• What order they are bound

Figure 220a
47
Secondary Structure

• Hydrogen bonds form spirals or pleats

Figure 220b
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Tertiary Structure

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

Figure 220c
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Quaternary Structure

• Final protein shape
• several tertiary structures together

Figure 220d
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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

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4. What are nucleic acids?
2.7 Nucleic acids

• Made of nucleotide subunits
• Function in the cell to make proteins
• Includes DNA and RNA
• DNA ? deoxyribonucleic acid
• RNA ? ribonucleic acid

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DNA and RNA

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

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KEY CONCEPT

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

54
Nucleotides

• Are the building blocks of DNA
• Have 3 molecular parts
• sugar (deoxyribose)
• phosphate group
• nitrogenous base (A, G, T, C)

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What are the 3 parts of a nucleotide?
2.7 Nucleic acids
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The Bases
Figure 222b, c
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RNA and DNA

• RNA
• a single strand
• DNA
• a double helix joined at bases by hydrogen bonds

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Protein SynthesisThree 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

59
Summary of DNA and RNA structural differences?
2.7 Nucleic acids

• RNA
• Sugar is ribose
• Bases include A, U, C and G
• Single stranded

• DNA
• Sugar is deoxyribose
• Bases include A, T, C and G
• Double stranded

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ATP An Energy Carrier

• Adenosine triphosphate (ATP)
• Adenine ribose 3 phosphate groups (tri3)
• Chemical energy stored in phosphate bonds

Figure 224
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Summary of the macromolecules