Download - Chapter 2 Chemistry of Life Mader, Sylvia S. Human Biology. 13 th Edition. McGraw-Hill, 2014
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Chapter 2
Chemistry of Life
Mader, Sylvia S. Human Biology. 13th Edition. McGraw-Hill, 2014.
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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?
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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
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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
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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
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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
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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
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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:
• 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
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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
Figure 2–3a
- Atoms donate or take on electrons- Results in a stable outer shell- Occurs between particles that are charged (ions)
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Covalent bonds:• Atoms in this type of bond share electrons• Results in a stable outer shell
2.1 From atoms to molecules
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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
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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
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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
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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
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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
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pH Scale
Figure 2–9
• Has an inverse relationship with H+ concentration: – more H+ ions mean lower pH, less H+ ions
mean higher pH
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Looking at the pH scale2.2 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
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Organic and Inorganic Molecules
• Organic: – molecules based on carbon and hydrogen
• Inorganic: – molecules not based on carbon and hydrogen
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What organic molecules are found in living organisms?
• 1. Carbohydrates
• 2. Lipids
• 3. Proteins
• 4. Nucleic acids
2.3 Molecules of life
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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
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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?
• 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
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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
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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
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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
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The Ruminant StomachRuminant stomach is polygastric: four compartments
-Rumen -Reticulum
-Abomasum -Omasum
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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
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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
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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
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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
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The structure of a Fat Molecule
• A glycerol molecule and 3 fatty acid tails• Fat molecule = triglyceride
2.5 Lipids
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Phospholipids and GlycolipidsCombination Lipids
Figure 2–17a, b
Diglyceride
Cell Membranes are Composed of these lipids
Hydrophilic
Hydrophobic
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Phospholipids Vs. GlycolipidsCombination Lipids
Figure 2–17c
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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
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What are steroids?
• A lipid
• Structure is four fused carbon rings
• Examples are cholesterol and sex hormones
2.5 Lipids
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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?
• 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
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Figure 2–20a
Primary Structure
• Polypeptide:– Linear sequence of amino acids
• How many amino acids were bound together• What order they are bound
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Secondary Structure
Figure 2–20b
• Hydrogen bonds form spirals or pleats
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Figure 2–20c
Tertiary Structure
• Secondary structure folds into a unique shape
• Global coiling or folding due to R group interaction
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Quaternary Structure
Figure 2–20d
• Final protein shape: – several tertiary structures together
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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?
• 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
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DNA and RNA
DNA• Determines inherited characteristics• Directs protein synthesis• Controls enzyme production• Controls metabolismRNA• 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
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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 2–22b, 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 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
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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
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Figure 2–24
ATP: An Energy Carrier
Adenosine triphosphate (ATP): – Adenine + ribose + 3 phosphate groups (tri=3)
• Chemical energy stored in phosphate bonds
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Summary of the macromolecules