Transcript Slide 1

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?
2.1 From atoms to molecules
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
Isotopes
• 2 or more elements with equal numbers of
protons but different numbers of neutrons
Electron
shell
n
e
p+
(a) Hydrogen-1
(electron-shell model)
p+
e
(b)
n
Hydrogen-2
deuterium
e
p+
(c)
n
Hydrogen-3,
tritium
2.1 From atoms to molecules
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
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.
2.1 From atoms to molecules
Molecules:
• Are made of atoms that are bonded
together
• Can be made of the same atom or
different atoms
• If atoms are different = compound
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
- Atoms donate or take on electrons
- Results in a stable outer shell
- Occurs between particles that are charged (ions)
Figure 2–3a
2.1 From atoms to molecules
Covalent bonds:
• Atoms in this type of bond share electrons
• Results in a stable outer shell
Covalent Bond
Molecule
Electron-Shell Model and
Structural Formula
Hydrogen
(H2)
H–H
Oxygen
(O2)
O=O
Carbon
Dioxide
(CO2)
O=C=O
Nitric
Oxide
(NO)
N=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 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
2.2 Water and living things
What bond holds water molecules
together?
• Hydrogen bonds
occur between a
hydrogen in a
covalent bond and
a 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
pH Scale
• Has an inverse relationship with H
concentration:
+
– more H+ ions mean lower pH, less H+ ions
mean higher pH
Figure 2–9
2.2 Water and living things
Looking at the pH scale
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
2.3 Molecules of life
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?
2.4 Carbohydrates
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 as
found 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
Carbohydrate Functions
Polysaccharides
Glycogen: made and stored in muscle cells
Cellulose: structural component of plants
-Ruminant Animals: Cattle, sheep, and deer
Table 2–5
The Ruminant Stomach
Ruminant stomach is polygastric: four compartments
-Rumen
-Reticulum
-Abomasum
-Omasum
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
2.5 Lipids
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
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
2.5 Lipids
The structure of a Fat Molecule
• A glycerol molecule and 3 fatty acid tails
• Fat molecule = triglyceride
Phospholipids and Glycolipids
Combination Lipids
Cell Membranes are Composed of these lipids
Hydrophilic
Diglyceride
Hydrophobic
Figure 2–17a, b
Phospholipids Vs. Glycolipids
Combination Lipids
Figure 2–17c
2.5 Lipids
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
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.
2.
3.
4.
central carbon
hydrogen
amino group (—NH2)
carboxylic acid group
(—COOH)
5. variable side chain or
R group
Figure 2-18
2.6 Proteins
What do amino acids look like?
Peptide Bond
• A dehydration
synthesis between:
– amino group of 1
amino acid
– and the carboxylic acid
group of another amino
acid
– producing a peptide
2.6 Proteins
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
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
• Hydrogen bonds form spirals or pleats
Figure 2–20b
Tertiary Structure
• Secondary structure folds into a unique shape
• Global coiling or folding due to R group
interaction
Figure 2–20c
Quaternary Structure
• Final protein shape:
– several tertiary structures together
Figure 2–20d
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
2.7 Nucleic acids
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
DNA and RNA
DNA
• Determines inherited characteristics
• Directs protein synthesis
• Controls enzyme production
• Controls metabolism
RNA
• 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)
2.7 Nucleic acids
What are the 3 parts of a nucleotide?
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
2.7 Nucleic acids
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
ATP: An Energy Carrier
Adenosine triphosphate (ATP):
– Adenine + ribose + 3 phosphate groups (tri=3)
• Chemical energy stored in phosphate
bonds
Figure 2–24
Summary of the macromolecules