Transcript Bio_130_files/Organic chemistry

Comparison of Ionic, Polar Covalent, and
Nonpolar Covalent Bonds
Formation of an Ionic Bond
• A valance electron from Na is transferred to Cl
• Cl now has 18e and 17p resulting in a – charge
• Na has 10e and 11P resulting in a + charge.
Nonpolar and Polar Covalent Bonds
Non polar covalent Bonds
equally share electrons
Polar covalent bonds
share electrons unequally
Hydrogen Bonds
• Too weak to bind atoms together
– (intra-molecular bonds= within molecule)
• Important as inter-molecular bonds
– between to different molecules
– Important for giving proteins (enzymes) and
DNA both shape and functionality.
• Hold water molecules together
– Responsible for surface tension in water
Hydrogen Bonds in Water
Hydrogen Bonds
Properties of Water
• Water makes up to 50-80% of all living cells.
• Water stabilizes internal temperature of the body
– Hydrogen bonds stabilize large shifts in
temperature
• Evaporate cooling (sweating) is critical from
maintaining 98.6 degrees temperature in hot
environments or increased physical workloads.
• Water is necessary for all biochemical reactions that
take place in the body.
Polarity of Water
• Oxygen has a greater
electronegativity.
• Hydrogen’s one electron spend more
time in Oxygen's outermost energy
level.
• The result is more electrons around
the oxygen making it more negative.
• Hydrogen losses its electron. Its
proton is unopposed making it more
positive.
Properties of Water
• Water makes up to 50-80% of all living cells.
• Water stabilizes internal temperature of the body
– Hydrogen bonds stabilize large shifts in
temperature
• Evaporate cooling (sweating) is critical for
maintaining 98.6 degrees temperature in hot
environments or increased physical workloads.
• Water is necessary for all biochemical reactions
that take place in the body.
Properties of Water
• Water is a powerful splitting agent. (Hydrolysis) means
water splitting. Occurs in breaking down reactions
• Is known as the universal solvent. ( Polarity allows it to
dissolve stuff.) water molecules slit the ionic bonds in
Na+Cl-
Polarity
• Polar molecules associate with water and will
dissociate from lipids (fats) .
– Polar = hydrophilic (philic = loving)
– Lipophobic (lipid fearing)
• Non-polar molecules associate with lipids will
not associate with water and are considered to
be
– Non-polar = hydrophobic (water fearing)
– Lipophilic= Lipid loving
Organic Compounds
• Organic compounds contain carbon as the backbone.
• It has the ability to create 4 covalent bonds which is
important for making large complex structures.
• Organic compounds include :
–
–
–
–
Carbohydrates (sugars)
Lipids (fats and oils)
Proteins ( muscle, enzymes)
Nucleic acids (DNA and RNA)
• They may be built up or broken down depending on
what the system requires.
• May have a variety of functional groups
Dehydration Synthesis
•
•
•
Dehydrate( remove water)/ Synthesis( Build)
Monomers bond together to form a polymer with the
removal of a water molecule (dehydration)
Removal OH– of one and H+ of the other hydroxyl
group forms the water.
–
A covalent bond will result.
Hydrolysis
• Translates into Water/splitting
• Addition of a water to a polymer causes (lysis) of the
covalent bond joining the 2 monomers.
– Reestablishes the hydroxyl groups in both monomers
• All digestion reactions consists of hydrolysis reactions
Monomers/Polymers
Carbohydrates
 Monosaccharides
Polysaccharides
Fats (lipids)
 Glycerol + 3 fatty Acids
Triglycerides
Protein
 Amino acids
Polypeptide
Nucleic Acids
nucleotides
Dehydration Synthesis
Hydrolysis
DNA, RNA
Carbohydrates
Hydrophilic organic molecule that : contain carbon, hydrogen, and
oxygen 1:2:1 atomic ratio( carbo/carbon:hydrate/H2O)
– i.e. glucose = C6H12O6
• Names of carbohydrates
– word root sacchar- or the suffix -ose often used
• Glucose is a monosaccharide which functions as a major
fuel source for the cells.
Carbohydrates
• Dehydration synthesis reactions allow the cell store
excess carbohydrates in the form of glycogen.
• Hydrolysis reactions allow the cell to break the bonds
holding the polysaccharide together allowing it to
release more simple sugars.
Disaccharides
• Major disaccharides
– sucrose = table sugar
• glucose + fructose
– Lactose = sugar in milk
• glucose + galactose
– Maltose = grain products
• glucose + glucose
• All digested carbohydrates
converted to glucose
broken down in ATP
(Cellular fuel).
Glycogen
• Glycogen is an energy storage polysaccharide produced
by animals. 2 storage sites:
– Liver cell: synthesize glycogen after a meal which can be broken
down later to maintains blood glucose levels.
– Muscle cells: Store glycogen within the muscle at is only used by
the muscle cell.
Starch and Cellulose
• Starch: is the storage form of sugar produced by plants. We
produce an enzyme that breaks the bonds between the sugars
allowing digestion to occur. i.e. potatoes and grains
• Cellulose: provides structure to plants but contains a different
type of bond. The β form is insoluble because we don’t
produce the enzyme .i.e. dietary fiber
Lipids
• Hydrophobic organic molecule
– Composed of carbon, hydrogen and oxygen
– Better fuel source since it contains many more carbon and
hydrogen molecules.
• There is an unlimited supply.
• Chain of 4 to 24 carbon atoms
– carboxyl (acid) group on one end, methyl group on the other
and hydrogen bonded along the sides
• Classified
– saturated - carbon atoms saturated with hydrogen
– unsaturated - contains C=C bonds without hydrogen
Lipids Found in the Body
• Neutral fats – found in subcutaneous tissue and around
organs.
• Phospholipids – chief component of cell membranes
• Steroids – cholesterol, bile salts, vitamin D, sex
hormones, and adrenal cortical hormones
• Eicosanoids – prostaglandins, leukotrienes, and
thromboxanes:
– These play a role in various reactions in the body such as
inflammation and immunity.
• Lipoproteins – transport fatty acids and cholesterol in the
bloodstream
• Fat-soluble vitamins – A,D, E, and K
Triglycerides
• Functions
– energy storage in adipose (fat) tissue
– Fats contain 9 kcal per gram where as
carbohydrates and proteins contain 4 kcal per
gram.
• They contain more energy rich hydrogen.
– insulation
• Prevent heat loss from the body
– protection
• Adipose tissue cushions the organs.
Triglycerides (Neutral Fats)
• Contain C, H, and O, but the proportion of oxygen in
lipids is less than in carbohydrates 3
• Fatty acids are bonded to a glycerol molecule during
dehydration synthesis.
• At room temperature : Contain double bonds.
– when liquid called oils
• often mono and polyunsaturated fats from plants
– when solid called fat
• saturated fats from animals.
– No double bonds.
• Function - energy storage, insulation and shock
absorption
Neutral Fats (Triglycerides)
• Composed of three fatty acids bonded to a
glycerol molecule
Phospholipids
• Modified triglycerides with two fatty acid groups
and a phosphorus group
Protein Functions
– Catalysts
• proteins which are enzymes significantly increase the rate
of a chemical reaction i.e. Salivary Amylase increases the
rate of hydrolysis of starch.
– Structural
• hold the parts of the body together i.e. collagen, elastin
and keratin
– Communication
• act as chemical messengers between body areas .i.e.
hormones such as insulin.
– Transport
• allow substances to enter/exit cells
• Carry things in the blood i.e. hemoglobin, lipoproteins,
Protein Functions
– Movement
• Actin and myosin function in muscle contraction
– Defense
• Antibodies( immunoglobulins) recognize and
inactivate foreign invaders( bacteria, toxins, and
some viruses)
– Metabolism
• Help regulate metabolic activities, growth and
development
– Regulation of pH
• Plasma proteins such as albumin can function both
as an acid or a base. Therefore have an important
role as a buffer
Amino Acids Structure
• Building blocks of protein
• Amino and carboxyl
group groups are
common in all Amino
acids.
• R-group (radical group):
20 amino acids are
different both structurally
and from a functional
level.
Different R- groups
Protein
• Macromolecules composed of combinations of 20 types of amino
acids bound together with peptide bonds
• Animal ,dairy and right combination of beans and rice are good
sources of protein.
• Enzymes are specific types to proteins that enable reactions.
Protein Structure
• Primary structure
– amino acid linked together by peptide bonds. The order of
the amino acids critical for both form and function. No
hydrogen bonds formed.
• Secondary structure :The primary structure will now form
hydrogen bonds and take one of 2 forms:
– α helix (coiled), β-pleated sheet (folded)
• Tertiary structure
– more hydrogen bonds form and increased interaction
between R groups in surrounding water results in protein
taking a globular 3 dimensional shape.
• Quaternary structure
– two or more separate polypeptide chains conjugate and form
a functional protein
• Hemoglobin.
Structural Levels of Proteins
• Primary – amino acid sequence
• Secondary – alpha helices or beta pleated
sheets
Structural Levels of Proteins
• Tertiary – superimposed folding of secondary structures
– Most enzymes are in this form.
• Quaternary – polypeptide chains linked together in a
specific manner
Functional Proteins (Enzymes)
• Enzymes are chemically specific. They fit a specific
substrate like a lock and key.
• Enzyme names usually end in –ase
– for example Lactase will be specific for the substrate
lactose ( Glucose
Galactose)
» Gycosidic bond
• Frequently named for the type of reaction they catalyze
i.e. hydrolases add water during hydrolysis reactions.
• lipase/lipids, protease/ proteins,
• Act as biological catalysts which lower activation energy
allowing reactions to occur at faster rates.
Activation Energy
• Activation energy refers to the extra energy
required to break an existing chemical bonds
and initiate a chemical reaction.
– Activation energy determines rate of reaction
(higher activation energy = slower reaction)
– catalyst - substance that lowers the activation
energy by influencing (stressing) chemical
bonds
Characteristics of Enzymes
Enzymatic Reaction
Steps
Enzyme Substrate Complex
• Enzymes need their 3
dimensional structure
– created by both Hydrogen
and disulfide bonds which
is specific to a certain
substrate.
– Proper conditions are
needed to keep these
enzymes functioning.
– pH
– Temperature
Protein Denuaturation
• Hydrogen bonds are broken and tertiary
level protein reverts back to primary
structure. Peptide bonds are still intact.
Protein Denuaturation
• Proteins will become
denatured if:
– ∆ pH
– ↑ temperature
• Hydrogen bonds are broken
from complex tertiary level
proteins to basic primary
structure.
– Peptide bonds are still
intact.
• Visible changes you see
when frying an egg
Nucleic Acids
• Two major classes – DNA and RNA
• Composed of carbon, oxygen, hydrogen,
nitrogen, and phosphorus
• Five nitrogen bases contribute to
nucleotide structure
• Adenine (A)
Thymine (T)
• Guanine (G)
Cytosine (C)
• Uracil (U) replaces Thymine in RNA
Nucleotides
The structural unit of the a nucleotide is composed of
• N-containing base A,T,C,G and U in RNA
• Pentose sugar: Ribose, and deoxyribose
• Phosphate group
Deoxyribonucleic Acid (DNA)
• Double-stranded helical molecule confined in the
nucleus of the cell
• Helical shape is a result of H-bonds between a
purine on one strand and a pyramidine on the
other strand
– A only pairs with T
– G only pairs with C
• Replicates itself before the cell divides, ensuring
genetic continuity
• Provides instructions for protein synthesis
Structure of DNA
Structure of DNA
Ribonucleic Acid (RNA)
•
•
•
•
1.
Single-stranded molecule
Made from the nucleotides that complimentary pair
A
U
G
C
Three varieties of RNA:
messenger RNA: transcribe DNA and carry it out of
nucleus.
2. transfer RNA: Bring amino acids to site of protein
synthesis (ribosome).
3. ribosomal RNA: building blocks of ribosomes ,made
in the nucleolus
Adenosine Triphosphate (ATP)
 Adenine-containing RNA nucleotide with three
phosphate groups
• Second and third phosphate groups are
attached by high energy covalent bonds
• The 3rd high energy phosphate bond of ATP is
hydrolyzed producing ADP + P + energy
– The cell can recycle the ADP and P back into
ATP using the energy harvested from dietary
foods primarily carbohydrates and lipids.
• Source of immediately usable energy for the cell.
– It is the currency that all cellular reactions
accept.
Adenosine Triphosphate (ATP)
Figure 2.22
How ATP Drives Cellular Work
Figure 2.23