Transcript biochemistry

Biochemistry
• Organisms are composed of matter,
which is anything that takes up space and
has mass. All matter is composed of
elements, pure substances that can not
be broken down by chemical reactions.
These elements combine together in fixed
ratios of atoms to form compounds.
Compounds are held together by chemical
bonds. The reactivity of an atom and the
chemical bond that it forms are determined
by the number of electrons it has.
Chemical Bonds & Compounds
• Covalent – very strong chemical bond in
which electrons are shared. Results in a
very stable compound called a molecule.
– Examples – water, glucose, ethanol
Covalent bonds
Chemical Bonds & Compounds
• Ionic – weaker bond in which electrons
are transferred – that is one atom strips
electron(s) away from the other. Results in
2 oppositely charged particles called ions.
– Cation – positively charged
– Anion – negatively charged
• These ions are attracted to each other
due to the difference in charge.
– Examples – sodium chloride (NaCl) ~ table salt
• Ionic bonds
Ionic bonds
Chemical Bonds & Compounds
• Chemical Formula – Description of a
compound. Identifies the ratio of atoms of
elements that make up the compound.
– H2SO4 = 2 Hydrogen atoms, 1 Sulfur atom, 4
oxygen atoms
• Total # of atoms = 7
– C6H12O6 = 6 Carbon atoms, 12 Hydrogen
atoms, 6 Oxygen atoms
• Total # of atoms = 24
Polarity
Water is a molecule formed by covalent bonds.
• The atomic number of hydrogen is 1 and the
atomic number for oxygen is 8. This means that
oxygen’s nucleus has 8 protons and hydrogen’s
nucleus has 1 proton; therefore oxygen’s
nucleus has a much stronger positive charge.
• **More protons = More positive Charge =
Greater attraction to Electrons**
Polarity
• Shared electrons orbiting around a water molecule are
more attracted to oxygen’s nucleus (great
electronegativity).
• **Greater attraction to electrons = greater
electronegativity**
• This gives the 2 hydrogen ends of the water molecule a
slightly positive charge, and the oxygen end, a slightly
negative charge. This is not a true charged particle or
ion because the electrons are not transferred; they are
still shared, just not equally. At any given moment the
electrons tend to be closer to the more strongly positive
oxygen nucleus.
Hydrogen Bonds
• A hydrogen bond is not a true chemical bond
because it does not result in the formation of a
new compound. This bond is simply an attraction
between the slightly positively-charged
hydrogen end of one polar molecule and the
slightly negative charged end (usually oxygen,
nitrogen, &/or sulfur) of another polar molecule.
• In water, Hydrogen bonds form between the
positive charged hydrogen end and the
negative charged oxygen end. Hydrogen bonds
are extremely important in organisms and life
processes.
• Hydrogen bonds
• Polar covalent bonds
Hydrogen bonds
Properties of Water
• Polarity gives water some unique
properties important in maintaining
homeostasis in organisms.
– Cohesion & adhesion.
– Water is the solvent of life.
– Water has a high heat of vaporization.
Properties of water
Cohesion & Adhesion
Water is “sticky” – water molecules tend to stick
together, called cohesion and results in
surface tension. Water molecules also tend to
stick to other surfaces due to slightly charged
ends – adhesion.
• Surface tension – due to cohesion and adhesion
properties of water
• Cohesion causes water to form drops,
surface tension causes them to be nearly
spherical, and adhesion keeps the drops
in place.
Properties of water
Solvent
• Water is the solvent of life – slightlycharged ends of water molecules attract
and separate atoms that make up other
compounds. Anything dissolved in water is
referred to as a solution. Many important
compounds in cells are in solution.
Properties of water
Phase Changes
• Water has a high heat of vaporization –
perspiring cools us because it requires
heat to change water from a liquid to a
gas.
– When perspiration evaporates, the heat
required is drawn from our skin.
Phases of water
• Gas
liquid
solid
Acids & Bases
• Although the covalent bonds holding a water
molecule together are very strong, at any given
moment a tiny fraction of these bonds split
apart, resulting in the formation of a hydrogen
ion (H+) and a hydroxide ion (OH-).
• As a result, pure water always has a minute, but
equal concentrations of H + and OH- ions. Any
substance that, when added to water, changes
the concentration of H + or OH – is known as an
acid or a base, depending on the change to the
reaction.
Acids & Bases
• Acid is a substance that increases hydrogen
concentration when dissolved in water.
•
Ex. HCl, HNO3
• Base is a substance that increases hydroxide
concentration when dissolved in water
•
Ex. NaOH
• Water is a neutral substance because for every
hydrogen produced or hydroxide is also
produced; therefore, the net concentration of
hydrogen and hydroxide does not change.
pH Scale
• Scientists use the pH scale to measure the strength of
an acid or base. The pH scale ranges from 0 to 14.
• pH < 7 = acid
• The lower the pH, the stronger the acid, the greater
concentration of hydrogen ions.
• pH > 7 = base
• The higher the pH, the stronger the base, the greater
concentration of hydroxide ions
• pH = 7 = neutral
• concentrations of Hydrogen ions and hydroxide ions are
equal
Carbon
• Although a cell is composed of 70% to 95% water, most
of the rest consist of carbon – based compounds.
Carbon’s importance is due largely to the arrangement
of its electrons. One carbon atom can form stable,
covalent bonds with as many as 4 other atoms. This
allows carbon to form very large and complex molecules.
• Carbon compounds are called organic compounds. In
general, organic compounds may be defined as any
carbon-containing compound. All other compounds are
known as inorganic compounds.
Carbon
• Organic molecules associated with living
organisms are called biomolecules. Most
biomolecules are polymers. The prefix
“poly” means “many”.
• A polymer is a large molecule composed
of many identical or similar building
blocks. The sub-units, or building block
molecules, of a polymer are called
monomers.
Biomolecules
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There are 4 major classes of biomolecules
Carbohydrates
Lipids
Proteins
Nucleic acids
Carbohydrates
• Includes sugars and starches.
• Carbohydrates are used for immediate and
stored energy and as a building material.
Carbohydrates contain the elements C, H, O.
• The ratio hydrogen atoms to oxygen atoms is
2:1. In other words, for every two hydrogen
atoms in a carbohydrate, there is one oxygen
atom.
•
There are 3 groups of carbohydrates:
• Monosaccharides, Disaccharides, & Polysaccharides
Monosaccharides – “one” sugar
• Simplest of all sugars. Most monosaccharides
taste sweet and dissolve in water. They vary in
number of carbon atoms that make up the
molecule, but the ratio of 2H:1O is always
present
• 5-Carbon Monosaccharides
– examples – ribose & deoxyribose
• These 2 sugars are main components in DNA & RNA
• 6-Carbon Monosaccharides
– Examples are glucose, fructose, & galactose.
Monosaccharides – “one” sugar
• Each of these molecules have the same
chemical formula, C6 H12 O6. They are
isomers – compounds with the same
chemical formula, but the atoms are
arranged differently giving each
molecule different characteristics.
Monosaccharides – “one” sugar
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Glucose – preferred energy source for
most organism, including humans. Found
in fruit, honey, etc.
Fructose - Very sweet! – found in fruit
Galactose – Monomer of milk sugar
• Monosaccharides are the monomers or
building blocks for the more complex
carbohydrates – disaccharides and
polysaccharides
Disaccharides – “2” sugars
•
Diasaccharides - 2 monosaccharides
covalently bonded together
1. Sucrose – Table sugar. Composed of glucose +
Fructose
2. Lactose – Milk sugar. Composed of Glucose +
Galactose
3. Maltose – Found in seeds, grain, beer. Composed of
Glucose + Glucose
Polysaccharides – “many” sugars
• Polysaccharides - many monosaccharides
covalently bonded together.
– They are divided into 2 groups based on
function – storage & structural
Storage Polysaccharide
• Long polymers of glucose broken down
as needed for energy.
» Glycogen – storage form of glucose in animals. In
humans, most glycogen is stored in liver and muscle
cells.
» Starch – storage form of glucose in plants. Humans
are able to break down starch for energy.
Structural Polysaccharides
• Used as a strong building material in
plants, fungi, and some animals.
» Cellulose – major component of plant cell walls.
Composed of glucose monomers covalently bonded
together differently than starch or glycogen. Humans
cannot break down cellulose for energy, but it is
important to our diet as a source of fiber.
» Chitin – Major component of fungi cell walls and
insect (and other arthropods) exoskeletons.
carbohydrates
• Monosaccharide
– Ex. fructose
• Disaccharide
– Ex. sucrose
• Polysaccharide
– Ex. cellulose
Lipids
• Very diverse group of molecules defined
by their insolubility in water due to their
non-polar structure. Made up of C,H, & O,
but lipids do not have the 2H:1O ratio
found in carbohydrates.
• Our bodies need lipids for cushioning,
insulation, energy, storage, etc.
• There are 3 important groups of lipids:
fats, oils, phospholipids, and steroids.
• Fats & Oils – made up of glycerol
molecule + 3 fatty acid tails.
• Generally referred to as fat if lipid is solid
at room temperature and an oil if the lipid
is liquid at room temperature.
• Fats and oils may be classified as
saturated or unsaturated, depending on
the type of covalent bonds in the fatty
acids.
• Saturated Fats – Saturated fats contain all
single covalent bonds. This means each
carbon shares one pair of electrons with another
atom.
– They usually come from animal source and are solid
at room temperature. May contribute to heart
disease.
• Unsaturated Fats – Unsaturated fats contain
some double covalent bonds, meaning some
carbons in the molecule share 2 pairs of
electrons with another atom.
– They are usually from a plant source and liquid at
room temperature. Lower health risk.
lipids
• Saturated fat
• Unsaturated
• Triglyceride
•
3 fatty acides + glycerol
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Phospholipids – Molecule with a polar
end and non-polar end that is an
important component of all cell
membranes.
Steroids – differ from other lipids in that they lack
fatty acid tails. An important example of a steroid
is cholesterol.
• Cholesterol is an important component of cell
membranes in animals and is also used to
synthesize some hormones.
Proteins
• The molecular tools of the cell; proteins are
instrumental in almost everything organisms do,
including support, structure, movement,
protection against infection, etc.
• In addition to C, H, & O, proteins contain N. The
monomers of proteins are amino acids. There
are 20 amino acids that combine together in
different numbers, orders, and arrangements to
form proteins.
• Proteins are divided into 4 categories: Structural,
Carriers, Regulatory, & Enzymes
• Protein structure
•
Structural Proteins – Major
components of bones, muscles, skin
•
Transport (carrier) Proteins – Help
move substances across the cell
membrane or through blood
•
Regulatory (messenger) Proteins –
include hormones which help maintain
homeostasis by serving as signals for
changes in cell activities.
•
Enzymes – Trigger metabolic reactions in the
body by serving as a catalyst. In otherwords,
an enzyme speeds up a reaction without
being used up in the reaction. A chemical
reaction is a process in which one set of
chemicals, known as reactants are changed
into another set of chemicals known as the
product. An enzyme works by lowering the
activation energy required to the reaction
started.
• enzymes
•
Enzymes share 4 common features:
1. Enzymes work best within a narrow pH and
temperature range.
2. Enzymes do not make a reaction happen that could not
happen on its own; they simply make the react occur
much faster.
3. Enzymes are not used up or changed in the reaction.
The same enzyme may be used over and over again.
4. Enzymes are substrate-specific. A substrate is the
reactant. Enzymes are substrate-specific because of
their shape. The substrate fits into a portion of the
enzyme called the active site. This fit between the
active site of the enzyme and the substrate allows the
enzyme to be specific for a certain type of reaction.
Nucleic Acids
• Nucleotides are the monomers of nucleic
acids, therefore nucleic acids are
polymers.
• Nucleotides play an important role as a
cell’s power supply and in storing and
carrying out the genetic code. Nucleotides
contain C, H, O, N, & P.
Nucleotides
• Each Nucleotide consists of 3 parts:
– 5-carbon sugar
– phosphate group
– N-containing base
Nucleic Acids
• Nucleic acids are polymers that are
composed of thousands of nucleotides.
There are 2 important nucleic acids:
– Deoxyribonucleic acid – DNA. Contains the
instructions and the genetic code for the cell.
– Ribonucleic acid – RNA. Carries out the
instructions in DNA.
• Suggested Question
• p. 57
(2,3,5,6,7,8,10,15,17,18,19,20,21,25)
• Acids taste sour, are corrosive to metals,
change litmus (a dye extracted from
lichens) red, and become less acidic when
mixed with bases.
• Bases feel slippery, change litmus blue,
and become less basic when mixed with
acids.