Transcript Chemistry of Life Part 2 (Updated)

Missing Pieces:
 Dipoles (Polar molecules)
 Cohesion
Biochemistry and Cell Compounds
 we will now look at biologically important molecules that are based
around carbon atoms. It is said that life on Earth is "Carbon
Based..."
 Biochemistry: the chemicals of life and their study.
 Organic chemistry is the study of carbon compounds. As will see,
a lot of biochemistry revolves around organic chemistry.
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Why Carbon?
1.has four available covalent bonds -- allows for other atoms to bind.
2.capable of forming strong bonds with itself
therefore can form long chains -- can be straight or branched -->
great VARIETY of possible combinations.
 carbon atoms in chains can rotate, forming single, double, and
multiple ring structures (e.g. glucose, nucleotides, lipids, proteins)
Macromolecules
 The next slides will examine the four major molecules
of life and the process by which they are combined and
separated.
 Two terms to be familiar with:
 Polymer:
 Monomer
Polymer and monomer
 Look at the term: polymer, Poly- means "many.”
 So what does polymer mean?
 Polymer means many monomers. Sometimes polymers
are also known as macromolecules or large-sized
molecules. A monomer is a molecule that is able to
bond in long chains. Here is a monomer:
Here is a
polymer:
Large Organic Molecules Have Monomers
 1. Each small organic molecule can be a unit of a large
organic molecule called a macromolecule.
 2. Small organic molecules (e.g., monosaccharides,
glycerol and fatty acid, amino acids, and nucleotides)
that can serve as monomers, the subunits of polymers.
 3. Polymers are the large macromolecules composed of
three to millions of monomer subunits.
 4. Four classes of macromolecules (polysaccharides or
carbohydrates, triglycerides or lipids, polypeptides or
proteins, & nucleic acids such as DNA & RNA) provide
great diversity.
Dehydration Synthesis and Hydrolysis
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a POLYMER is a large molecule formed from
repeating subunits of smaller molecules (e.g. proteins,
starch, DNA are all polymers).
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DEHYDRATION SYNTHESIS: forms large
molecules (polymers) from small molecules.
(Dehydration = to remove water) In the process water
is produced. (Also called condensation)
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HYDROLYSIS (hydro = water, lysis = to split): is
the opposite reaction. Water breaks up another
molecule. The addition of water leads to the
disruption of the bonds linking the unit molecules
together.
Details, details….
 DEHYDRATION SYNTHESIS: one molecule loses an
H+, one molecule loses an OH-. Amino acids can
continue to be added to either end of the dipeptide to
form polypeptides. Large polypetides are called
proteins.
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HYDROLYSIS: One molecule takes on H+ and
the other takes an OH-. This also requires the action
of helping molecules called enzymes. Enzymes that
do this are called hydrolytic enzymes.
Dehydration:
Carbohydrates
 Carbohydrates contain the elements carbon,
hydrogen, and oxygen in the ratio of 1C:2H:1O.
 The building blocks or monomers that make up more
complex carbohydrate polymers are called
monosaccharides and have a ring structure with five
or six sides. Examples of monosaccharides are
glucose and fructose. Two monosaccharides can be
combined to produce disaccharides such as sucrose
(table sugar) and maltose. The large complex
carbohydrate polymers that are produced include
starch, glycogen, and cellulose. (Polysaccarides)
Carb Functions:
 used for ENERGY, FOOD STORAGE, & STRUCTURAL
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SUPPORT in plants and animals. Carbohydrates are very
important in living systems for the following functions:
1.
Short-term energy supply (e.g. glucose is used by all cells
to produce ATP energy)
2. Energy storage (e.g. glycogen is stored in liver and muscles
and can be rapidly converted to glucose: starch has a similar
role in plants)
3. Cell membrane markers (receptors & “identification tags”)
4. As structural material (e.g. plant cell walls are made of
cellulose, insect exoskeletons are make of the carbohydrate
chitin)
 Starch
Carb Structure
Lipids: Fats, oils and waxes
include fats oils (neutral fats),phospholipids, & steroids.
 Fats and oils, called neutral fats, are composed of a glycerol
backbone and three fatty acids. Glycerol is a 3-carbon molecule.
Fatty acids are long carbon chains with an acid group at the end.
Fatty acids can be saturated or unsaturated with hydrogen atoms.
 Phospholipids are similar in structure to neutral fats but have
one of the fatty acid molecules replaced with a phosphate group.
They are the main component of cell membranes.
 Steroids are easily recognized by a backbone of four fused
carbon rings. Cholesterol found in cell membranes can be
transformed into common steroid hormones such as
testosterone and estrogen.
THE MAIN TYPES OF LIPIDS: Fatty Acids
 i. Fatty Acids: a long chain of carbons with hydrogens attached,
ending in an acid group (-COOH). There are two main types:
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Saturated fatty acids - no double bonds between carbons.
All carbons are "saturated" with hydrogens. Saturated fats tend to
be solid at room temp. These are the "bad" dietary fats (e.g. butter,
lard, meat fat), which are known to contribute to heart disease,
strokes, and cancer.
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Unsaturated fatty acids - have one (monounsaturated) or
more (polyunsaturated) double bonds between carbons in chain.
That means that the carbons are not “saturated” with hydrogens.
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Unsaturated fats tend to be liquid at room temperature. e.g.
vegetable oils, Omega-3 unsaturated fatty acids. Are thought to be
better for your heart than saturated fats.
Continued: Neutral/Triglycerides
 ii.
NEUTRAL FATS: (also called TRIGLYCERIDES)
 formed by dehydration synthesis reaction between
glycerol (a molecule of 3 hydrated carbons and 3 fatty
acids.
continued
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All triglycerides are non-charged, non-polar
molecules.
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They do not mix with water. This property of not
mixing with water is called “hydrophobic” which
literally means “water-fearing.” This is the opposite of
polar molecules, which mix readily with water and are
called “hydrophilic” which means “water-loving.”
STEROIDS: a different
type of lipid
 They are multi-ringed structures,
all derived from CHOLESTEROL
 essential molecule found in
every cell in your body (it forms
parts of cell membranes, for
example).
 Steroids can function as chemical
messengers, and form many
important HORMONES (e.g.
testosterone, estrogen,
aldosterone, cortisol) that have a
wide variety of effects on cells,
tissues, and organs.
Lipid Function
 1.
Long-Term Energy storage: (fat is excellent for
storing energy in the least amount of space, and packs
9.1 calories of energy per gram, versus 4.4 for
carbohydrates and proteins).
 2. Insulation ("blubber")
 3. Padding of vital organs
 4. Structural (e.g.cell membranes are mostly
composed of phospholipids, white matter of brain
contains a high proportion of lipid material)
 5. Chemical messengers (e.g. steroid hormones like
testosterone, estrogen, prostaglandins).
Short Hand: Triglyceride
Proteins
 polymers constructed from amino acid monomers.
 Amino acids have a central carbon atom. This central carbon
is bonded to a hydrogen atom and three groups. An amino
group (-NH2), an acid Carboxyl group (COOH), and an Rgroup. The R-group is unique to an amino acid and
determines its identity. When amino acids bond together to
form proteins the amino group of one combines with the acid
group of another producing a (C-N) or peptide bond. This
peptide bond is easily seen in a dipeptide containing two
amino acids.
 There are 20 different amino acids in living things. Our
bodies can make 12 of these. The other 8, which we must get
from food, are called “Essential Amino Acids.”
Identify: Amino Group, Carboxyl
Acid, Central Carbon and R-Group.
Peptide bonds through
Dehydration Synthesis.
Protein Functions
 provide STRUCTURAL SUPPORT (e.g. elastin, collagen in cartilage
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and bone, muscle cells)
MOVEMENT (actin and myosin etc. in muscle cells)
METABOLIC FUNCTIONS:
ENZYMES (biochemical catalysts that speed up biochemical
reactions). Crucial to life.
ANTIBODIES: proteins of your immune system that fight disease.
Transport: HEMOGLOBIN is a protein that transports oxygen in your
blood. Proteins in cell membranes act as channels for molecules
entering or leaving the cell.
Hormones: many hormones, like insulin, are proteins. Hormones
control many aspects of homeostasis.
Protein Structure
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Dipeptide: two amino acids joined together
 iii. Polypeptide (abreviation = ppt): >2 amino acids
joined together. Usually short: less than 20 amino
acids or so.
 iv. Protein: a polypeptide chain is called a protein
when it gets large (usually ~75 or more amino acids in
length – though there is no absolute rule here)
Structure continued
 Primary, secondary, tertiary, quatrenary
DENATURING
PROTEIN
protein shape is critical to its function
 changes in temperature or pH, or the presence of
certain chemicals or heavy metals, can disrupt the
bonds that hold a protein together in its particular
shape.
 If a protein is DENATURED, it has lost normal
structure/shape because normal bonding between -R
groups has been disturbed.
 heating an egg white (raising the temperature above
50°C will reliably denature most animal enzymes)
 adding vinegar to milk (this is the same thing as
changing the pH, since vinegar is an acid)
 adding heavy metals such as lead and mercury also
denature proteins
Nucleic Acids
 Nucleic Acids are double-stranded DNA
(Deoxyribonucleic Acid) and a single-stranded cousin
RNA (Ribonucleic Acid). Both of these polymers are
built from nucleotides.
 Nucleotides are composed of three parts; a sugar, a
phosphate, and a nitrogenous base.
 There are four different nucleotides found in DNA
(adenine, thymine, guanine, and cytosine). In
RNA the thymine nucleotide is replaced with a uracil
nucleotide. If a polymer is made from nucleotides it is
a nucleic acid.
Nucleic Acid
From Nucleotides to Chromosomes.
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Sections of DNA form functional units called
GENES. A gene is one instruction for making one
polypeptide (protein), and is about 1000 nucleotides
long, on average.
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DNA is packaged into chromosomes, and is
located in the nucleus. You have about 4 billion
nucleotide pairs in each of your cells. Each of your 46
chromosomes (23 from mom, 23 from dad) contains
one very long polymer of DNA around 85,000,000
nucleotides long!
 http://www.biologyjunction.com/biochemistry_notes
_bi_ch3.htm
 http://www.chemistrypictures.org/v/cell_structure/cel
l_structure.jpg.html
 Acid, acid (carboxyl) group, adenine, adenosine triphosphate
(ATP), alpha helix, amine group, amino acid, base, beta pleated
sheet, bonding, buffer, carbohydrate, cellulose, complementary
base pairing, cytosine, dehydration synthesis, deoxyribonucleic
acid (DNA), deoxyribose, dipeptide, disaccharide, double helix,
glucose, glycerol, guanine, glycogen, hemoglobin, hydrogen
bonding, hydrolysis, lipid, lubricant, maltose, monomer,
monosaccharide, neutral fat, nitrogenous base, nucleic acids,
nucleotide, organic, peptide bond, pH, phosphate, phospholipid,
polarity, polymer, polypeptide, polysaccharide, primary
structure, protein, quaternary structure, R-group, ribonucleic acid
(RNA), ribose, saturated fatty acid, secondary structure, solvent,
starch, steroid, sugar-phosphate backbone, temperature
regulator, tertiary structure, thymine, unsaturated fatty acid,
uracil