BIO130H1 Lecture Notes - Lecture 3: Disaccharide, Chief Operating Officer, Expose

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Published on 16 Oct 2011
School
UTSG
Department
Biology
Course
BIO130H1
Professor
Chapter 2: Cell Chemistry and Biosynthesis
THE CHEMICAL COMPONENTS OF A CELL
An atom often behaves as if it has a fixed radius
Space-filling models give us a more accurate representation of molecular structure
A solid envelope represents the radium of the electron cloud at which strong repulsive
forces prevent a closer approach of any second, non-bonded atom the so-called van der
Waals radius for an atom
At slightly greater distances, any two atoms will experience a weak attractive force, known as a van der Waals
attraction
There is a distance at which repulsive and attractive forces precisely balance to produce an energy min in each
atom’s interaction with an atom of a second, non-bonded element
Water is the most abundant substance in cells
Water accounts for 70% of a cell’s weight
Hydrogen bond: the electrical attraction when a + charged region of
one water approaches a charged region of a second water;
weaker than covalent bonds and are easily broken by the random
thermal motion due to the heat energy of the molecules so each
bond lasts only a short time
Explains why water is a liquid at room temp, with a high bp and high surface tension
Molecules that contain polar bonds can form H bonds with water dissolve readily in water
Ions likewise interact favourably with water
Such molecules are hydrophilic (water loving)
Hydrophobic (water hating) are uncharged and form few or no H bonds, and so go not dissolve in water
Some polar molecular are acids and bases
Proton (): a molecule that had largely given up its electron to the companion atom
When water molecules surround the polar molecule, the proton is attracted to the partial negative charge on
the O atom of an adjacent water molecule and can dissociate from its original partner to associate instead with
the oxygen atoms of the water to generate a hydronium ion ()
Acids: substances that release protons to form when they dissolve in water
Base: accepts protons to lower the concentration of ions, and thereby raise the concentration of 
[   
The concentration of is
expressed using a log scale called
the pH scale
The interior of a cell is kept close to
neutrality, and it is buffered by the
presence of many chemical groups
that can take up and release
protons near pH 7
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Four types of noncovalent attractions help bring molecules together in cells
In aqueous solutions, covalent bonds are 10-100x stronger than the other attractive forces between atoms
Much of biology depends on the specific binding which is mediated by a group of noncovalent attractions that
are individually quite weak, but whose energies can sum to create an effective force between two separate
molecules
1. Electrostatic attractions
a. Result from the attractive forces between oppositely charged atoms
b. Quite strong in the absence of water
c. Readily form between permanent dipoles but are greatest when the 2 atoms involves are fully charged
d. Water cluster around both full charged ions and polar molecules, greatly reducing the attractiveness of
these charged species for each other in most biological settings
2. Hydrogen bonds
a. Represents a special form of polar interaction in which an electropositive H atom is partially shared by 2
electronegative atoms
b. H can be viewed as a proton that has partially dissociated from a donor atom, allowing it to be shared by
a second acceptor atom
c. Highly directional being strongest when a straight line can be drawn between all 3 of the involved
atoms
d. Water weakens these bonds by forming competing H-bond interactions
3. Van der Waals attraction
a. Electron cloud around any nonpolar atom will fluctuate, producing a flickering dipole which will
transiently induce an oppositely polarize flickering dipole in a nearby atom
b. Generates a very weak attraction
c. Water does not weaken these attractions
Fourth effect is not a bond at all, strictly speaking
A very important hydrophobic force is caused by a pushing of nonpolar surfaces out of the H-bonded water
network
Brining any 2 nonpolar surfaces together reduces their contact with water; the force is nonspecific
A cell is formed from carbon compounds
Because C is small and 4 e and 4 vacancies, nearly all the molecules in a cell are based on C
High stable covalent C-C bonds form chains and rings and hence generate large and complex molecules
Certain combination of atoms occur repeatedly in organic molecules; these chemical groups have distinct
physical and chemical properties that influence the behaviour of the molecule in which the group occurs
Cells contain 4 major families of small organic molecules
Some organic molecules are used as monomer subunits to construct macromolecules proteins, nucleic acids,
and large polysaccharides - of the cell
Small organic molecules are much less abundant that the organic macromolecules
3 major families: sugars, fatty acids, the amino acids, and the nucleotides
Sugars provide an energy source for cells and are the subunits of polysaccharides
The simplest sugars monosaccharides are compounds with the general formula , where n is usually
3, 4, 5, 6, 7, or 8
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Called carbohydrates because of this simple formula
The formula, however, does not fully define the molecule; same
set of C, H and O can be joined together by covalent bonds in a
variety of ways
Eg. Glucose can be converted into a different sugar simply by
switching the orientation of specific OH groups
Each of these sugars can exist in either of 2 forms, D-form and L-form, which
are mirror images of each other
Isomers: same chemical formula but different structures
Optical isomers: mirror-image pairs
In their open chain forms of sugars, they contain a number of OH groups and a
carbonyl group
The carbonyl group can react with a OH group in the same molecule to convert
the molecule into a ring
Once the ring is formed, this same C can become further linked, via O, to one of
the C bearing a OH on another sugar, creating a disaccharide
Larder sugar polymers range from oligosaccharides up to giant polysaccharides
A bond is formed between an OH group on one sugar and an-OH group on
another by a condensation reaction, in which a molecule of water is expelled as
the bond is formed
The covalent bond between two sugar molecules are known as a glycosidic bond
The bonds created can be broken by the reverse process of hydrolysis, in which water is consumed
Glucose is a key energy source for cells; in a series of reaction, it is broken down to smaller molecules, releasing
energy
Cells use simple polysaccharides composed only of glucose: starch in plants and glycogen in animals
Sugars can also be used to mechanical supports; eg. Cellulose and chitin
Other polysaccharides are components of slime, mucus and gristle
Smaller oligosaccharides can be covalently linked to proteins to form glycoproteins and to lips to form
glycolipids, which are recognized selectively by other cells through their side chains
Fatty acids are components of cell membranes, as well as a source of energy
Have two chemically distinct regions: a long hydrocarbon chain (hydrophobic and not reactive) and carboxyl
group (behaves as an acid, ionized in solution, hydrophilic and chemically reactive)
Almost all fatty acids in a cell are covalently linked to other molecules by their carboxylic acid group
saturated: no double bonds between C atoms and contains the max possible # of H
Unsaturated: one or more double bonds along their length, creating kinks and interfering with their ability to
pack together in a solid mass
Are stored in the cytoplasm in the form of droplets of triacylglycerol molecules, which consist of 3 fatty acid
chains joined to a glycerol molecule (the animal fats found in meat, butter and cream)
When required to provide energy, the fatty acid chains are released from triacylglycerols and broken down into
2-C units which are identical to those derived from the breakdown of glucose
Triacylglycerols serve as a concentrated food reserve in cells because they can produce about 6x energy than glu
Lipids: loosely defined collection of biological molecules that are insoluble in water, while being soluble in fat
and organic solvents
Either long HC chains, or multiple linked rings (steroids)
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Document Summary

An atom often behaves as if it has a fixed radius. Space-filling models give us a more accurate representation of molecular structure. A solid envelope represents the radium of the electron cloud at which strong repulsive forces prevent a closer approach of any second, non-bonded atom the so-called van der. At slightly greater distances, any two atoms will experience a weak attractive force, known as a van der waals attraction. There is a distance at which repulsive and attractive forces precisely balance to produce an energy min in each atom"s interaction with an atom of a second, non-bonded element. Water is the most abundant substance in cells. Water accounts for 70% of a cell"s weight. Explains why water is a liquid at room temp, with a high bp and high surface tension. Molecules that contain polar bonds can form h bonds with water dissolve readily in water.

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