Download Chapter 3 Biochemistry

Chapter 3
Biochemistry
Here- Bio molecule art by
David Goodsell, creates
hyperrealist paintings
the molecular world
Here,a depiction of HIV
shown in cross-section- the
structural biology & electron
microscopy — gives a much
-maligned pathogen a unique
artistic quality.
AC
Examples of bio molecules: Hemoglobin
• the oxygen-carrying molecule of erythrocytes,
formed by developing erythrocytes in the bone
marrow;
• a protein made up
of 4 polypeptide
chains that contain
141 - 146 amino
acids each.
Examples of biological molecules:
• The Helicase enzyme
unzips the DNA
molecule, to expose
the nitrogenous bases
so we can read the
genetic code & do
everything that is in
the instructions for
life.
Inside leaves, solar energy is transferred to
the chemical bonds in biological molecules
like GLUCOSE – food.
Examples: Biological molecules
• Hormones are chemical messengers that
regulate imperative bodily functions in living
organisms.
• For example pheromones are hormones used by
ants & other insects as a
communication system to
send messages among one
another or to attract the
opposite sex.
http://www.reciprocalnet.org/edumodules/commonmolecules/biochemical/index.html
Examples:
biological molecules
• Other examples of biomolecules are poisons
found in animals. Batrachotoxin, a poison at the
skin of the golden poison frog
• Phyllobates terribilis is considered
to be one of the most deadly poisons to humans,
however it is harmless to predator,
the snake Liophis epinephelus .
bio.davidson.edu
• Before you can study any of these complex
systems, you must understand the molecules
that are behind all the wonder…..
CHNOPS: the 6 most common elements in living things
• Biological molecules, are built by joining
atoms through covalent bonds.
• Although more than 25 types of elements can
be found in biomolecules, 6 elements are most
common. These are called the CHNOPS
All compounds can be classified
into 2 broad categories:
1. Organic compounds
•
•
made primarily of carbon atoms.
Most matter in living organisms that is not
water is made of organic compounds.
2. Inorganic compounds
• Compounds that, with a few exceptions, do not
contain carbon atoms. (an exception is CO2- not
organic!) water is ex. of an inorganic compound.
What do people think organic means?
• A survey showed most people think
“organic” refers to organic foods (limited
use of synthetic materials during growth
& production), and only a few science
majors said carbon compounds.
• Organic chemistry is - the study of
the structure, properties, and
reactions of carbon compounds.
I. What is an Organic Compound?
• Contains carbon
atoms
• Even though organic chemistry focuses on carbon,
many organic compounds also contain hydrogen
(H), nitrogen (N)-, oxygen (O), phosphorous (P)
or other elements.
• Carbon molecules make up the bodies of all living
things and have many different functions;
• They are also commonly used in medicine, food,
paints, and gasoline.
Where is Carbon on the Periodic Table?
It forms 4 covalent bonds
Carbon has 4 electrons in
its outmost electron shell.
(It has a valence of 4)
• it forms 4 covalent bonds
A. Carbon Bonding:
C atoms form many different shaped
molecules:
• It can form straight chains, branched chains
with a single bond.
• A carbon atom can also share two or even
three pairs of electrons with another atom.
Carbon bonds: Chains, Branched, Rings
Each line represents a single covalent bond
Carbon also forms
double & triple bonds
A good site for more explanation:
www.biologyjunction.com
Examples: carbon bonding in molecules
B. Functional Groups
- A specific group of atoms that gives a
known type of behavior to molecules
– changes the characteristics of the compound(See page 52 in your textbook for more on functional groups)
Hydrocarbons - C and H only
Alcohols
- OH
Acids
- COOH
Amines
- NH2
An excellent site to look more closely at functional groups:
http://www.phschool.com/science/biology_pl
More Functional groups
Example -adding a hydroxyl group
– makes ethane into an alcohol-
Example - adding an amino
group
- makes methane or ethane into- an amine
C. Naming Hydrocarbons
The simplest organic compounds are hydrocarbons. Hydrocarbons
are compounds that consist of hydrogen and carbon atoms.
When naming hydrocarbons, the prefixes vary depending on the
number of carbons in a compound, the prefixes are:
Number of
Carbon(s):
Prefix:
Number of
Carbon(s):
Prefix:
1
2
3
4
5
MetEthPropButPent-
6
7
8
9
10
HexHeptOctNonDec-
http://chemwiki.ucdavis.edu/index.php?title=Organic_Chemistry/Case_Studies/What_is_Organic%3F#Carbon-containing_Compounds
Methane
- the simplest carbon compound-
1 Carbon & 4 hydrogen atoms
Other simple organic molecules
• Butane
cyclohexane
D. Drawing Molecules: ways that
a molecule can be drawn:
1. Skeletal Structure (Kekulé Structure)
• In this form of representation, atoms are
placed on a plane and lines are drawn
between atoms to represent bonding
electrons.
2. Condensed Structure
• A simplified version
of the bond-line structure that omits the lines. When
there are 2 or more of the same kinds of atoms
attached to a central atom, a subscript is used to
indicate how many of these atoms are attached.
3. Lewis Structure
• valence electrons are represented
as dots. This structure shows what
atoms are bonded together, which electrons are
involved in bonding, lone pairs, any formal charges.
E. Isomers- same chemical
formula, different structure!
• Organic molecules are three-dimensional
• the same set of atoms can be put together in
different ways, resulting in “isomers”
• Example: The atoms found in a simple sugar, with
the structural formula C6H12O6, can be arranged in
over a dozen different ways.
sonefe.org
F. Polarity: Unequal electron sharing
• In covalent bonds e sharing is not always equal.
• Example: Water - oxygen contains a higher
negative charge density than hydrogen. So electron
distribution is asymmetric, or polar, and the oxygen
atom is said to be electronegative.
• This asymmetry results in regions
of slight negative & positive
charge in different regions of the
molecule, denoted by the Greek
symbol δ (delta), for "partial" charge.
Electronegativity is a measure of
the tendency of an atom to attract
a bonding pair of electrons
• Oxygen is a very
electronegative atom &
pulls electrons to itself.
• That would leave the
oxygen side of a
molecule fairly
negative and the carbon
fairly positive.
http://www.chemguide.co.uk/basicorg/bonding/eneg.html
G. Sizes of Molecules
Monomers- small simple molecules
2. Polymers- big molecules formed
1.
when monomers bonded to each other
3. Reactions to build or
break down molecules
• Condensation Reaction
– 2 monomers join together- a water
is released
(an H from 1 end and an OH from the other
end are cut loose when the monomers join.)
• Hydrolysis Reaction
– polymers are broken back down- they
need a water added.
Hydrolysis of sucrose
Condensation Reactions (also called
dehydration synthesis) -builds monomers into polymers
http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html
Hydrolysis Reactions- break down
polymers into monomers by adding water
H. Energy from ATP
• Life needs a constant supply of energy
• Chemical bonds store energy.
• One molecule that living things use to store
energy is in the bonds of the ATP molecule
• Adenosine Triphosphate
Adenosine Triphosphate
Blue = ribose (a 5-carbon sugar)
Green = adenine (a nitrogenous base)
Yellow = phosphate groups
Energy is stored in bonds joining
the phosphate groups
ATP-ADP Cycle.
Energy is stored in ATP (ADP + P)
Energy is used as needed & ATP is
converted back to ADP + phosphate.
ATP further explained
• A nitrogen-containing compound, adenine, is
represented by the two rings & The three
linked phosphate groups, -PO4- are
represented by the small circles with a “P.”
• Because the phosphate groups are close
together and have negative charges. When
a bond between the phosphate groups is
broken, energy is released.
• This hydrolysis of ATP is used by the cell to
provide the energy needed to drive the
chemical reactions in an organism
II. Four Classes of
Organic Molecules
• Much of biochemistry deals with the
structures, functions and interactions of
cellular components, basically:
•
•
•
•
Carbohydrates
Proteins,
Lipids
Nucleic Acids
Monomers & Polymers
• Each group has small
molecules
(monomers)
• linked to form larger macromolecules
(polymers) three to millions of subunits.
A. Carbohydrates
the most important energy source for cells
–
short-term energy storage (sugar)
–
intermediate-term energy storage
• starch for plants
• glycogen for animals
–
as structural components in cells
• cellulose cell walls of plants
• chitin -exoskeleton of insects
Monomers & Polymers
1. Monosaccharides
- single sugar units glucose
2. Disaccharides
- two monosaccharides. Lactose, maltose
3. Polysaccharides
- linking many sugar units together
Examples: starch, glycogen, cellulose
Carbohydrates
• General formula
[CH2O]n
• where n is a number
between 3 and 6.
• Ex- glucose=
C6H12O6
Maltose & Lactose are examples of disaccharides
What does it
mean to be
“lactose
intolerant”?
Got Milk?
- milk’s sugar is lactose
• Infant mammals are fed on milk from mom
• Enzyme lactase digests
the molecule into its two
subunits for absorption.
• in most species, including humans,
the production of lactase gradually
ceases with maturity, & they are
then unable to metabolize lactose…
becoming “Lactose
intolerant”
A Polysaccharide
Lots of monomers linked together
B. Proteins
• Important as control and structural elements.
– Control –enzymes,
–
hormones.
Structural -cell membrane, muscle tissue, etc.
• Amino acids are the
building block of proteins
• All living things (and even viruses) use various
combinations of the same 20 amino acids.
1. An Amino Acid
an amino end (NH2)
a carboxyl end (COOH).
R is the variable (R-group) of each amino acid.
*Amino acids are linked together by joining
the amino end of one molecule to the
carboxyl end of another.
*Removal of water (condensation reaction)
links amino acids with a peptide
bond.
2. PEPTIDE BONDS
Condensation reaction- (also called
dehydration synthesis) To build a peptide chainadd monomers & lose a water! Makes a peptide bond!
http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html
• your amino acid pun
for the day: The
cysteine chapel.
http://popperfont.net/tag/biochemistry/
Some examples of proteins
• Antibodies: they recognize molecules of
invading organisms.
• Receptors: part of the cell membrane, they
recognize other proteins, or chemicals, and
inform the cell... 'The Door Bell'.
• Enzymes: assemble or digest.
• Neurotransmitters and some hormones:
Trigger the receptors... (the finger on the door
bell...)
• Channels, and pores: holes in the cell
membrane (with or without a gate). Usually,
filter the flow...
3. Enzymes• Organic molecules that act as catalysts
• Enzymes & substrates (the reactants) fit
together like a “lock & key”
• This fit weaken bonds so that less energy is
needed for reaction.
Enzymes- really important little guys!
• protein molecules, (or RNA molecules) can
act as biological catalysts -are essential for
the functioning of any cell.
• Enzyme reactions depend on a physical fit
between the enzyme, at its active site on a
specific substrate.
• the substrate and enzyme link together, it
causes a slight change in the enzyme’s
shape, which weakens some chemical bonds
in the substrate, that reduce the amount of
activation energy needed.
http://alevelnotes.com/Enzymes/144
How Enzymes Work
Most reactions in a cell require high temperatures to
start, which would destroy the cell. Enzymes work
by lowering the Activation Energy of a reaction.
Examples
• Enzymes like DNA polymerase make important
molecules (like DNA) in cells.
• Enzymes are used for a wide variety of purposes,
such as Pepsin & Trypsin in digestion.
• Enzymes are also used to destroy invading
Microorgansims. Phagocyte cells engulf
pathogens and the endocytosed
vesicle then fuses with Lysosomes
which contain enzymes that destroy
the pathogen's cell membrane.
tutorvista.com
Enzymes Need Optimal Temperatures:
-Unwind if too hot, don’t work if too cool.
• At high temperatures, enzymes denature
(unwind) and lose their catalytic properties.
• at low temperatures, the reaction rate decreases.
Enzymes also need optimal pH!
• The pH at which enzymatic activity is
maximal is known as the optimum pH.
• Within limits, enzymatic activity increases
as substrate concentration increases.
http://classes.midlandstech.com/carterp/Courses/bio225/chap05/ss2.htm
C. Lipids
• Functions:
1. Long-term energy storage.
-Generally insoluble in polar substances
(water)
• phospholipids are the major building
block in cell membranes
• hormones ("messengers") play roles in
communications within and between
cells.
1. Structure of
Fatty Acids
• The carboxyl head is
polar- therefore it is
HYDROPHILIC –
water loving
• The hydrocarbon CH2
units are
HYDROPHOBICwater fearing
(not water soluble).
Fatty acids
• Can be saturated (meaning they have as many
hydrogens bonded to their carbons as possible)
• Unsaturated (with one or more double bonds
connecting their carbons, hence fewer
hydrogens).
• A fat is solid at room temperature, while an oil is
a liquid under the same conditions. The fatty
acids in oils are mostly unsaturated, while those
in fats are mostly saturated.
2. Triglycerides
• Triglycerides are composed of three fatty
acids (usually) covalently bonded to a 3carbon glycerol.
Fats and oils function in energy storage.
• Animals convert excess
sugars into fats.
• Most plants store excess
sugars as starch,
although some seeds and
fruits have energy stored
as oils (e.g. corn oil,
peanut oil, palm oil,
canola oil, and
sunflower oil).
– Fats yield 9.3 Kcal/gm,
while carbohydrates yield
3.79 Kcal/gm. Fats store
six times as much energy
as glycogen.
Diets & Fat Intake
• Attempts to reduce the amount of fats present in
specialized cells known as adipose cells that
accumulate in certain areas of the human body.
• By restricting the intakes of carbohydrates and
fats, the body is forced to draw on its own stores
to makeup the energy debt.
• The body responds to this by lowering its
metabolic rate, often resulting in a drop of "energy
level."
• Successful diets usually involve three things:
decreasing the amounts of carbohydrates and fats;
exercise; and behavior modification
3. Phospholipids
• One fatty acid is
replaced with a
phosphate.
• The negative charge(s) of the phosphate makes
the “head” of the phospholipid hydrophilic.
The long, hydrocarbon tail is non-polar and,
therefore, hydrophobic.
•
*The water loving edge of the molecule orients
toward water- the inside and outside of the cell.
*The water fearing edges of the molecule orient
toward each other to make a lipid “bilayer”
- the construction of the cell membrane.
4. Cholesterol and steroids:
• Structure is a lipid with 4
carbon rings with various
functional groups attached
• Cholesterol has many
biological uses, such as its
occurrence in the cell
membranes, and its role in
forming the sheath of
some neurons. Excess
cholesterol in the blood
has been linked to
atherosclerosis, hardening
of the arteries.
• Steroids are mainly used
as hormones in living
things
•Structure of four steroids. Image from Purves et al., Life:
The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.
D. Nucleic Acids
•Function - informational molecules –
heredity/genetic, protein synthesis, and energy
•A nucleotide is formed from a 5 carbon
sugar, a phosphate and a nitrogen base.
•Polymers formed by linking together long
chains of nucleotide monomers.
3 Nucleic Acids
1. DNA-deoxyribonucleic acid
Double strand of nucleotides
Double Helix shape
• RNA-ribonucleic acid
Single strand nucleotides
1. ATP -Adenosine Triphosphate
Structure of DNA
double strand of nucleotides
Structure of tRNA -single strand of nucleotides
RNA differs from DNA in the
following ways:
• RNA is single stranded while DNA is
double stranded.
• RNA has a sugar called ribose while
DNA has a sugar called deoxyribose.
• RNA has the base uracil while DNA has
the base thymine.
How DNA & RNA work together
• DNA(deoxyribonucleic acid) is the genetic material.
• It functions by storing information regarding the
sequence of amino acids in each of the body’s
proteins.
• This "list" of amino acid sequences is needed when
proteins are synthesized.
• Before protein can be synthesized, the instructions in
DNA must first be copied to another type of nucleic
acid called messenger RNA.
•
3 types RNA
• Messenger RNA, or mRNA.
– carries the code for building a protein from the nucleus to
the ribosomes in the cytoplasm. It acts as a messenger.
• Transfer RNA or tRNA.
– picks up specific amino acids in the cytoplasm & brings
them into position on ribosome where they are joined
together in specific order to make a specific protein.
• Ribosomal RNA or rRNA –place for protein synthesis
How a protein is built