Chapter 3 Biochemistry

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Chapter 3 Biochemistry
AC

• 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.

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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.

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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.

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Inside leaves, solar energy is transferred to the
chemical bonds in biological molecules like
GLUCOSE food.
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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/commonmole
cules/biochemical/index.html
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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
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• Before you can study any of these complex
  systems, you must understand the molecules that
  are behind all the wonder..

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Remember!
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

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All compounds can be classified into 2 broad
categories

• Organic compounds
• made primarily of carbon atoms.
• Most matter in living organisms that is not water
  is made of organic compounds.
• 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.

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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.

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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.

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Where is Carbon on the Periodic Table?
It forms 4 covalent bonds
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Carbon has 4 electrons in its outmost electron
shell. (It has a valence of 4)

• it forms 4 covalent bonds

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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.

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Carbon bonds Chains, Branched, RingsEach line
represents a single covalent bond
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Carbon also forms double triple bonds
A good site for more explanation
www.biologyjunction.com
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Examples carbon bonding in molecules
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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_place/biocoach/biokit/function.html
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More Functional groups
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Example -adding a hydroxyl group makes ethane
into an alcohol-

• Example - adding an amino group
• - makes methane or ethane into- an amine

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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 Met- 6 Hex-
2 Eth- 7 Hept-
3 Prop- 8 Oct-
4 But- 9 Non-
5 Pent- 10 Dec-
http//chemwiki.ucdavis.edu/index.php?titleOrgani
c_Chemistry/Case_Studies/What_is_Organic3FCarbon
-containing_Compounds
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Methane - the simplest carbon compound- 1
Carbon 4 hydrogen atoms
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Other simple organic molecules

• Butane cyclohexane

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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.

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• 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.

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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
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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 d (delta), for "partial" charge.

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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.h
tml
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G. Sizes of Molecules

• 1. Monomers- small simple molecules
• 2. Polymers- big molecules formed when monomers
  bonded to each other

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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.

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Hydrolysis of sucrose
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Condensation Reactions (also called dehydration
synthesis) -builds monomers into polymers
http//nhscience.lonestar.edu/biol/dehydrat/dehydr
at.html
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Hydrolysis Reactions- break down polymers into
monomers by adding water
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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

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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
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ATP-ADP Cycle.
The energy is released when the last P is taken
off
Energy is stored in ATP (ADP P) Energy is used
as needed ATP is converted back to ADP
phosphate.
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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

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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

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Monomers Polymers

• Each group has small molecules (monomers)
• linked to form larger macromolecules
• (polymers) three to millions of subunits.

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• 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

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Monomers Polymers
1.   Monosaccharides - single sugar units
glucose 2.   Disaccharides - two
monosaccharides. Lactose, maltose    3.   Polysacc
harides - linking many sugar units
together Examples starch, glycogen,
cellulose
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Carbohydrates

• General formula CH2On
• where n is a number between 3 and 6.
• Ex- glucose C6H12O6

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Maltose Lactose are examples of disaccharides
What does it mean to be lactose intolerant?
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Got Milk?- milks 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

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A Polysaccharide
Lots of monomers linked together
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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.

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1. An Amino Acid
an amino end (NH2) a carboxyl end (COOH).
R is the variable (R-group) of each amino acid.
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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.
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2. PEPTIDE BONDS
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Condensation reaction- (also called dehydration
synthesis) To build a peptide chain- add
monomers lose a water! Makes a peptide bond!
http//nhscience.lonestar.edu/biol/dehydrat/dehydr
at.html
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• your amino acid pun for the day The cysteine
  chapel.

http//popperfont.net/tag/biochemistry/
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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...

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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.

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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 enzymes shape, which
  weakens some chemical bonds in the substrate,
  that reduce the amount of activation energy
  needed.

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How Enzymes Work

• How Enzymes Work
• Most reactions in a cell require very high
  temperatures to get going, which would destroy
  the cell. Enzymes work by lowering the Activation
  Energy of a reaction.

http//alevelnotes.com/Enzymes/144

• 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.

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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.

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tutorvista.com
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Enzymes Need Optimal Temperatures -Unwind if too
hot, dont work if too cool.

• At high temperatures, enzymes denature (unwind)
  and lose their catalytic properties.
• at low temperatures, the reaction rate decreases.

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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/bi
o225/chap05/ss2.htm
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C. Lipids

• Functions
• 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.

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Structure of Fatty Acids

• The carboxyl head is polar- therefore it is
  HYDROPHILIC water loving
• The hydrocarbon CH2 units are HYDROPHOBIC- water
  fearing
• (not water soluble).

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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.

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2. Triglycerides

• Triglycerides are composed of three fatty acids
  (usually) covalently bonded to a 3-carbon
  glycerol.

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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.

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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

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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.

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•     

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.
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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.

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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.

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• 3 Nucleic Acids
• DNA-deoxyribonucleic acid
• Double strand of nucleotides
• Double Helix shape
• RNA-ribonucleic acid
• Single strand nucleotides
• ATP -Adenosine Triphosphate

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Structure of DNA Structure of tRNA
-double strand of nucleotides -single
strand of nucleotides
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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.

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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 bodys
  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.

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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

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How a protein is built
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