Transcript biochemistry notes w packet edit

ADVANCED BIOLOGY
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 Matter – anything that has mass and takes up space
 Everything is made of matter
 “Physical Stuff” in the universe
 All elements are composed of atoms
 Atoms – smallest basic unit of matter
 Millions could fit on this period
.
 Made of three smaller components called subatomic particles
 Protons: + charge, in nucleus
 Neutrons: no charge, in nucleus
 Electrons: - charge, surrounding nucleus
(nucleus of atom contains most of the atom’s mass)
 Element – a pure substance that cannot be broken down
into other substances
 Molecule- two or more atoms chemically combined, or
bonded.
The formula for this molecule is H2O
 Compounds Substance made of 2 or more elements that are chemically
combined in a fixed ratio
 Ex: Water, Sodium Chloride (salt), sugar, proteins
 Cannot be physically separated
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 Elements can be found on the Period Table
 About 25 elements are essential to life
 96% of living matter is Oxygen (O), Carbon (C), Hydrogen ( H) ,
& Nitrogen (N)
 Ca, P, K, & S make up most of the other 4%
 Organic chemistry is the study of carbon compounds
 Deals with carbon based molecules
 Can be simple like hydrocarbons (methane)
 Can be very complex (starches)
 Life without carbon would be as unlikely as life without
water
 Other than water, most molecules of a cell are carbon
based
 No other element is capable of forming molecules as large
and complex as carbon based molecules (without carbon
chains and rings, there could be no DNA!)
 deoxyribose sugar unit contains five carbon atoms
 Out of all the elements on the periodic table, carbon is
arguably the best at bonding.
 Because of carbon’s 4 valence electrons, it can make up
to four bonds with other atoms
 An endless variety of carbon skeletons can be formed
leading to many combinations
 Carbon can also bond to another carbon in a straight
chain, branched chain or ring bond.
 The shape of an organic molecule determines its
function. (can become different macromolecules)
 Inorganic molecules are
 Non-carbon based molecules
 Water, oxygen, ammonia (NH3)
 Functional groups give different properties to the
organic compound to which they attach.
 Hydroxyl group in an alcohol, that determines the
chemical behavior of the compound (oxygen atom
connected by a covalent bond to a hydrogen atom).
 Polymers – long chain of smaller molecular units
 Can be a simple straight chain or large multiple branching
chains
 Essential to life
 Built from fewer than 50 kinds of monomers
 Life’s major large molecules (polymers)
 Carbohydrates, Lipids, Proteins, Nucleic Acids
 Monomers – smaller molecular units
 Mono= one
 Building blocks of larger molecules
 Can be “usable” by themselves
 Dehydration synthesis links small molecules or
monomers together by removing molecules of water.
 Hydrolysis involves adding a molecule of water in order
to break bonds.
 Ionic bonds – occurs when electrons are transferred
between atoms
 Usually between a metal and non-metal
 Each atom becomes charged
 1 is + and the other is -
 Covalent bonds – occur when atoms share electrons
 Usually between 2 non-metals
 Forms molecules (2 or more atoms covalently bonded)
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 Oxygen has a stronger attraction of the shared electrons
 Creates a V-shaped molecule
 Oxygen has 8 electrons and hydrogen has one electron.
 Creates a polar molecule
 A molecule in which the opposite ends are oppositely
charged
 Creates a hydrogen bond
 An attraction between a slightly
positive atom and a slightly
negative atom
• This allows for water to have very
unique properties
 Cohesion – water molecules “sticking” together
◦ Spider “skating” on water
◦ Dew drops
◦ Surface tension
 Adhesion – water molecules “sticking” to other molecules
◦ Surface tension
◦ Sticking to surfaces
◦ Water moving up tubes (plants)
 High Specific Heat
◦ Water resists changes in temperature
◦ Water takes longer to heat up and cool down
◦ Evaporation causes cooling of body
◦ Large bodies of water change temp or land nearby
 Low Density of ice
 Normally solids are more dense than liquids
 Ice is less dense than liquid water
 Bodies of water freeze top down, lets things live underneath
 Water is an excellent solvent
 Can dissolve many things easily
 Allows living things to absorb different substances
 Occurs due to charges being used to attract substances and
hold onto them
 Solutions – a mixture of substances that is the same
throughout (evenly mixed)
 Many important life solutions: blood plasma, saliva
 Solvent – substance present in great amount; it dissolved the other
substance (water in Kool-Aid)
 Solute – substance that is dissolved (sugar in Kool-Aid)
 Some substances cannot be dissolved in water
 These are non-polar (not charged) molecule
 Oils and Fats do not mix with water
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 Solutions will have some hydrogen and hydroxide ions in
the solution
 Acids – compound that donates H+ ions to an aqueous
solution
 Acids have more H+ ions
 Bases – compound that removes H+ ions from an
aqueous solution
 Bases have more OH- ions
 An acid is a compound that releases a proton- a
hydrogen ion (H+ ) – when it dissolves in water.
 A base is a compound that removes H+ ions from a
solution
 Most organisms need to keep their pH between 7.357.45
 Slightly basic
 pH is regulated in organisms by substances called
buffers
 pH scale measures amount of H+ ions
 Lower numbers indicate acid
 0-6.9  lower = more acidic
 Higher numbers indicate base
 7.1-14  higher = more basic
What happens when acids and bases are
mixed together?
When they are mixed together, a chemical reaction occurs.
This chemical reaction is called neutralisation reaction. It is
called so because they both neutralise each other to produce
a salt and water. Also remember the following points.
• When a strong acid and weak base are mixed, the salt formed
is an acidic salt.
 When a strong base and weak acid are mixed, the salt formed
is a basic salt.
 When both the acid and base are strong, then the salt formed
is a neutral salt
 Low Acid Foods
 Foods that have a low acid content include dairy products and
vegetable oils.
 Medium Acid Foods
 Foods that have a medium acid content include bananas,
eggs, nuts, oats, whole wheat bread and potatoes.
 High Acid Foods
 Foods that have a high acid content include sugars, beef,
white flour products and black tea. These are also low in base.
Source: http://www.livestrong.com/article/29548-list-acid-base-foods/#ixzz2iYHlK7MD
 Low Basic Foods
 Foods that have a low base content include almonds, honey,
mushrooms and olive oil.
 Medium Basic Foods
 Foods that have a medium base level include apples, avocados,
peaches and figs.
 High Basic Foods
 Foods with a high base content include papaya, asparagus,
watermelon, and parsley. These are also low in acid.
Source: http://www.livestrong.com/article/29548-list-acidbase-foods/#ixzz2iYHlK7MD
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Carbohydrates
 What are they?
 a large group of organic compounds occurring in foods and living tissues
and including sugars, starch, and cellulose. They contain hydrogen and
oxygen in the same ratio as water (2:1) and typically can be broken down
to release energy in the animal body.
 Functions? Source of energy
Lipids
 What are they?
 any of a class of organic compounds that are fatty acids or their
derivatives and are insoluble in water but soluble in organic solvents.
They include many natural oils, waxes, and steroids.
 Functions? Energy storage
Proteins
 What are they?
 nitrogenous organic compounds that consist of large
molecules composed of one or more long chains of amino
acids and are an essential part of all living organisms.
 Functions? Structural components of body tissues such as
muscle, hair, collagen, etc. along with enzymes and
antibodies
Nucleic Acids
 What are they?
 a complex organic substance present in living cells, especially
DNA or RNA, whose molecules consist of many nucleotides
linked in a long chain
 Functions? Make up DNA & RNA
 Carbs- organic molecule made up of sugar
molecules (C, H, O atoms bonded)
 Ratio: 1 C & O, 2 H
 Base formula is CH2O
 Divided into 3 major categories
 Monosaccharides
 Disaccharides
 Polysaccharides
Carbohydrates names end in- saccharide
Major Function: Main Energy supply for cells
 Monosaccharides –
 Simple sugars with just 1 sugar unit
 Examples:
 Fructose – C6H12O6- found in fruit
 Glucose - C6H12O6 -found in plants
 Galactose - C6H12O6 -found in milk
 Provide energy quickly
 Are not “big” molecules and are easier to breakdown
 Disaccharides (di- means= two)
 Combination of two monosaccharides
 Combined in a dehydration reaction
 Sucrose (example)
 Table sugar, maple syrup
 Easily broken down by cells into mono- and then used for
energy

Molecules of Sugars
1.
Sucrose
Made of GLUCOSE and FRUCTOSE
2.
Maltose
GLUCOSE and GLUCOSE
3.
Lactose
Made of GALACTOSE and GLUCOSE
 Polysaccharides – long polymer chains of
monosaccharides (aka: complex carbs)
◦ Starch – found in plants Glucose monomers
 Serve as sugar storage units
 Eaten when we need large energy supply later
◦ Cellulose – found in plants, structural supports plants
 Serve as building materials, know as fiber
 Fiber cleans out your intestinal tract (regularity) 
◦ Glycogen – found in animals
 Stored usually in liver cells
The energy from carbohydrates comes from the breaking of the
bonds between carbon and hydrogen.
Chitin- structure support for insects and fungi
 Grains:
 Fiber – whole grains
 Starches
 Fruits:
 Fiber – usually skins
 Starches
 Some Mono & Di
 Junk Food:
 Processed/refined
 Simple sugars, not
healthy though
 Vegetables:
 Fiber – lots of it
 Starches
 Milk Products:
 Lactose -disaccharide
 Meat:
 No carbs unless added
 Liver does have glycogen
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 Lipids are made up of Carbon, Hydrogen, and
Oxygen
 The ratio is Carbon: Hydrogen: Oxygen 1:2:very few
(.05)
 Hydrophobic – avoiding water, not mixing with
water molecules (hydro=water, phobic= fear)
 Hydrophillic – ability to attract water molecules
 Lipids – a class of water-avoiding compounds
 Lipids include oils, fats, steroids, & cholesterol
 Each will avoid or repel water (do not mix)
 Non-polar molecules
 Fats
 Consist of three –C backbone





called glycerol attached to 3
fatty-acids
Primary Function: Energy
Storage
Lipids contain more energy
than carbohydrates
Other functions: cell
membrane, insulation, organ
cushioning
Lipids store
Saturated Fats
 Animal fats
 Solid at room temp
 Unsaturated Fats
 Plant & fish oils
 Liquid at room temp
 Steroids
 Carbon skeleton is a fused
ring (not line)
 Lipid since they are
hydrophobic
 Chemical messengers
(hormones EX:
Corticosteroids & androgenic/
anabolic)
 Cholesterol
 Type of steroid
 Forms cell membranes
 Produces other steroids
 Needed, but can harm
 Glycerols
 a.) Glycerols are the monomers of the lipid.
 Fatty Acids
 a.) Long chain of carbon and hydrogen called a fatty acid
chain.
 The monomers (building blocks) that make up lipids are
called glycerol and fatty acids.
 The most commonly occurring lipids, called triglyceride,
have 3 fatty acids bonded to a lone glycerol molecule.
 These subunits are joined together by removing water.
 Saturated fatty acids
 Contain fatty acids in
which all carboncarbon bonds are
single bonds.
 Solid at room temp.
 Unsaturated fatty
acids
 Have fatty acids with
at least one carboncarbon double bond
 Liquid at room temp.
 Steroids
 Carbon skeleton is a fused ring (not line)
 Lipid since they are hydrophobic
 Chemical messengers (hormones)
 Cholesterol
 Type of steroid
 Forms cell membranes
 Produces other steroids
 Needed, but can harm
 Good:
 How we get it
 Energy storage
◦ Unused
 Insulation
carbohydrates energy
stored as fat
◦ From fatty foods
 Membrane Formation
 Bad:
 Cause heart disease
 Clog arteries
 Animal meats
 Oily foods (peanuts)
 Dairy products
◦ Good vs. Bad
 Omega 3 Fatty Acids
 (good)
 LDL (bad)
 Nucleic acids are Polymers that are made of
monomers called nucleotides
 Nucleotide = sugar, phosphate group, & a
nitrogen containing base
 Examples:
 DNA is a nucleic acid that stores information for
putting amino acids together.
 RNA is a nucleic acid that helps put proteins
together
 Nucleic Acids work together to make proteins
A phosphate group
nitrogen-containing molecule,
called a base
deoxyribose (sugar)
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 Proteins are made from the following atoms: N,H,O,C, P
 Proteins are made up on monomers called amino acids
 20 different amino acids create many possible functions
and uses.
 Functions:
 Form Structures – hair, muscles
 Immune defense
 Acts as chemical signals
 Controls reactions in cells
 Transport- Hemoglobin, cell membrane
 Hydrogen: H
 Amino Group: NH2
 Carboxyl Group: COOH
 “R” Group
 There are 20 different amino acids. The difference is in the R group.
 Amino Acids
 Carbon with 4 bonded partners
 1 partner is different in each Amino Acid
 All others are same
 Different = side group or R-group Polypeptides





Long chains of linked amino acids
Polymers
Proteins are made of 1 or more linked polypeptide chains
Usually 100 AA in length
20 AA = many combos
 Amino acids are linked together by dehydration synthesis and held
together by peptide bonds.
 Build Muscles,
ligaments, and tendons
 Many enzymes are
protein based
 Needed for basic use
 Form hemoglobin
 Carries oxygen in blood
 Form cells that fight
disease
 White blood cells
 Foods rich in protein
 Any meat
 Fish!
 Dairy products
 ICE CREAM!
 Milk, cheese
 Most beans
 Soy products
 Peanuts
 Peanut butter
 Grains (bread/pasta)
As always, structure determines function.
1.) Linear sequence of amino
acids (chain)
PRIMARY STRUCTURE
2.) When amino acid chains are
folded
SECONDARY STRUCTURE
3.)The 3-D shape of the protein
TERTIARY STRUCTURE
4.) Two or more separate
proteins interacting
QUATERNARY STRUCTURE
 Proteins differ in the number and order of amino
acids.
 – Amino acids interact to give a protein its shape.
 – Incorrect amino acids change a protein’s structure
and function.
Denaturing in a
protein involves
changing its
structure so it no
longer works.
hydrogen bond
 Chemical reactions are constantly occurring in
the cells of living organisms
 In order to occur more efficiently, the rate of the
reaction needs to be changed
 Catalysts – compounds that speed up chemical
reactions
 Lowers activation energy needed.
 Many proteins act as enzymes, or biological
catalysts.
 Enzymes – specialized proteins that act as
catalysts in living organisms
 Enzymes in cells may break chemical bonds and
lower the amount of activation energy needed for
the reaction.
 Only certain enzymes work on certain molecules
 Shape of enzyme fits a specific molecule
 Substrate – reactant acted upon by an enzyme
 Substrate fits into active site of an enzyme
 Example: Sucrase = enzyme that breaks apart sucrose
(disaccharide)
 Enzyme breaks it into a glucose & fructose
PAGE 27
 Breaking of old and formation of new chemical
bonds that result in new substances
 Breaking bonds releases energy!
 Chemical reactions change substances into
different substances by breaking or forming bonds.
 Chemical reactions have two parts
 Reactants – starting materials of a reaction
 Products – ending materials of a reaction
 Reactants  products
 2H2 + O2  2H2O
 Bond Energy is the amount of energy that will
break a bond between two atoms.
 All chemical reactions involve changes in energy
(absorbed or released)
 Activation energy – amount of energy that needs to
be absorbed to start a reaction
 Exothermic Reaction – chemical reaction that
RELEASES more energy than it absorbs
 Endothermic Reaction – chemical reaction that
ABSORBS more energy than it releases
 Mixtures
 Substance made of 2 or more substances joined together
physically
 Can be separated by physical means
 Ex: blood, synovial fluid, gastric juices, bile, saliva