biochemistry bio 1 ch2 notes. atomic structure all atoms have the same basic structure in the center...
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BIOCHEMISTRYBIOCHEMISTRYBio 1Bio 1
CH2 NOTESCH2 NOTES
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Atomic Structure
• All atoms have the same basic structure• In the center of the atom is the nucleus
which contains the protons and neutrons– Protons have a positive charge– Neutrons have a neutral charge
• Moving at high speed around the nucleus in a circular orbit is the electron– Electrons have a negative charge– There are multiple orbits for the electrons to move in –
in the first orbit there are only 2 electrons and then 8 electrons in each subsequent orbit
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= protons - -
= neutrons - -
= electrons -
-
-
_______________=center of an atom.Home to protons and neutrons.
Carbon Atom
Positively charged1 amu
No charge
1 amu
Electronegative charge1/1840 amu
electrons travel in regions outside the nucleus called orbitals
Nucleus
If the # of _________ = # of _________ the atom is _____________ (no overall charge)Ex. 6 protons = ++++++ 6 electrons = ------
protons electrons neutral
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Elements• Something that is made
up only one type of atom
• All elements that have been discovered are listed on a periodic table – describes the weight of
the element, the number of electrons and gives the symbol that is used to describe the element
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Reading the Periodic Table Example: The element Carbon (only made of carbon atoms)
6
CCarbon12.011
Section 2-1
An Element in the Periodic Table
____________usually 1-2
letters
_______________= # Protons + # neutrons in an atom; the average of one element’s isotopes
____________ of the element
Atomic number =
SYMBOL
MASS NUMBER
NAME
Number of protons in an atom; different for each element
Isotopes are the various forms of an atom that differ based on the number of neutrons in the nucleus such as C 14. The isotopes that differ from the most common form are often radioactive or unstable.
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Isotopes• An element that has more
neutrons than published on the periodic table
• The isotope weighs more than the original form of the element because of the extra neutrons
• Because the number of electrons is the same as the original element the isotope behaves the same in chemical reactions
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Radioactive Isotopes• isotopes with nucleus that is
unstable • Over time the neutrons are released
into the environment as the isotope breaks down
• The break down of the isotope occurs at a constant rate– used to date fossils by comparing the
concentrations of radioactive isotopes in the fossil to the concentration in the current environment
• Radiation can be good or bad• It can cause cancer and other life
threatening diseases– Can be used to diagnose disease and treat
cancer
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Compounds
• More than one element joined together with a bond
• The chemical properties of the compound are often very different than those of the individual elements
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Ionic Bonds
• two or more electrons are transferred from one atom to another
• atom that loses electrons has a positive charge
• atom that gains electrons has a negative charge
• The opposite charge of the ions forms a strong attraction between the ions
IONS
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Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl-)
Transferof electron
Protons +11Electrons -11
Charge 0
Protons +17Electrons -17
Charge 0
Protons +11Electrons -10
Charge +1
Protons +17Electrons -18
Charge -1
Section 2-1
Figure 2-3 Ionic Bonding
Ionic Bonding
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COvalent Bonds (Co = sharing)
• two or more electrons shared between two elements
• covalent bonds formed between two elements >>resulting compound is a molecule
• These bonds are stronger and harder to break than ionic bonds graphite
diamond
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WATER Cbio pp72-73; Ch2-2 Bio
• Universal solvent– Most things will dissolve in it
• Can exist in all three stages on earth– Water – liquid– Ice – solid– Water vapor – gas
• The ability to bond and dissolve most things is due to the polarity of the molecule– Positive charge on one end and
negative charge on the other– Covalent bonds between the
hydrogen and the oxygenCOVALENT BONDS
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Water Molecule
Creates polar nature of water
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WATER, DIAMOND, GRAPHITE SALT
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Mixtures• Two or more substances
mixed together but not chemically bonded together– Example is salt and pepper
• All the materials are evenly distributed through the area
• The compounds remain intact• Mixtures Solution or
Suspension
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Solutions• All materials undergo physical
but not chemical change• One thing is dissolved into
something else– Solvent – the thing that does the
dissolving– Solute – the thing that is dissolved
• The best type of mixture – the individual parts can not be seen even under a microscope
• The compounds are split apart and release the individual ions
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Ionic solutionsIonic compounds dissociate in water to become their individual ions.
Note how Hs of water are nearest Cl- and O of water is nearest Na+
Solute: Solvent:
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Section 2-2
Figure 2-9 NaCI Solution
Cl-
Na+
Water
•Acids release Acids release hydrogen (H+)hydrogen (H+)
• Hydrogen - most Hydrogen - most chemically reactive chemically reactive ion known; attacks ion known; attacks other chemical other chemical bondsbonds
•Bases release Bases release hydroxides (OH-)hydroxides (OH-)•pH is the pH is the measurement of the measurement of the concentration of concentration of hydrogens and hydrogens and hydroxides in the hydroxides in the solutionsolution
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More Hydroxideions (OH-)
More Hydrogenions (H+)
BASE (Alkaline)
Acid
pH Scale
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Suspensions
• Materials that don’t mix but instead float at a constant level in liquid
• The material is too small and light to sink– Blood – red blood cells
are suspended in the plasma
– Oil and water
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Chemical Reaction
CHEMICALS REACT TO BECOME OTHER CHEMICALS
REACTANTS PRODUCTS
H2O2 H20 + O2
Hydrogen peroxide on wound bubbles
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ENERGY FROM CHEMICAL REACTION
• HEAT
• SOUND
• LIGHT
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CHEM REVIEW
• 3 PARTICLES THAT MAKE UP AN ATOM
•ELECTRONS IN SPACE AROUND NUCLEUS
•NUCLEUS HAS PROTONS AND NEUTRONS
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ISOTOPES
• ATOMS OF THE SAME ELEMENTS
• SAME NUMBER OF PROTONS
• SAME NUMBER OF ELECTRONS
• DIFFERENT NUMBER OF NEUTRONS
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RADIOACTIVE ISOTOPES
• AGE OF ROCKS AND FOSSILS
• TREAT CANCER AND KILL BACTERIA
• USE TO “TRACE” MOVEMENTS OF SUBSTANCES IN ORGANISMS
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TWO OR MORE ELEMENTS MAKE A…..
• COMPOUND
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ATOMS & ELEMENTS MAKING UP WATER?
• ONE ATOM OF OXYGEN
• TWO ATOMS OF HYDROGEN
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IONIC VS COVALENT• IONIC – TRANSFER
e-• COVALENT –
SHARED e-
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MacromoleculesCarbon Compounds 2-3
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Types of Compounds• Inorganic
– Any compound that does not contain carbon• Example is water – H2O (water and oxygen)
– The body contains some inorganic compounds• Therefore the association with life is not a good
indicator about whether or not something is organic
• Organic– Any compound that contains carbon– Contains strong covalent bonds which make a
great backbone for life
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Methane Acetylene Butadiene
Benzene Isooctane
Section 2-3
Figure 2-11 Carbon Compounds
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Polymerization
• The process of joining two smaller organic compounds to form one large organic compound
• The small pieces of the compound are called monomer – Two monomers form one polymer
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CarbonCompounds
include
that consist of
which contain
that consist of that consist of that consist of
which contain which contain which contain
Section 2-3
Concept Map
Carbohydrates Lipids Nucleic acids Proteins
Sugars and starches
Fats and oils Nucleotides Amino Acids
Carbon,hydrogen,
oxygen
Carbon,hydrogen,
oxygen
Carbon,hydrogen,oxygen, nitrogen,
phosphorus
Carbon,hydrogen,oxygen,
nitrogen,
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Carbohydrates• More commonly known as sugars and
starches• Made up of different arrangements of carbon,
hydrogen and oxygen– There are two hydrogens for every oxygen in the
chain
• Carbohydrates are the main energy source for the body
• Plants use carbohydrates for support of cell structures (cellulose)
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Carbs. cont.• Monosaccarides
– easiest for the body to digest in order to produce energy (energy is released for use when bonds are broken)
– All have the same chemical structure with different arrangements
– C6H12O6 remember this formula, it will haunt you later
– Include glucose, fructose and galactose
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Carbs. Cont.
• Polysaccharides– combination of many monosaccharides– This is how extra sugars are stored– Starch is this type of compound and is
produced by plants– The animal equivalent of starch is glycogen– Humans break down starch and glycogen
through the process of hydrolysis• C6H12O6 CO2 + H2O + energy
• The extra oxygen comes from the air we breathe (that’s why we need oxygen)
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Starch
Glucose
Section 2-3
Figure 2-13 A Starch
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Lipid• Also known as fats and oils• Do three main things for the human body
– Stores energy– Composes the cell membranes– Can act as a chemical messenger (hormones)
• The difference between a fat and an oil is that fats are solid at room temperature and oils are liquid
• Most lipids are a combination of fatty acids and glycerol (P46)– Fatty acid = a long chain of Cs and a COO group– Glycerol = an alcohol with a hydroxyl group– When these two things are joined water is released
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Lipids Cont.• Saturated lipids
– Every carbon atom is bonded to a hydrogen by a single bond
– Found in meats and dairy products• Unsaturated lipids
– There is at least one carbon to carbon double bond which limits the number of hydrogens present
– This is the healthiest to digest because it is harder for the body to break down (margarine as opposed to butter)
• Polyunsaturated lipids– Many double bonds are present between the carbons
in the fatty acid chain
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Nucleic Acids• The basis for genetics because
it makes up your DNA and RNA• Composed of individual
nucleotides– Each nucleotide is made up
of • 5 carbon sugar• A phosphate group• A nitrogenous base
– Each nucleotide is joined to the next by a covalent bond
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Proteins• Macromolecules made of nitrogen, carbon, hydrogen
and oxygen• C,H,O,N join together to form polymers called amino
acids– These make up DNA and RNA– More than 20 amino acids exist in the human body
• Covalent bonds between amino acids are called peptide bonds– They are formed by the dehydration synthesis
• Perform 4 main functions in the human body– Carry out chemical reactions– Act as membrane pumps– Move cells– Join to contain genetic information
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General structure Alanine Serine
Section 2-3
Figure 2-16 Amino Acids
Amino group Carboxyl group
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Aminoacids
Section 2-3
Figure 2-17 A Protein
Protein Structure: Turn to p 48
Proteins:1.Amino acids connected to become a protein chain.
2.Amino acids fold or twist
3.Protein chain itself can be folded.
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CHEMICAL REACTIONS, ENZYMES
2-4
http://www.biologie.uni-hamburg.de/b-online/library/cat-removed/enzyme_.gif
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Chemical reactions need help to get started.
Ex: A fire needs a match to get it started.
http://www.chuckwagondiner.com/art/matches.jpghttp://plato.acadiau.ca/COURSES/comm/g5/Fire_Animation.gif
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______________ to get a chemical reaction _______________
= ________________________
Image from: Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved
ACTIVATION ENERGY
REACTANTSPRODUCTS
ACTIVATIONENERGY
Energy requiredSTARTED
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___________ HELP CHEMICAL REACTIONS _______________
Catalysts work by ____________ the___________________________to get a chemical reaction started.
Image from: Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved
DECREASING
CATALYSTS
ACTIVATION ENERGY required
HAPPEN FASTER
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IT’S LIKE PUSHING A SNOWBALL UP A HILL
Once it gets to top . . . it can roll back all by itself
http://www.gifs.net
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CATALYSTS in Living Things
In living systems __________ that
________________to control chemical reactions are called
= _________
Image from: http://www.hillstrath.on.ca/moffatt/bio3a/digestive/enzanim.htm
PROTEINS
act as catalysts
ENZYMES
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Video 4
• Click the image to play the video segment.
Video 4
Enzymatic Reactions 2D
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PROTEINS CAN BE ENZYMES
SUBSTRATE
ENZYME-SUBSTRATE COMPLEX
PRODUCTSENZYMEUnchanged& Reusable
ENZYME
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ENZYMES _____ like a _______________
to only _________of _________.
Enzymes are ___________ by thereaction and ___________
LOCK AND KEY
REUSABLEUNCHANGED
FIT
ONE KIND SUBSTRATE
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FACTORS THAT AFFECT ENZYME ACTIVITY
__________ & ______________
Conditions that are TOO ACIDIC
or TOO HOT cause proteins to________ or _________
pH temperature
UNWIND DENATURE
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See a movie
Choose narrated
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Denaturing _______ the _______ of the ______________ so enzyme ______________ to ____________
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_______________ (keeping pH and temperature constant) is ______________ for maintaining ____________________
HOMEOSTASIS
changes shapeACTIVE SITE
CAN’T BINDSUBSTRATE
IMPORTANT ENZYME FUNCTION
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Many enzyme NAMES end in _____and the beginning of the name tells what it does
DNA Polymerase= “polymerizes” joins monomers to make DNA
Protease= breaks down proteins
ATP synthase= synthesizes ATP
-ASE