biochemistry bio 1 ch2 notes. atomic structure all atoms have the same basic structure in the center...

BIOCHEMISTRYBIOCHEMISTRYBio 1Bio 1

CH2 NOTESCH2 NOTES

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

= 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

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

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.

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

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

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

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

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

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

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

Water Molecule

Creates polar nature of water

WATER, DIAMOND, GRAPHITE SALT

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

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

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:

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

More Hydroxideions (OH-)

More Hydrogenions (H+)

BASE (Alkaline)

Acid

pH Scale

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

Chemical Reaction

CHEMICALS REACT TO BECOME OTHER CHEMICALS

REACTANTS PRODUCTS

H2O2 H20 + O2

Hydrogen peroxide on wound bubbles

ENERGY FROM CHEMICAL REACTION

• HEAT

• SOUND

• LIGHT

CHEM REVIEW

• 3 PARTICLES THAT MAKE UP AN ATOM

•ELECTRONS IN SPACE AROUND NUCLEUS

•NUCLEUS HAS PROTONS AND NEUTRONS

ISOTOPES

• ATOMS OF THE SAME ELEMENTS

• SAME NUMBER OF PROTONS

• SAME NUMBER OF ELECTRONS

• DIFFERENT NUMBER OF NEUTRONS

RADIOACTIVE ISOTOPES

• AGE OF ROCKS AND FOSSILS

• TREAT CANCER AND KILL BACTERIA

• USE TO “TRACE” MOVEMENTS OF SUBSTANCES IN ORGANISMS

TWO OR MORE ELEMENTS MAKE A…..

• COMPOUND

ATOMS & ELEMENTS MAKING UP WATER?

• ONE ATOM OF OXYGEN

• TWO ATOMS OF HYDROGEN

IONIC VS COVALENT• IONIC – TRANSFER

e-• COVALENT –

SHARED e-

MacromoleculesCarbon Compounds 2-3

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

Methane Acetylene Butadiene

Benzene Isooctane

Section 2-3

Figure 2-11 Carbon Compounds

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

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,

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)

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

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)

Starch

Glucose

Section 2-3

Figure 2-13 A Starch

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

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

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

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

General structure Alanine Serine

Section 2-3

Figure 2-16 Amino Acids

Amino group Carboxyl group

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.

CHEMICAL REACTIONS, ENZYMES

2-4

http://www.biologie.uni-hamburg.de/b-online/library/cat-removed/enzyme_.gif

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

______________ to get a chemical reaction _______________

= ________________________

Image from: Pearson Education Inc, publishing as Pearson Prentice Hall. All rights reserved

ACTIVATION ENERGY

REACTANTSPRODUCTS

ACTIVATIONENERGY

Energy requiredSTARTED

___________ 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

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

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

Video 4

• Click the image to play the video segment.

Video 4

Enzymatic Reactions 2D

PROTEINS CAN BE ENZYMES

SUBSTRATE

ENZYME-SUBSTRATE COMPLEX

PRODUCTSENZYMEUnchanged& Reusable

ENZYME

Image modified from: http://www.biologie.uni-hamburg.de/b-online/library/cat-removed/enzyme_.gifArrow: http://www.gifanimations.com/action/ImageDisplay/1/2/11/next

ENZYMES _____ like a _______________

to only _________of _________.

Enzymes are ___________ by thereaction and ___________

LOCK AND KEY

REUSABLEUNCHANGED

FIT

ONE KIND SUBSTRATE

http://www.grand-illusions.com/images/articles/toyshop/trick_lock/mainimage.jpg

FACTORS THAT AFFECT ENZYME ACTIVITY

__________ & ______________

Conditions that are TOO ACIDIC

or TOO HOT cause proteins to________ or _________

pH temperature

UNWIND DENATURE

http://www.desktopfotos.de/Downloads/melt_cd.jpg http://www.nealbrownstudio.com/adm/photo/163_nb_fried_egg.jpg

See a movie

Choose narrated

Denaturing _______ the _______ of the ______________ so enzyme ______________ to ____________

Image modified from: http://www.lewport.wnyric.org/jwanamaker/animations/Enzyme%20activity.html

_______________ (keeping pH and temperature constant) is ______________ for maintaining ____________________

HOMEOSTASIS

changes shapeACTIVE SITE

CAN’T BINDSUBSTRATE

IMPORTANT ENZYME FUNCTION

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