Chemistry

Adv an ced Bio lo g y Chemistry

Cla ssific atio n o f Ma tter  Elements  pure substances made of only one type of atom

 Compounds  pure substances made of two or more different elements

Elements Oxygen Sodium Lead

Compounds Dihydrogen oxide (H2O) Sodium chloride (NaCl) Lead nitrate

2.1

???  Turn to your neighbor  Name four other elements  Try to make two compounds from them

Em ergent Pr opertie s

+

Sodium

Chloride

Sodium Chloride

When elements are combined to form compounds new properties are exhibited

Com mon Organi c Elem en ts  Carbon, hydrogen, oxygen, and nitrogen are essential elements  They make up 96% of living matter  The remaining elements may are also essential to life, but in small quantity 2.2

De fic ie ncie s in esse ntia l ele ments Normal crop

Abnormal growth

Goiter

Nitrogen deficiency

Iodine deficiency

Deficiencies can lead to abnormal growth or disease

Cla ssic At omic Mo del

Electron Energy Levels 2.3

Ele ctron En ergy L eve ls  Electrons move very fast in energy levels called orbitals  The orbitals represent the area where an electron is most likely to be at a given moment

S orbital

P orbitals

D orbitals 2.3

At omic Co mposit ion Protons

Neutrons

Electrons

Location

Nucleus

Nucleus

Electron orbital

Charge

Positive (+)

Neutral (0)

Negative (-)

Mass

1 dalton

1 dalton

0.0005 daltons

1 dalton = 1 amu = 1.7 x 10-24 g 2.4

Th e Pe rio dic Ta ble Atomic number Chemical symbol

238

U

92

Chemical name Atomic Mass 2.4

Th e Pe rio dic Ta ble  Atomic number = the number of protons Because protons and neutrons have a mass of 1 dalton...  Mass number = the number of protons plus neutrons

 Atomic mass = the average of all the mass numbers for an element 2.4/2.5

Ca lc ula tin g P/N /e   

Protons = atomic # Neutrons = mass # – atomic # Electrons = atomic # in a neutral atom 1. Atomic # = 92 = protons

238

U

92

3. Mass # = 238

P

N

e

5. Neutrons = 238-92

92

146

92

7. Electrons = protons = 92

2.5

???  Find P/N/e for the following elements P/N/e  Fe

26/30/26

N

7/7/7

 Cl

-1

+1

 Na

17/18/18 11/12/10

Iso topes  Isotopes have the same number of protons and electrons, but different numbers of neutrons  Some isotopes spontaneously give off energy (radioactivity) Isotopes of Carbon 12

14

6

6

C

C 2.6

Usin g i soto pes i n rese arch  Radioactive tracers  The radioisotope are used to replace normal atoms in a molecule  The radioisotopes can then be traced using a scintillation counter

 Radiocarbon dating  Over time carbon 12 decays into carbon 14. The amount of carbon 14 present in a fossil is a relative estimate of its age.  Useful up to ~50,000 years 2.7

Usin g Radioactiv e T racers APPLICATION Scientists use radioactive isotopes to label certain chemical

substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. TECHNIQUE 1

Ingredients including Radioactive tracer (bright blue)

Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H.

1

10°C

Human cells

4

25°C

7

40°C

2

15°C

5

30°C

8

45°C

3

20°C

6

35°C

9

50°C

DNA (old and new)

2 The cells are placed in test

tubes, their DNA is isolated, and unused ingredients are removed.

Incubators

1

2 3

4

5 6

7

8 9

2.7

3

A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter.

Counts per minute (x 1,000)

RESULTS The frequency of flashes, which is recorded as counts per minute, is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.

30 20

Optimum temperature for DNA synthesis

10 0

10

20 30 40 Temperature (°C)

50

2.7

Usin g Radioactiv e T racers  Bone scans use technetium as a radioactive tracer  It concentrates in areas of high blood flow and inflammation 98 Post.

Metastatic Bone Carcinoma

Ant.

43

Tc 2.7

Ele ctrons a nd e nergy Third energy level

• Electrons closer to the nucleus are held tightly

Energy absorbed

Second energy level

• They have less potential for motion as a result

First energy level Energy lost Nucleus

ENERGY = MOTION

• The further from the nucleus the more potential energy electrons have 2.8

???  When light is emitted (such as turning on a light bulb) electrons change energy levels  Do the electrons move toward the nucleus or away from it?

Va le nce electrons  Valence electrons  

Are those in the outermost, or valence shell Determine the chemical behavior of an atom

2.9

Ele ctron Sh ell Dia grams Hydrogen 1H

2 e’s

First shell Beryllium 4Be

Boron 3B

Helium 2He

Element symbol

Carbon 6C

Nitrogen 7N

Silicon 14Si

Phosphorus 15P

Oxygen 8O

Fluorine 9F

Neon 10Ne

Sulfur 16S

Chlorine 17Cl

Argon 18Ar

Second shell Sodium Magnesium Aluminum 13Al 11Na 12Mg

18 e’s

Atomic number

Electron-shell diagram Lithium 3Li

8 e’s

Atomic mass

2 He 4.00

Third shell

2.10

Val ence El ectr ons and Chem ical Propert ies  Atoms need full outer energy levels to be stable (8 electrons)  Atoms form bonds to fill their outer energy levels  Atoms with the same number of valence electrons have similar bonding properties

2.9

Lewi s ( electron) Dot Formu la s  Show the atom’s chemical symbol  Show the atom’s valence electrons as dots

H

C

O

H

O

H

???  Draw Lewis Dot Structures for: N

F

H 2O

Cl 2

Co va le nt Bo nds  Formed when two atoms share a pair of electrons  Electrons are shared so that each atom has a full outer energy level

Formati on of a coval ent bond Hydrogen atoms (2 H)

1

2

3

In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus.

When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus.

The two electrons become shared in a covalent bond, forming an H2 molecule.

+

+

+

+

Representing Covalent Bonds

+

+

Hydrogen molecule (H2)

H H

Lewis Dot Structure

H H

Structural Formula

Single and double bonds Name (molecular formula)

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

Electronshell diagram

Structural formula

H

H

O

O

Spacefilling model

•Single bond - the sharing of one pair of valence electrons •Double bond - the sharing of two pairs of valence electrons

Co va le nt c ompounds Name (molecular formula) Water (H2O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. Methane (CH4). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane.

Electronshell diagram

Structural formula

O

H

H

H H

C H

H

Spacefilling model

Po la r v s. No n-p olar  Electronegativity  Is the attraction of an atom for the electrons in a covalent bond

 The more electronegative an atom  The more strongly it pulls shared electrons toward itself

 In a Non-polar Covalent Bond  The atoms have similar electronegativities  Share the electron equally 2.11

Highly e le ctronegat ive at oms    

Fluorine Oxygen Chlorine Nitrogen

Po la r Co va le nt Bonds  In a polar covalent bond  The atoms have differing electronegativities  Electrons are shared unequally Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

δ–

This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens.

O

δ+

H

H H2O

δ+

2.11

Weak Bo nds

 Hydrogen bonds

 Form when a hydrogen atom bonded to one electronegative atom is attracted to another electronegative atom δ– δ+ H

Water (H2O)

O H δ+ δ–

Ammonia (NH3)

N H δ+

H δ+

A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen H atom of δ+ ammonia.

2.13

Weak Bo nds  Van der Waals interactions  Occur when temporarily positive and negative regions of molecules attract each other

The gecko’s “spiderman” grip is due to Van der Waals attractions 2.13

Weak b onds are esse ntia l  Weak chemical bonds  

Reinforce the shapes of large molecules Help molecules adhere to each other

2.13

Ionic Bonds

 Electron transfer between two atoms creates ions  Ions  Are atoms with more or fewer electrons than usual  Are charged atoms

Cl

-1

 An anion  Is negatively charged ions

 A cation  Is positively charged

2.12

Ionic Bonds  An ionic bond  Is an attraction between anions and cations The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1

2

Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions.

+

Na

Cl

Na

Cl

Sodium atom (an uncharged atom)

Chlorine atom (an uncharged atom)

Na

Na+ Sodium on (a cation)

–

Cl

Cl– Chloride ion (an anion)

Sodium chloride (NaCl)

2.12

Mo lecula r shape and function  The precise shape of a molecule  Is usually very important to its function in the living cell  Determines how biological molecules recognize and respond to one another with specificity

2.15

Mo lecula r shape and function Natural endorphin Structures of endorphin and morphine The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

Binding to endorphin receptors Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Carbon

Nitrogen

Hydrogen

Sulfur Oxygen

Morphine

Natural endorphin

Brain cell

Morphine

Endorphin receptors

2.15

Th e Formatio n of Bo nds w ith Ca rbon  Carbon has four valence electrons  This allows it to form four covalent bonds with a variety of atoms

2.16

The bondin g ve rsati lit y of carbon  Carbon forms many diverse molecules Name and Comments

Molecular Structural Formula Formula

Ball-andStick Model

SpaceFilling Model

H

(a) Methane

CH4

H C

H

H

(b) Ethane

H H

C2H6

H C C H H H

(c) Ethene (ethylene)

C2H4

H H

C C

H H

2.16

Versa til ity of Carbon  The electron configuration of carbon  Gives it covalent compatibility with many different elements Hydrogen

Oxygen

Nitrogen

Carbon

(valence = 1)

(valence = 2)

(valence = 3)

(valence = 4)

H

O

N

C

2.16

Car bon S kele ton Var iation  Carbon chains  

Form the skeletons of most organic molecules Vary in length and shape H H H

H H

(a) Length

C C H H H

H C C C H H H

H H H H C C C C H H H H

H H C H H H H C C C H H H

H

Ethane

(b) Branching

H

Propane

H

Butane H H H

1-Butene

2-Butene

(c) Double bonds H C C C C H

(d) Rings

H H H H

H H C C C C C C

H H H H

Cyclohexane

H

Isobutane H H H C C C C H H

H H

H

H H

H

H

H

H

C C

C C C

Benzene

H

2.16

Functional Gr oups  Functional groups 

Estradiol

Are the chemically reactive groups of atoms within an organic molecule

OH CH3

HO

Female lion



Give organic molecules distinctive chemical properties

Testosterone

OH CH3

CH3 O

Male lion

2.17

Functional Gr oups HYDROXYL

FUNCTIONAL GROUP

CARBONYL

CARBOXYL O C

OH C

(may be written HO)

NAME OF COMPOUNDS

Alcohols

EXAMPLES H

H

H

C

C

OH

O

Ketones or Aldehydes

H OH

H H Ethanol, the alcohol present in alcoholic beverages

H

H

O

C H

Carboxylic Acids

H

C H

H

C H

Acetone, the simplest ketone

C H

O C OH

Acetic acid, which gives vinegar its sour tatste

2.17

Functional Gr oups FUNCTIONAL GROUP

AMINO

SULFHYDRYL

PHOSPHATE

H

O

N

O P OH

H

SH

OH

(may be written HS)

NAME OF COMPOUNDS

EXAMPLES

Thiols

Amines

H

O C HO

C

H N

H

Glycine

H H

H

H

C

C

H

H

Ethanethiol

Organic Phosphates

OH OH H SH

H

C

C

C

H

H

H

O O

O−

P O−

Glycerol phosphate

2.17