Regents Biology

Basic Chemistry

Define: Chemistry & Biochemistry

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Basic Chemistry Chemistry is the study of matter

Anything that has volume and takes up space Solid, liquid, and gas Exists as elements in pure form and in chemical

combinations called compounds

All matter is composed of

atoms

Organism

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Basic Chemistry Atoms

The smallest unit of an element that still retains the properties of an element

Elements A substance made of only one kind of atom

Cant be broken down into simpler substances by a chemical reaction

Ex: Iron is an element – it consists of only iron atoms

Each element has its own unique symbol

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FACTS:• 118 known elements• 92 occur in nature • arranged according to similar properties and atomic number

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96% of living organisms is made of: carbon (C) hydrogen (H) oxygen (O) nitrogen (N)

Elements of Life

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A few other elements make up the remaining 4% of living matter

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Other Elements

Table 2.1

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If there is a deficiency of an essential element, disease results

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Deficiencies

(a) Nitrogen deficiency(b) Iodine deficiency

(Goiter)

Figure 2.3

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Trace elements Are required by an organism in only minute quantities

Minerals such as Fe and Zn are trace elements

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Trace Elements

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Explain the relationship between an atom and an element.

What are the four major elements that make up living organisms?

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Are substances consisting of two or more elements combined in a fixed ratio

Have characteristics different from those of their elements

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Compounds

Sodium Chloride Sodium Chloride

+

Figure 2.2

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Molecule of Glucose

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Atomic Structure

• Atoms of each element are composed of subatomic particles

• Nucleus

• Protons (p+)

• Neutrons (n0)

• Outside of nucleus

• Electrons (e-) in a cloud, electron shells

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Identifying Elements

C12.011

6

Atomic Mass

Atomic Number

= # protons + # neutrons

= # of p+ and # of e-

Carbon has ___ p+ and ___ e-

Carbon has ___ n0

6 6

6

protons (+) = electrons (-)Atoms are electrically NEUTRAL

Atoms of various elements differ in their number of subatomic particles

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C6

2 4

Carbon12.011

Atomic number – the number of protons –

unique to each element

Electron configuration –

placement of electrons in energy levels

Atomic symbol – used to represent both the element and one atom of

that element

Atomic mass – the total mass of the atom – sum of

the mass of the protons and neutrons – average mass of

all isotopes

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Mass number – number of

protons plus the number of neutrons

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Identifying Elements Practice

Atomic number

Mass number

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Identifying Elements Practice

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Identifying Elements Practice

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Identifying Elements Isotopes – varieties of an element that have

different number of neutrons Same number of protons, different neutrons Same ____________, different ____________

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Can be used in medicine to treat tumors

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Other uses

Cancerous throat tissue

Figure 2.6

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Energy Is defined as the capacity to cause

change Potential energy

- Is the energy that matter possesses because of its location or structure

Kinetic Energy

- Is the energy of motion

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Energy

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The electrons of an atom Differ in the amounts of potential energy

they possess

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Electrons and Energy

A ball bouncing down a flightof stairs provides an analogyfor energy levels of electrons,because the ball can only reston each step, not betweensteps.

(a)

Figure 2.7A

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An atom’s electrons vary in the amount of energy they possess

Electrons further from the nucleus have more energy

Electron’s can absorb energy and become “excited”

Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels

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Energy Levels of Electrons

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Are represented by electron shells

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Energy Levels

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Energyabsorbed

Energylost

An electron can move from one level to another only if the energyit gains or loses is exactly equal to the difference in energy betweenthe two levels. Arrows indicate some of the step-wise changes inpotential energy that are possible.

(b)

Atomic nucleus

Figure 2.7B

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The number of valance electrons determine the chemical behavior of an element

Atoms seek to have “full” outer most electron shells

Why do elements react?

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The sharing of a pair of electrons Results in a molecule

Two or more atoms combine and act as a single particle

Example: H2O (water)

1+

Hydrogen Atom Oxygen Atom

8+

= WATER MOLECULE

wants to fill this

Covalent Bonds

Regents Biology 26

Multiple Covalent Bonds

(a)

(b)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

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.

H H

O O

Figure 2.11 A, B

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Compounds & Covalent BondsName

(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

(c)

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

(d)

HO

H

H H

H

H

C

Figure 2.11 C, D

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Electronegativity Is the attraction of a particular kind of atom

for the electrons in a covalent bond The more electronegative an atom

The more strongly it pulls shared electrons toward itself

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Covalent Bonding

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In a nonpolar covalent bond The atoms have

similar electronegativities

Share the electron equally

Covalent Bonding

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In a polar covalent bond The atoms have differing

electronegativities Share the electrons unequally

Covalent Bonding

Figure 2.12

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

d–

O

H Hd+ d+

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

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Formed by the transfer of electrons between atoms Results in ions

an atom that has lost or gained electrons = electric charge

Example: NaCl (table salt)

11+

Sodium Atom Chlorine Atom

17+

Sodium Ion +1 (Cation) Chlorine Ion -1 (Anion)

Ionic Bonds

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Ionic compounds Are often

called salts, which may form crystals

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Ionic Substances

Na+

Cl–Figure 2.14

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Several types of weak chemical bonds are important in living systems

This includes: hydrogen bonds Van der Waals interactions

Weak Chemical Bonds

Weak chemical bonds are important because◦ Reinforce the shapes of large molecules◦ Help molecules adhere to each other

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Van der Waals Interactions Even non-polar

molecules can have some positively and negatively charged region briefly and can very weakly bind to another.

Plasma membrane are stabilized by the additive affect of Van der Waals interactions between non-polar fatty acid tails of

phospholipids.

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Hydrogen Bonds Forms when a hydrogen atom that is

covalently bonded to on electronegative atom is attracted to another electronegative atom

Formed between two partially charged atoms

Weaker than ionic bondsH bonds

The two strands of a DNA molecule are held together tightly by the additive affect of many, many weak

Hydrogen Bonds

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Molecules of Life Put C, H, O, N together in different

ways to build living organisms What are bodies made of?

carbohydrates sugars & starches

proteins fats (lipids) nucleic acids

DNA, RNA

Regents Biology 37

Morphine

CarbonHydrogen

NitrogenSulfurOxygenNatural

endorphin

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

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

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Determines how biological molecules recognize and respond to one another with specificity

Molecular Shape Determines Function