Chapter 2 The Molecules of Cells Pages 19-44. Matter - a substance that occupies space and has...

Chapter 2

The Molecules of CellsPages 19-44

Matter- a substance that occupies space and has ________;

- a substance composed of _________

Atom- the smallest unit of an _________

that possesses all the characteristics of that element

- unit of an element that is not easily divisible by ordinary chemical means

Atom• Composed of :

1 or more _________ (positive charge),usually 1 or more neutrons (no charge),and 1 or more __________

(negative charge)

Often the number of protons and electrons are equal. The resulting atom has no net charge.

similar to Fig. 2.2

____________• a pure substance composed of only one kind

of atom

e.g. hydrogen (H), carbon (C), oxygen (O)

(See Blackboard for a list of chemical symbols you should know.)

Different elements MUST have a different number of protons in the nucleus

Isotope• an atom of an element that differs in the

number of ____________ in the nucleus

e.g. Carbon 12 (12C) and Carbon 14 (14C)

both are carbon, must have 6 protons

12C has 6 protons and 6 neutrons

14C has 6 protons and 8 neutrons

____________ Isotope• an unstable isotope; an atom that will

decay (change) into a different element as subatomic particles are lost from the nucleus

e.g. 14C 14N + 1e-

6p + 8n 7p + 7n

Ion• an atom of an element that has gained

or lost one or more ___________

e.g. H+, Na+ - both have lost one electron

Cl- - has gained one electron

outer electron is lost

_____________• a substance composed of two or more

atoms; the atoms may be identical or may be different elements (compound).

e.g. water H2O

glucose C6H12O6

oxygen gas O2

Chemical Bond• an attractive force between two atoms

• Three different types:

__________

______________

_____________

Ionic Bond• the chemical bond that results from the

attractive force between two oppositely charged _________

e.g. table salt Na+- Cl-

Ionic bonds are not extremely strong.

Fig. 2.7

Covalent Bonds

• chemical bonds that result from two atoms sharing one or more pairs of ____________;produces a relatively strong bond

• Two types of covalent bonds:Nonpolar covalent bond – the pair(s) of

electrons are shared equallyPolar covalent bond – the pair(s) of

electrons are not shared equally

Nonpolar covalent bondChlorine atoms share 1 pair of electrons

similar to Fig. 2.8

Polar covalent bondsO and H do not share electrons equally

similar to Fig. 2.9

O and H have partial charges due to polar covalent bonds

Pg. 26

OH H

_____________ Bond• an attractive force between two atoms

with opposite partial charges

• The atoms are not ions, the partial charges result from the atoms being polar covalently bonded to some other atom.

• weak bonds, but very important in living systems

O forms hydrogen bonds with H BETWEEN water molecules

Fig. 2.9

Properties of water

• very good __________ for polar substances

• water molecules are adhesive and cohesive

• takes a lot of energy to warm (high heat capacity) or vaporize (high heat of vaporization) water

• ice (solid water) is ________ dense than liquid water

________________- the substance is attracted to

water; will form H bonds with water; contains some polar covalent bonds

________________- the substance is repelled by

water; will not form H bonds with water; contains mostly nonpolar covalent bonds

Hydrophilic – e.g. glucoseO-H bond is polar covalent

A fatty acid – all the C-C and C-H bonds are nonpolar covalent

Will this molecule form any H bonds with water?

see also Fig. 2.20

See page 110 in Chapt. 6

____________ – the loss of one or more electrons from an atom or molecule

_____________ – the gaining of one or more electrons from an atom or molecule

Usually linked; referred to as oxidation/reduction (redox) reactions

Oxidation/reduction is important in living systems because energy is transferred from molecule to molecule with the electrons.

Oxidation – loss of e- and _______

Reduction – gaining of e- and energy

NADox + e- + H+ NADHre

lower energy higher energy

Acid- a substance that releases _________ ions when placed in solution

e.g. HCl H+ + Cl-

________- a substance that combines with H+ or releases OH- when placed in solution

e.g. HCO3- + H+ H2CO3

NaOH Na+ + OH-

_____- a measure of the hydrogen ion concentration of a solution

- ranges from 0 to 14 0 – the most acidic, lots of H+ 14 –

the least acidic, very few H+ (most alkaline or basic)

7 – neutral, neither acidic or basic

pH is the negative logarithm of the hydrogen ion concentration

Based on logarithms, each whole number change represents a 10-fold change in H+.

pH 6 is ______ more acidic than pH 7

Negative log is why larger pH numbers represent lower acidity.

100 = 1 10-1 = 0.1 10-2 = 0.01 10-14 = 0.000,000,000,000,01

__________- a substance, that within a certain range, maintains a constant pH by combining with H+ when mixed with an acid, or releasing H+ when mixed with a base

- Buffers do not necessarily maintain a pH of 7.

H2O + CO2 H2CO3 HCO3- + H+

Organic Chemistry “Organic chemistry nowadays almost drives me mad. To me it appears like a primeval tropical forest full of the most remarkable things, a dreadful endless jungle into which one does not dare enter for there seems to be no way out.”

Fredrich Wohler 1835

Organic Chemistry- the study of ___________ containing compounds

Organic molecule- a molecule synthesized by living organisms (no longer useful)- a molecule containing 2 or more carbon atoms (What about methane, CH4?) - a molecule containing at least the elements ________ and __________

Functional Groups- parts of organic molecules

• Hydroxyl group -OH

• Methyl group -CH3

• Carboxyl (acidic) group -COOH

• Amino group -NH2

• Phosphate group -PO3

Can you identify the functional groups?


_____________, -COOH


__________, -CH3


_____________, -OH


______________, -PO3


__________, -NH2

Families of Organic Molecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic AcidsNote – this list does not contain all the different

kinds of organic molecules

____________________• Contain only C, H and O• Lots of hydroxyl groups• Three groups we’ll look at

Monosaccharides – simple sugars

Disaccharides – made from 2 simple sugars

Polysaccharides – polymers of simple sugars

_____________- a large molecule composed of repeating subunits, monomers

e.g. polysaccharides, proteins, DNA, plastics, etc.

Monosaccharides – simple sugars• Contain only C, H, and O

• Ratio of these three elements is:

___C : ___H : ___O

• Lots of hydroxyl groups, -O-H

• Dissolve easily in water. Why?

e.g. glucose or fructose, C6H12O6

ribose, C5H10O5

_________________• Composed of 2 simple sugars bonded

together

• C:H:O ratio not quite 1:2:1

e.g. sucrose, C12H22O11, made from joining glucose and fructose, both C6H12O6

Easily digested to simple sugars

Fig. 2.16

Dehydration aka

______________________• Contain only C, H and O

• Ratio not 1C:2H:1O, but still contains

lots of O

• Size limits solubility in water

e.g. starch and cellulose are both polysaccharides made from only glucose

starch – easily digested

cellulose – undigestible by most organisms

similar to Fig. 2.17

__________• Usually contain only C, H and O

• Ratio of C:H:O nowhere near 1:2:1

lots of C and H, relatively little O

• 4 types we’ll look at:

Fatty Acids Glycerides

Phospholipids Steroids

Fatty Acids• Consist of a carboxyl group and a

____________________ chain


________________ Fatty Acids

• at least 2 H atoms bonded to each of the C in the hydrocarbon chain

Common in animal fats; solid at room temperature

from Fig. 2.20

_________________ Fatty Acids

• One or more C atoms in the hydrocarbon chain have less than 2 H atoms bonded to them.

Common in vegetable oils; liquid at room temp.

Trans fats - partially hydrogenated vegetable oils, not typically made by living organisms

from Fig. 2.20

Glycerides• Glycerol and 1, 2 or 3 ________ _____

(mono-, di-, or triglycerides)

How are they synthesized?

How do you digest them?

When did your great grandmother use hydrolysis of

triglycerides?


Dehydration

Will this molecule form any H bonds with water?

Is it hydrophilic or hydrophobic?

Fig. 2.20

________________• A diglyceride + phosphate group + R group

• Lipid end is hydrophobic

• Phosphate and R group end is hydrophilic

• Form the basic structure of all cell membranes

Steroids• Non-fatty acid lipids• Contain only lots of C, H and little O• Behaves like other lipids• e.g. _________________• Absolutely necessary –

e.g. cell membranes, sex hormones

Proteins• Contain __________, in amino groups

• Made from long chains of amino acids

• Very diverse group of molecules;

very diverse functions

• Shape is extremely important

Amino Acids• An _________ group and a

____________ group bonded to the same carbon atom

• Differ in the R group attached to the central carbon atom

Amino Acids• All proteins made from different

combinations of the same 20 amino acids

• Humans have 8 (children 9) _____________ amino acids – must be present in diet

Polypeptide• A small polymer of ______ _____;

part of a protein molecule.

• Peptide bonds – a covalent bond between the carboxyl group of one amino acid and the amino group of the following amino acid.

• Synthesis? Digestion?


Dehydration

_______________• A change in the shape of a molecule.

• Shape is very important in organic molecules, especially proteins.

e.g. frying an egg; sickle-cell anemia

_____________ _______

• An organic molecule composed of long chains of nucleotides.

e.g. DNA, RNA

Nucleotides• An organic molecule composed of:

1 or more phosphate groups,

a 5-carbon sugar,

and a _______________ base

Adenosine Triphosphate - ______

• A nucleotide involved in most of the reactions in which energy is transferred in living organisms

• Composed of Adenine (N-base), 5-C sugar and three phosphate groups

Chapter 2 The Molecules of Cells Pages 19-44. Matter - a substance that occupies space and has...

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