the chemistry of life sbi4u, biology, grade 12, university preparation

The Chemistry of Life

SBI4U, Biology, Grade 12, University Preparation

BWilliams

1.1 Chemical Fundamentals



Elements: make up earth & organisms

(O, C, H, N,S, P, K, Si, Al, Fe,

Ca)cannot be broken down by a

chemical process into a simpler substance



Molecules: a substance made up of two or more non-metal atoms that are covalently bonded together



Compounds: substances formed by the combination of two or more elements in a fix ratio. (ex. Hemoglobin (compound) contains Fe (element)

Organic compounds: all contain carbon -ex. Carbohydrates,

lipids, proteins, nucleic acids



Inorganic compounds: not based on carbon example: Table salt (NaCl)

Chemical Formula: C6H12O6 – 24 total atoms

6 carbon atoms12 hydrogen atoms6 oxygen atoms


How many atoms are in this molecule?

C55H72MgN4O5

137



Atoms: smallest particle of an element that can exist and still have the properties of that element


Atomic Structure

Bohr-Rutherford Model atoms are made of a dense positively charged

central nucleus with negative particles surrounding it at specific energy levels

protons (+) neutrons (no charge) electrons (-)

protons and neutrons together make up the nucleus

electrons are used to form bonds with other elements



Changes in the number of electrons cause atoms to become + or –

Outermost energy level (orbit) likes to be full – more stable that way

Atoms will give up, gain, or share electrons to fill the outer orbit

1st level – 2 electrons 2nd level – 8 electrons 3rd level – 8 or 18 electrons



Sodium – 11 protons and 11 electrons 2 electrons in the 1st level 8 electrons in the 2nd

1 electron in the 3rd



Chlorine – 17 protons, 17 electrons 2 electrons in the 1st level 8 electrons in the 2nd level 7 electrons in the 3rd level

Sodium wants to give up the last electron whereas Chlorine wants to gain an electron to fill the 3rd level with 8 electrons

Atoms bond with other atoms to become more stable



Chemical Bond The force that holds atoms together



Ionic bond: a bond b/w oppositely charged ions. One element loses e- & the other element gains e-. These bonds are formed between metals and nonmetals.

Covalent bond: a bond where electrons are shared (carbs, lipids, proteins & nuc. Acids); Three types: single, double, triple


IONIC BOND



Ions - atoms that gain or lose an electron and have a

chargeCharged particle


IONIC BONDING

Electrons are lost by one element and gained by another

Outer energy level in both elements is full (stable)


COVALENT BONDING

Electrons shared in a chemical bond (each atom donates one electron)

Outer energy level in both elements is full (stable)

Double covalent bonds have four electrons

Triple covalent bonds have six electrons


COVALENT BOND



Polar Covalent – bond w/ unequal sharing of electrons that results in slightly positive & slightly negative ends

Water – an example of a polar covalent molecule


POLAR COVALENT


NONPOLAR COVALENT


COVALENT VS. IONIC



There are three types of intermolecular bonds (collectively referred to as van der Waals forces)

London Forces – exist between all atoms, very weak, unequal distribution of electrons

Dipole-Dipole forces – hold molecules together (+-+-)

Hydrogen Bonds – H of one molecule and N, O, F of a nearby polar molecule



Hydrogen Bonds – bonds that hold molecules together rather than atoms. These bonds are weaker than ionic or covalent bonds

* like in water – hydrogen bonds are the force that holds water molecules together


Isotopes atoms of the same element that

have a different number of neutrons



radioisotopes - have an unstable nucleus that breaks apart giving off energy in the form of radiation

used to tell age of fossilspreserve foodtreat cancerSBI4U, Biology, Grade 12, University Preparation


Water is found in all living organisms Water is a polar molecule Being polar allows water to dissolve ionically

bonded compounds easily When compounds dissolve in water they form

a solution Living things are composed of 70-90% water


Properties of water



Solutions Water is known as the universal

solventChemical properties of water are

important b/c they allow it to form solutions (aka. Uniform mixtures)



Solute :That which is being dissolved (sugar)

Solvent: That which does the dissolving (water)



Ionic compounds: dissolve readily in water b/c water

is polar Polar covalent compounds

dissolve in water



Properties of water: Cohesion – “sticking together” b/c of

hydrogen bondingr Adhesion _ water molecules are

attracted to other substances



surface tension – water is pulled together creating the smallest surface area possible water strider walking on water



Capillary Action

Because water has both adhesive and cohesive properties, capillary action is present.

Capillary Action = water’s adhesive property is the cause of capillary action. Water is attracted to some other material and then through cohesion, other water molecules move too as a result of the original adhesion.

Ex: Think water in a straw

Ex: Xylem in plants carry water this way


Expansion – water expands when it freezes, which is opposite to most substances results in ice having a lower

density than liquid water so the ice floats



ponds “freeze on top” so organisms are able to

live underneathProblem for roads



High Heat CapacityIn order to raise the temperature of water, the average molecular speed has to increase.

It takes much more energy to raise the temperature of water compared to other solvents because hydrogen bonds hold the water molecules together!

Water has a high heat capacity.

“The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.”

Properties of Water

Density

Water is less dense as a solid! This is because the hydrogen bonds are stable in ice – each molecule of water is bound to four of its neighbors.

Solid – water molecules are bonded together – space between fixed

Liquid – water molecules are constantly bonding and rebonding – space is always changing


Acids, Bases & Salts Acids – release Hydrogen

ions (H+) in water (ex. HCl in stomach acid)



Bases – Produce hydroxide (OH-) ions in solution (ex. NaOH in soap & egg whites)

Salts – yields other ions (ex. NaCl and KCl)When salt is dissolved in water; sodium & chlorine “disassociate” or temporarily separate



pH --“power of H+”

-pH scale measures the concentration of

Hydrogen ions

Scale 0-14

acid: 0 to < 7bases: > 7 to 14



Blood - 7.4 (lethal if more acidic than 7 and more basic than 7.8)

Stomach acid - 2

A change in pH --in your body results in halting some enzyme functions


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•Buffers resist changes to the pH of a solution when H+ or OH- is added to the solution.

•Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.


Acid rain - contains sulfuric acid and nitric acid

Acid rain pH < 5.6 Acid rain washes away vital minerals from soil,

kills aquatic organisms & strips nutrients from plants


1.2The Chemicals of Life (most contain carbon)

Carbohydrates - store energy & provide shape (composed of C,H&O)

Starch - plants stored energy that is made of sugars

(monosaccharides,disaccharides &polysaccharides)


1.2 CARBON

Carbon is an important biological element because it can form four bonds with other elements and long chains or rings

Polymer – large molecule made up of many smaller units like starch

Monomer – unit that makes up polymer; glucose is the monomer for starch


1.2 The Chemicals of Life

Glycogen - animals stored

energy made from sugars

(same saccharides)Cellulose - simple sugars that

make structural carbohydrates in plants


GLUCOSE

Monomer of starch, glycogen, and cellulose



Lipids - long term energy storage; four types; not soluble in water

Fats - provide insulationWax - repel waterPhospholipids – give structure

to cell membranesSBI4U, Biology, Grade 12, University Preparation


Steroids - cholesterol in cell membranes



Proteins - large, complex molecules composed of many smaller molecules called amino acids (only 20 amino acids make different combinations & proteins)


A protein’s structural characteristics determine its function.

The genetic information in DNA codes specifically for the production of proteins and nothing else.

Proteins accomplish more tasks than any other group of biological molecules.



Proteins - make enzymes that help control chemical reactions (ex. Speed up digestion, releasing energy during cellular respiration, building up proteins)



1. Defense2. Movement3. Structure

4. Regulation5. Transport6. nutrition



Amino Acids Amino acids are held together by peptide bonds to form proteins

An amino acid is an organic molecule possessing a central atom to which are attached an amino group, a carboxyl group, a hydrogen and a variable group of atoms called a side chain (R)



Globular Proteins Protein molecules composed of one or more

polypeptide chains that take on a rounded spherical shape

Primary Structure – the sequence of amino acids in a polypeptide strand



Secondary Structure Coils and folds in a polypeptide caused by

hydrogen bonds between nearby amino acids Alpha helix – a type of polypeptide secondary

structure characterized by a tight coil that is stabilized by hydrogen bonds

Beta pleated sheets – polypeptide secondary structures that form between parallel stretches of polypeptides and are stabilized by hydrogen bonds



Tertiary Structure – supercoiling of a polypeptide that is stabilized by side-chain interactions, including covalent bonds, such as disulphide bridges

Disulphide Bridges – a covalent bond between cysteine residues in a polypeptide that stabilize tertiary structure



Quaternary Structure (QS)– two or more polypeptide subunits forming a functional protein

Examples of proteins with a QS: collagen- found in bones, skin, tendons, and

ligaments keratin – found in hair hemoglobin – found in red blood cells



The Denaturing of Proteins The final shape of a polypeptide (tertiary

structure) can be altered by environmental factors.

These include: Temperature changes pH Ionic concentration

A denatured protein cannot carry out its biological functions



Chaperone proteins – special proteins that aid a growing polypeptide to fold into tertiary structure


1.2 The Compounds of Life

Nucleic Acids - large, complex molecules that contain hereditary or genetic info – two types

monomer – nucleotide (made up of a nitrogenous base, a phosphate group, and a five carbon sugar)



DNA - carries instruction that control activities of cell (blueprint)



RNA - makes the proteins (builder)Reads the information in DNA

and transports it to the protein building apparatus of the cell



Comparing DNA and RNADNA contains the sugar

deoxyriboseRNA contains riboseThe only difference between these

two monosaccharides is the lack of an oxygen atom at carbon 2 in deoxyribose.



There are five types of organic bases found in nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)

DNA has nucleotides containing the bases A, G, C, and T, while RNA contains A, G, C and U.



DNA Helical in structure Composed of two strands There is a strict rule regarding base pairing: The two strands are held together by

hydrogen bonds between nitrogenous bases Adenine (A) will always bond to Thymine (T) with

two hydrogen bonds; Guanine (G) will always bond to Cytosine (C) with

three hydrogen bonds



Each strand of the DNA molecule has a free phosphate group at one end and a free sugar (deoxyribose) at the other end.

Hydrogen bonds will only form if one strand is upside down compared to the other (antiparallel)

Every nucleotide pair consists of a purine (double ring) facing a pyrimidine (single ring)



Other nucleotides Nucleotides are not only used in the

construction of DNA and RNA They are important intermediates in a cell’s

energy transformations



ATP (adenosine triphosphate) – drives energy requiring reactions

Nucleotide derivatives such as nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD), are used in the production of ATP.

cAMP is used as a “second messenger” in various hormone interactions.


1.2 Chemical Reactions and Enzymes

Chemical Reaction creation of new substances by

breaking or forming chemical bonds

Carbohydrates broken for energyAll chemical reactions involve

energy (absorbed or released)



2H2 + O2 2H2O

_C6H12O6 + __ O2 __C02 + __ H2O



Reactions happen in living & nonliving things all the time Can be sped up by increasing temp or by involving a catalyst Catalyst - in organisms are called

enzymes (see sucrose example, fig. 2.15)

Enzymes - break bonds others help form bonds



*Type of protein

*Act as a catalyst, speeding up chemical reactions

1. Substrate- substance being changed by enzyme

2. Active site- region on enzyme where substrate attaches (this is the enzyme substrate complex)



3. Substrate is altered (bond weakened) so that bond is broken

4. Products released and enzyme is unchanged (only the substrate changes)

5. Enzyme is free to bond with another substrate


*Enzymes catalyze specific reactions- only specific substrates will fit into the active site

*Enzymes work by either breaking or forming compounds

*Enzymes work only within specific ranges of temperature and pH.

1.2 Chemical Reactions and

Enzymes


*Enzyme affected by high temperature


*Enzymes are also affected by the concentration of the substrate and the enzyme

Application: bee sting home remedy- meat tenderizer (enzyme) on bee

sting (protein in venom)


the chemistry of life sbi4u, biology, grade 12, university preparation

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