cell compounds and biological molecules

Cell Compounds and Biological Molecules

Biology 12Unit 2 – Cell Compounds and Biological Molecules

Inquiry into Life pages 20 - 44

Basic Chemistry

Matter – anything that has mass and volume

Element – comprises all matter, living or non-living

Atom – the smallest unit of matter to function in chemical reactions; composed of 3 subatomic particles

Isotope – atoms with the same atomic number but different atomic mass

Basic Chemistry

SubatomicParticle

Charge Relative Mass

electron – 1 0

proton + 1 1

neutron no charge 1

Basic Chemistry

6 12.0107

CCarbon

atomic number

atomic mass

element symbol

element name

Basic Chemistry

Isotopes are different forms of the same atom

The only difference is the number of neutrons present

Neutrons only add mass and do not change chemical properties

Some isotopes are unstable and emit radiation radioactive isotope

Molecules vs Compounds

A molecule is any chemical unit that contains more than 1 atom. They can contain the same atom or different atoms

A compound is any chemical unit that contains more than 1 atom, but the atoms cannot be the same.

Ionic Compounds

Ionic compounds are formed when a metal and a non-metal are attracted resulting in the transfer of electrons from metal to non-metal

Ionic compounds require ions or charged atoms

Ions can be positive or negative, but never neutral

Ionic Compounds

Positive ions are metals and have lost electrons

Negative ions are non-metals and have gained electrons

Ionic Compounds

Because electrons are negative particles, having more electrons means the ion is more negative

Fewer electrons means more positive

Ionic Compounds

This represents electron shells

1st shell = 2 e-

2nd shell = 8 e-

3rd shell = 8 e-

Ionic Compounds

C

Ionic Compounds

Remember, ionic bonds transfer outer shell electrons from the metal to the non-metal

Covalent Compounds

Covalent reactions occur between two non-metals

Electrons are shared in covalent compounds instead of transferred

The shared outer shell electrons spend equal time between the two atoms

Covalent Compounds

Each pair of electrons form a single covalent bond

When two pairs of electrons are shared, they form a double bond

When three pairs of electrons are shared, they form a triple bond

The more bonds between atoms, the more difficult it is to separate them

Covalent Compounds

Electrons in the overlapping regions are shared

Each H shares 1 e- with the carbon

Covalent Compounds

The hydrogens share their electron with each other, forming a molecule of hydrogen gas

Water

OH H

Water

Water

Water is a polar molecule

Since oxygen has a larger nucleus, the shared electrons spend slightly more time near the oxygen nucleus than the hydrogen nuclei

This differential in time gives water a slight + and – charge at its poles

OH H

–

+

Water

Polar covalent molecules form weak bonds between compounds called hydrogen bonds

A hydrogen bond occurs when the slight positive charge of a bound hydrogen attracts the slight negative charge of a neighbouring atom

It is represented by a dashed line

Water

Water

Properties of Water

1. Liquid at room temperature

2. Facilitates chemical reactions

3. Molecules are cohesive

4. Changes temperature slowly

5. Has a high heat of vapourization

6. Solid water is less dense than liquid water

Roles of Water in Living Organisms

1. Temperature Regulator

2. Lubricant

3. Solvent

Acids and Bases

Water spontaneous breaks up into two component ions, H+ and OH –

Acids are compounds that release H+ when dissociated in water

Bases are compounds that release OH – when dissociated in water

Acids and Bases

Acids

Strong acids are characterized by the amount of H + ions that dissociate

The more complete the dissociation, the stronger the acid

The more H + added to the water, the more acidic the solution

Bases

Strong bases are characterized by the amount of OH – ions that dissociate

The more complete the dissociation, the stronger the base

The more OH – added to the water, the more basic the solution

pH Scale

This scale is used to indicate the acidity or the alkalinity of a solution

Values range from 0 – 14

The lower the value, the more acidic the solution

The higher the value, the more basic the solution

pH Scale

pH is a logarithmic scale:

pH 1 is 10X more acidic than pH 2

pH 1 is 100X more acidic than pH 3

pH 2 is 1000X more acidic than pH 5

pH 8 is 10X more basic than pH 7

pH 12 is 10 000X more basic than pH 8

pH 14 is 100 000 000 000 000X more basic than pH 0!

Buffers and pH

A buffer is a chemical that keeps pH within certain limits

Buffers resist changes in pH by absorbing excess hydrogen and hydroxide ions

Buffers in human blood are carbonic acid and bicarbonate ions

Organic Molecules

Characterized by the presence of carbon and hydrogen

Organic Molecules

Organic Molecules

Carbon molecules can link to other carbon molecules forming a hydrocarbon molecule

Organic Molecules

Functional groups can be added to hydrocarbons to impart certain characteristics

Two important functional groups are:

carboxyl (COOH)

amine (NH3)

Carbohydrates

Carbohydrates

Short-term energy storage

Structural molecule in plants and bacteria

Cell membrane communication

Carbohydrates

Monosaccharides are simple carbohydrates that can be characterized by having 5 or 6 carbons (pentose and hexose)

Common monosaccharides are:

glucose

fructose

galactose

Carbohydrates

Disaccharides are links of two monosaccharides (di meaning two and mono meaning one)

Common disaccharides:

sucrose

lactose

maltose

Polysaccharides contain many monosaccharides linked together

Polysaccharides are considered polymers

A polymer is a long chain of monomers

A monomer is a single unit

Carbohydrates

Carbohydrates

monomer

polymers

Carbohydrates

Polysaccharides are formed through a process called condensation synthesis

synthesis = making of

condensation = releases water

Carbohydrates

Breaking apart polysaccharides involves a process called hydrolysis

hydro means water

lysis means to break apart

Hydrolysis reactions break down polysaccharides by adding water

Carbohydrates

monomers polymer + H2O

http://www.biotopics.co.uk/as/disaccharidehydrolysis.html

Carbohydrates

Starch and glycogen store glucose in plants and animals

Starch is a polymer of glucose with few side branches

GLYCOGEN is similar to starch except it is highly branched

Carbohydrates

Cellulose is found only in plants

The glucose molecules are linked differently than in glycogen and starch

This linkage causes the greater strength of this molecule

Lipids

Lipids are the greatest energy source in biological molecules

carbohydrates = 17 kJ/g

proteins = 17 kJ/g

lipids = 38 kJ/g

However, most lipids are not used as energy stores

Lipids

Lipids have different structures and functions:

long-term energy storage

steroids (sex hormones)

membrane components

What links all lipids is that they are all insoluble in water

Lipids

Fats and oils

usually of animal origin and is solid at room temperature

Fats have two functions:

long term energy storage

insulation and cushioning

Lipids

Fats and oils form when one glycerol molecule react with three fatty acid molecules

Sometimes called trigylcerides

Lipids

Emulsification is the process of mixing fat with water

Elmulsifiers are made of a polar molecules (polar head and nonpolar tail)

Lipids

Fat globule Emulsifier

(bile)

(soap)

polar head

nonpolar tail

Fat Emulsification

Fatty Acids

A fatty acid is a hydrocarbon chain that ends with the acidic group -COOH

Saturated Fatty Acids

Saturated fatty acids have no double bonds between carbon atoms, and it is saturated, or full of, all the hydrogens that can fit

Saturated fatty acids are solid at room temperature

Animal fats are often saturated

Unsaturated Fatty Acids

Unsaturated fatty acids have double bonds somewhere within the carbon chain, often causing kinks in the chain

They occur where the carbon does not have two hydrogens attached to it

Unsaturated fatty acids are liquid at room temperature

Plant fats are often unsaturated

Phospholipids

Phospholipids are polar molecules containing a phosphate or a phosphate/nitrogen group attached to the lipid tail

They are found in cell membranes and will spontaneously form a bilayer with hydrophobic tails facing in and hydrophilic heads facing out

Phospholipids

Lecithin is a common phospholipid found in soybeans and eggs

It is used to emulsify fats and is basis of mayonnaise, an emulsified fat

Steroids

Steroids have the common stucture of 4 fused carbon rings

Steroids

Steroids differ by their atom arrangement and the functional groups attached to them

Cholesterol is an important component in the cell membrane, adding to rigidity as well as the starting point for sex hormones like estrogen and testosterone

Steroids

Examples of common steroids:

cholesterol

estrogen (estradiol)

testosterone

cortisol

vitamin D

Proteins

Proteins have many functions, from movement to antibodies to enzymes to biological messengers

Proteins are polymers of amino acids monomers

Proteins

Proteins

The R group is what makes the 20 amino acids different from each other

R groups can be as simple as a single hydrogen (glycine) or as complex as a double benzene ring (tryptophan)

Proteins

Proteins

Amino acids combine through a peptide bond, which is a condensation synthesis reaction

Proteins

A chain of amino acids is called a polypeptide

Proteins

Four Levels of Organization (p. 39)

primary structure

the linear sequence of amino acids joined by peptide bonds

secondary structure

polypeptides form a 3-D shape

hydrogen bonds between peptide bonds keep the shape

Proteins

Tertiary Structure

the final 3-D shape of proteins

this shape is maintained by different covalent, ionic, and hydrogen bonds between R groups, including the covalent disulphide bond between 2 cysteine amino acids

Quaternary Structure

two or more polypeptides arranged together (mostly enzymes)

Proteins

Protein structure is extremely important because structure is related to function

If protein structure is changed (denatured) then the protein cannot function

Nucleic Acids

Two types:

Deoxyribonucleic Acid (DNA)

Ribonucleic Acid (RNA)

Both are polymers of nucleotides

Nucleotide

Nucleotides

All nucleotides are composed of a sugar (either ribose or deoxyribose), a phosphate and a nitrogenous base

There are five bases:

Adenine

Thymine (DNA only)

Cytosine

Guanine

Uracil (RNA only)

Nucleotide Chains

Nucleotides join via condensation synthesis – the same process as joining monosaccharides and amino acids!

Nucleic Acids

Nucleic acids form strands made up of a sugar-phosphate backbone

Nitrogenous bases stick out of the sides

DNA

DNA is double stranded, each twisting about the other

RNA

RNA is a single strand of DNA

There are three types:

Messenger RNA (mRNA)

Ribosomal RNA (rRNA)

Transfer RNA (tRNA)

We will look more into DNA at a later time.

ATP

ATP

ATP (adenosine triphosphate) is composed of adenine (a nitrogenous base), a ribose 5-sided sugar and three phosphate groups. This structure is actually a modified nucleotide.

ATP

ATP is the "energy currency" of the cell and is spent to drive chemical reactions

Glucose is converted into ATP in the mitochondria via cellular respiration.

Energy is derived from breaking the bond between phosphate 2 and 3, releasing energy stored in the bond.

ATP

ATP

Breaking this bond results in the production of ADP or adenosine diphosphate and a phosphate group.

These molecules can be recycled and used to produce more ATP in the mitochondria.

Quiz

Quiz on Lipids, Proteins, Nucleic Acids, and ATP

This used to be Unit 6 – EnzymesTextbook Ch 6

MetabolismMetabolism refers to the total of all chemical and

physical reactions that occur in a cell

Most of these activities are driven by ATP

MetabolismMetabolism is controlled by thyroxine, a hormone

produced in the thyroid gland

Metabolism

Thyroxine is made from the addition of iodine to the amino acid tyrosine

Thyroxine stimulates all cells to produce more ATP through cellular respiration resulting in overall increase in metabolism

Metabolism

The level of thyroxine in the blood is determined by a negative feedback loop which goes like this:

Thyroxine levels drop causing hypothalamus to release TRH

TRH acts on the anterior pituitary to release TSHTSH acts on the thyroid causing it to produce more

thyroxineHigh levels of thyroxine cause the hypothalamus to

stop TRH production and anterior pituitary to stop TSH production

Thyroxine Control Feedback Loop

EnzymeEnzymes are protein molecules with particular shapes

(active sites) to bond with particular substrates

Enzymes are catalysts for cellular reactions, bringing substrates together where they can react and form new substances

http://highered.mcgraw-hill.com/sites/dl/free/0072421975/196646/lw03_enzymes_final.html

SubstrateSubstrates are molecules that react to produce new

products with the help of an enzyme

Reactions can be hydrolysis (breaking down) or synthesis (building) reactions

CoenzymeCoenzymes are smaller molecules that help enzymes

function properly and are often contain vitamins

Activation EnergyActivation energy refers to the amount of energy

needed to make a reaction occur

Enzymes reduce the activation energy needed

“Lock and Key” ModelEnzymes are locks. Locks can only be opened by a

specific key.

Substrates are keys. They only work on a specific lock.

Starch is the substrate, amylase is the enzymePeptides are the substrates, peptidase is the enzymeLipids are the substrates, lipase is the enzymeLactose is the substrate, lactase is the enzyme

pH – enzymes work at specific pHs. Enzymes in the blood work at pH 7.4 while enzymes in the stomach work at pH 2.

Factors Affecting Enzyme Action

Temperature – Enzymes in our bodies work efficiently at 37oC but their action starts to drop off dramatically after 40oC

Factors Affecting Enzyme Action

Substrate Concentration – The higher the concentration the more reactions that can occur up to a certain point

Factors Affecting Enzyme Action

Competitive Inhibitors – fight for active sites with the substrate and prevents them from binding.

Enzyme Inhibition – Products made by an enzymatic pathway prevent the binding of other substrates

Factors Affecting Enzyme Action

Factors Affecting Enzyme Action

Heavy Metals – Some metals act as enzyme cofactors (helps the enzyme function) but others (Hg and Pb) causes the enzymes to denature and no longer function

Factors Affecting Enzyme Action

Factors Affecting Enzyme Actionhttp://highered.mcgraw-hill.com/sites/dl/free/0072421975/196644/feedback_inhibition.html

Enzyme InhibitionEnzyme inhibition occurs when the enzyme

cannot bind substrate molecules

The purpose of this enzyme inhibition is to limit the amount of product made by the enzyme so levels do not rise too high

Enzyme InhibitionAs product molecules are produced, their level or

concentration will rise

Eventually these product molecules will interfere or inhibit the enzymes producing them, by binding the active site on the enzyme or attaching to the enzyme in a manner that alters the active site on the enzyme.

Enzyme InhibitionWhen the product molecules are used up or their

concentration lowers, the enzyme will no longer be inhibited by the product molecules

The enzyme active site will be available to bind with substrate and make new product once again

Enzyme InhibitionEnzyme inhibition is controlled by a negative

feedback loop

Enzymes Lab - CatalaseCatalase is an enzyme found in liver and catalyzes the

reaction decomposing hydrogen peroxide into oxygen and hydrogen

Enzymes Lab - CatalaseIn this lab, you will combine the reactants in the test

tubes and record your observations

When you are finished your observations, you will explain your observations with respect to the factors affecting enzyme action.

The lab sheet is provided and all reactants are included

Summary

Learn your basic chemistry

Water is a polar molecule and is the universal solvent – meaning lots of things can dissolve in it

Acids and bases dissociate into different ions and their strength can be measured using the pH scale

Summary

Organic molecules contain C and H

Carbohydrates are composed of monosaccharides or polymers of them

Lipids are composed of gylcerol and 3 fatty acids and form fats and oils, phospholids, and steroids

Summary

Proteins are composed of polymers of amino acids called polypeptides

There are 4 levels of protein organization

Protein function is dependent on maintaining proper structure

Unit 2 Review

Reread textbook pages 20-41

Read section summaries on page 42

Answer all review questions on pages 42 – 43

Define all keyterms on page 44

Use the website listed on page 44 for extra practice

Test is on __________