Reactions and Biomolecules

Biology

• Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones– Such changes in the chemical composition of

matter are called chemical reactions

Hydrogen gas Oxygen gas Water

Reactants Products

Chemical Reactions

All chemical reactions• have two parts• Reactants - the substances you

start with• Products- the substances you end

up with• The reactants turn into the products.• Reactants Products

Chemical Reactions

Reactants: on the left side of the equation – the starting

materials

Chemical Equations: symbolize chemical reactions

Products: on the right side of the equation – the ending materials

(the stuff produces)

Law of Conservation of MatterMatter is neither created or destroyed in a

chemical reaction.– Chemical reactions do not create or

destroy matter—they only rearrange it!

Describing chemical reactions• The way atoms are joined is changed• Atoms aren’t created or destroyed.• Can be described several ways

– In a sentence

• Copper reacts with chlorine to form copper (II) chloride.– In a word equation

• Copper + chlorine copper (II) chloride

• Cu(s) + Cl2(g) CuCl2(aq)

Chemical Reactions

Symbols used in equations

• 2 Cu or 2 H2O – the number in front of the chemical symbol or formula is the coefficient, it tells you how many atoms or molecules there are in the equation, (note: there are 4 hydrogen atoms and 2 oxygen atoms in 2 H2O

• Cu2 or H2O – a small number after an atom is called a subscript and tells you how many of that type of atom there are in that molecule (note: there are 2 hydrogen atoms in water but only one oxygen)

Chemical Reactions

Symbols used in equations

• (s) after the formula – solid Cu(s)

• (g) after the formula – gas H2 (g)

• (l) after the formula - liquid H2O(l)

• (aq) after the formula - dissolved in water, an aqueous solution. CaCl2 (aq)

• “produces” or “yields,” indicating the result of the reaction

• reaction in which products can reform into reactants; final result is a mixture of products and reactants

Chemical Reactions

Reaction Energy

All chemical reactions are accompanied by a change in energy. Exothermic - reactions that release energy to their surroundings (usually in the form of heat)

Endothermic - reactions that need to absorb heat from their surroundings to proceed.

Chemical Reactions

Reaction Energy

Spontaneous Reactions - Reactions that proceed immediately when two substances are mixed together.  Not all reactions proceed spontaneously. 

Activation Energy – the amount of energy that is required to start a chemical reaction.

•Once activation energy is reached the reaction continues until you run out of material to react.  

Chemical Reactions

Activation energy• The least amount of energy needed for a chemical reaction to take place.

Some elements and compounds react together naturally just by being close to each other, and their activation energy is zero. Others will react together only after a certain amount of energy is added to them.

Chemical Reactions

What is a catalyst?• A substance that speeds up a reaction without

being changed by the reaction. • Enzymes are biological or protein catalysts.

Chemical Reactions

Catalysts (enzymes) lower the activation energy required for the reaction.

Diatomic elements• There are 8 elements that never want to be

alone.• They form diatomic molecules.

• H2 , N2 , O2 , F2 , Cl2 , Br2 , I2 , and At2

Water

Balancing EquationsBalancing EquationsBalancing EquationsBalancing Equations

______ HH22(g) + ___ O(g) + ___ O22(g) ---> ___ H(g) ---> ___ H22O(l)O(l)2 2•What Happened to the Other Oxygen Atom?

•This equation is not balanced!

•Two hydrogen atoms from a hydrogen molecule (H2) combines with one of the oxygen atoms from an oxygen molecule (O2) to form H2O. Then, the remaining oxygen atom combines with two more hydrogen atoms (from another H2 molecule) to make a second H2O molecule.

1

• Life on Earth began in water and evolved there for 3 billion years

• The abundance of water is a major reason Earth is habitable– Modern life still remains tied to water– Your cells are composed of 70%–95%

water

WATER AND LIFE

Water

• The water molecule:– two hydrogen atoms joined to one oxygen

atom by single covalent bonds

The Structure of Water

H

O

H

Water

• The electrons of the covalent bonds are shared unequally between oxygen and hydrogen– unequal sharing of electrons makes water a polar

molecule– hydrogen atoms: partially positive (d ) Why?– oxygen atom: partially negative (d -) Why?

() ( )

( )

Water: a polar molecule

• The polarity of water results in weak electrical attractions between neighboring water molecules– These interactions

in molecules with hydrogen are called hydrogen bonds

(b)

()

Hydrogen bond()

()()

()

()

()()

The Structure of Water

The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties

• Versatility of water as a solvent• Water’s cohesive nature • Water’s ability to moderate

temperature• Floating ice

Water’s Life-Supporting Properties

Water

• A solution is a liquid consisting of two or more substances evenly mixed

Water as the Solvent of Life

– The dissolving agent is called the solvent

– The dissolved substance is called the solute

Ion in solutionSalt crystal

Dissolving of Sodium Chloride (NaCl) in Water

Salt

Water

Electricalattraction

Watermolecules(H2O)

Hydrogenbonds

Edge of onesalt crystal

Ionic bond

Water molecules dissolve NaCl,breaking ionic bond

• Water molecules stick together as a result of hydrogen bonding– This is called

cohesion– Cohesion is vital

for water transport in plants

The Cohesion of Water

Microscopic tubes

Water

• Surface tension – is the measure of how

difficult it is to stretch or break the surface of a liquid

– Hydrogen bonds give water an unusually high surface tension

Figure 2.13

Water

• Because of hydrogen bonding, water has a strong resistance to temperature change

• Water can absorb and store large amounts of heat while only changing a few degrees in temperature– Earth’s Oceans cause temperatures to

stay within limits that permit life

Water Moderates Temperature

Water

Reactions & BiomoleculesMetrics_and_Measuring.ppt

Water

Hydrogen bond

Liquid waterHydrogen bonds

constantly break and re-form

IceStable hydrogen bonds

• When water molecules get cold, they move apart, forming ice– A chunk of ice has fewer molecules than

an equal volume of liquid water

• Since ice floats, ponds, lakes, and even the oceans do not freeze solid– Marine life could not survive if bodies of

water froze solid

The Biological Significance of Ice Floating

Water

• Main idea: Organisms are made up of carbon-based molecules.

• Objectives:– Describe the role of carbon in living organisms.– Summarize the four major families of biological

macromolecules.– Compare the functions of each group of biological

macromolecules.• Review Vocabulary:

– Organic compound: carbon-based substance that is the basis of living matter.

Biomolecules

Organic Chemistry• The element carbon is a

component of almost all biological molecules.

• Carbon has four electrons in its outermost energy level.

• One carbon atom can form four covalent bonds with other atoms.

Biomolecules

Macromolecules

• Carbon atoms can be joined to form carbon molecules.

• Large molecules that are formed by joining smaller organic molecules together are called macromolecules.

• Polymers are molecules made from repeating units of identical or nearly identical compounds linked together by a series of covalent bonds.

Biomolecules

Carbon Compounds• Carbon compounds can be in the shape of straight chains,

branched chains, and rings.• Together carbon compounds lead to the diversity of life on

Earth.

Biomolecules

Biological MacromoleculesGroupGroup ExamplesExamples FunctionFunction

CarbohydratCarbohydrateses

Pasta, breads & Pasta, breads & grainsgrains

Stores energyStores energy Provides structural supportProvides structural support

LipidsLipids Beeswax, fat & oilsBeeswax, fat & oils Stores energyStores energy Provides steroidsProvides steroids Waterproofs coatingsWaterproofs coatings

ProteinsProteins HemoglobinHemoglobin

and Amylaseand Amylase

Transport substancesTransport substances Speeds reactionsSpeeds reactions Provides structural supportProvides structural support Provides hormonesProvides hormones

Nucleic AcidsNucleic Acids DNA stores genetic DNA stores genetic info in the cell’s info in the cell’s nucleusnucleus

Stores and communicates Stores and communicates genetic informationgenetic information

Biomolecules

The Role of Carbon in Organisms

Carbon compounds vary greatly in size.

When carbon atoms bond to each other, they can form straight chains, branched chains, or rings.

Cells make a huge number of large molecules from a

small set of small molecules

Biomolecules

Most of the large molecules in living things are macromolecules called polymers

Polymers are long chains of smaller molecular units called monomers (building blocks)

A huge number of different polymers can be made from a small number of monomers

SIZE: monomer<polymer<macromolecule

(poly ~ many ; mono ~ one)

Biomolecules

Making and Breaking of POLYMERS

Cells link monomers to form polymers by dehydration synthesis (building up); also called condensation reaction

Short polymer Unlinked monomer

Removal ofwater molecule

Longer polymer

Biomolecules

Making and Breaking of POLYMERS

Polymers are broken down to monomers by the reverse process, hydrolysis

(hydro ~ add water; lysis ~ to split)

Addition ofwater molecule

Biomolecules

IsomersMolecules that have the same simple chemical formula but have different structural formula are called Isomers (both have the chemical formula C6H12O6)

CARBOHYDRATES

composed of carbon, hydrogen, and oxygen with a ratio of about two hydrogen atoms and one oxygen atom for every carbon atom.

The structure of carbohydrates

The monomer (building block) of a carbohydrate is a simple sugar called a monosaccharide* (mah noh SA kuh ride). (ie. glucose, fructose)

are the fuels for cellular work

*(Mono ~ one; sacchar ~ sugar)

Monosaccharides can join to form disaccharides*, such as sucrose (table sugar) and maltose (brewing sugar)

*di ~ two; sacchar ~ sugar

Polysaccharides are long chains of sugar units

polymers of hundreds or thousands of monosaccharides linked by dehydration synthesis

Polysaccharides are long chains of sugar units

Function as

Energy storageStarch (plants)Glycogen (animals)

StructureCellulose (plants cell walls)Chitin ( insects)

Chitin

Structural polysaccharide Structural componemt of cell walls in fungi Exoskeleton of invertebrates like insects, crustaceans like crawfish, shrimp etc. Suture material for surgery (breaks down as wound heals)

Lipidscomposed largely of carbon and

hydrogen

They are not true polymersThey are grouped together because they do not mix with water (Nonpolar) (ie. fats, oils, waxes, steroids)

Lipids include fats and oils, Fats and oils are lipids whose main function is long term energy storage

Other functions: Insulation in higher vertebrates“shock absorber” for internal organs

Fatty acid

Fatty acid

Lipids include fats like a triglyceride,

Fatty acid

Fatty acid

Saturated & Unsaturated fatsfatty acids of unsaturated fats

(plant oils) contain a double bond.

These prevent them from solidifying at room temperature

Saturated fats (lard) lack double bonds

They are solid at room temperature

Saturated & Unsaturated fats

No double bonds between carbon and carbon

One or more double bonds between carbon and carbon

Phospholipids

Partial exception to the hydrophobic (non-polar) lipid rule

Have a polar region and a nonpolar region on each molecule

Nonpolar Region

Polar Region

Compared to a Triglyceride Phosphate group replaces 3rd fatty acid

Phospholipids Major component of all cell membranes!Phospholipids form a double layer in each cell membrane. The polar heads are oriented towards the aqueous areas and the nonpolar fatty acid tails form a nonpolar lipid barrier between the inside and outside of the cell.

Thus, membranes have two sides, each facing the aqueous environment inside and outside of the cell.

THE STEROIDS Fused Rings Found in all steroid compounds

Important part of cell membranes

Obtain in diet and make it in the liver.

Anabolic steroids: Testosterone mimics

Cholesterol:

Precursor in living organisms for: sex hormones ( testosterone in male, estrogen and progesterone in female) Corticosteroids from adrenals Vitamin D Bile salts

PROTEINSEssential to the structures and activities of life

Make up 50% of dry weight of cells Contain carbon, hydrogen, & oxygen PLUS nitrogen and sometimes sulfur Proteins are involved in

Cellular structure Movement (muscles) Defense (antibodies) Transport (blood) Communication

Monomers are called amino acids

The structure of proteins 20 common amino acids that can make literally

thousands of proteins.

Their diversity is based on different arrangements of amino acids

R = variable group- which distinguishes each of the 20 different amino acids

Amino acids can be linked by Peptide Bonds

Cells link amino acids together by dehydration synthesis (condensation reaction)

The bonds between amino acid monomers are called peptide bonds

Dehydrationsynthesis

Amino acid Amino acid

PEPTIDEBOND

Dipeptide

A protein’s specific shape determines its function

A protein consists of polypeptide chains folded into a unique shape

The shape determines the protein’s function

A protein loses its specific function when its polypeptides unravel

Enzymes are proteins that catalyze (i.e., increase the rates of) chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products.

Enzymes

Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

Enzymes

LEVELS OF STRUCTURE IN PROTEINS:

Function of a protein is determined by its overall conformation. (Failure to achieve the

proper confirmation can result in a non-functioning protein, with disastrous results.)

PRIMARY LEVEL (Primary Structure) - the specific sequence of amino acids joined together

LEVELS OF STRUCTURE IN PROTEINS: SECONDARY LEVEL (Secondary structure) This level is defined as the way the polypeptide chain is coiled and folded upon itself.

Two Types of Secondary Structures:

Alpha Helix

Beta pleated sheet

Alpha Helix

Beta pleated sheet

LEVELS OF STRUCTURE IN PROTEINS: TERTIARY LEVEL (tertiary structure) the overall 3-D

conformation of a protein

tertiary structure

LEVELS OF STRUCTURE IN PROTEINS: QUATERNARY LEVEL (quaternary structure) Found only proteins composed of two or more polypeptide chains (each

with its primary, secondary, tertiary structure).

REMEMBER:

Without correct conformation, protein will be

dysfunction or non-functional.

LEVELS OF STRUCTURE IN PROTEINS: DENATURATION OF PROTEIN: loss of native conformation -unfolding of tertiary and secondary structures -biologically inactive in this state

Proteins are sensitive to: temperature pH salt concentration solvent

Effect of denaturing agent:

Proteins will unfold and lose conformation.

PRIONS Prions – abnormally folded proteins

In some diseases, these agents have the ability to subvert normal proteins to unfold and refold abnormally

See this in some forms of:

Alzheimer’s Kuru Scrapie Creutzfeld-Jakobs Bovine spongiform encephalopathy (Mad cow disease) Transmissible mink encephalopathy

Nucleic acids A nucleic (noo KLAY ihk) acid is a complex biomolecule that

stores cellular information in the form of a code.

DNA (deoxyribonucleic acid) contains the instructions used to form all of an organism’s proteins.

RNA (ribonucleic acid) forms a copy of DNA for use in making proteins.

They ultimately control the life of a cell

Nucleic acidsThe monomers of nucleic acids are called nucleotides

Each nucleotide is composed of a sugar, a phosphate, and a nitrogenous base

Phosphategroup

Sugar

Nitrogenousbase (A)

Basic Structure of Nucleotide

One 5 carbon sugar

One Phosphate group

One Nitrogen base

For a given nucleic acid, the phosphate groups are identical in each nucleotide. The sugars differ between DNA and RNA.

The real difference is in the nitrogen bases. Therefore each type of nucleotide is named for the nitrogen base it contains.

The DNA and RNA nucleotides differ in the 5-carbon sugar: DNA – deoxyribose, RNA – ribose

In DNA, the hydroxyl group on C2 has been replaced by a hydrogen. In other words, an oxygen is missing at that site. (deoxyribose has one carbon without a hydroxyl group) Hence, the name: Deoxyribose.

In RNA, the ribose has the hydroxyl group on C-2.

The nitrogen bases:

A,G, C are found in allNucleic acids.

T is found only in DNA.

U is found only in RNA.

There are two main groups of bases with five types of bases.

Condensationreaction or dehydration synthesis joins nucleotides between the phosphate group on one nucleotide and the sugar on the other nucleotide. This linkage is referred to as : The “Sugar-Phosphate” backbone of the nucleic acid.

ATP - Adenosine Triphosphate

Energy source used by all Cells

Organic molecule containing high-energy Phosphate bonds

A nucleotide with adenine as the nitrogenous base, ribose as the 5-carbon sugar and 3 phosphate groups instead of one.

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