(Bio)Chemistry and Cytology

BIOL241Introduction or Recap of Cell

Structure & chemistry

INTERCONNECTEDNESS

• Matter and Energy• Atoms, molecules, and chemical bonds• Importance of organic and inorganic nutrients

and metabolites• Structure and function of carbohydrates,

lipids, proteins, and nucleic acids• Enzymes and ATP help run the metabolic

reactions of the body

Energy• The capacity to do work (put matter into

motion)• Types of energy

– Kinetic – energy in action– Potential – energy of position; stored

(inactive) energy: chemical energy• Energy is easily converted from one form

to another• During conversion, some energy is “lost”

as heat

Chemistry• Chemistry is the science that deals with

matter• Matter is anything that takes up space and

has mass• Smallest stable units of mass are atoms

But I thought this was biology?

• Mathematics (the language of science)• Physics (the structure of matter & energy)• Chemistry (organic and inorganic structure)• Biology: uses them all to understand Life.

Atoms, Elements, Molecules

• Elements are atoms of one particular type (see the periodic table)

• Molecules are groups of atoms that (usually) contain more than one element

Biologically significant elements

• 13 principal elements– Carbon (C)– Oxygen (O)– Hydrogen (H)– Nitrogen (N)– Calcium (Ca), phosphorus (P), potassium (K),

Sulphur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)

• 13 trace elements – (e.g. zinc, manganese)

Atoms with unfilled electron shells are reactive

• Octet Rule• To become stable they form chemical bonds.• Three main types of chemical bonds

– Intramolecular:• Ionic bonds (charged atoms resulting from the gain

or loss of electrons)• Covalent bonds (electrons are shared)

– Intermolecular• Hydrogen bonds

Covalent & Ionic Bonds• Molecules: atoms held together by

covalent bonds• Salts: molecules held together by ionic

bondsQ: What are the strongest type of bonds?

H2O

The body is mostly water (~2/3rd of total body weight) so all chemical reactions in the body occur in water

Covalent bonds are much stronger than ionic bonds in water

H2O – “Special” Properties

• Water can dissolve organic and inorganic molecules making a solution

• Water is needed for chemical reactions• Water absorbs and retains heat• Water is an effective lubricant

H2O

• What is it about water that makes it so special?

• Water has all these amazing properties due to its molecule’s ability to form hydrogen bonds

H-bonds b/t + & - charges

Mixtures and Solutions• Mixtures – two or more components physically

intermixed (not chemically bonded)– Solutions – homogeneous mixtures of components– Colloids (emulsions) – heterogeneous mixtures

whose solutes do not settle out– Suspensions – heterogeneous mixtures with visible

solutes that tend to settle out

Essential Molecules

• Nutrients: – essential molecules obtained from food (you

have to eat them to get them)• Metabolites:

– molecules made or broken down in the body

Organic vs. inorganicOrganic molecules:• Always contain carbon with hydrogen, and

sometimes oxygen• Often soluble in waterInorganic: Electrolytes, minerals, and compounds that

do not contain carbon with hydrogen. • Important examples: oxygen, carbon dioxide, water,

inorganic acids and bases, salts

Vitamins and Minerals• Vitamins and minerals are essential nutrients

that are required in very small amounts for healthy growth and development.

Examples? • They cannot be synthesized by the body and

are essential components of the diet.

Vitamins• Organic substances necessary for metabolism • There are 13 known vitamins (e.g. A, B1, D, K) • Some are fat soluble while others are water

soluble• Are Coenzymes that help carry out the

reactions of metabolism

Minerals• Inorganic compound (often salts or elements)

necessary for proper body function• Can be bulk or trace minerals• Are Cofactors in metabolic reactions

Electrolytes

• Inorganic ions (usually minerals) that conduct electricity in solution

• Electrolyte balance is maintained in all body fluids; imbalance seriously disturbs vital body functions

Electrolytes

Table 2–3

Biological Macromolecules

• Life depends on four types of organic macromolecules:1. Carbohydrates2. Lipids3. Proteins4. Nucleic acids

Can you think of an example of each?

1. Carbohydrates• Contain carbon, hydrogen and oxygen in a

ratio of 1:2:1• Account for less that 1% of body weight• Used as energy source• Called saccharides (sugars, starches)

Glucose is a monosaccharide

DisaccharidesSucrose

Lactose

Polysaccharides

• Starch• Glycogen• CelluloseAll are long strings of glucose moleculesDifference lies in how they are bonded together

Polysaccharides

• Polysaccharides or polymers of simple sugars

Figure 2.14c

PLAY Polysaccharides

Polymers

• A polymer is any molecule made up of several repeating units. Starch is a polymer of glucose.

2. Lipids• Contain carbon, hydrogen, and oxygen but the

ratio of C:H is 1:2 (much less O)• May also contain other elements,

phosphorous, nitrogen, and sulfur• Form essential structures in cells• Are important energy stores

Lipids: Triglycerides (Fats and Oils)

• Consist of 3 fatty acids and glycerol– Insulation– Energy– protection

Q: What’s the difference between saturated and unsaturated?

Lipids: Steroids and Cholesterol

• All consist of a complex ring structure

Lipids: Phospholipids

Amphipathic

3. Proteins

• Consist of chains of amino acids liked together by peptide bonds

• Enzymes are proteins

Protein Structure• Proteins are the most abundant and

important organic molecules• Basic elements:

– carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)

• Basic building blocks: – 20 amino acids

Figure 2–20a

Protein Structure – 4 levelsPrimary: amino acid sequenceSecondary: Hydrogen bonds form spirals or

pleats (α-helix, β-sheet)Tertiary: Secondary structure folds into a unique

shapeQuaternary: several tertiary structures together:again: Shape!!

Protein structure

Shape and Function• Protein function is based on shape• Shape is based on sequence of amino acids• Denaturation:

– loss of shape and function (due to heat, pH change or other factors)

Protein Functions

– support: • structural proteins

– movement: • contractile proteins

– transport:• transport proteins

– buffering: regulation of pH

– metabolic regulation:

• enzymes– coordination and

control: • hormones

– defense:• antibodies

Figure 2–7

Activation Energy

• Chemical reactions in cells cannot start without help

• Activation energy gets a reaction started

Characteristics of Enzymes

Figure 2.20

Energy In, Energy Out

• Exergonic reactions: – produce more energy than they use

• Endergonic reactions: – use more energy than they produce

KEY CONCEPT• Most chemical reactions that sustain life

cannot occur unless the right enzymes are present

How Enzymes Work

• Substrates: – reactants in enzymatic reactions

• Active site: – a location on an enzyme that fits a particular

substrate

Figure 2–21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

How EnzymesWork

4. Nucleic acids

• Contain C, H, O, N, and P

• DNA and RNA are nucleic acids

• Nucleotide consists of– Sugar– Phosphate group– Nitrogenous base

Structure of DNA

Figure 2.22b

A nucleotide: ATP

• Energy storage for cells

• Many enzymes use ATP

• Provides a way to run reactions that are otherwise endergonic (require energy)

Figure 2.24

Solute Solute transported

Contracted smoothmuscle cell

Product made

Relaxed smoothmuscle cell

Reactants

Membraneprotein

P Pi

ATP

PX X

Y

Y

+

(a) Transport work

(b) Mechanical work

(c) Chemical work

Pi

Pi

+ADP

ATP is the energy currency

of the cell

Compounds Important to Physiology

Table 2–8

Summary

• Energy and matter• Atoms, molecules, and chemical bonds• Importance of organic and inorganic

nutrients and metabolites• Structure and function of carbohydrates,

lipids, proteins, and nucleic acids• Enzymes and ATP help run the metabolic

reactions of the body