Biomolecules

Overview 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

Energy

The capacity to do work (put matter into motion)

Types of energy Kinetic – energy in action Potential – energy of position; stored (inactive)

energy Energy is easily converted from one form to

another During conversion, some energy is “lost” as

heat

Why is chemistry important to anatomy and physiology?

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

Elements vs. Molecules

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

Molecules are groups of atoms that contain more than one element

Elements found in the body

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

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

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

Elements with unfilled electron shells are reactive

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

Ionic and covalent bonds

Molecules: atoms held together by covalent bonds

Salts: molecules held together by ionic bonds

Q: What are the strongest type of bonds?

Importance of water

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

Covalent bonds are much stronger than ionic bonds in water

Water properties

Water can dissolve organic and inorganic molecules making a solution

Water is needed for chemical reactions Water can absorb and retain heat Water is an effective lubricant

Water properties

Water has all these amazing properties due to their ability to form hydrogen bonds

Hydrogen bonds: weak bonds between molecules

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. inorganic

Organic 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

Biological Macromolecules

Life depends on four types of organic macromolecules:1. Carbohydrates

2. Lipids

3. Proteins

4. 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

Glucose is a monosaccharide

DisaccharidesSucrose

Lactose

Polysaccharides

Starch Glycogen Cellulose

All are long strings of glucose molecules

Difference lies in how they are bonded together

Polysaccharides

Polysaccharides or polymers of simple sugars

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 Chemistry

Proteins

are very important biological molecules

that play crucial roles in virtually all

biological processes

BIOLOGICAL FUNCTIONS OF PROTEINS

1. Catalytic function: Nearly all chemical reactions in biological systems are catalyzed

by specific enzymes.

2. Transport and storage: For example;

Hemoglobin transports oxygen in erythrocytes Myoglobin carries & stores oxygen in muscle. Albumin transports free fatty acids in blood. Transferrin transports iron in blood.

3. Coordinated motion:Actin and myosin are contractile proteins in muscle.

BIOLOGICAL FUNCTIONS OF PROTEINS (cont.)

4. Structural and Mechanical support: For Example; collagen, a fibrous protein in skin and bone.

5. Defense function: For Example Clotting factors prevent loss of blood. Immunoglobulins protects against infections.

6. Generation and transmission of nerve impulses: For example, rhodopsin is the photoreceptor protein in retinal

rod cells. 7. Control of growth and differentiation: For Example

growth factor proteins. hormones such as insulin and thyroid-stimulating

hormone.

General structure of protein

All biologically known protein are polymers of a set of twenty known amino acids.

All biologically known amino acids are α L amino acids.

They are composed of carboxylic end COOH and amino end NH2 and α carbon attached to both of them and special side chain (R) attached to this α carbon .

This side chain is characteristic of every amino acid.

AMINO ACIDS are the basic building

blocks of

PROTEINS

Each AMINO ACID has

An amino group,A carboxyl group,

A hydrogen atom and a specific side chain (R group)

Bonded to the α-carbon atom

Classification of amino acids

Side chain reaction classification Biological classification Metabolic classification

Side chain classification

Glycine (Gly-G)Alanine (Ala-A)Valine (Val-V)Leucine (Leu-L)Isoleucine (Ile– I) Methionine (Met– M)Proline (Pro– P)Phenylalanine (Phe– F) Tryptophan (Trp–W)

2- Hydrophilic (polar) R-group

UnchargeUnchargedd

Aspargine Aspargine (Asn – N) (Asn – N) Glutamine Glutamine (Gln – Q ) (Gln – Q ) Serine Serine

(Ser – S) (Ser – S) Threonine Threonine (Thr – T ) (Thr – T ) TyrosineTyrosine

(Tyr – Y) (Tyr – Y) Cysteine Cysteine (Cys – C )(Cys – C )

PositivelPositively y chargedcharged

LysineLysine

(Lys – (Lys – K ) K )

Arginine Arginine

(Arg – R) (Arg – R)

HistidinHistidine e

(His – (His – H )H )

Negatively Negatively chargedcharged

Aspartic Aspartic acid acid

(Asp – D)(Asp – D)

Glutamic Glutamic acid (Glu – E acid (Glu – E ))

1- Hydrophobic (non-polar) R-group)

Non polar (hydrophobic) amino acids

Side chains of non polar (hydrophobic) a.a. can not participate in hydrogen or ionic bonds, but they form hydrophobic interactions.

In aqueous environment, non polar a.a. tend to be present in the interior of proteins.

They include: Amino acids with aliphatic R group (glycine, alanine, Amino acids with aliphatic branched R group (valine,

leucine and isoleucine). Amino acids with aromatic R group (phenylalanine,

tryptophan) Amino acids with sulfur group (methionine) and Imino acid (proine).

Polar (hydrophilic) amino acids

Side chains of polar (hydrophilic) a.a. can participate in hydrogen or ionic bonds.

Therefore, in aqueous environment polar a.a. tend to be present on the surface of proteins.

Polar (hydrophilic) amino acids are classified into: - Polar charged amino acids include

acidic (Negatively charged): (aspartic and glutamic a.) and basic (Positively charged group): (arginine, lysine, histidine)

amino acids. Polar non charged amino acids include:

Amino acids with OH group (serine, threonine, tyrosine) Amino acids with SH group (cysteine) Amino acids with amide group (glutamine, asparagines)

Biological classification 1- Non essential amino acids: These are

Glycine, Alanine, Serine, Tyrosine, Cysteine, Arginine, Asparagine, Aspartic, Glutamic acid , Glutamine and Proline.

2- Essential amino acids:

They include Valine, Leucine, Isoleucine, Threonine, Methionine,, Lysine, Histidine, Phenylalanine and Tryptophan.

Metabolic classification Glucogenic amino acids: These amino acids

could give intermediates which finally can give glucose.

Purely ketogenic amino acids: They include Leucine & Lysine. They give ketone bodies after its degradation in the body, but no glucose.

Mixed amino acids: These are amino acids that can give both ketone bodies and glucose intermediates. These are Phenylalanine, Tyrosine, Tryptophan, Isoleucine and Lysine.

* The rest of amino acids are all purely glucogenic.

Ionic properties of amino acids

Amino acids have amphoteric properties . They contain acidic (COOH) and Basic (NH2) groups. The amino acids are usually ionized at physiological pH . In acidic medium ; amino acid is positively charged

( behave as a base : proton acceptor ) In alkaline medium ; the amino acid is negatively charged

( behave as an acid: Proton donor)

Isoelectric point or “pI”

At certain pH “ specific for each amino acid “ the amino acid can exist in the dipolar from : fully ionized but with no net electric charge .

The characteristic pH at which the net electric charge is zero is called the Isoelectric point or “pI”.

The amino acid at the isoelectric pI is called

“ Zwitter Ion “ and is electrically neutral not migrating in an electric field

“Zwitter in German means hybrid or hermaphrodite”.

Isoelectric point or “pI” At certain pH “specific for

each amino acid” the amino acid can exist in the dipolar from : fully ionized but with no net electric charge.

The characteristic pH at which the net electric charge is zero is called the Isoelectric point or “pI”.

The amino acid at the isoelectric pI is called “Zwitter Ion” and is electrically neutral not migrating in an electric field.

Zwitter ion

N

H

HCH

C

O

OH

R

N

H

CHC

O

R

N

H

CHC

O

R'

N

H

CHC

O

R''

N

H

CHC

O

R''''

N

H

CHC

O

R'''

Amide links

An -amino acid A portion of a protien molecular

Primary structure: the exact sequence of the different α-amino acids along the protein chain.

Second and tertiary structure: the folding of the polyamide chain which give rise to higher levels of complexity.

Although hydrolysis of natural occurring proteins may yield as manyas 22 different amino acids, the amino acids have an importantstructural feature in common.

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

Protein Structure – 4 levels

Primary: amino acid sequence

Secondary: Hydrogen bonds form spirals or pleats

Tertiary: Secondary structure folds into a unique shape

Quaternary: several tertiary structures together

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

Proteins: Enzymes

Enzymes are catalysts: proteins that lower the activation energy of a

chemical reaction are not changed or used up in the reaction

Other factors that speed up reactions: Increased temperatures Smaller particles Higher concentrations

Activation Energy

Chemical reactions in cells cannot start without help

Activation energy gets a reaction started

Characteristics of Enzymes

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

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

A nucleotide: ATP

Energy storage for cells

Many enzymes use ATP

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

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

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