An Introductory Overview of Cells, Chemical Bonds Energy Part-II Lecture no.4 BCH 361/ Section: xxxxx 25/02/20161

An Introductory Overview of An Introductory Overview of Cells, Chemical Bonds & EnergyCells, Chemical Bonds & Energy

Part-IIPart-II

Lecture Lecture no.4no.4

BCH 361/ Section: BCH 361/ Section: xxxxxxxxxx

06/05/231

What We Will Be Covering-II?Covalent and non-covalent bonds.The four macromolecules and their building blocksChemical reactions and delta GCoupling chemical reactions to ATP hydrolysis


06/05/232

Chemical Hierarchy structure in living Chemical Hierarchy structure in living cellscells

Organization of molecules in cells:1. Atoms.

2. Small molecules.

3. Macromolecules.

4. Supramolecular aggregates.

06/05/233


06/05/234

Continue…Continue…

Organization is the key to the chemistry of life.


AtomsAtoms Each atom has a nucleus

(protons and neutrons) with electrons orbiting it.

H, C, O, and N make up 96.5% weight of a living organism.

Na, K, Cl, Ca, Fe, Zn are each present at less than 1%.

Two types of atomic interaction: Covalent & Non-covalent Bonds.

06/05/235


ContinueContinue……

06/05/236

Atomic InteractionAtomic Interaction

Covalent Bonds

Non-Covalent Bonds

Non-polar interaction

Polar interaction

Hydrogen Bonds

Van der Waals

Hydrophobic effects

Ionic interactions

1 21 2

3 4


06/05/237

Hi, plz remember this regarding the covalent bonds:• It form the backbones of molecules.• Electrons are shared between atoms.• Single bonds allow rotation, double bonds are rigid


Molecules are covalently bonded atoms, covalent bonds result from sharing electrons and depend on valence (C: +4, N: -3, O: -2, H:+1).

Nonpolar Hormones Pass Through Cell Membranes; Nonpolar Hormones Pass Through Cell Membranes; Polar Hormones Use Extracellular Receptor ProteinsPolar Hormones Use Extracellular Receptor Proteins


06/05/238

Covalent And Noncovalent Bonds Play Different Roles Covalent And Noncovalent Bonds Play Different Roles In Maintaining Molecular StructureIn Maintaining Molecular Structure

Covalent bonds assemble atoms into molecules, but noncovalent bonds determine the shape of large molecules and the way in which molecules interact with each other.

Covalent bond = approx. 350 kJ/mol and difficult to break, Noncovalent bond = 1- 30 kJ/mol and readily reversible by thermal movement or interactions with other molecules.


06/05/239

Hydrogen Bonds In BiomoleculesHydrogen Bonds In Biomolecules

Hydrogen has a low electronegativity (it has only one proton to attract electrons with).

Oxygen and nitrogen are highly electronegative.

When there is a bond between O and H, or N and H, the molecule forms a dipole -- the O or N will become δ- (hydrogen bond acceptor), and the H will become δ+ (hydrogen bond donor).


06/05/2310

Hydrogen Bonds Hold The Hydrogen Bonds Hold The DNA Double Helix TogetherDNA Double Helix Together

An AT pair has 2 H bonds, while a CG pair has 3 H bonds.

The helix is harder to unwind in a CG-rich region than in an AT-rich region.

H-bonds play pivotal roles in different aspects of the central dogma of MB DNA.


06/05/2311

Noncovalent Bonds Influence Molecular Noncovalent Bonds Influence Molecular Structure--Hydrophobic InteractionsStructure--Hydrophobic Interactions

Lipids form micelles, in which the hydrophilic groups line the outside of the micelle and the hydrophobic groups cluster inside it, away from the water.

The first stage of lipid digestion involves breaking up huge globs of fat into smaller globs and micelles


06/05/2312

They determine the shape of macromolecules (i.e. the double stranded helical shape of DNA is determined by hydrogen bonds between complementary base pairs A-T and G-C).

They produce reversible self-assembly of pre-synthesized subunits into specific structures (i.e. membrane lipid bi-layer, protein "polymers" like microtubules).

They determine the specificity of most molecular interactions (i.e. enzyme substrate specificity and catalysis).

Molecules or supramolecular aggregates denature (unfold) upon environmental changes (pH, temperature, or ionic strength) which affect the strengths of weak bonds.


06/05/2313

Hemoglobin is a heterotetramer-2 alpha globin chains plus 2 beta-globin chains.

Glutamic acid (negative charge) is replaced by valine (uncharged) in the beta-globin polypeptide.

If beta-globin shape changes, hemoglobin's solubility decreases, hemoglobin precipitates into rod-like aggregates in red blood cells.

Disrupting Noncovalent Bonding Disrupting Noncovalent Bonding Causes Sickle-Cell AnemiaCauses Sickle-Cell Anemia


06/05/2314


Hemoglobin aggregation causes sickling of the red blood cell, and the aggregates punctures the cell when it gets squeezed through capillaries


06/05/2315

The Molecules of LifeThe Molecules of Life

Cells are 70% water, nearly 30% carbon compounds.


06/05/2316

Continue…Continue…

06/05/2317

All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids.


• Concept 1: Macromolecules are polymers, built from monomers.

• Concept 2: Carbohydrates serve as fuel and building material.

• Concept 3: Lipids are a diverse group of hydrophobic molecules.

• Concept 4: Proteins include a diversity of structures, resulting in a wide range of functions.

• Concept 5: Nucleic acids store, transmit, and help express hereditary information

06/05/2318

Overview: The Molecules of LifeOverview: The Molecules of Life


MonosaccharideMonosaccharide The simplest carbohydrates form.

It serve as a major fuel for cells and raw material for building molecules

Polysaccharides, polymers composed of many sugar building blocks.

Monosaccharides are classified by: The location of the carbonyl group (as aldose or

ketose). The number of carbons in the carbon skeleton.


06/05/2319

LipidsLipids Lipids are the one class of large biological molecules that do not

form polymers.

The unifying feature of lipids is having little or no affinity for water.

Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bond.

The most biologically important lipids are fats, phospholipids, and steroids.


06/05/2320

Amino acidsAmino acids

Subunits of proteins.

20 major types of amino acids.

Side groups of amino acids dictate protein structure (non-polar, polar, and charged subgroups).


06/05/2321

Made up of 5 carbon sugar,

phosphate & nitrogenous base

(adenine, cytosine, thymosine,

guanine, Uracil).

Subunits of DNA and RNA.

ATP - the main energy source.

NucleotidesNucleotidesLecture Lecture no.4no.4

06/05/2322

SummarySummary

06/05/2323


The Adenosine triphosphate (ATP)The Adenosine triphosphate (ATP)

Adenosine-5'-triphosphate (ATP) is a multifunctional nucleotide used in cells as a coenzyme.

ATP transports chemical energy within cells.

ATP is produced by phosphorylation and cellular respiration and used by enzymes and structural proteins in many cellular processes, including:

• Metabolism, synthesis, and active transport. • Roles in cell structure and locomotion. • Cell signaling.


06/05/2324

06/05/2325

The phosphoryl groups, starting with the group closest to the ribose, are referred to as the ( )α , ( )β , and ( ) γphosphates.

ATP molecule as it exists in the intact cell is highly charged at pH 7, the three phosphate groups are completely ionized (4 negative charges) near the linear phosphate structure.

Continue…Continue…Lecture Lecture no.4no.4

Metabolic processes that use ATP as an energy source convert it back into its precursors.

ATP is therefore continuously recycled in organisms.

06/05/2326


ATP has several negatively-charged groups in neutral solution, it can chelate metals with very high affinity.

ATP forms stable complexes with certain divalent cations as Mg2+. Most of ATP in the cell present as Mg2+-complex Mg2+.

Ionization in biological systemsIonization in biological systems

06/05/2327


Gibbs Free Energy (G)

The energy associated with a chemical reaction that can be used to do work.

• Reactions can also be classified as:

exergenic (G < 0) or endergenic (G > 0).

06/05/2328

Reactant

Product

Energymust besupplied. En

ergy

sup

plie

dEn

ergy

rele

ased

Reactant

Product

Energy isreleased.

Gibbs Free Energy (G)Gibbs Free Energy (G)Lecture Lecture no.4no.4

• Example: the phosphorylation of glucose to glucose 6-phosphate:

Glucose + phosphate G-6 phosphate ΔG°' = +3.3 kcal/mol (unfavorable)

Consider the hydrolysis of ATP:ATP ADP + Pi

Δ G°' = - 7.3 kcal/mol (favorable)

Summing these reactions together:ATP + glucose ADP + G- 6-phosphate

Δ G°' = +3.3 + (-7.3) = -4kcal/mol (still favorable)

06/05/2329


06/05/2330


06/05/2331


The energy released in the formation of noncovalent bonds is on the order of 1-5 kcal per mol


Time to relax ...Time to relax ...Later we will start Later we will start with the main part with the main part of the course of the course ““Nucleic acids”..Nucleic acids”..

Good luckGood luck

06/05/2332


Documents

An Introductory Overview of Cells, Chemical Bonds Energy Part-II Lecture no.4 BCH 361/ Section: xxxxx 25/02/20161