section 1 lecture notes

8/6/2019 Section 1 Lecture Notes

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Resources

Textbook: Biology, 8th Edition, Campbell &Reece.

Websites:

www.pubmed.gov

www.who.int/en/

www.cdc.gov

www.cdc.gov/mmwr/


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Basic Biochemical Molecules

Matter consists of chemical elements in pure form and incombinations called compounds

Organisms are composed of matter.

Matter is anything that takes up space and has mass.

An element is a substance that cannot be broken down toother substances by chemical reactions.

There are 92 naturally-occurring elements.

Each element has a unique symbol, usually from thefirst one or two letters of the name, often from Latin orGerman.


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A compound is a substance consisting oftwo or more elements in a fixed ratio.

Table salt (sodium chloride or NaCl) is acompound with equal numbers of chlorine andsodium atoms.

While pure sodium is a metal and chlorine is agas, their combination forms an ediblecompound, an emergent property.

Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 2.3


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The Essential Elements

About 25 of the 92 natural elements areknown to be essential for life.

Four elements - carbon (C), oxygen (O),hydrogen (H), and nitrogen (N) - make up96% of living matter.

Most of the remaining 4% of an organisms

weight consists of phosphorus (P), sulphur(S), calcium (Ca), and potassium (K).


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Trace elements are required by anorganism but only in minute quantities.

Some trace elements, like iron (Fe), arerequired by all organisms.

Other trace elements arerequired only by some species. For example, a daily intake

of 0.15 milligrams of iodineis required for normalactivity of the human

thyroid gland.

Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2.4


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Atoms & Molecules

Each element consists of unique atoms. An atom is the smallest unit of matter

that still retains the properties of an

element. Atoms are composed of even smaller

parts, called subatomic particles.

Two of these, neutrons and protons, arepacked together to form a dense core, theatomic nucleus, at the center of an atom.

Electrons form a cloud around the

nucleus.


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Each electron has one unit of negativecharge.

Each proton has one unit of positive charge. Neutrons are electrically neutral.

The attractions between the positive

charges in the nucleus and the negativecharges of the electrons keep the electrons

in the vicinity of the nucleus.



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A neutron and a proton are almostidentical in mass, about 1.7 x 10-24 gram

per particle. The dalton, is used to measure the mass

subatomic particles, atoms or molecules.

The mass of a neutron or a proton is close to1 dalton.

The mass of an electron is about 1/2000th

that of a neutron or proton. the contribution of electrons when

determining the total mass of an atom isusually ignored.


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Atoms of a particular element have thesame number of protons in their nuclei.

Each element has a unique number of protons,the atomic number.

Unless otherwise indicated, atoms have

equal numbers of protons and electrons - nonet charge.

the atomic number is the number of protons andthe number of electrons that are found in a

neutral atom of a specific element.


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The mass number is the sum of the numberof protons and neutrons in the nucleus of an

atom. the number of neutrons in an atom = the mass

number - the number of protons (the atomicnumber).

The atomic weight of an atom, a measureof its mass, can be approximated by the

mass number.

For example, He has a mass number of 4 andan estimated atomic weight of 4 daltons.

More precisely, its atomic weight is 4.003

daltons.


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Atoms of a given element have the samenumber of protons, but they may differ in

the number of neutrons. Isotopes = two atoms of the same element

that differ in the number of neutrons.

In nature, an element occurs as a mixture ofisotopes. For example, 99% of carbon atoms have 6 neutrons

(

12

C). Most of the remaining 1% of carbon atoms have 7

neutrons (13C) while the rarest isotope, with 8 neutronsis 14C.


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Most isotopes are stable; they do nottend to loose particles.

Both 12C and 13C are stable isotopes.

The nuclei of some isotopes areunstable and decay spontaneously,emitting particles and energy.

14C is an unstable or radioactiveisotopes.

In its decay, an neutron is converted to aproton and electron.

This converts 14C to 14N, changing theidentity of that atom.


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Interaction of Elements

When two elements interact during a chemical reaction, itis actually their electrons that are actually involved.

The nuclei do not come close enough to interact

The electrons of an atom may vary in the amount of

energy that they possess

Electrons have potential (stored) energy because of theirposition relative to the nucleus.

The negatively charged electrons are attracted to the

positively charged nucleus.

The farther electrons are from the nucleus, the morepotential energy they have.


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Energy Levels

The different states of potential energy thatthe electrons of an atoms can have arecalled energy levels or electron shells.

The first shell, closest to the nucleus, has thelowest potential energy.

Electrons in outer shells have more potentialenergy.

Electrons can only change their position if theyabsorb or release a quantity of energy thatmatches the difference in potential energybetween the two levels.


16/80Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2.8


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The chemical behavior of an atom isdetermined by its electron configuration

electron configuration = the distribution ofelectrons in its electron shells.

The first 18 elements can be arranged in 8

columns and 3 rows. Elements in the same row use the same shells.

Moving from left to right, each element has asequential addition of electrons (and protons).


18/80Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2.9

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00

Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3Li

Beryllium

4BeBoron

3B

Carbon

6CNitrogen

7N

Oxygen

8OFluorine

9F

Neon

10Ne

Sodium

11Na

Magnesium

12Mg

Aluminum

13Al

Silicon

14Si

Phosphorus

15P

Sulfur

16S

Chlorine

17Cl

Argon

18Ar


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Electron Orbitals

An electron occupies a three-dimensionalspace, an orbital.

The first shell contains a single spherical

orbital for its pair of electrons. The second shell can contain pairs of electrons

into a spherical orbital and three p orbitals(dumbbell-shaped).


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Fig. 2.10 Electron Orbitals


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Atoms interact by either sharing ortransferring electrons.

Atoms remain close together, held bychemical bonds.

The strongest chemical bonds are covalentbonds and ionic bonds.

Chemical Bonds


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A covalent bond is the sharing of a pair ofvalence (outermost) electrons by two

atoms. If two atoms come close enough that their

unshared orbitals overlap, each atom cancount both electrons toward its goal of fillingthe valence shell.

For example, if two hydrogen atoms comeclose enough that their 1s orbitals overlap,

then they can share the single electrons thateach contributes.


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Figure 2.11

Formation of a covalent bond

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

+ +

+ +

+ +

In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.

1

When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.

2

The two electronsbecome shared in acovalent bond,forming an H2molecule.

3


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A molecule

Consists of two or more atoms held togetherby covalent bonds

A single bond

Is the sharing of one pair of valence electrons

A double bond

Is the sharing of two pairs of valence electrons


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(a)

(b)

Name

(molecularformula)

Electron-

shelldiagram

Structural

formula

Space-

fillingmodel

Hydrogen (H2).Two hydrogenatoms can form a

single bond.

Oxygen (O2).Two oxygen atomsshare two pairs ofelectrons to forma double bond.

H H

O O

Figure 2.12

Single and double covalent bonds


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Name

(molecularformula)

Electron-

shelldiagram

Structural

formula

Space-

fillingmodel

(c)

Methane (CH4).Four hydrogen

atoms can satisfythe valence ofone carbonatom, formingmethane.

Water (H2O).Two hydrogenatoms and oneoxygen atom are

joined by covalentbonds to produce amolecule of water.

(d)

HO

H

H H

H

H

C

Figure 2.12

Covalent bonding in compounds


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Molecule = Two or more atoms heldtogether by covalent bonds.

Structural formula - substitute a line foreach pair of shared electrons, H-H = the

structural formula for the covalent bondbetween two hydrogen atoms.

The molecular formula indicates thenumber and types of atoms present in asingle molecule.

H2 is the molecular formula for hydrogen gas.


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Covalent bonds can form between atoms ofthe same element or atoms of differentelements to form a compound. Water, H2O, is a compound in which two

hydrogen atoms form single covalent bondswith an oxygen atom.



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Electronegativity = the attraction of anatom for the electrons of a covalent bond.

Strongly electronegative atoms attempt to pullthe shared electrons toward themselves.

Nonpolar covalent bond = electrons in a

covalent bond that are shared equally. A covalent bond between two atoms of the

same element is always nonpolar.

A covalent bond between atoms that havesimilar electronegativities is also nonpolar.

Because carbon and hydrogen do not differ greatly inelectronegativities, the bonds of CH4 are nonpolar.


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Polar covalent bond = electrons in acovalent bond are not shared equally by

the two atoms,. The bonds between oxygen and hydrogen in water

are polar covalent because oxygen has a muchhigher electronegativity than does hydrogen.

Compounds with a polarcovalent bond have regionsthat have a partial negativecharge near the strongly

electronegative atom and apartial positive charge nearthe weakly electronegativeatom.


Fig. 2.13


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Ionic bond = two atoms are so unequal intheir attraction for valence electrons thatone atom strips an electron completely

from the other. For example, sodium with one valence electron in

its third shell transfers this electron to chlorine with

7 valence electrons in its third shell. Now, sodium has a full valence shell (the second)and chlorine has a full valence shell (the third).


Af l f


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After an electron transfer, atoms are nolonger neutral, but are charged and arecalled ions.

Sodium has one more proton thanelectrons and has a net positive charge. Atoms with positive charges are cations.

Chlorine has one more electron thanprotons and has a net negative charge. Atoms with negative charges are anions.



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Cations and anions are attracted to eachother to form an ionic bond.

This attraction is due to charge differences


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Weak chemical bonds between moleculesare important to a number of processes.

signal molecules from one neuron use weakbonds to bind briefly to receptor molecules onthe surface of a receiving neuron.

This triggers a momentary response by the

recipient. Weak interactions = ionic bonds (weak in

water), hydrogen bonds, and van der Waals

forces.

Importance of Weak Bonds


Copyright 2002 Pearson Education Inc publishing as Benjamin Cummings


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Hydrogen (H) bonds

A H bond is formed when a hydrogen atom

covalently bound to a stronglyelectronegative atom is attracted to anotherstrongly electronegative atom.

The electronegative atoms

are usually nitrogen or oxygen

The H bond joins H in water

with N in ammonia

Fig. 2.16



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Molecules with nonpolar covalent bonds canhave partially negative and positive regions.

Because electrons are constantly in motion, there

can be periods when they accumulate randomly inone area of a molecule.

This creates random regions of negative andpositive charge within a molecule.

Molecules or atoms in close proximity can beattracted by these charge differences, creatingvan der Waals forces/interactions.


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In chemical reactions chemical bonds arebroken and reformed, leading to newarrangements of atoms.

reactants products In a chemical reaction, all of the atoms in

the reactants must be accounted for in the

products.

Chemical Reactions


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Formation of Water

H2 + O2 = H2O.

Two molecules of H2 combine with onemolecule of O2 to form two molecules of H2O.



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Some chemical reactions go to completion;that is, all the reactants are converted to

products. A + B C

Most chemical reactions are reversible, theproducts in the forward reaction becoming the

reactants for the reverse reaction.

A + B AB


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Equilibrium

The rate of formation of products will equal

the rate of breakdown of products, thus thesystem approaches a chemical equilibrium.

At equilibrium, products and reactants are

continually being formed There is no net change in the concentrations of

reactants and products.


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Water

Solution = a liquid that is a completely homogeneousmixture of two or more substances.

A sugar cube in a glass of water will eventuallydissolve to form a uniform mixture of sugar and

water. Solvent = the dissolving agent

Solute = substance that is dissolved

for example, water is the solvent and sugar the

solute. In an aqueous solution, water is the solvent.

Water is not a universal solvent, however, it isversatile because of the polarity of water molecules.


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Water

Water is an effective solvent as it readilyforms hydrogen bonds with charged andpolar covalent molecules.

A substance that has an affinity for water ishydrophilic.

A substance that has no affinity for water ishydrophobic.


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Macromolecules

Cells join smaller organic moleculestogether to form macromolecules.

Macromolecules are composed ofthousands of atoms and weigh over100,000 daltons.

4 major classes of macromolecules:carbohydrates, lipids, proteins, and

nucleic acids.


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Polymers

Three of the four classes ofmacromolecules form molecules calledpolymers.

Polymers consist of many similar oridentical units linked by covalent bonds.

The repeated units are small molecules

called monomers.


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1. Carbohydrates

Carbohydrates include sugars andpolymers.

The simplest carbohydrates aremonosaccharides or simple sugars.

Disaccharides consist of two

monosaccharides. Polysaccharides are polymers of

monosaccharides.


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Function of Carbohydrates

Monosaccharides (sugars), the smallestcarbohydrates = source of fuel and carbonsources e.g. glucose

Polysaccharides = energy storage

macromolecules that are hydrolyzed as

needed e.g. starch

Polysaccharides = building materials for

the cell or organism e.g. cellulose, chitin


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2. Lipids

3 important families: Fats, phospholipids,steroids

Lipids are an exception among

macromolecules, they do not havepolymers.

Lipids have little or no affinity for water.

This is because their structures are dominatedby nonpolar covalent bonds.

Are lipids hydrophilic or hydrophobic?

Lipids are diverse in structure and function.


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Fats

Fats are not polymers but they are largemolecules assembled from smallermolecules.

A fat is made from 1 glycerol and 3 fatty

acids.

Glycerol consists of a three carbon skeleton

with a hydroxyl group attached to each. A fatty acid consists of a carboxyl group

attached to a long carbon skeleton, often 16to 18 carbons long.


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Fat & Fatty Acids

The three fatty acids in a fat can be the sameor different.

Fatty acids vary in the number of carbons and

in the number and locations of double bonds. saturated fatty acid = no carbon-carbon double

bonds

unsaturated fatty acid = one or more carbon-carbon double bonds


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Saturated & Unsaturated Fats

Fats with saturated fatty acids are saturated fats. Most animal fats are saturated.

Saturated fat are solid at room temperature.

A diet rich in saturated fats may contribute to

cardiovascular disease (atherosclerosis) through plaquedeposits.

Fats with unsaturated fatty acids are unsaturatedfats.

Plant and fish fats, known as oils, are liquid are roomtemperature.


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Function of Fats

The major function of fat is energy storage. A gram of fat stores more than twice as much

energy as a gram of a polysaccharide.

Plants use starch for energy storage when mobility

is not a concern but use oils when dispersal andpacking is important, as in seeds.

Humans and other mammals store fats as long-term energy reserves in adipose cells.

Fat functions to cushion vital organs. A layer of fat can function as insulation.

This subcutaneous layer is especially thick inwhales, seals, and most other marine mammals.


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Phospholipids

Phospholipids = two fatty acids attached toglycerol and a phosphate group at thethird position.

Phospholipids + water: they self-assembleinto aggregates, the hydrophobic tailspoint inward and the hydrophilic heads

point outward. This structure is called a micelle.

At th f f ll h h li id


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At the surface of a cell phospholipids arearranged as a bilayer.

Again, the hydrophilic heads are on the outsidein contact with the aqueous solution and thehydrophobic tails from the core.

The phospholipid bilayer forms a barrier between

the cell and the external environment. They are the major component of

membranes.


See Fig. 5.13


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Steroids

Steroids are lipids with a carbon skeletonconsisting of four fused carbon rings.

Cholesterol, an important steroid, is a componentin animal cell membranes.

Cholesterol is also the precursor from which allother steroids are synthesized.

Many of these other steroids are hormones,

including the vertebrate sex hormones. While cholesterol is clearly an essential molecule,

high levels of cholesterol in the blood maycontribute to cardiovascular disease.

3 P t i


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3. Proteins

Proteins are structurally complex molecules.

Each type of protein has a complex three-dimensional shape or conformation.

All protein polymers are constructed from thesame set of 20 monomers, called amino acids.

Polymers of proteins are called polypeptides.

A protein consists of one or more polypeptidesfolded and coiled into a specific conformation.

P i


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Proteins

Protein functions include structural support,storage, transport of other substances,intercellular signaling, movement, and

defense against foreign substances.

Humans have 1000s of different proteins,

each with their own structure and function


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Protein Form & Function

A functional proteins consists of one or morepolypeptides that have been precisely folded,into a unique structure.

It is the order of amino acids that determines

what the three-dimensional conformation willbe.

A proteins specific conformation determines

its function.

Protein function usually depends on its abilityto recognize and bind to some othermolecule.


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4. Nucleic Acids

There are 2 types of nucleic acid,deoxyribonucleic acid and ribonucleicacid (DNA and RNA)

The amino acid sequence of apolypeptide is programmed by a gene.

A gene consists of regions of DNA, a

polymer of nucleic acids.

DNA (and their genes) is passed by themechanisms of inheritance.

The flow of genetic information is from DNA >


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The flow of genetic information is from DNA ->RNA -> protein.

Protein synthesis occursin cellular structurescalled ribosomes.

In eukaryotes, DNA is

located in the nucleus,but most ribosomes arein the cytoplasm withmRNA as an

intermediary.


Fig. 5.26

First some definitions


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First, some definitions.

Genome All the genes in a cell or virus

Gene A linear sequence of nucleotides with definite end and start

points


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DNA Building Blocks

Nucleotides A nucleoside with one or more phosphate groups

attached

Nucleosides A purine or pyrimidine base joined to either ribose

or deoxyribose

Purine & Pyrimidine Cyclic nitrogenous structures:

purines have 2 rings, adenine and guanine

pyrimidines have 1 ring, cytosine, thymine (DNA) and

uracil (RNA)

C iti f N l i A id


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Composition of Nucleic Acids

S


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DNA Structure

2 polynucleotide chains coiled together toform a double helix, 2.0 nm in diameter

Each chain is comprised of purine and

pyrimidine deoxyribonucleosides (bases)joined by phosphodiesterase bridges

The bases are stacked on top of each other

& paired specifically A--T, C---G (- = H bonds) = base pairing

Base pairing enables 2 stands of DNA in the

helix to be complementary

The sugar phosphate backbones of the two


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The sugar-phosphate backbones of the twopolynucleotides are on the outside of the

helix. Pairs of nitrogenousbases, one from eachstrand, connect the

polynucleotide chainswith hydrogen bonds.

Most DNA moleculeshave thousands to

millions of base pairs.


Fig. 5.28

Base Pairing


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Base Pairing

Adenine (A) always pairs with thymine (T) Guanine (G) always pairs with cytosine (C).

With base-pairing rules, the sequence of

bases on one strand is the mirror image ofthe sequence on the opposite strand.

The two strands are complementary.


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Function of Nucleic Acids

Storage of genetic information

We will come back to DNA in more detaillater in the course.

M b li


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Metabolism

Metabolism = the totality of an organismschemical reactions.

Metabolic pathways change molecules in astepwise fashion.

Enzymes selectively accelerate each step.

The action of enzymes is regulated to allow

the correct amount of each pathwayproduct to be produced/degraded.

Bioenergetics is the study of how organismsmanage their energy resources.


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Metabolism = Catabolism + Anabolism

Catabolic pathways release energy bybreaking down complex molecules to simplercompounds.

This energy is stored in organic molecules. Anabolic pathways consume energy to build

complicated molecules from simplercompounds.

The energy released by catabolic pathways isused to drive anabolic pathways.

E


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Energy

Energy = the capacity to do work - to move matteragainst opposing forces.

Kinetic energy = the energy of motion.

e.g. objects in motion, photons, and heat Potential energy = the energy that matter

possesses because of its location or structure.

Chemical energy is a form of potential energy inmolecules because of the arrangement of atoms.

Free Energy = portion of a systems energy that isavailable for work


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Two Laws of Thermodynamics


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Two Laws of Thermodynamics

The first law of thermodynamics: energy can

be transferred and transformed, but it cannotbe created or destroyed.

Plants transform light to chemical energy; they do

not produce energy.

The second law of thermodynamics: every

energy transformation must make the

universe more disordered. Entropy is a quantity used as a measure of

disorder, or randomness.


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Enzymes

A catalyst is a chemical agent thatchanges the rate of a reaction withoutbeing consumed by the reaction.

An enzyme is a catalytic protein.

Enzymes regulate the movement ofmolecules through metabolic pathways.

Activation energy is the amount of energy


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Activation energy is the amount of energynecessary to push the reactants over anenergy barrier.

At the summit themolecules are atan unstable point,

the transition state. The difference between

free energy of theproducts and the freeenergy of the reactantsis the delta G.


Fig. 8.14

Enzyme speed reactions by lowering EA


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Enzyme speed reactions by lowering EA.

The transition state can then be reached evenat moderate temperatures.

Enzymes do not change delta G.

It hastens reactions that would occureventually.

Because enzymesare so selective,they determine

which chemicalprocesses willoccur at any time.


Fig. 8.15


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A substrate is a reactant which binds to anenzyme.

When a substrate or substrates binds to anenzyme, the enzyme catalyzes the

conversion of the substrate to the product.

Enzymes are unaffected by reactions andare reusable.

Substrates & Enzymes

The active site of an enzymes is a pocket or


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y pgroove on the surface of the protein into whichthe substrate fits.

The specificity of an enzyme is due to the fitbetween the active site and that of the substrate.

As the substrate binds, the enzyme changesshape leading to a tighter induced fit, bringing

chemical groups in position to catalyze thereaction.


Fig. 8.16

The catalytic cycle of an enzyme


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The catalytic cycle of an enzyme

Substrates

Products

Enzyme

Enzyme-substrate

complex

1 Substrates enter active site; enzymechanges shape so its active site

embraces the substrates (induced fit).

2 Substrates held in

active site by weakinteractions, such ashydrogen bonds andionic bonds.

3 Active site (and R groups ofits amino acids) can lower EAand speed up a reaction by

acting as a template forsubstrate orientation,

stressing the substrates

and stabilizing thetransition state,

providing a favorable

microenvironment,

participating directly in thecatalytic reaction.

4 Substrates areConverted intoProducts.

5 Products areReleased.

6 Active siteIs available fortwo new substrateMole.

Figure 8.17

How do Enzymes operate?


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How do Enzymes operate?

The active site orients substrates in the correctorientation for the reaction.

As the active site binds the substrate, it mayput stress on bonds that must be broken,making it easier to reach the transition state.

R groups at the active site may create aconducive microenvironment for a specificreaction.

Enzymes may even bind covalently tosubstrates in an intermediate step beforereturning to normal.

Concentration Dependence:


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p

At low substrate concentrations, an increasein substrate increases binding to availableactive sites.

This does not happen at highconcentrations.

At some substrate concentrations, the activesites on all enzymes are full, called enzymesaturation.

The only way to increase productivity at thispoint is to provide more active sites.

How can we provide more active sites?

Factors affecting Enzyme Activity


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The structures of enzymes depend onenvironmental conditions.

Changes in shape influence the reaction

rate. pH

Temperature

Co-factors

Factors affecting Enzyme Activity

section 1 lecture notes

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