8/18/15

1

Ch2: Chemical Components of Cells

BSC 300 Lecture 2

Tuesday, August 25

Subatomic parDcles

posiDvely charged nucleus composed of protons (+) and neutrons (no charge)

Number of protons is invariant for a given element and denes its atomic number

Electrical charge of protons is equal and opposite to that of electrons surrounding the nucleus

8/18/15

2

Subatomic parDcles

For electrically neutral atoms, the number of protons and electrons is the same

Chemical reacDvity the ability to form bonds is determined

by the atomic number: which also denes the # of electrons

Number of neutrons can vary (isotopes). This contributes to nuclear stability, but doesnt alter chemical reacDvity of atoms

Nuclear parDcles and atomic measures

Atomic weight and molecular weight is the mass of atom or molecule relaDve to a hydrogen atom = number of protons plus the number of neutrons.

Measured in units of Daltons = mass of one H atom (1 proton)

1 gram of H atoms contains 6.022 x 1023 atoms: Avogadros number

1 mole of a substance contains 6.022 x 1023 (atoms, molecules, marbles, what ever)

8/18/15

3

Atomic measures

Well oZen refer to the concentra2ons of substances in solu2on so be familiar with the concept of molar concentraDon (M)

Hydrogen: H = 1 proton = 1g/mol 1M = 1g/L

Glucose: C6H12O6= 180 protons and

neutrons = 180g/mol 1M = 180g/L

There are only a small number of biologically relevant elements

~25 elements essenDal for life

4 major elements in organic material (96% of organic weight): Carbon, hydrogen, oxygen and nitrogen

8/18/15

4

There are only a small number of biologically relevant elements

Other 4%: Calcium, sulfur, phosphorous and potassium are criDcal for organic molecules

While trace elements make up the rest: several metals like iron and sodium, as well as chlorine and iodine

The outermost electrons determine how atoms interact

Atomic nuclei do not parDcipate in chemical reacDons

Electrons are rearranged to form chemical interacDons

Electrons occupy discrete energy levels aka energy shells

Electrons closest to the nucleus are acracted most strongly and are the most Dghtly bound

8/18/15

5

The outermost electrons determine how atoms interact

Each shell can hold only a specic number of electrons

A lled outer shell renders the atom chemically inert

Atoms with unlled outer shell are chemically reacDve and can parDcipate in chemical bonds

The outermost electrons determine how atoms interact

This outer most shell is referred to as the valence shell and for low atomic weight atoms, the electrons in this shell are the chemically reacDve electrons, aka the valence electrons.

8/18/15

6

Chemical bonds occur via the sharing or transfer of electrons

Atoms without a lled valence shell react with other atoms to form chemical bonds, achieving stability by reaching a full valence state.

Ionic bonds: electrons are donated from one atom to another. The result is an ionic compound.

Covalent bonds: Electrons are shared between two atoms. The result is a molecule.

Covalent bonds form by the sharing of electrons

The valence shell of hydrogen can hold only 2 electrons, therefore H can form only one covalent bond

8/18/15

7

Covalent bonds are characterized by parDcular geometries

Common organic elements can form mulDple covalent bonds

Bond number generates specic geometric arrangements around the central atom.

Ex., Carbon can form 4 single bonds producing a tetrahedron.

There are dierent types of covalent bonds

Single bonds result from sharing a single pair of electrons by two atoms allows rotaDon in the molecule around such bonds

double and triple bonds share 2 or 3 electron pairs are shorter and stronger bonds which prevent rotaDon.

AlternaDng double bonds are common in carbon chains. Electrons are actually shared across the molecule (or a part) and stabilize it.

8/18/15

8

Polar and non-polar covalent bonds

In non-polar bonds electrons are shared equally, such as between two carbon atoms, or in diatomic oxygen

In polar covalent bonds one atom has stronger anity (electronegaDvity) for the shared electrons which are pulled closer to that atom.

Such molecules are polar parDal posiDve and negaDve charges are formed in the pair of atoms due to this unequal sharing

Oxygen and nitrogen are highly electronega2ve.

Covalent bonds are strong and vary in strength

Bond strength reects the energy required to break the bond

Usually measured in units of kilocalories (or kilojoules) / mol

1 kcal is the amount of energy needed to raise the temperature of one L or water by 1C. = 4.2 kJ.

Covalent bond strength is on average about 100 Dmes greater than the kineDc energy of molecules in cells, making them very stable

Therefore breaking bonds requires considerable cellular energy and the funcDon of important biological catalysts called enzymes (CH 3)

8/18/15

9

Ionic bonds: Gain and loss of electrons

Atoms that obtain a lled valence by the gain or loss of a singe electron can form ionic bonds

Sodium and chlorine for example

Loss of an electron produces an ion with a full posiDve charge: a caDon. Gain of an electron full negaDve charge: an anion

Oppositely charged ions form salts via electrosta2c a6rac2on. But ionic bonds are weak and disassociate in water, a polar molecule.

Many biologically important ions

Noncovalent bonds help bring molecules together in cells

Though weak and transient, ionic bonds and other noncovalent interacDons play important roles in forming large organic molecules

CollecDvely thousands of such acracDons help shape and hold together large molecules

Even weaker than ionic bonds are electrostaDc acracDons between parDally charged regions of molecules that result from polar covalent bonds: hydrogen bonds

8/18/15

10

Hydrogen bonds

Polarity of water molecules provides electrostaDc acracDon between oppositely charged regions. Each water molecule can form 4 H-bonds one at each H and two at the O.

Extremely weak and can be broken by thermal moDon, but collecDvely, thousands or millions are formed between molecules, within molecules or between molecules and the water in which they are dissolved.

Charge, polarity and dissolvability

Hydrophilic: Polar covalent molecules and ions readily dissolve in water. H-bonds lead to aqueous shell forming around them.

Hydrophobic: Molecules without polarity, such as oils and fats, aka hydrocarbons, contain only, or mostly, carbon and hydrogen. Have no polarity in their bonds and therefore are not acracted to water.

8/18/15

11

Some polar molecules form acids and bases in water

In strong polar covalent bonds H has very weak hold on electron pair

In soluDon, the H nucleus (a proton) is acracted to water molecules; it dissociates and joins water to form a hydronium ion (H30+)

Acids are substances that release protons when dissolved in water

Even occurs between water molecules

ConcentraDon in pure water 10-7M

Some polar molecules form acids and bases in water

By convenDon the concentraDon of H30+ is wricen as H+ and is expressed in a logarithmic scale where pH= - log10[H+]

Strong vs. weak acids reects their tendency to give up protons readily in soluDon

8/18/15

12

Some polar molecules form acids and bases in water

bases accept protons when dissolved in water and in doing so increase the OH- concentraDon of the soluDon

H+ and OH- are highly reacDve. Can modify chemistry and funcDon of biological molecules by associaDon/disassociaDon of H+.

Buers: Molecular agents within cells that maintain a relaDvely neutral pH (pH=7) funcDoning as both acids and bases, Ex. carbonic acid hydrogen carbonate:

Small molecules in cells Organic molecules: compounds that contain carbon

Carbon can form large molecules due to: 4 unpaired electrons can form up to 4 covalent bonds C-C bonds are highly stable can form long chains (straight or

branched) as well as rings

Several important chemical groups can be acached to these carbon skeletons to form an endless variety of organic molecules with highly specialized funcDons

Review panel 2-1 and be able to idenDfy (by composiDon or descripDon): methyl, hydroxyl, carboxyl, carbonyl, phosphoryl and amino groups

8/18/15

13

Chemical groups

Chemical groups

8/18/15

14

Cells contain 4 major families of small organic molecules

These are in turn the building blocks for the 4 large macromolecules

Sugars, amino acids and nucleoDdes serve as monomers to build the larger polymers (polysaccharides, proteins and nucleic acids)

Facy acids are subunits of (but not monomers) of fats and lipids

Sugars are both energy sources and subunits of polysaccharides

Sugars and their polysaccharides are aka carbohydrates sugar monomers have the formula (CH2O)n where n=3-6

All contain one carbonyl group All other carbons: one hydroxyl group Arrangement of these groups can

vary so that molecules with same chemical formula have dierent structure: isomers

This does li6le to alter their chemical proper2es but aects the ability of specic enzymes to recognize and process them.

8/18/15

15

Sugars are both energy sources and subunits of polysaccharides

In aqueous soluDons sugars adopt a ring structure

monosaccharides are linked to form disaccharides

condensaDon reacDon: bond between OH groups on two sugars releases a H2O molecules forming a glycosidic linkage

The reverse reacDon breaks the glycosidic linkage by consuming a molecule of water: Hydrolysis

Large number of OH in sugar monomers allows branching and the generaDon of diverse polysaccharides

Energy storage/transport, structural support, protein and lipid modicaDon

8/18/15

16

monosaccharides are linked to form disaccharides

In soluDon the OH on the anomeric carbon alternates between up () and down () posiDons

ResulDng glycosidic linkages are either or

Karp, Cell and Molecular Biology, Fig 2-16

monosaccharides are linked to form disaccharides

HydrolyDc enzymes are specic to one form or another

This is why we can digest storage polysaccharides like starch (with linkages) , but not structural polysaccharides like cellulose (with linkages).

Karp, Cell and Molecular Biology, Fig 2-17

8/18/15

17

AddiDons to sugars modify their chemistry

Such modied sugars play a variety of import roles including protein modicaDon and prokaryoDc cell walls.

Facy acids and derivaDves are Lipids Lipids are a diverse group of nonpolar molecules dened as facy

acids or their derivaDves and being insoluble in water but soluble in organic solvents.

FAs are unbranched hydrocarbons with one carboxyl group; thus they are amphipathic.

Saturated FAs lack C=C double bonds and are solid at room temperature. Unsaturated FAs have one or more C=C double bonds and are liquid at room temperature.

Soaps consist of facy acids

Karp, Cell and Molecular Biology, Fig 2-20

8/18/15

18

Facy acids and derivaDves are Lipids

FA tails vary in length and can be saturated or

unsaturated

UnsaturaDon (C=C double bonds) produces kinked tails that inhibit packing

Facy acids as a source of energy

Triacylglycerols: Fat droplets are composed of 3 FA tails joined by ester bonds to glycerol

About 6 Dmes as much energy, weight for weight, as glucose

8/18/15

19

Steroids: another category of lipids

Hydrocarbon in a linked 4-ring structure diverse roles in cell signaling and structure (especially the plasma membrane)

Phospholipids form membrane lipid bilayers

One FA of a triglyceride is replaced by a negaDvely charged phosphate group linked to polar funcDonal groups (like choline in this example) making them strongly amphipathic.

As a result they readily form a bilayer in aqueous soluDon with the hydrophobic FA tails facing one another and the charged head group interacDng with water on both surfaces.

8/18/15

20

Amino acids are the subunits of proteins

General structure of all amino acids: a central alpha carbon covalently bound to a H, and amino group and a

carboxyl group At neutral pH, the amino and carboxyl groups are ionized: ie, they are

dipolar ions 4th posiDon: unique side group that denes chemistry of the amino acid Thousands of possible side groups, but only 20 encoded geneDcally and

used in protein construcDon

Amino acids are the subunits of proteins

Be able to nd the side chain and determine which family the amino acid belongs to. You will not be expected to recognize and know names of all amino acids.

There are a few that bear special consideraDon: hisDdine, proline, glycine and cysteine

8/18/15

21

Amino acids are the subunits of proteins

Though stereoisomers are possible, all biological systems use and synthesize only the L isomer

Basic amino acids

5 amino acids form ions in soluDon and therefore carry charge 3 basic amino acids

8/18/15

22

Two acidic amino acids

Uncharged polar

Five have polar side chains and can therefore parDcipate in H-bonding

8/18/15

23

Remainder are uncharged nonpolar

The pepDde bond Covalent link between the carboxylic acid of one AA and the amino

group of another

Because of the direcDon of translaDon, the pepDde sequence is always wricen and presented with the amino terminus (N-terminus) toward the leZ and C-terminus toward the right.

8/18/15

24

NucleoDdes are the subunits of DNA and RNA Know the general structure of a nucleoDde Contain a nitrogen containing ring compound a base Bound to a 5 carbon sugar, ribose or deoxyribose Which is bound to one or more phosphate groups Nucleosides lack phosphate groups

Be able to disDnguish pyrimidine from purine and know which bases/nucleoDdes fall into these two families and which are used in RNA vs DNA

Two types of pentoses are used

Know the dierence between ribose (RNA) and deoxyribose (DNA)

8/18/15

25

NucleoDdes can act as short term energy carriers

As with the well known ATP, but GTP as well

Can be combined with other groups to form coenzymes necessary to acDvate specic enzymes

And serve as important intracellular messenger molecules

Nucleic acids are polymers of nucleoDdes

NucleoDdes are joined by phosphodiester bonds between the 5 and 3 carbons of two monomers

By convenDon nucleic acid sequences are read from the 5 to the 3 direcDon

8/18/15

26

Macromolecules in cells

Each macromolecule contains a specic sequence of subunits

Nucleic acids, polysaccharides and pepDdes/proteins result from condensaDon reacDons between monomeric subunits

Facilitated by cellular enzymes that process these reacDons only in one direcDon (for example, 5 3 nucleic acids and C-term N-term in proteins).

Specic order of the polymer leads to unique funcDon of the polymer

Huge diversity in sequences (especially for nucleic acids and proteins)

8/18/15

27

Noncovalent interacDons

Are principle forces behind the 3-dimensional shape (conformaDon) of macromolecules: This includes ionic bonds, H-bonds, as well as Van der Waals acracDons and hydrophobic interacDons

Such interacDons depend on specic linear sequence of the polymer

Noncovalent interacDons

Are principle forces behind the 3-dimensional shape (conformaDon) of macromolecules: This includes ionic bonds, H-bonds, as well as Van der Waals acracDons and hydrophobic interacDons

Such interacDons depend on specic linear sequence of the polymer

8/18/15

28

Van der Waals acracDon

Electrons are not in xed posiDons, but rather occupy spaces of probability

Random uxuaDons in electron posiDons create regions of charge even in nonpolar bonds

CollecDvely, such electrostaDc forces can create signicant acracDon between molecules with complementary shapes

Hyrdrophobic interacDons

Are not acracDve forces, but instead result from repulsion of hydrophobic regions from the aqueous environment. Water forces such groups together to minimize their interacDon with water.

8/18/15

29

Non covalent interacDons

Can be disrupted by changes in pH or salinity, but in biological systems many are formed and increase molecular binding

Such forces provide highly specic inter- and intra-molecular interacDons