cell compounds

8/12/2019 Cell Compounds

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Cell Compounds2/25/09

Cell Biology 1 Cell Compounds

A. Bonding- When substances react together, the tendency is

always for their atoms to gain, lose or share electrons

so that they each acquire a full outershell. The

attractive force that holds atoms together is a

chemical bond

Compounds

- consist of atoms of two or more elements that arejoined by chemical bonds e.g., Water (H2O)

1. Ionic bond (= ionic compound)

- two ionic, and oppositely charged atoms (ions)are attracted to one another

- one donating electron(s) and the other acceptingthe electron(s)

- e.g., Na++ Cl-= NaCl

- This a biologically weak bond, as ioniccompounds will readily solvate in water (diagram

solute/solvent, solvation)

- An ionic compound is not a molecule

2. Covalent bond (= molecule)

- forms when two or more atoms share one or morepairs of electrons (to form a stable outer energy

shell)

-e.g., Polar, H2O;Nonpolar, N2- Non-Polar covalent bond

- is formed where the electrons are pulled exactlyequally by the atoms involved, e.g., N

2, O

2,

CO2, CH4.

Notes

source:http://www.accessexcellence.org

/AB/GG/


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Cell Compounds


Source: LifeThe Science of Biology, 7thed.

b. Polar covalent bond

- is formed when atoms of two different elementsshare e-, such that the charge between them is

asymmetrically distributed, e.g., H2O, NH3(Ammonia) (diagram)

- (*) lone e- pair which are not part of thebond - found in outermost shell

- Forms biologically strong bonds- Covalent compounds are usually gases or liquids at

room temperature

- Carbon (organic compounds) bond covalently- a molecule is a group of atoms held together by

covalent bonds

3.Two Other Important Bonds

- Hydrogen Bond- Are formed when a single hydrogen atom

(H+)is shared between two electronegative

atoms, (usually N or O).


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Cell Compounds


1. pH

- is a measure of the relative amounts ofhydronium (oxonium)[H3O+]and hydroxide

(hydroxyl) [OH-]dissolved in solution

- [H3O+] > [OH-]is an acid- [H3O+]< [OH-] is a base/alkali- the scale is logarithmic, a difference of one

pH unit represents a tenfold change

- a pH of 5is ten times greater than thatof a sample with a pH of 6, and 100x

greater than7

- Hydrogen ion concentration and pH areinversely related, i.e.,- the higher the [H+]ion concentration, the

lower the pH

- the lower the [H+] ion concentration, thehigher the pH

2.Acid

- if hydrogen chloride (HCl) is dissolved in water,some of its molecules dissociateto form

hydrogen ions (H+) and chloride ions (Cl-). The

hydrogen combines with water molecules toform hydronium ions (H3O+). Such a solution

contains many more [H3O+]than [OH-]and is

therefore defined as an acid.

- sour taste; tingling or burning sensation onskin; can be corrosive, e.g., citric acid in

citrus fruits, like oranges; detergents

3. Base / Alkaline

- NaOH (sodium hydroxide) dissolved in waterdissociates to form Na+and adds more OH-,shifting the concentration in favour of OH-,

([H3O+]< [OH-]) abase

- bitter taste; slippery to the touch, e.g., bakingsoda; soap

Note:

If pH is increasing, it is morealkaline/basic!

If pH is decreasing, it is moreacidic"

Reminder:

H3O+!H2O+ H

+

Abbreviation:

In chemistryconcentrationis

indicated by use of square

brackets [ ].


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Cell Compounds


4. Buffer

- biological buffers stabilize fluctuating pHlevels, by donating or accepting excess H+ ions.

(diagram)

Primary Biological Buffers

1. Bicarbonate (HC03-)HC03

-+ H+!H2C03!CO2+ H2O [these

substances can easily be excreted by the kidneysand lungs]

2. Phosphates H2PO4-/ HPO43. Protein Buffers

a. Amino acid residues of proteins take up H+NH2(Amine)!NH3

-Ammonia ion

NH3- + H+!NH4[Ammonium, is relatively

non-toxic]

b. Red Blood Cells (hemoglobin)Hb + H+!HHb [reduced hemoglobin]

Relative Buffering Power- HC03- 1- Phosphate 0.3- Plasma proteins 1.4- Hemoglobin 6.5- Most important buffer is protein. 75% of all

buffering power of the body is within cells as

protein. Hemoglobin is important due to highconcentration and its increased buffering capacity

when deoxygenated.

- Lung and Kidney respond with excretion & denovo synthesis.

- buffersDO NOTneutralize pH, buffers helpkeep the pH constant by compensating forchanges

Homeostasis:

- Respiratory acidosis cause - hypoventilation- Retention of CO2

- Respiratory alkalosis cause - hyperventilation

To first understand how amino acids and

proteins function as buffers in the body, you

need to understand a little about the structure of

an amino acid (you might want to jump ahead in

your notes to our section on Biomolecules:

Proteins, or re-read this after we have discussedproteins). If we look at the general structure of

an amino acid, you can see that it has an amine

(NH3) group on one end and a carboxyl (COOH)

group on the other end.

Example: glycine 3HN-CH2-COOH

If the amino acid is in solution, as the pH

changes the amino and carboxyl

hydrogens (protons) will be affected.

Using glycine as an example again:

LOW pH [pH 2.3]

+3HN-CH2-COOH(+1 net charge)

|

NEUTRAL pH [pH 7]+3HN-CH2-COO

-

|

HIGH pH [pH 9.7]

2HN-CH2-COO

(-1 net charge)

As the pH changes an hydrogen can be lost or

gained affecting the charge (see above).

Glycine is a simple example since it doesn't have

any R groups attached to the carbon. Many R

groups can also gain or lose hydrogens, such as

arginine, glutamic acid, etc. This means that at

any particular pH an amino acid may have a net

(+ ) or (-) charge.

To complicate this a little bit more, proteins are

made up of many amino acids each of which

contributes to the proteins overall charge.

Remember that there will be only 1 terminal

amine and carboxyl group, BUT there will be

many R groups affecting the charge.

We now consider a basic definition of a buffer as

a solution that consists of a mixture of a weak

acid and its conjugate base. A good buffer will

tend to resist changes in pH upon addition of

moderate amounts of strong acid or base.

Amino acids that have this capability are glycine

and histidine. For proteins to act as buffers, you

must take into account all of the R groups and

the pH that they will gain or lose protons.

Source: Jeffrey Stiefel, http://www.madsci.org


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Cell Compounds


- Blow off CO2Defence against addition of acid.

1. Firstline of defence: bufferingH++ HCO3

- H2CO3

2. Respiratory component H2CO3 CO2 &H2O and the CO2excreted by the lungs.

- Advantage: in min pH can be restoredtowards normal.

- Disadvantage: One of the primaryextracellular buffers has been

depleted. i.e.#[HCO3-]

3, Renal - kidney excretes H+ and replenishes

[HCO3-]

- But, this is a slow process taking hours todays.

C. Water

- it provided a medium in which other molecules couldmove and interact without being bound by strongcovalent or ionic bonds

- life evolved as a result; and as such all liferequires it, and the greater the availability thegreater the array of life (oceans!tropical forest

!desert)

- all reproduction requires a water medium- Key to this, water has the ability to form weak

chemical associations with only 5-10% the strength

of covalent bonds

- This property derived from waters structure isdirectly responsible for the shape of life

a. Water Molecules- Water is a polar molecule

- it has positively and negatively chargedends; one portion of the molecule attractselectrons more strongly then

Body is

~70% water

~30% other chemicals

- ions, small molecules ~4%-phospholipids ~2%- DNA ~1%- RNA ~6%- Proteins ~15%- Polysaccharides ~2%


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Cell Compounds


- because of their polarity they tend to formhydrogen bonds with each other.

- The high degree ofcohesiveness between

water molecules due toH bonding results in

waters unusually high

surface tension,

melting pt., boiling pt,heat of vaporization,

and heat capacity.

-b. Water as Solvent

- since water moleculesare polar, they are ableto dissolve ionic

compound readily,e.g., NaCl

- i.e., 4 or 5 watermolecules can fit

around one Na+ion

or Cl-ion and the

sum of theircollective weak

charges is enough

to attract the ion

away from otherions in the crystal

(cf. hydration, solvation)

- NB.Electrically neutral (e.g., fats) and non-polar substances (e.g., O2) are not soluble in

water.

Source: LifeThe Science of Biology, 7thed.


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Cell Compounds


c. Water as a Regulator

- Water is also important in regulatingenvironmental temperatures, because it is able

to absorb much heat energy without a very large

increase in temp. (conversely it may also release

much heat energy without a great loss in temp.)

- It acts like a highly cost efficient rechargeableheat/energy battery

- dampens fluctuations in temperature- the amount of water vapour in the atmosphere

exerts a strong greenhouse effect

Property of Water Explanation Example for life

High polarity

(universal solvent)- polar water molecules

are attracted to ionsand polar compounds,

making them soluble

- many kinds of moleculescan move freely in cells,permitting a very diverse

array of chemical reactions

High specific heat - hydrogen bonds absorbheat when they break,

and release heat whenthey form, minimizing

temp. change

- water stabilizes body temp.,as well as that of the

environment

High heat of

vaporization*- many hydrogen bonds

must be broken for

water to evaporate

- evaporation of water coolsbody surfaces

Lower density of ice - water molecules in anice crystal are spaced

relatively far apartbecause of hydrogen

bonding

- because ice is less densethan water, lakes do not

freeze solid, and theyoverturn in spring to enrich

the lakes food/nutrient chain

Cohesion(surface tension)

- hydrogen bonds holdmolecules of watertogether

- leaves pull water upwardfrom roots; seeds swell andgerminate

* Ammonia (NH3) with a molecular weight of 17 (water is 18) has a

freezing pt. of ~ -78C and a boiling pt. of ~ -33C Why? H-bonds in

water mean water has a much higher freezing pt and boiling pt. (recall

our simile of a loan, principle and interest, you need to pay off the

interest first, a lot of E has to go into the H-bonds to break them before

Lubricant

Water is also an excellent lubricant,

blame those H-bonds (and surface

tension) for forming a sheet of water

between two bodies, thus reducing

friction.


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Cell Compounds


the water will boil). Household ammonia is a solution of NH3in water

(ammonium hydroxide).

D. Biomolecules: A Quick Introduction

Waterfunction - universal solventcomposition - H O

Carbohydratesfunction - energy source

composition - H O C

Lipids (Fats)function - energy storage

composition - H O C

Proteinsfunction - structural & catalytic

composition - H O C N (sometimes P, S)

Nucleic Acids (DNA & RNA)function - genetic code

composition - H O C N P

cell compounds

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