chap 4 biology bio
Post on 04-Jun-2018
231 Views
Preview:
TRANSCRIPT
-
8/13/2019 Chap 4 BIOLOGY BIO
1/82
Introduction to cell biology
Chemical Bonds and Water
-
8/13/2019 Chap 4 BIOLOGY BIO
2/82
Organisms are composed of matter.
Matter is anything that takes up space and has mass.
An elementis a substance that cannot bebroken down to other substances by chemicalreactions.
There are 92 naturally-occurring elements.
Each element has a unique symbol, usually from thefirst one or two letters of the name, often from Latinor German.
-
8/13/2019 Chap 4 BIOLOGY BIO
3/82
A compoundis a substance consisting of two ormore elements in a fixed ratio.
Table salt (sodium chloride or NaCl) is a compoundwith equal numbers of chlorine and sodium atoms.
While pure sodium is a metal and chlorine is a gas,their combination forms an edible compound, an
emergent property.
-
8/13/2019 Chap 4 BIOLOGY BIO
4/82
About 25 of the 92 natural elements are knownto be essential for life.
Four elements - carbon (C), oxygen (O), hydrogen(H), and nitrogen (N) - make up 96% of living matter.
Most of the remaining 4% of an organisms weightconsists of phosphorus (P), sulfur (S), calcium (Ca),
and potassium (K).
Life requires about 25 chemicalelements
-
8/13/2019 Chap 4 BIOLOGY BIO
5/82
-
8/13/2019 Chap 4 BIOLOGY BIO
6/82
Trace elementsare required by an organism but
only in minute quantities.
Some trace elements, like iron (Fe), are required by allorganisms.
Other trace elements arerequired only by some species.
For example, a daily intakeof 0.15 milligrams of iodineis required for normalactivity of the human
thyroid gland.
Fig. 2.4
-
8/13/2019 Chap 4 BIOLOGY BIO
7/82
An elementconsists of a single type of atomthat is different from other atoms that build
up another element. Is the smallest unit of matter in biological or
chemical organization. So small, symbolized with abbreviation used
for the elements that are made up of thoseatoms
C = Carbon, consists only single carbon atom
-
8/13/2019 Chap 4 BIOLOGY BIO
8/82
1. Subatomic particles Atom= Greek word= indivisible
Consists of many subatomic particlesNeutrons (Neutral)
Protons (+ve charge)
Electrons (-ve charge) Neutron + Proton = Atomic nucleus
Electron move around nucleus= electron cloud
-
8/13/2019 Chap 4 BIOLOGY BIO
9/82
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
(a) (b)
-
8/13/2019 Chap 4 BIOLOGY BIO
10/82
Protons and electrons attracted to each otherbecause of opposite charge, thus keeping theelectron orbiting around the nucleus.
Protons and neutrons have same mass Electrons are so light and small, their mass
considered zero.
Protons and neutrons contribute to mass ofatom Unit for atom mass = dalton Proton + neutron = closed to 1 dalton
-
8/13/2019 Chap 4 BIOLOGY BIO
11/82
2.Atomic number and atomic weight Atomic number= the number of protons in
the element The number is unique to that element
2He
Indicates atom of the element Helium has 2protons in its nucleus
-
8/13/2019 Chap 4 BIOLOGY BIO
12/82
Usually, an atom is neutral in electricalcharge.
Equal number of electrons must balance itsproton. Therefore, the atomic number indicates the
number of protons or the number ofelectrons in an electrically neutral atom.
-
8/13/2019 Chap 4 BIOLOGY BIO
13/82
Atomic mass = the sum of protons and neutronsin the nucleus atom (mass number)
Number of neutron= Atomic mass- Atomic number
Proton = 11Electron =11Neutron = Atomic mass-Atomic number
= 23-11=12
-
8/13/2019 Chap 4 BIOLOGY BIO
14/82
Atomic number= no. of proton= no. of electronProton = 2Electron = 2Neutron = Atomic mass- Atomic number
= 4- 2=2
-
8/13/2019 Chap 4 BIOLOGY BIO
15/82
-
8/13/2019 Chap 4 BIOLOGY BIO
16/82
-
8/13/2019 Chap 4 BIOLOGY BIO
17/82
-
8/13/2019 Chap 4 BIOLOGY BIO
18/82
Hydrogen, special case
Smallest atom
Made up of 1 proton, 1 electron, no neutron
-
8/13/2019 Chap 4 BIOLOGY BIO
19/82
3. Isotopes Name given to the atoms from the same
element, but shows differences in terms ofthe subatomic particle numbers.
Element consists of mixture of atoms withdifferent numbers of neutrons, and thusdifferent masses.
-
8/13/2019 Chap 4 BIOLOGY BIO
20/82
-
8/13/2019 Chap 4 BIOLOGY BIO
21/82
-
8/13/2019 Chap 4 BIOLOGY BIO
22/82
Radioactive isotope
Form of element that their nucleus decays
spontaneously Unstable, tend to give off particles and energy
easily.
-
8/13/2019 Chap 4 BIOLOGY BIO
23/82
Carbon-12, Carbon-13 are stable- unable to decayeasily
But, Carbon-14 are unstable or radioactive
When an atomic nucleus of an element experience
the decaying process, the atomic number change.
As a result, the process transforms the atom into
different atoms or different elements. E.g Carbon-14 transforms to N.
-
8/13/2019 Chap 4 BIOLOGY BIO
24/82
Radioactive isotopes applications:
Measurements of radioactivity in fossils to date
relics of past life Measure thickness of metal
Testing for corrosion and monitoring purpose
Treat cancerous cells
Tracers to follow atoms through metabolism-diagnostic tools in medicine (Kidney problem)
-
8/13/2019 Chap 4 BIOLOGY BIO
25/82
4. Electron configuration The arrangement and how electrons are
distributed in the atom Determines the chemical behavior of atoms Electrons orbiting nucleus in spherical
pathway- help from the opposite charge ofproton- right pathway
-
8/13/2019 Chap 4 BIOLOGY BIO
26/82
The pathway of electrons represents theirenergy level electron shell
Nucleus need less energy to attract theelectron when they are close to each other Periodic table shows the distribution of
electrons according to numbers of electronshell in their atom
-
8/13/2019 Chap 4 BIOLOGY BIO
27/82
Left-right; refers to additional sequence ofelectrons
Top-bottom sequence of elements in eachcolumn represents the number of electronshell in their configuration
Similar no. of electrons in valence shell=similar chemical behavior
Completed valence shell- unreactive Incomplete valence shell- reactive
Figure 2.9
-
8/13/2019 Chap 4 BIOLOGY BIO
28/82
g
First
shell
Secondshell
Third
shell
Hydrogen
1H
Lithium
3Li
Sodium
11Na
Beryllium
4Be
Magnesium
12Mg
Boron
5B
Aluminum
13Al
Carbon
6C
Silicon
14Si
Nitrogen
7N
Phosphorus
15P
Oxygen
8O
Sulfur
16S
Fluorine
9F
Chlorine
17Cl
Neon
10Ne
Argon
18Ar
Helium
2He2
He
4.00Mass number
Atomic number
Element symbol
Electron
distribution
diagram
-
8/13/2019 Chap 4 BIOLOGY BIO
29/82
Electron orbital Orbital- 3D space where electron spends
most of its time 1stelectron shell-single orbital- 2 electrons 2ndelectron shell-4 orbital- 8 electrons
2s
2p (2px,2py, 2pz)
-
8/13/2019 Chap 4 BIOLOGY BIO
30/82
-
8/13/2019 Chap 4 BIOLOGY BIO
31/82
The reactivity of atoms arises from the presence ofunpaired electron in one or more orbitals of their
valence shells
-
8/13/2019 Chap 4 BIOLOGY BIO
32/82
Atoms with incomplete valence shell interactwith each other to complete their own
valence shell Atom stays close to each other bind by
chemical bonds
Covalent bonds
Ionic bonds
Hydrogen bond
-
8/13/2019 Chap 4 BIOLOGY BIO
33/82
1. Covalent bond Attraction due to sharing valence electrons
by two atoms to fulfill their valence shells. Strong, not easily broken unless by
enzymatic catalysis.
-
8/13/2019 Chap 4 BIOLOGY BIO
34/82
Two or more atoms held together by covalentbonds constitute a molecule.
We can abbreviate the structure of this molecule
by substituting a line for each pair of sharedelectrons, drawing the structural formula. H-H is the structural formula for the covalent bond
between two hydrogen atoms.
The molecular formulaindicates the numberand types of atoms present in a single molecule. H2is the molecular formula for hydrogen gas
-
8/13/2019 Chap 4 BIOLOGY BIO
35/82
Single covalent bond: 2 atoms share a pairof electron valence- stable, completeconfiguration.
For example, if two hydrogen atoms comeclose enough that their 1s orbitals overlap,then they can share the single electrons
that each contributes.
-
8/13/2019 Chap 4 BIOLOGY BIO
36/82
Oxygen needs to add 2 electrons to the 6already present to complete its valence shell.
Two oxygen atoms can form a molecule bysharing twopairs of valence electrons.
These atoms have formed a double covalent
bond.
-
8/13/2019 Chap 4 BIOLOGY BIO
37/82
Every atom has a characteristic total number ofcovalent bonds that it can form - an atoms valence.
The valence of hydrogen is 1.
Oxygen is 2. Nitrogen is 3.
Carbon is 4.
Phosphorus should have a valence of 3, based onits three unpaired electrons, but in biological
molecules it generally has a valence of 5, forming
three single covalent bonds and one double bond.
-
8/13/2019 Chap 4 BIOLOGY BIO
38/82
Covalent bonds can form between atoms ofthe same element or atoms of differentelements.
While both types are molecules, the latterare also compounds.
Water, H2O, is a compound in which two
hydrogen atoms form single covalentbonds with an oxygen atom. This satisfies the valences of both
elements.
-
8/13/2019 Chap 4 BIOLOGY BIO
39/82
Methane, CH4, satisfies the valences of both C and H.
-
8/13/2019 Chap 4 BIOLOGY BIO
40/82
The attraction of an atom for the electrons ofa covalent bond is called itselectronegativity.
Strongly electronegative atoms attempt to pull
the shared electrons toward themselves.
If electrons in a covalent bond are shared
equally, then this is a nonpolar covalentbond.
A covalent bond between two atoms of the sameelement is always nonpolar.
-
8/13/2019 Chap 4 BIOLOGY BIO
41/82
If the electrons in a covalent bond are notshared equally by the two atoms, then this is
a polar covalent bond. The bonds between oxygen and hydrogen
in water are polar covalent because oxygenhas a much higher electronegativity thandoes hydrogen.
-
8/13/2019 Chap 4 BIOLOGY BIO
42/82
Compounds with a polarcovalent bond have regions
that have a partial negativecharge near the stronglyelectronegative atom and apartial positive charge near
the weakly electronegativeatom.
-
8/13/2019 Chap 4 BIOLOGY BIO
43/82
2. Ionic bonds
Forms because of the attraction between
positive and negative charged ion. For example, sodium with one valence electron in its
third shell transfers this electron to chlorine with 7valence electrons in its third shell.
Now, sodium has a full valence shell (the second) andchlorine has a full valence shell (the third).
-
8/13/2019 Chap 4 BIOLOGY BIO
44/82
-
8/13/2019 Chap 4 BIOLOGY BIO
45/82
After the transfer, both atoms are no longerneutral, but have charges and are called ions.
Sodium has one more proton than electrons
and has a net positive charge. Atoms with positive charges are cations.
Chlorine has one more electron than protons
and has a net negative charge. Atoms with negative charges are anions.
-
8/13/2019 Chap 4 BIOLOGY BIO
46/82
Atoms with 5, 6, 7 valence electron tend togain electrons- become negatively charged.
Atoms with 1, 2, 3 electrons tend to loseelectrons- become positively charged
-
8/13/2019 Chap 4 BIOLOGY BIO
47/82
3. Hydrogen bonds Is the attractive force between hydrogen
atom covalently bonded to oneelectronegative atom and is attracted toanother electronegative atom from othermolecules.
Usually oxygen or nitrogen atoms E.g H2O, NH3
-
8/13/2019 Chap 4 BIOLOGY BIO
48/82
Hydrogen bonds between water molecules
-
8/13/2019 Chap 4 BIOLOGY BIO
49/82
Weak, but important The advantages Support shapes of large molecules and help
molecules to attach to each other The contact can exist temporarily, not permanent Chemical signal in brain
One-brain cell signals other cell by releasing moleculesthat use weak bonds to tie up onto receptor moleculesof the receiving cell
If the signals strongly bonded, the transmission willcontinue to respond causing cell excited continuously
-
8/13/2019 Chap 4 BIOLOGY BIO
50/82
Do not the Unbelievers see that the heavens and theearth were joined together (as one unit of creation),
before we clove them asunder? We made fromwaterevery living thing. Will they not then believe?- Al-Anbiyaa 21: 30
-
8/13/2019 Chap 4 BIOLOGY BIO
51/82
Because water is the substance that makes possiblelife as we know it on Earth, astronomers hope tofind evidence of water on newly discovered planetsorbiting distant stars.
Life on Earth began in water and evolved there for 3billion years before spreading onto land.
Even terrestrial organisms are tied to water.
Most cells are surrounded by water and cells are about 70-95% water.
Water exists in three possible states: ice, liquid, andvapor.
-
8/13/2019 Chap 4 BIOLOGY BIO
52/82
a) Cohesive and adhesive properties Cohesive-capacity to stick to each other
tightly although under tension, normally
occur among similar atoms and held togetherby hydrogen bonds. The bonds are fragile, easily break and
reform with greater frequency.
Make water more structured than most liquids
hydrogen bonds hold water molecules,cohesion occur
-
8/13/2019 Chap 4 BIOLOGY BIO
53/82
Cohesion among water molecules plays a key role inthe transport of water against gravity in plants.
Water that evaporates from a leaf is replaced bywater from vessels in the leaf.
Hydrogen bonds cause water molecules leavingthe veins to tug on molecules further down.
This upward pull is transmitted to the roots.
-
8/13/2019 Chap 4 BIOLOGY BIO
54/82
Adhesive- ability to cling to other substances. Also contribute to water transportation
Adhesion of water to the wall of vessels helps to
counter against gravity
Ensure molecules move upward to every part of
higher plants.
Also can be seen during cleaning and cleansing-help things become wet and remove all impurities
Adhesion to cell walls byhydrogen bonds resist
-
8/13/2019 Chap 4 BIOLOGY BIO
55/82
hydrogen bonds- resistdownward pull of gravity
Cohesion due to hydrogenbonds between water
molecules helps holdtogether the column ofwater within the cells
-
8/13/2019 Chap 4 BIOLOGY BIO
56/82
Surface tension,a measure of the force necessaryto stretch or break the surface of a liquid, is relatedto cohesion.
Water has a greater surface tension than mostother liquids because hydrogen bonds amongsurface water molecules resist stretching orbreaking the surface.
Water behaves as if covered by an invisible film.
Some animals can stand,walk, or run on waterwithout breaking thesurface.
-
8/13/2019 Chap 4 BIOLOGY BIO
57/82
b. Water has high specific heat Specific heat- amount of heat that must be
absorbed or lost for 1g of substances to change its
temperature by 1C. Specific heat of water- 1 cal/g/1C. Unusually high compared to others
Ethanol- 0.6 cal/g/1C
Acetone- 0.5 cal/g/1C Allows water to absorb or release large amount of
heat without changing its temperature dramatically.
-
8/13/2019 Chap 4 BIOLOGY BIO
58/82
The property of specific heat closely relatedto hydrogen bonds.
Absorption of heat- break bond Released of heat- bond formation Water needs more heat to raise its
temperature as it need to break the
hydrogen bond first before raising up thekinetic energy that cause the temperature tobe increased.
-
8/13/2019 Chap 4 BIOLOGY BIO
59/82
When temperature drops, many additionalhydrogen bonds form, slowing down the kineticenergy and releasing large amount of energy
(heat). High specific water heat important in life forboth large water bodies or the living cells oforganisms. In the ocean, large water bodies can absorb and store
large amount of heat from sun, while warming outonly a few degrees,
Gradually, cooling water can warm the air at night. Coastal area have mild climate compared to desert.
-
8/13/2019 Chap 4 BIOLOGY BIO
60/82
Stabilizes ocean temperatures, sustainingfavorable environment for marine life.
Keeps earth temperature fluctuating in water and
on land within limit that permit life.
Cells can resist extreme change in their own
temperature so that it fluctuates within limits that
permit life activities.
-
8/13/2019 Chap 4 BIOLOGY BIO
61/82
-
8/13/2019 Chap 4 BIOLOGY BIO
62/82
The heat is used to break off hydrogen bondsfirst before it moves faster and transforms intogaseous state.
Advantages in moderating earths climate
Ocean capable of absorbing considerable amount ofheat for evaporation of surface water, it is then
changes to moist tropical air and circulates upwards. The hot, moist tropical air meets with cool air at
higher altitude and releases an amount of heat as itcondenses to form rain.
-
8/13/2019 Chap 4 BIOLOGY BIO
63/82
Due to evaporation, evaporative cooling occur as thehottest molecule transform into gas leavingremaining molecule to cool down.
Contributes to the stability of temperature in lakesand ponds, prevent overheating for terrestrialorganism.
Example
Evaporation of water from leaves and plants helpsto keep plant tissues from overheating on hot day
Evaporation of sweat from human skin transfersbody heat to surrounding.
-
8/13/2019 Chap 4 BIOLOGY BIO
64/82
-
8/13/2019 Chap 4 BIOLOGY BIO
65/82
d. Water expands as it freezes When water is cooled, it does contract as usual until
the temperature is approximately 4c, then expanding
slightly until it reach freezing point. Therefore, water become less dense as solid thanliquid-ice floats.
Temperature reaches 0c- water molecules lockedinto crystalline lattice; maximum 4 neighboring
partner through hydrogen bond, forming hexagon. Hydrogen bonds keep molecules at certain length , so
there are more empty space inside compared to liquidwater 10% less density.
-
8/13/2019 Chap 4 BIOLOGY BIO
66/82
-
8/13/2019 Chap 4 BIOLOGY BIO
67/82
Advantages to the fitness of environment
Floating ice insulate water below, prevent freezing.
Life under frozen surface.
Ice Liquid
-
8/13/2019 Chap 4 BIOLOGY BIO
68/82
e. Water is versatile solvent Because of their polarity-due to polar covalent bond
when a water molecule bears partial positve and
partial negative charges. Hydrogen atom of water molecule with its partial
positive charge attracted to oxygen atom of
neighboring water molecule.
Partial negative charge form hydrogen bond. The opposite charges attracted another ionic
compounds such as NaCl, sugar and protein.
-
8/13/2019 Chap 4 BIOLOGY BIO
69/82
The polarity of water-capable to dissolvemany substances, polar and ioniccompounds.
Water provides efficient medium infacilitating chemical rxn.
Able to interact with H2O hydrophilic Unable to interact with H2O hydrophobic
Oxygen- negatively charge,attracted to Na+
-
8/13/2019 Chap 4 BIOLOGY BIO
70/82
attracted to Na+
Hydrogen- positively charge,
Attracted to Cl-
NaCL- Solute Water- Solvent Mixture of more than one
substance in water-homogenous liquid- Solution
The region of water
molecules around dissolvedions-hydration cell
Any polar-molecules
compound can be dissolved
-
8/13/2019 Chap 4 BIOLOGY BIO
71/82
Mixture in which water is the solvent. Solute- must be hydrophilic substance, dissolve and
interact readily with water. Important for physiological and enzymatic activity. Solute concentration
Units of mole (mol)= molecular weight of asubstance
Avogadros number= number of molecules in amole=6.02 x 1023
Molarity refers to the number of moles of solute perliter of solution- M or mol/l
-
8/13/2019 Chap 4 BIOLOGY BIO
72/82
How to prepare a 0.5 M of NaCl
0.5 M equals to 0.5 mol NaCl in 1 liter of watersolution
Na(23) + Cl (35) = 58 grams (1 mol)
= 0.5 x 58 g= 29 g
-
8/13/2019 Chap 4 BIOLOGY BIO
73/82
1. How to prepare a 2.0 M of K2HPO4?
39K 1H 31P 16O
2. How many grams of salt (NaCl) must bedissolved in water to make 2 L of a 2M salt
solution?23Na 34Cl
-
8/13/2019 Chap 4 BIOLOGY BIO
74/82
Acids and bases Acid-substances that dissociate in solution to yield
hydrogen ion (H+) andanion inside aqueoussolution
HClH++ Cl-
Proton donor because of the +ve charge Acidic solution- always has higher hydrogen ion
[H+] concentration compared to hydroxide ion [OH-]
Strong acid-If the dissociation happens completely Weak acid- incomplete, reversible Litmus paper- blue -> red
-
8/13/2019 Chap 4 BIOLOGY BIO
75/82
Base- substance that dissociates to yieldhydroxide ion [OH-]and cationwhen dissolved inwater.
Proton acceptor Basic solution- lower hydrogen ion [H+]
concentration than hydroxide ion [OH-] .
[OH-] acts as base by accepting a proton to form
H2O indirectly. Strong base- dissociate completely in water
Litmus paper- red -> blue
-
8/13/2019 Chap 4 BIOLOGY BIO
76/82
Neutral-solution which have equalconcentration of [H+] and [OH-].
When acid and base added to each other,they react to neutralize each other provided ifan equal number of hydrogen andhydroxide ionspresent.
Produce salt and water
-
8/13/2019 Chap 4 BIOLOGY BIO
77/82
pH scale Measure the strength of acid and base
Ranges from 0-14
pH of solution= the negative logarithms (base 10)of the hydrogen ion concentration:pH = - log [H+]
[ ] = the molar concentration for the substance.
Neutral, [H+] = 10-7= - log [10-7]= 7
-
8/13/2019 Chap 4 BIOLOGY BIO
78/82
In any solution, the product of H+and OH-
concentration = 10-14
Helps to determine pH if either concentrationof H+or OH- are given.
pH declines as concentration of H+increase pH scale based on H+ concentration, but also
can imply OH- concentration.
-
8/13/2019 Chap 4 BIOLOGY BIO
79/82
-
8/13/2019 Chap 4 BIOLOGY BIO
80/82
Buffers- substances that resists extremechangesin the concentrations of H+and OH-
in a solution. Resists changes in pH when acids or bases are
introduced. How? Buffer work by accepting H+from the
solution if excess, donating H+if depleted. Normally, buffer solutions contain weak acid
and weak base, which combine reversiblywith H+.
-
8/13/2019 Chap 4 BIOLOGY BIO
81/82
One important buffer in human blood and other
biological solutions is carbonic acid.
The chemical equilibrium between carbonic acid
and bicarbonate acts at a pH regulator.
The equilibrium shifts left or right as other
metabolic processes add or remove H+from the
solution.
-
8/13/2019 Chap 4 BIOLOGY BIO
82/82
FINVerily, after each difficulty, there arerelief- Al-Insyirah
top related