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Transcript of Chapter 2 - Fall 08
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Biol 213
Cell Structure and Function
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iClicker Registration
Go to: www.iclicker.com/registration
Your student ID is your GMU email
username (Example: gfondufe)
http://www.iclicker.com/registrationhttp://www.iclicker.com/registration -
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Chapter 2
The Chemical Context of Life
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Atomic Carbon, hydrogen, oxygen
Molecular DNA, proteins
Organelle Nucleus, mitochondria, etc.
Cellular Metabolism, cell signaling Tissue Smooth muscle, bone, etc.
Organ Heart, brain, liver, etc.
Organ System Circulatory, digestive, etc.
Organism Mouse, human, maize
Higher Levels Ecosystems, populations
Hierarchy of biological organization
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Fig. 1.4 Exploring levels of Biological Organization
The biosphere
Communities
PopulationsOrganisms
EcosystemsOrgans andorgan systems
CellsCell
Organelles
Atoms
MoleculesTissues
10 m
1 m50 m
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Cell Biology
Cell
Smallest unit that can carry out all the activities
required for the life of an organism
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Cell Biology
Cell Properties / Organism Properties
Ability to reproduce
Ability to grow
Ability to process energy
Ability to respond to the environment
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Cell Biology
Organisms are composed of cells
Some are unicellularsingle cell
Some are multicellularmultiple cells
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Cell Biology
Multicellular Organism
Starts as a single cell (zygote)
Reproduces by division (mitosis)
Cells differentiate
Have different form and/or properties
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Cell Biology
Cells may appear different, but they have
many similarities
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Cell Biology
In Cell Biology, we will be examining the many
similarities (and some differences) of cells
the similarities that make up the commonSTRUCTURAL and FUNCTIONAL
properties of cells
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Biology - Study of life, living things
Biology is a multidisciplinary science
Cell Biology- Study of cells
To understand structure and function of cells,we need a basic understanding of Chemistry
Cell Biology
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Basic Chemistry for Cell Biologists
Matter
Composed Elements and Compounds
Elements required by living organisms
Atomic structure
Chemical bonding
Chemical reactions
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Basic Chemistry -Matter
Matter
Anything which takes up spaceand has mass
Composed of elements
Exists in many forms
Rock, wood, water, air, plastic, human, etc
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Basic Chemistry - Matter
Element
Substance which cannot be broken down into
other substances by chemical means
92 natural elements + ~20 man-made
Has a symbolusually 1 or 2 letters of its
name (may be derived from Latin or German)
H = Hydrogen He = Helium
Na = Sodium (Natrium) Fe = Iron (Ferrum)
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Basic Chemistry - Matter
Compound
Substance consisting of two or more elements
combined in a fixed ratio
Examples:
Water: H2O = 2 Hydrogen : 1 Oxygen
Table salt: NaCl = 1 Sodium : 1 Chlorine
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Basic Chemistry - Matter
A compound has characteristics beyond those of
its combined elementsemergent properties
Example:Table salt: NaCl = 1 Sodium : 1 Chlorine
Sodium - very reactive (explosive) metal
Chlorine - poisonous gas
Combined = edible compound
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Basic Chemistry for Cell Biologists
Matter
Elements and Compounds
Elements required by living organisms
Atomic structure
Chemical bonding
Chemical reactions
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Basic chemistryElements Required for Life
Number required by living organisms
Only about 25 of 92 natural elements
96% of living matter composed of:
Carbon, Hydrogen, Oxygen, Nitrogen
Other 4% composed of:
Phosphorus, Sulfur, Calcium, Potassium,
others
T bl 2 1 N t ll O i El t i th
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Table 2.1 Naturally Occurring Elements in theHuman Body
Symbol Element % (by body weight)
Elements that make up 96% of the human bodyO Oxygen 65
C Carbon 18.5
H Hydrogen 9.5
N Nitrogen 3.3Elements that make up about 4% of the human body
Ca Calcium 1.5
P Phosphorus 1.0
K Potassium 0.4S Sulfur 0.3
Na Sodium 0.2
Cl Chlorine 0.2
Mg Magnesium 0.1Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings
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Basic Chemistry - Trace Elements
Trace Elements
required only in very small quantities
Examples:
Iron (Fe)hemoglobin, other proteins
Iodine (I)thyroid hormone
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Fig. 2.4b Goiter due toiodine deficiency
Iodine- thyroidhormone
a daily intake of0.15 mg of iodine isrequired for normalactivity of the humanthyroid gland
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Basic Chemistry for Cell Biologists
Matter
Elements and Compounds
Elements required by living organisms
Atomic structure
Chemical bonding
Chemical reactions
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Basic Chemistry - Atomic Structure
Atomic structure determines behavior of element
Atoms combine by chemical bonding to form
molecules
Weak chemical bonds are important
Shape of molecule is related to function
Chemical reactions make and break bonds
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Basic Chemistry - Atomic Structure
Atom
Smallest unit of matter that still retains
properties of an element
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Basic Chemistry - Atomic Structure
Atom
Composed of three types of particles
Neutrons - no electrical charge
Protons - positive electrical charge (+1)
Electrons - negative electrical charge (-1)
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Basic Chemistry - Atomic Structure
Atom
Neutrons and Protons
Packed together in dense core
Atomic Nucleus
Electrons
Located in a cloud or shell around thenucleus
Attracted to nucleus by positively charged
protons
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Cloud of negativecharge (2 electrons)
Nucleus2 protons2 neutrons
Electrons
(b)(a)
Basic ChemistryAtomic structure
Fig. 2.5 Models of a Helium (He) atom
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Basic Chemistry - Atomic Structure
Nucleus
Small in comparison to entire atom (5/1000)
Electrons orbit at a distance from nucleus
Accounts for nearly all of the weight Protons + neutrons (electron weight is
negligible)
Neutrons & protons - about the same mass ~1 dalton (~1.7 x 10-24g)
After John Dalton, a British scientist
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Basic Chemistry - Atomic Structure
Atomic Number
Number of protons in an atom
Unique for each element
Written as a subscript to left of chemical
symbol 2He, 8O, 16S, 26Fe
Number of protons and electrons are
generally the same - no net charge
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Basic Chemistry - Atomic Structure
Mass Number
Number of protons and neutrons
Written as a superscript to left of chemical
symbol - 4He, 16O, 32S, 55Fe Atomic Weight
approximately the mass number
proton and neutron each 1 dalton
4He has a mass number of 4
estimated atomic weight of 4 daltons (4.003)
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Basic Chemistry - Atomic Structure
Number of Neutrons
No. of protons = Atomic Number
No. of protons and neutrons = mass number
Mass number - Atomic Number =Number of neutrons
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Basic Chemistry - Atomic Structure
Number of Neutrons
Can the number of neutrons vary in atoms of
an element?
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Basic Chemistry - Atomic Structure
Yes! Number of Neutrons may vary!
Isotopes- different numbers of neutrons
Carbon- 12C - 6 protons + 6 neutrons
13C - 6 protons + 7 neutrons
14C - 6 protons + 8 neutrons
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Basic Chemistry - Atomic Structure
Isotopes
Stability of an isotope
Unstable (radioactive) -
breaks down (decays) and loses particles
12C and 13C are stable
14C is unstable (radioactive isotope)
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Basic Chemistry - Atomic Structure
Radioactive IsotopesUseful in scientific research and medicine
Tracing atoms through metabolic processes
Diagnosing medical disorders
Also useful in dating fossils
Unfortunately, they pose a hazard to life
Decay particles damage cellular molecules
From nuclear reactor accidents or a dirty
bomb
Fi 2 6 U i R di ti I t
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Fig. 2.6 Using Radioactive Isotopes
Compounds includingradioactive tracer(bright blue)
Humancells
Incubators
1 2 3
4 5 6
7 8 9
50C45C40C
25C 30C 35C
15C 20C10C
Humancells are
incubatedwith compounds used tomake DNA. One compound islabeled with 3H.
1
2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds are
removed.
DNA (old and new)
Fig 2 6 Using Radioacti e isotopes
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Fig. 2.6 Using Radioactive isotopes
The test tubes are placed in a scintillation counter.3
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U i R di ti I t
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Using Radioactive Isotopes
Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Cells containing
radioactive DNA
are exposed to
a photographicemulsion. Then
the emulsion is
developed and
viewed under amicroscope.
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Fig. 2.7 PET(Positron Emission Tomography) SCAN
Cancerous
throattissue
Radioactively-taggednutrient is given
and monitored
Decay of isotope is
detected and colorindicates amount of
isotope present
Intensely coloredareas indicate high
metabolic rate - i.e.,
CANCER
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Basic Chemistry - Atomic Structure
Electrons
Involved in chemical reactions between atoms
Energy levels of electrons vary (potential
energy)
Discrete steps called electron shells
Low energy near nucleus
High energy further away
Fig 2 8 Energy levels of an atoms electrons
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Fig. 2.8 Energy levels of an atoms electrons
(a) A ball bouncing down a flightof stairs provides an analogy
for energy levels of electrons
Third shell (highest energy
level)
Second shell (higherenergy level)
Energyabsorbed
First shell (lowest energylevel)
Atomicnucleus
(b)
Energylost
Different amounts of
potential energy are
stepwise changes
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Basic Chemistry - Atomic Structure
Electron configuration
Determines chemical properties of elements
Depends upon the number of electrons in its
outermostshell
Termed valence shelland valence
electrons
The periodic table of elements shows the
electron distribution of elements
Fig 2-9 Electron distribution diagrams for the first 18
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Fig. 2-9 Electron distribution diagrams for the first 18elements in the periodic table
Hydrogen
1H
Lithium
3LiBeryllium
4BeBoron
5BCarbon
6CNitrogen
7NOxygen
8OFluorine
9FNeon
10Ne
Helium
2HeAtomic number
Element symbol
Electron-distributiondiagram
Atomic mass
2He
4.00Firstshell
Secondshell
Third
shell
Sodium
11NaMagnesium
12MgAluminum
13AlSilicon
14SiPhosphorus
15PSulfur
16SChlorine
17ClArgon
18Ar
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Basic Chemistry - Atomic Structure
Electron configuration
Valence shell and valence electrons
Completed shell is unreactivechemicallyinert
Helium, Neon, Argon
Other atoms transfer or share electrons to
complete valence shell
Chemical bonds
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Basic Chemistry - Atomic Structure
Electron shells or Orbitals
Once thought to be like planets orbiting the
sun, but dont know exact path
An orbitalis where electron is 90% of time
Only 2 electrons per orbital at any time
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Basic Chemistry - Atomic Structure
Electron orbitals
First energy shell - 2 electrons
1s orbital - 2 e-
Second energy shell - 8 electrons
2s orbital - 2 e-
Three 2p orbital - 6 e-
Neon, with two filled shells (10 electrons)Fig. 2.10 Electron Orbitals
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Electron-distributiondiagram
(a)
(b)
Separate electronorbitals
First shell Second shell
1sorbital 2sorbital Three 2porbitals
(c)
Superimposed electronorbitals
1s, 2s, and 2porbitals
x y
z
Fig. 2.10 Electron Orbitals
B i Ch i t At i St t
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The presence of unpaired electrons in one ormore orbitals of their valence shells accounts for
the reactivity of an atom
Atoms interact with certain other atoms in order
to complete their valance shells
Such interactions result in atoms stayingclose together, and held by attractions
called chemical bonds
Basic ChemistryAtomic Structure
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Basic Chemistry for Cell Biologists
Matter
Elements and Compounds
Elements required by living organisms
Atomic structure
Chemical bonding
Chemical reactions
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Covalent Chemical Bonds
Sharing of valence electrons
Strongest of the chemical bonds
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Covalent Bond
Sharing of a pair of valence electrons by two
atoms
If unshared orbitals overlap, each atom cancount both electrons toward its goal of filling the
valence shell
Fig. 2.11 Formationof aHydrogen
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covalent bondHydrogen
atoms (2 H)
Hydrogen
molecule (H2)
When two hydrogen atoms approach,the electron of each atom is also attracted
to the proton in the other nucleus.
The two electrons become shared in a
covalent bond, forming an H2 molecule
In eachhydrogen atom, the single
electron is held in its orbital by itsattraction to the proton in the nucleus
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Basic Chemistry - Molecules
Two or more atoms held together by covalentbonds constitute a molecule
The molecular formulaindicates the number
and types of atoms present in a single molecule
For molecular hydrogen: H2
Structural formulaFor molecular hydrogen: HH
Covalent Bonds
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A single covalent bond, or single bond
sharing of one pair of valence electrons
A double covalent bond, or double bond
sharing of two pairs of valence electrons
Covalent Bonds
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Animation: Covalent Bonds
Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Covalent Bonds - Animation
http://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.html -
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Oxygen has 6 electrons in valence shell
Needs to add 2 e-to complete its valence
shell
Two oxygen atoms can form a molecule by
sharing two pairs of valence electrons
Forms a double covalent bond
Covalent Bond - O2
Fi 2 12 C l t B d O
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Fig. 2.12 Covalent Bond - Oxygen
(b) Oxygen (O2)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
B i Ch i t V l
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Basic Chemistry - Valence
Every atom has a characteristic total number
of covalent bonds that it can form - an atoms
valence
The valence of hydrogen is 1Oxygen is 2
Nitrogen is 3
Carbon is 4
Phosphorus has a valence of 5, forming 3
single covalent bonds and 1 double bond
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Covalent Bonds
Can form between atoms of the same element or
atoms of different elements.
While both types are molecules, the latter are
also compounds
Water, H2O, is a compound in which two
hydrogen atoms form single covalent bonds
with an oxygen atom
Fig. 2.12 Covalent Bond - Hydrogen
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Fig. 2.12 Covalent Bond Hydrogen
(a) Hydrogen (H2)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
Fig 2 12 Covalent Bond - Water
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Fig. 2.12 Covalent Bond - Water
(c) Water (H2O)
Name and
MolecularFormula
Electron-
distributionDiagram
Lewis Dot
Structure andStructuralFormula
Space-
fillingModel
Fig. 2-12 Covalent Bond - Methane
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g Co a e t o d et a e
(d) Methane
(CH4)
Name and
MolecularFormula
Electron-
distributionDiagram
Lewis Dot
Structure andStructuralFormula
Space-
fillingModel
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Covalent Bonds
Sharing of electrons between atoms
Equal- nonpolar covalent bond
Unequal- polar covalent bond
Some atoms have a greater attraction for an
electron
Electronegativityis a measure of the degree
of attraction
P l C l B d
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Polar Covalent Bonds
Form between atoms with different
electronegativity
Water: Oxygen - high electronegativity
Hydrogen - low electronegativity
partial negative charge near the strongly
electronegative atom
partial positive charge near the weakly
electronegative atom
Fig. 2.13 Polar covalent bonds in a water
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gmolecule
+ +H H
O
H2OPartial positive Partial positive
Partial negative
Oxygen is more electronegative than hydrogen
Basic Chemistry for Cell Biologists
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Basic Chemistry for Cell Biologists
Chemical Bonds
Covalent bonds
Nonpolar
Polar
Ionic bonds
Hydrogen bonds
Van der Waals interactions
Basic Chemistry Ionic Bonds
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Basic Chemistry - Ionic Bonds
Transfer of electrons between atoms
After such a transfer, both atoms have charges
A charged atom (or molecule) is called an ion
A cationa positively charged ion
An aniona negatively charged ion
An ionic bondis the attraction between ananion and a cation
Basic Chemistry Ionic Bonds
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Basic Chemistry - Ionic Bonds
Sodium and Chlorine
Sodium has one electron in valence shell
Chlorine has seven
Transfer one electron from sodium to chlorine
Sodium becomes positively charged - cation
Chlorine becomes negatively charged - anion
Both have complete valence shell
Fig. 2.14 Electron Transfer and Ionic Bonding
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Fig. 2.14 Electron Transfer and Ionic Bonding
Na Cl Na Cl
NaSodium atom Chlorine atom
Cl Na+Sodium ion(a cation)
ClChloride ion
(an anion)
Sodium chloride (NaCl)
Electron Transfer
Ionic Bonds - Animation
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Animation: Ionic Bonds
Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Ionic Bonds Animation
Ionic Compounds
http://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.html -
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Ionic Compounds
Compounds formed by ionic bonds
Formula indicates ratio of elements
NaCl - 1 atom of sodium: 1 atom of chlorine
MgCl2: 1 atom of Mg : 2 atoms of Cl
Strength of ionic bonds depends on
environmental conditions
dry conditions - salts are hard
aqueous conditions - salts dissolve
C f C
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Basic Chemistry for Cell Biologists
Chemical Bonds
Covalent bonds
Nonpolar
Polar
Ionic bonds
Hydrogen bonds
Van der Waals interactions
B i Ch i H d B d
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Basic Chemistry - Hydrogen Bonds
Weak type of bonding
Hydrogen atom covalently bonded to one
atom (strongly electronegative) is attracted toanother atom (also strongly electronegative)
The partially positive charged hydrogen atomin a covalent bond is attracted to negatively
charged (partial or full) molecules, atoms, oreven regions of the same large molecule.
Fig. 2.16 A hydrogen bond between water and ammonia
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+
+
+
+
+
Water (H2O)
Ammonia (NH3)
Hydrogen bond
Basic Chemistry for Cell Biologists
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Basic Chemistry for Cell Biologists
Chemical Bonds
Covalent bonds
Nonpolar
Polar
Ionic bonds
Hydrogen bonds
Van der Waals interactions
Van der Waals Interactions
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Van der Waals Interactions
Because electrons are constantly in motion,there can be periods when partially positiveand negative regions accumulate by chancein one area of a molecule
This creates ever-changing regions ofnegative and positive charge within amolecule.
Molecules or atoms in close proximity can beattracted by these fleeting charge differences,creating van der Waals interactions.
Van der Waals Interactions
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Van der Waals Interactions
Such bonds, collectively, can be strong
as between molecules a geckos toe hairsand the surface of a wall
Function Relates to Shape
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Function Relates to Shape
Shape of a molecule
determined by the arrangement of electron
orbitals that are shared by the atoms involved
in a bond
A molecule with two atoms is always linear
However, a molecule with more than twoatoms has a more complex shape
Function relates to Shape
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sorbitalz
x
y
Three porbitals
Hybridization of orbitals
Four hybrid orbitals
Tetrahedron
(a)
For atoms with electrons in both s and p orbitals, the
formation of a covalent bond leads to hybridization ofthe orbitals to form four new orbitals in a tetrahedron
shape
Fig. 2.17a Hybridization of orbitals
Function Relates to Shape
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Function Relates to Shape
In a water molecule the hybrid orbitals thatoxygen shares with hydrogen atoms are
spread in a V shape.
In a methane molecule (CH4),
all four hybrid orbitals are shared
hydrogen nuclei are at the corners of thetetrahedron
Space-fillingModel
Ball-and-stickModel
Hybrid-orbital Model(with ball-and-stick
Fig. 2.17b
Molecular-shape
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Model Model (with ball-and-stickmodel superimposed)
Unbonded
electronpair
104.5
Water (H2O)
Methane (CH4)
Molecular shape
models
Function Relates to Shape
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Function Relates to Shape
Molecules with similar shapes can interact in similar
ways
Opiate drugs (such as morphine) are similar to
endorphins (the bodys natural pain killers)
Both morphine and endorphins can bind to
endorphin receptors on the surface of brain cells
thereby relieving pain and producing euphoria
Key
Carbon NitrogenFig 2.18 A molecular
mimic
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(a) Structures of endorphin and morphine
(b) Binding to endorphin receptors
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
Morphine
Natural endorphinHydrogen
gSulfurOxygen
mimic
Basic Chemistry for Cell Biologists
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Basic Chemistry for Cell Biologists
Matter
Elements and Compounds
Elements required by living organisms
Atomic structure
Chemical bonding
Chemical reactions
Basic Chemistry - Chemical Reactions
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y
The making and breaking of chemical bonds
Chemical bonds are broken and reformed,
leading to new arrangements of atoms
The molecules at the beginning of a chemical
reaction are called reactants
The molecules at the end of a chemical
reaction are called products
B
Basic Chemistry Chemical reactions
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Reactants Reaction Products
2 H2 O2 2 H2O
Basic ChemistryChemical reactions
All of the atoms in the reactants must be accounted
for in the products
The reaction must be balanced
Basic Chemistry - Chemical Reactions
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Basic Chemistry - Chemical Reactions
Reactants Products
In Photosynthesis (summarized reaction):
6 CO2 + 6 H2O C6H12O6 + 6 O2
This is not what happens chemically, but is a
balanced equation of the summarized reaction
Basic Chemistry - Chemical Reactions
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Basic Chemistry Chemical Reactions
Reactants Products
Some reactions can go forward or reverse
3 H2 + N2 2 NH3
Reversible reactions indicated by the opposite headed arrows
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