L1.2.Biochemistry BB
L1.2.Biochemistry BB
L1.2.Biochemistry BB
1
Matter
• Takes up space
and has mass
• Exists as chemical
elements (pure
form) and in
chemical
combinations
called compounds
2
Elements
• Can’t be broken down into simpler
substances by chemical reaction
• Presented as atoms
• Each element has a unique symbol
3
Essential Elements
• Are elements that an
organism needs to live a
healthy life and reproduce
• Include 17-25
Which different
element is
elements,
toxicamong which
to human?
– C, H, O, and N making up
96% of living matter;
– Other elements make up the
remaining 4% of living matter
(some even at trace amount)
5
Deficiencies
• If there is a deficiency of an essential
element, disease results
6
Trace Elements
• Are required by an
organism in only
minute quantities
(< 0.01%)
• Minerals such as Fe
and Zn are trace
elements Iodine deficiency
(Goiter)
7
Compounds
• Are substances consisting of two or more
elements combined in a fixed ratio
• Have characteristics different from
those of their elements
Nucleus
(a) This model represents the (b) In this even more simplified
electrons as a cloud of model, the electrons are
negative charge, as if we had shown as two small blue
taken many snapshots of the 2 spheres on a circle around the
electrons over time, with each nucleus.
dot representing an electron‘s
position at one point in time.
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Atomic Number
❖ The number of protons in the nucleus is
unique for each element = atomic number
•Carbon = 6 Nitrogen = 7 Oxygen = 8
13
Atomic Mass
14
15
Question
16
Isotopes of an element
• Different atomic forms of the same element
• Have the same number of protons, but
different number of neutrons
• Behave identically in chemical reactions
• May be radioactive spontaneously giving off
subatomic particles and energy (i.e. decay)
• May be used for certain purposes
– to date fossils (14C) or
– as medical tracers
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Use of radioactive isotope
– Can be used in medicine to detect tumors
(with high metabolic activity)
Radioactively
labeled
glucose
Cancerous
throat
tissue
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Energy Levels of Electrons
• Electrons of an atom vary in
the amount of energy they
possess
• Electrons further from the
nucleus have more energy
(higher potential energy)
• Electron can absorb energy
and become “excited”
• Excited electrons gain
energy and move to higher
energy levels or lose energy
and move to lower levels
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Bohr atom animation.gif
• Energy: Is defined
as the capacity to
cause change
• Potential
energy: Is the
energy that matter
possesses because
of its location or
structure
• Kinetic Energy:
Is the energy of https://www.quora.com/How-do-hydroelectric-power-plants-produce-
energy-How-much-pollution-do-they-generate
motion
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Electrons and Energy
• Energy levels are represented by electron shells
• Changes in the potential energy of electrons can
occur only in steps of fixed amounts
(a) A ball bouncing down a flight (b) An electron can move from one level
of stairs provides an analogy to another only if the energy it gains
for energy levels of electrons, or loses is exactly equal to the
because the ball can only rest difference in energy between the two
on each step, not between levels.
steps.
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Electron Configuration and
Chemical Properties
• The chemical behavior of an atom
– Is defined by its electron configuration,
which is the distribution of electrons in the
atom’s electron shells
22
Other information referred from Periodic table
Second
shell
Third
shell
23
Why do some elements react?
• Valence electrons
– Are those in the outermost shell (valence shell)
– Determine the chemical behavior of an atom (full
valence shell vs incomplete valence shell)
Hydrogen 2 Atomic number Helium
He 2He
1H 4.00 Element symbol
Atomic mass
First Electron-shell
shell diagram
Second
shell
Third
shell 24
Electron Orbitals
• An orbital
– Is the three-dimensional space where an
electron is found 90% of the time
https://www.presentermedia.com/index.php?
target=closeup&maincat=animsp&id=714
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Electron Orbitals
• Each electron shell
– Consists of a specific number of orbitals
• No more than 2 electrons can occupy a single orbital
Electron orbitals.
Each orbital holds
up to two electrons. x Y
Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.
(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
2 electrons) 8 electrons)
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Chemical Bonding
• Is a lasting attraction between atoms, ions
or molecules that enables the formation of
chemical compounds
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Covalent Bonds
• Resulted from Hydrogen atoms (2 H)
electrons
attracted to the proton
in the other nucleus.
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Covalent Bonding
• A molecule
– Consists of two or more atoms held
together by 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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Orbitals & Covalent Bonds
• In a covalent bond
– The s and p orbitals may hybridize,
creating specific molecular shapes
Three p orbitals Four hybrid orbitals
Z
s orbital X
Y
Tetrahedron
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Ways of presenting
Bonding
capacity
(atom’s
valence):
To indicate
the number
of covalent
bonds the
atom can
form
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Ways of presenting
Bonding
capacity
(atom’s
valence)
1
Bonding capacity (Atom’s valance)
usually equals the number of unpaired
electrons required to complete the
atom’s outermost shell
2
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Compounds & Covalent Bonds
34
Covalent Bonding
• Electronegativity
– Is the attraction of a particular atom in the
molecule for the electrons in a covalent bond
• The more electronegative an atom
– The more strongly it pulls shared electrons
toward itself
35
Covalent Bonding
• In a nonpolar covalent
bond
– The atoms have similar
electronegativities
– Shares the electron
equally
36
Covalent Bonding
• In a polar covalent bond
– The atoms have differing electronegativities
– Share the electrons unequally
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
d–
This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.
H H
d+ d+
H2O
37
Ions
• In some cases, atoms strip electrons away
from their bonding partners
• Electron transfer between two atoms
creates ions
• Ions: Are atoms with more or fewer electrons
than usual (charged atoms)
* An anion: Is negatively charged
* A cation: Is positively charged
• The term ion also applies to entire molecules
that are electrically charged (e.g. NH4+)
38
Ionic Bonding
• Established by the attraction (electrostatic
force) between anions and cations
1 2 Each resulting ion has a completed
The lone valence electron of a sodium
atom is transferred to join the 7 valence valence shell. An ionic bond can form
electrons of a chlorine atom. between the oppositely charged ions.
+ –
Na Cl Na Cl
Na+ Cl–
Sodium on Chloride ion
Na Cl
(a cation) (an anion)
Sodium atom Chlorine atom
(an uncharged (an uncharged
atom) atom)
Sodium chloride (NaCl)
39
Ionic Substances
• Ionic compounds
– Are often called salts,
which may form crystals
• Unlike a covalent
compound which consists
of molecules having a
definite size and number
of atoms, an ionic
compound does not
consist of molecules
40
Weak Chemical Bonds
41
Weak Bonds
• Weak chemical bonds
– Reinforce the shapes of large molecules
– Help molecules adhere to each other
42
Molecular Shape and Function
• Structure determines
Function!
• The precise shape of a
molecule
– Is usually very important to
its function in the living cell
– Determines how biological
molecules recognize and
respond to one another with
specificity
– Is determined by the positions
of its atoms’ valence orbitals
43
Hydrogen Bonds
• A hydrogen bond
– Forms when a hydrogen atom covalently
bonded to one electronegative atom is also
attracted to another electronegative atom
d+ 44
Van der Waals Interactions
• Van der Waals interactions
– Occur when transiently
positive and negative regions
of molecules attract each
other
45
Chemical Reactions
• A Chemical reaction
– Is the making and breaking of chemical
bonds
– Leads to changes in the composition of
matter
46
Chemical Reactions
• Chemical reactions
– Convert reactants to products
2 H2 + O2 2 H2O
Coefficient
indicate the Reaction
number of
Reactants Product
molecules
involved
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Chemical Reactions
• Photosynthesis
– Is an example of “a chemical reaction” (actually
many chemical reactions take place!)
48
Chemical Reactions
• Chemical equilibrium
– Is reached when the forward and reverse
reaction rates are equal (dynamic
equilibrium)
– The relative concentrations of products
and reactants stop changing
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Lecture highlights
• Matter consists of chemical elements in
pure form and in combinations called
compounds
• An element’s properties depend on the
structure of its atoms
• The formation and function of molecules
depend on chemical bonding between atoms
• Chemical reactions make and break
chemical bonds
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