Bio 2
Molecules, Organelles, Cells, Cellular
Metabolism
What is a Cell?
•
Small
•Membrane- enclosed
•Filled with a concentrated aqueous solution of chemicals= cytoplasm
•Endowed with the ability to create copies of themselves
What is Life?
Characteristics of living things include:
•Growth and development
•Respiration
•Nutrition
• Excretion
• Reproduction
•Death
•Response to stimuli
•Adaptation to the environment
Viruses: non-living: acellular infectious agents
How Do Genes Evolve?
-Lethal changes
-Selectively Neutral Changes
-Change for the better
Through endless repetitions of mutation and
natural selection, organisms evolve their genetic
specifications
-Gives them new ways to exploit their
environment more effectively.
-Survive in competition with others.
-Reproduce successfully.
New Genes are Generated from Preexisting Genes
•Intragenic mutation- gene modified by mutation
•Gene duplication- creates pair of closely related genes within a
single cell.
•Segment shuffling- 2 or more existing genes are broken and
rejoined to make a hybrid gene.
•Horizontal transfer- DNA is transferred from the genome of
one cell to another. From one bacteria cell to another bacterial
cell. Not typical in Eukaryotes.
Thus, over many millions of years, repeated rounds of duplication and
divergence have enabled one gene to give rise to a whole family of genes
within a single genome
ARCHETECTURALLY SPEAKING vs
EVOLUTIONARILLY SPEAKING
Prokaryotes
•Archaebacteria
•Eubacteria
Eukaryote
Attachment
Prevents the bacterial cell from lyses
Mobility
Prokaryotes vs eukaryotes: prokaryotes do not have membrane-bound organelles
Eukaryotic organelles comprise four
functional categories
• Manufacture
• Breakdown
• Energy Processing
• Support, movement, and communication
between cells
Similarities between prokaryotes and
eukaryotes
• Basic cellular processes:
– Carbon and nitrogen metabolism
– Energy cycles: making and breaking of ATP
• Basic chemical composition of building
blocks:
– Nucleic acids DNA and RNA
– Proteins
– Carbohydrates
– Lipids
What about…
• Viruses: noncellular infectious agents.
Composed of proteins and nucleic acids.
• Viroids: also noncellular infectious agents.
Composed of only RNA ( infects plants)
• Prions: noncellular infectious agents. Composed
of proteins ( mad-cow disease or scrapies)
Functionality of the nucleus
Based on the central dogma of molecular
biology: DNA > RNA > proteins
Information > intermediary > executors
The nucleus:
• Houses the genetic material (DNA)
• DNA replication
• RNA synthesis
Not all genetic material because there is mitochondrial dna
The Chemical Nature of Life
Table 2-1
Protein: only
polysaccharide
composed of
hydrogen
Hint: Know the
molecules: be able
to identify them.
Electrons Rule!
The chemical behavior of an atom is
determined by the distribution of
electrons in electron shells
The periodic table of the elements shows the electron distribution for each element
ELECTRONS
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electrondistribution
diagram
Lithium
3Li
Beryllium
4Be
Sodium
11Na
Magnesium Aluminum Silicon
12Mg
13Al
14Si
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
Valence electrons are those electrons located in the outermost shell
-free to participate in chemical bond formation
Molecules May Change Their Shapes
• Atoms combine to form a molecule with three
dimensional shape
• The shape is determined by the arrangement and
number of bonds between atoms
• Angles that form between atoms give molecules
specific shapes
• Covalent bonds are not rigid and rotation around
single covalent bonds allows molecules to change
shape
• Molecular shape defines function.
Covalent bonds are forces that hold
atoms together
• Formed when the atoms of a molecule share
electrons
– The angles formed are specific and defined
– Have definite and predictable shapes
– Not easily broken under normal biological
conditions of temperature and pressure
• Polar and nonpolar covalent bonds ( difference
in electronegativites)
Carbon
• Carbon has 4 electrons in its outer shell
• It can make up to 4 bonds
❑ Usually single or double bonds
• Carbon can form non polar or polar bonds
❑ Molecules with polar bonds are water soluble
❑ Molecules with nonpolar bonds (like
hydrocarbons) are not very water soluble
20
Fig. 2-13
Electronegativity is an atom’s attraction for the electrons in a covalent bond
δ–
O
H
δ+
H
H2O
δ+
The more electronegative an atom, the more strongly it pulls shared
electrons toward itself
Polar and Nonpolar Covalent Bonds
• Polar covalent bonds are important because
these kinds of bonds allow the formation of
another kind of weak bond called a hydrogen
bond.
• Molecules consisting of mainly nonpolar
covalent bonds are hydrophobic.
NON-COVALENT BONDS
Weak
Bonds
Like hydrogen bonds- you do not need energy to break them
Hydrogen Bonds
• Force of attraction between a hydrogen in a
polar molecule and electronegative portion in
another molecule
– Has only about 5% of the strength of a covalent
bond
– When multiple hydrogen bonds can form within a
molecule or between 2 molecules, the bond can
be sufficiently strong and stable
Hydrogen Bonds
• Examples of the role of hydrogen bonds
include
– Holding 2 strands of DNA together
– Holding polypeptides ( proteins) together
– Assist enzyme in substrate bonding ( substrate
needs to “clasp” to enzyme)
– Assist antibodies in substrate bonding ( antigen
would be the substrate)
Other Non-covalent Bonds
• Ionic bonds
– Electrons are removed from one atom and transferred
to another
• Van der Waals Interactions
– Weak, nonspecific attractive force
– Requires atoms or molecules to be close together
• If electrons are distributed asymmetrically in molecules or
atoms, they can result in “hot spots” of positive or
negative charge
• Van der Waals interactions are attractions between
molecules that are close together as a result of these
charges
Weak Chemical Bonds
• Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
• Weak chemical bonds ( hydrogen breinforce
shapes of large molecules and help molecules
adhere to each other
– A molecule’s shape is usually very important to its
function
– A molecule’s shape is determined by the positions of
its atoms’ valence orbitals
– In a covalent bond, the s and p orbitals may hybridize,
creating specific molecular shapes
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Biological molecules recognize and interact with
each other with a specificity based on molecular
shape
• Molecules with similar shapes can have similar
biological effects
Endorphine vs Morphine
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Not just a solvent
• Water has many important functions in living
organisms:
❑ Participates in chemical reactions
(macromolecules: hydrolysis- breaks covalent or
condensation synthesis- forms covalent )
❑ Provides force or support
❑ Removes tax waste compartments
❑ Evaporative cooling
❑ Cohesion and adhesion
❑ Surface tension
❑ Lubrication
❑ Water resists temperature change, both for heating and cooling.
• The specific heat of a substance is the amount of heat that must be
absorbed or lost for 1 g of that substance to change its temperature
by 1ºC
• The specific heat of water is 1 cal/g/ºC
• Water resists changing its temperature because of its high specific
heat
• Water’s high specific heat can be traced to hydrogen bonding
❑ Heat is absorbed when hydrogen bonds break
❑ Heat is released when hydrogen bonds form
❑ The high specific heat of water minimizes temperature fluctuations to within
limits that permit life
Fig. 3-3
Cohesion helps the transport of water
against gravity in plants. ( attraction of
water to itself)
Adhesion
Water-conducting
cells
Direction
of water
movement
Cohesion
150 µm
Adhesion is an attraction between
different substances, for example,
between water and plant cell walls
Capillarity ( adhesion + cohesion) water
molecules will “tow” each other along
Effects of pH
• The pH of a solution can affect
❑ The shapes and functions of molecules
❑ The rates of many chemical reactions
❑ The ability of two molecules to bind to each other
❑ The ability of ions or molecules to dissolve in
water
Fig. 4-5
Carbon Skeletons Can Vary
Propane
Ethane
(a) Length
Butane
(b) Branching
1-Butene
2-Butene
(c) Double bonds
2-Methylpropane
(commonly called isobutane)
Memorize this
Cyclohexane
(d) Rings
Benzene
Carbon Isomers
Isomers are compounds with the same
molecular formula but different structures and
properties
• Geometric isomers
❑ Require double bond
Pentane
2-methyl
butane
(a) Structural isomers
• Cis or trans
• Enantiomers
cis isomer: The two Xs are
on the same side.
❑ Have asymmetric carbon (b) Geometric isomers
❑ Never superimposable
( always different)
❑ Have biological
relevance
L isomer
(c)
trans isomer: The two Xs are
on opposite sides.
D isomer
Enantiomers
Fig. 4-7
Biological Importance of Enantiomers
Functional Groups- need to know!!!
• Groups of atoms with special chemical
features that are functionally important
• Each type of functional group exhibits the
same properties in all molecules in which it
occurs
37
Fig. 4-10e
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
(may be
written HS—)
EXAMPLE
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
Cysteine
Cysteine is an important
sulfur-containing amino
acid.
Cross-linking of
cysteines in hair
proteins maintains the
curliness or straightness
of hair. Straight hair can
be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
FUNCTIONAL
PROPERTIES
Fig. 4-10f
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
Glycerol phosphate
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
Contributes negative charge
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Has the potential to react
with water, releasing energy.
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES
Four major types of organic molecules
and macromolecules
CH2OH
O H
H
H
OH
H
HO
OH
H
OH
Lipids
Carbohydrates
glycosidic bonds
ester bonds
Proteins
Nucleic Acids
peptide bonds
44
phosphodiester bonds!!!!
Carbohydrates serve as fuel and building material
• Carbohydrates include sugars and the polymers
of sugars
• The simplest carbohydrates are
monosaccharides, or single sugars
❑ Monosaccharides serve as a major fuel for cells and as
raw material for building molecules
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks
Glucose and galactose are structural isomers
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Linear and ring structures
of α-D-glucose
H
H
HO
H
H
H
2
3
4
5
6
C
OH
C
H
C
C
C
H
6
OH
OH
OH
H
D-glucose
(linear)
H
HO
5
3
H
3
H
1
H
2
H
OH
β-D-galactose
CH2OH
O H
H
OH
4
O OH
H
OH
4
C
CH2OH
5
HO
O
1
6
H
2
6
1
H
OH
OH
α -D-glucose
(ring)
Ring glucose in living systems
6
CH2OH
5
O OH
H
OH
4
HO
Isomers
of glucose
3
H
1
H
2
H
H
H
OH
β-D-glucose
5
HO O
1
2
OH
CH2OH
H
OH
3
4
HO
H
β-L-glucose
Enantiomers
H
Many monosaccharides linked together to form long polymers = polysacchraides
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Starch
α-1,4-Glycosidic linkages form linear chains.
6
6
CH OH
2
5
H
OH
4
O
H
3
H
2
2
5
O H
O H
H
1 O4
OH
H
OH
H
3
H
2
HO O
Moderately branched
1
α-1,6-Glycosidic linkages
form branches.
6 CH
CH O H
2
O H
H
O
Branching patterns
CH OH
H
OH
H
H
OH
CH OH
2
O
H
OH
H
H
OH
C H OH
2
O H
H
O
2
O H
H
H
OH
H
H
OH
O H
H
O
H
OH
H
H
OH
O
Glycogen
6
6
CH2OH
5
4
O
H
OH
H
3
H
2
CH2OH
5
O H
1 O4
OH
H
OH
H
3
H
2
HO O
6
CH2OH
O H
H
HO
O H
H
H
OH
H
H
OH
Highly branched
1
CH2
O H
H
O
H
OH
H
H
HO O
CH2OH
CH2
O H
H
O
H
OH
H
H
OH
H
O
CH2OH
O H
H
OH
H
H
OH
O H
H
O
H
OH
H
H
HO
O
Unbranched
β-1,4-Glycosidic linkages form chains.
Cellulose
6
CH2OH
H
4
O
H
5
O
H
OH
1 O 4
H
H
H
3
2
OH
3
OH
H
H
5
CH2OH
6
2
CH2OH
OH
H
H
O
1 O
O
H
H
OH
OH
OH
OH
H
H
H
H
H
H
H
O
H
CH2OH
O
O
Fiber: irritates cell wall of large intestine and makes it produce mucuous
Lipids
• Composed predominantly of hydrogen and
carbon atoms
• Defining feature of lipids is that they are non
polar and therefore very insoluble in water
• Include fats, phospholipids, steroids, waxes
• Lipids comprise about 40% of the organic
matter in the average human body
49
Fats
• Also known as triglycerides or triacylglycerols
• Formed by bonding glycerol to 3 fatty acids
• Joined by dehydration; broken apart by hydrolysis
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The hydrogens from
each hydroxyl group in
glycerol are removed.
The hydroxyl groups from each
carboxyl group of the 3 fatty acids
are removed.
H
H
C
O
OH
HO
C
H
CH2
(CH2)15
C
OH
+
HO
C
H
CH3
C
O
O
Dehydration
CH2
(CH2)15
CH3
H
C
O
C
OH
HO
C
CH2
(CH2)15
CH3
(CH2)15
CH3
C
CH2
(CH2)15
CH3
3 H2O
H
C
O
C
CH2
(CH2)15
CH3
H
H
Glycerol
CH2
O
O
H
C
O
O
H
The new bond created is
called an ester bond.
3 Fatty acids
Triglyceride (fat)
50
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O
HO
C CH2
CH2
CH2
CH2
CH2
CH2
Saturated fatty acid
(Stearic acid)
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
saturated= no double bond
O
HO
C CH2
CH2
CH2
CH2
CH2 CH2
CH2 CH
CH
CH2
CH
CH
CH2
CH2 CH2
Unsaturated fatty acid
(Linoleic acid)
unsaturated= double bond, causes a kink, fluidity
51
CH2
CH3
Phospholipids
• Formed from glycerol, two fatty acids and a
phosphate group
• Phospholipids are amphipathic molecules
❑ Phosphate head – polar / hydrophilic
❑ Fatty acid tail – nonpolar / hydrophobic
52
Proteins
• Composed of carbon, hydrogen, oxygen,
nitrogen, and small amounts of other
elements, notably sulfur
• Building blocks of proteins are amino acids
❑ 20 different amino acids ( amino acids with
different side chains changes the way a protein
folds)
❑ Common structure with variable side chain that
determines structure and function
53
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H 3C
Side chains
H
Nonpolar
H 3N +
H 3N +
CH3
COO–
C
H 3N +
C
CH3
H
H
Glycine (Gly; G)
Alanine (Ala; A)
H 3N +
C
CH3
CH
CH2
CH2
CH
COO–
CH3
COO–
H 3N +
H
COO–
C
H 3C
H 3N +
H
Valine (Val; V)
CH2
H 3N +
H
Leucine (Leu; L)
Isoleucine (IIe; I)
CH3
S
Polar (uncharged)
H 3N +
O
H 3N +
C COO–
H 3N +
H
H 3N +
H
Serine (Ser; S)
H 3N +
C COO–
Methionine (Met; M)
OH
NH2
CH2
CH2
C COO–
Proline (Pro; P)
C
NH2
C
HO CH3
CH
CH2
COO–
H
Cysteine (Cys; C)
O
OH
C
CH2
C COO–
H
Tryptophan (Trp; W)
CH2
H 2N +
CH2
CH2
C COO–
CH2
H 2C
H
N
H
Phenylalanine (Phe; F)
C
H
CH2
C COO–
COO–
H
SH
H 3N +
CH
CH2
C COO–
H 3N +
H
C COO–
CH2
H 3N +
H
Threonine (Thr; T) Asparagine (Asn; N) Glutamine (Gln; Q)
C COO–
H
Tyrosine (Tyr; Y)
Better know the shape of the amino acid!! Be able to determine which one is an amino acid
Basic
NH2
Polar (charged)
Acidic
O
O
C
O–
C
C COO–
H
Aspartic acid (Asp; D)
HN
CH2
CH2
CH2
H 3N +
O–
H 3N +
C COO–
NH+
CH2
H 3N +
C COO–
NH3+
C NH2+
CH2
NH
CH2
CH2
CH2
CH2
CH2
CH2
H 3N +
C COO–
H 3N +
C COO–
H
H
H
H
Glutamic acid (Glu; E)
Histidine
54(His; H)
Lysine (Lys; K)
Arginine (Arg; R)
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Formation of a peptide bond
Alanine
Glycine
H
H
H
N+
C
H
H
O
+
C
H
O–
Carboxyl
group
H
CH3
N+
C
H
H
O
H
C
O–
H
H
O
N+
C
C
H
H
Amino
group
CH3
N
C
H
H
O
C
O–
Peptide
bond
Polypeptide—a linear chain of amino acids
O
H
H
H
O
N+
C
C
H
H
Free amino
group
CH3 O
N
C
H
H
C
O–
OH
C
CH2 O
CH2 O
N
C
H
H
C
N
C
H
H
H 3C
C
CH2 O
N
C
H
H
C
SH
CH3
CH O
N
C
H
H
C
CH2 O
N
C
H
H
C
CH2
N
C
H
H
O
C
O–
Free carboxyl
group
One side is also amino group and another side is the carboxyl group ( N and C termin
1
2
3
4
5
6
7
8
H 3N +
N-terminus
COO–
Gly
Ala
Ser
Asp
Phe
Val
Tyr
Cys
C-terminus
55
Secondary Structure
• Chemical and physical interactions cause protein
folding
• A helices and B pleated sheets
❑ Key determinants of a protein’s
characteristics
• “Random coiled regions”
❑ Not α helix or β pleated sheet
❑ Shape is specific
and important to function
56
-
The protein chains are held together by intermolecular hydrogen bonding.
In a β sheet, strands of protein lie adjacent to one another, interacting laterally via
H bonds between backbone carbonyl oxygen and amino H atoms. The strands may
be parallel or antiparallel
Tertiary structure
Copyright © The McGraw-Hill Companies, Inc.
Permission required for reproduction or display.
• Folding gives protein
complex 3D shape
• This is the final level
of structure for a single
polypeptide chain
59
Five factors that promote protein folding and stability ( tertiary structure)
Secondary
structure is just hydrogen bonding.
NH
3
+
1
2 Ionic bond: Bonds form
between oppositely
charged side chains.
O
Hydrogen bonds: Bonds form
between atoms in the polypeptide
backbone and between atoms in
different side chains.
CH2
C
+
O–
NH3
CH2
CH2
CH2
H O
CH
H N
3
H
NH2 C CH2
CH 3
H
CH 3 OH
CH 2
CH 3
CH 3
4
CH2
CH
3
CH
O
CH
CH
2
CH3
N
CH 2
C
CH
CH
O
CH2 OH
CH 2
CH2
2
H
HC CH3
3
CH
CH2
H O
3
Hydrophobic effect:
Nonpolar amino
acids in the center
of the protein avoid
contact with water.
H3
CH
CH2
CH2
3
S
S CH2
5 Disulfide bridge:
A covalent bond
forms between 2
cysteine side chains.
van der Waals
forces: Attractive
forces occur
between atoms
that are optimal
distances apart.
60
COO–
Quaternary structure
• Made up of two or more polypeptides
❑ Individual polypeptide chains are protein subunits
❑ Protein can be formed from several copies of the
same polypeptide
❑ Or may be multimeric
– composed from
different polypeptides
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61
Protein Folding in the Cell
• It is hard to predict a protein’s structure from its primary
sequence
• Most proteins probably go through several states on their way
to a stable structure
• Chaperones are protein molecules that assist the proper folding
of other proteins. Proteins do not fold early and providing
proper environment so the protein will in fact fold correctly.
• aggregate= improperly folded protein
Correct
Copyright © 2008 Pearson Education,
Inc., publishing as Pearson Benjamin
Cummings
Misfolded
Aggregate
Chaperones participate in many actions
-folding and refolding
-preservation of unfolded state
-facilitation of transport
-block aggregation ( once proteins are aggregated
are denatured)
-disaggregation
-degradation
-assembly/disassembly of oligomeric complexes
-facilitation of signaling processes
Fig. 5-24
HSP60s – Chambered Chaperones
Polypeptide
Correctly
folded
protein
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
Steps of Chaperonin 2 The cap attaches, causing the 3 The cap comes
Action:
cylinder to change shape in
off, and the properly
such a way that it creates a
folded protein is
1 An unfolded polyhydrophilic
environment
for
released.
peptide enters the
cylinder from one end. the folding of the polypeptide.
Nucleic Acids
• Responsible for the storage, expression, and
transmission of genetic information
• Two classes
❑ Deoxyribonucleic acid (DNA)
• Stores genetic information encoded in the sequence of
nucleotide monomers
❑ Ribonucleic acid (RNA)
• Decodes DNA into instructions for linking together a
specific sequence of amino acids to form a polypeptide
chain
65
Bases stick together
Draw a pyrimidine and label it, or draw a purine and label it. Draw it correctly, and tell me which
one u drew correctly.
NUCLEOSIDE numbering
4
"Prime" mark: '
5
3
6
2
The 3' and 5' positions
are very important for
understanding DNA and
RNA structure and
function
3’ hydroxyl, 5’
phosphate
1
5
4
'
1
'
3
'
2
'
'
How are mononucleotides linked together to
form the polymers DNA and RNA?
3',5'-phosphodiester
bond
O
5'
3'
5'
O
O
P
O
O-
3'
POLARITY
A
C
5'
Enzymes: DNA
polymerase and RNA
polymerase, can only
synthesis DNA or RNA in
a 5’ to 3’ direction
O
3'
C
5'
O
Single-stranded
polynucleotides have one free
5' end and one free 3' end —
they exhibit POLARITY
3'
5'
O
3'
What information did Watson and Crick use
in 1953 to arrive at their "double helix"
structure for DNA?
%A = %T
• NUCLEOTIDE
• CHARGAFF's
"rules"
%G = %C
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Adenine
N
H
P O
CH2
–
O
H
H
N
O
H
H
HH
H
O
N
O–
CH2 O P
H
H N
N
H 2N
O
O
O
O
HO
H
O
O
N
H
H
H
H
Guanine H
O
O
N
CH O P O
ThymineH N
N
H H
H
CH3
–
2
2
O
O
O
P O CH2
O–
H
O
N
H
H
H
OH
H
H
N
O
N
O
N
O
H
NH2
H
H
Cytosine
DNA strand
71
O
Opposite
DNA strand