Transcript Biochemistry Notes

MOLECULAR BIOLOGY
Elements present in your body other
than water…
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Carbon-30% of all biomass, original source of C is
CO2 from photosynthesis
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
If carbon is present then the compound is considered
organic.
 Carbon is the most versatile element b/c of its ability to
bond to itself and other elements. It is tetravalent (4 bonds).
 If C and H are present it is a hydrocarbon: most are energy
sources (fossil fuels)
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Molecules in living organisms: proteins, carbohydrates,
lipids, nucleic acids
Most are polymers of smaller, covalently bonded,
molecules called monomers.
Functional groups: groups of atoms with specific
chemical properties and consistent behavior.
 The
consistent behavior of functional groups allows one
to recognize the properties of molecules that contain
them. i.e. polarity, electronegativity
Figure 3.1 Some Functional Groups Important to Living Systems (Part 2)
Aminescontain
N, act as
a base
Phosphat
esinvolved
in E
transfers
Sulfur in
sulfhydrls
make
disulfide
bridges
in protein
Figure 3.1 Some Functional Groups Important to Living Systems (Part 1)
Hydroxyls
- act as
an alcohol
or polar
Aldehydes
, Ketones,
have one
double
bond to O
Carboxyls
have two
Os, one
double,
one single
bond
FUNCTIONAL GROUPS SERVE IMPORTANT
PURPOSES IN MOLECULES
Estradiol
Female lion
Testosterone
Male lion
Isomers
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Structural Isomers
Structural isomersame chemical
formula, different
arrangement of atoms.
Figure 3.2 Optical Isomers
Optical Isomers
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Same chemical
formula, arranged
Bio around an
differently
asymmetrical carbon
Biochemical Unity
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Biochemical unity-organisms can acquire needed
biochemicals by consuming other organisms.
 Because
all macromolecules have the same chemistry:
 The four biological molecules are present in the same
proportions in all living things.
 Argument
for common ancestor
Figure 3.3 Substances Found in Living Tissues
70%
water
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The function of macromolecules is directly related to
their 3-D shape and their chemical
properties/formula.
 This
will determine molecular interactions such as
solubility.
Synthesis Question
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Question: Carbon is an extremely important
element to all life forms on the planet. Life on Earth,
as we know it, could not exist without this element.
In no more than three sentences,
A) Identify the ultimate source of all Carbon for
living organisms alive today and
B)provide two brief explanations of why Carbon is
important molecularly speaking.
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Scoring Rubric: 1pt. The ultimate source is CO2
from the atmosphere.
1pt. Discussion of source of carbon for making
Carbohydrates, Lipids, Proteins, and
Nucleic Acids.
1pt. Discussion of the tetravalence allowing for a
wide range of different molecules.
1pt. Correct use of scientific terms.
1pt. Answer has no more than three sentences.
(Following Directions.)
Molecular Biology
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Polymers are formed in condensation reactions AKA
dehydration synthesis.
Condensation reactions result in monomers joined by
covalent bonds.
These require E
http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html
The reverse of a dehydration synthesis is hydrolysis reaction
which break apart polymers and turn them into monomers.
These make E
Figure 3.4 Condensation and Hydrolysis of Polymers (A)
Figure 3.4 Condensation and Hydrolysis of Polymers (B)
DEHYDRATION
AND
HYDROLYSIS
REACTIONS
Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water
molecule, breaking a bond
Hydrolysis of a polymer
Carbohydrates
See the Carbonyls and Hydroxides?
Carbohydrates (C,H,O 1:2:1)
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Molecules that contain carbons flanked by a H
group and an OH group.
Four major types of carbs: mono, di, poly, and oligo
saccharides.
Two major functions:
 Source
of energy that can be released in a usable form
to body tissues
 Serve as carbon skeletons for other 3 macromolecules.
Monosaccharides
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Produced through photosynthesis.
All living cells contain glucose.
Most monosaccharides are in the D series of optical
isomers (proteins are L)
Figure 3.13 Glucose: From One Form to the Other (Part 2)
Figure 3.14 Monosaccharides Are Simple Sugars (Part 1)
Figure 3.14 Monosaccharides Are Simple Sugars (Part 2)
Structural These are structural isomers.
Glycosidic Linkages
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Monosaccharides covalently bind together in
condensation reactions to form glycosidic linkages.
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Glycosidic linkages can be α or β.
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Examples of disaccharides
sucrose — table sugar = glucose + fructose
lactose — milk sugar = glucose + galactose
maltose — malt sugar = glucose + glucose
Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 1)
Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages (Part 2)
ThiThis is cellobiose, a subunit of cellulose, humans don’t have the enzymes to break
this down, but cows do. To us it is merely roughage.
Cellulose is a very stable glucose polymer, and is the principle component of cell
walls.
Oligosaccharides (3-20)
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Often covalently bonded to proteins and lipids on cell
surfaces and act as recognition signals.
ABO blood groups
Polysaccharides
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Formed by glycosidic linkages, animal and plant
energy storage form.
Three forms: starch, glycogen, cellulose, and chitin.
Starch and glycogen easily hydrolyzed for energy.
Starch- all contain alpha linkages, stored in plants.
Cellulose- plant cell wall structure; most abundant
organic molecule on earth
Glycogen-energy storage in animals
Chitin- found in exoskeletons and fungi cell walls
Polysaccharides
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Glucose must be stored as glycogen because
glycogen does not exert as much osmotic pressure
on the cell as one glucose molecule
Figure 3.16 Representative Polysaccharides (A)
Carbohydrate Energy Storage
Figure 3.16 Representative Polysaccharides (B)
Cellulose, Starch, & Glycogen
Chemically Modified CHOs
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Some CHO can be modified by adding functional
groups such as a phosphate or amino group.
 Phosphate
sugars and amino sugars
Lipids –C,H,O
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Lipids are hydrocarbons that are insoluble in water
because of their nonpolar, covalent bonds.
All the extra H= 2x E of CHO
Hydrophobic.
One lipid molecule consists of a glycerol (alcohol)
bonded to 3 fatty acid chains.
The fatty acids are held together through van der
Waals forces not covalent bonds; therefore they are
not true polymers.
Lipids
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The bond that holds each fatty acid molecule to the
glycerol is formed through dehydration synthesis,
and is called an ester linkage.
The ester linkage is a covalent bond.
ESTER LINKAGE AND
LIPIDS
Fatty acid
(palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
Math Quiz
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Tell if each pH or pOH is an acid, base, or neutral by
writing ACID, BASE, or NEUTRAL on the line next to the
prompt. (1 points each)
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pH 3
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pH 14 _______________
pOH 7 ______________
pH 7
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pH 4 ______________
pOH 14 ____________
pOH 2 ____________
pOH 0 ______________
pOH 9 _____________
pH 10 _____________
Calculate pH differences in H concentration
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pH 2- pH 5
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pH 1- pH 3
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pH 1- pH 2
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pH 10- pH 14
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pH 3- pH 8
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pH 3- pH 7
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pH 7 – pH 10
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pH 5 – pH 10
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pH 1- pH 14
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pH 1- pH 11
Figure 3.18 Synthesis of a Triglyceride
Lipid Functions
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Fats and oils store energy
Phospholipids in cell membrane for structure
Carotenoids
Hormones and vitamins
Fat = insulation (Camels)
Lipids coat neurons for electrical insulation
Oil and wax on skin surface repel water
Lipids
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One lipid unit is called a triglyceride/triglycerol.
Triglycerides solid at room temp. are fats.
 Saturated
fatty acid- all C-H bonds are single
 Animal fat, least healthy.
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Triglycerides liquid at room temp. are oils.
 Unsaturated
fatty acid (mono, poly) some of the C-H
bonds are double causing kinking in the hydrocarbon
chain.
 Plant
oils, lower melt. pt., healthier
 Polyunsaturated
Fats- many double bonds, usually in plants
 Hydrogenated or Trans Fat- Unsaturated turned saturated
Saturated vs. Unsaturated
Figure 3.19 Saturated and Unsaturated Fatty Acids
Phospholipids
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A phosphate molecule bonds to the glycerol
replacing one hydrocarbon chain (fatty acid).
Since phosphate functional group is (-) it is
hydrophilic and attracts polar H20 molecules.
In aqueous environment, phospholipids line up with
hydrophobic region “tails” on one end, and
hydrophilic “heads” on the other.
Phospholipids form a bilayer.
Figure 3.20 Phospholipids (A)
Figure 3.20 Phospholipids (B)
Phospholipid bilayers form biological membranes.
Waxes
Steroid Structure
LE 4-9
Estradiol
Female lion
Testosterone
Male lion
Cell Membranes
Lipid storage
Energy and Macromolecules Data Set
6
Proteins- suffix “lin” eg insulin
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Contain: C, H, O, N, P, and S
Protein monomers are known as amino acids, which
then fold into the polypeptide form of proteins.
50% of organisms biomass
Essential Amino Acids
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Over 20 amino acids
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 11
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non-essential
 9 essential
 These
9 are essential
because they cannot
be synthesized by the
body and must be
supplemented.
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Phenyalanine
Valine
Threonine
Tryptophan
Isoleucine
Methionine
Leucine
Lysine
Histidine
Protein Structure
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Can be made of more than one polypeptide chain
The sequence of amino acids in each polypeptide
chain is the source of diversity in protein structure
and function.
What Are the Chemical Structures and Functions of Proteins?
Amino acids have carboxyl and amino groups—they
function as both acid and base.
Rgroup= property
Table 3.2 (Part 1)
These hydrophylic amino acids attract ions of opposite charges.
Table 3.2 (Part 2)
Hydrophylic amino acids with polar but uncharged side chains form hydrogen bonds
Table 3.2 (Part 3)
Hydrophobic amino acids
Table 3.2 (Part 4)
Proteins
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Amino acids bond together covalently by peptide
bonds to form the polypeptide chain.
The beginning of all polypeptides begin with the
amino group of an amino acid: the N terminus and
the end of the chain is the carboxyl group: the C
terminus
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NC orientation
Figure 3.6 Formation of Peptide Bonds
The peptide bond is inflexible—no rotation is possible.
Protein Structure
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Primary Structure-sequence of amino acids in the
polypeptide chain. Peptide backbone –N-C-C.
Secondary Structure- determined by hydrogen
bonds, alpha helix and beta pleated. Bonds
between amino (H) and carboxyl (C and O)
Tertiary Structure- additional folding between the R
groups (side chains). Folded by disulfide bridges,
cysteine has the sulfur.
Quarternary Structure- result from subunits
(separate tertiary structures) folding together.
Multiple polypeptides together.
Figure 3.7 The Four Levels of Protein Structure (A)
Figure 3.7 The Four Levels of Protein Structure (B, C)
Figure 3.7 The Four Levels of Protein Structure (D, E)
Primary (1’) sequence
Primary Structure is IMPORTANT
SICKLE CELL AND OXYGEN
TRANSPORT
Sickle-cell hemoglobin
Normal hemoglobin
Primary
structure
Val
His
1
2
Leu
Thr
3
4
Pro
Glu
5
6
Secondary
and tertiary
structures
Function
7
 subunit
Normal
hemoglobin
(top view)
Molecules do
not associate
with one
another; each
carries oxygen.
Primary
structure
Secondary
and tertiary
structures
His
1
2
Leu
Thr
3
4
Function
Val
Glu
5
6
7
 subunit
Sickle-cell
hemoglobin
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a
Pro
Exposed
hydrophobic
region
a
Quaternary
structure
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Val

a
Quaternary
structure
Glu
Molecules
interact with
one another to
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.

a
2’ structure
3’ Structure
4’ Structure
Protein’s Natural Form
Protein Function
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Structural support
Protection
Transport
Catalysis- speeding up a chemical reaction
Defense
Regulation
Movement
Protein denaturation
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Denaturation= loss of 3-D shape and function
(unfold due to environmental stressors)
Proteins are sensitive to their environment due to
weaker bonds in the 2nd and 3rd structure. 3
Denaturing factors:
 Increased
temperature
 Alterations in pH
 Salt concentration changes
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Denaturation is usually irreversible
Figure 3.11 Denaturation Is the Loss of Tertiary Protein Structure and Function
Protein Shape
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Sometimes proteins will bind to the wrong ligand
(molecule) while completing their folding process.
E.g. alzheimer’s
Chaperonins- type of protein that prevents
misfolding.
Enzymes
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Enzymes are proteins that are catalysts that speed
up chemical reactions in cells.
Words that end in “ase” are enzymes
Enzymes form an enzyme-substrate complex
Animation: How Enzymes Work
Nucleic Acids- C,H,O,P,N
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Nucleic acids are polymers designed for storage,
transmission, and use of genetic information.
DNA & RNA
DNA encodes our heredity info.
DNA contains the info, uses RNA to create an amino
acid sequence (proteins) which carry out life’s
functions.
Pyrimidines: cytosine, thymine, uracil
Purines: adenosine, guanine
Nucleotide
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Nucleotides are the monomers for nucleic acids.
Each nucleotide consists of a pentose sugar,
phosphate group, and nitrogenous base.
Nitrogenous bases can be pyrimidines (single ring)
or purines (2 fused rings)
Pyrimidines-C,T,U
Purines-G, A
3.5 What Are the Chemical Structures and Functions of Nucleic Acids?
DNA—deoxyribose
RNA—ribose
DNA & RNA Backbone
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Alternate pentose sugar and phosphate groups (SP-S-P-S-P…)
The nitrogen bases project off the backbone.
Nucleotides bonded by phosphodiester linkages.
Phosphodiester linkages form between the sugars
linked by the phosphate.
Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1)
DNA
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Hydrogen bonds link nitrogenous bases together.
Base pairing rule-purine and pyrimidine always
pair up.
 A-T
and C-G in DNA
 A-U and C-G in RNA
 Know why base pairing is complimentary p.59
Figure 3.24 Distinguishing Characteristics of DNA and RNA (Part 1)
DNA Relationships
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DNA in all organisms, chimps and humans share
98% base sequence with humans.
Scientists use DNA to determine evolutionary
relationships.
Nucleotides also are used in energy reactions. (ATP
and GTP).
Nucleotides are used in hormones and the nervous
system (cAMP).
HW: Due Friday 8-30-13
Macromolecule
Type
Name of
Molecule
Source
Role in
Organisms (What
does it do?)
5 Carbohydrates
glucose
plants
Immediate
energy
5 Lipids
5 Proteins
4 Nucleotides
How did life begin?
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Could life have come from outside earth?
 Allan
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Hills region of Antartica, meteorite from Mars
Miller and Urey experiment 1953- chemical
evolution. Took inorganic substances and made them
organic
Miller and Urey Experiment
RNA world before DNA- RNA less stable than DNA
 RNA
ribozymes could replicate itself
 Ribozymes are responsible for peptide bonds
Figure 3.27 Was Life Once Here?
Energy Source- Stanley Miller
Figure 3.28 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1)
4 Steps for Life to Emerge on Earth
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1. Abiotic synthesis of amino acids and nucleic acids.
2. Monomers must join to make polymers
3. RNA/DNA form and gain ability to reproduce
and stabilize using bonds and complimentary
bonding.
4. Evolution of the “protobiont” first life form
Evidence for #1: Abiotic synthesis
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Miller and Urey- hypothesized about early earth’s
organic composition…
H2, CH4, NH3 and H2O vapor…
These things formed amino acids and oils…
The compounds came from volcanic eruptions and
the energy from lightning…
These compounds collected in the oceans and wala
life…
Evidence for #2: Polymerization
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Researchers have taken fool’s gold, sand, and clay,
and exposed to it to intense heat…
In the presence of water (tides) amino acids and oils
become polymers
Evidence for #3: RNA/DNA
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Some RNA can act as ribozymes that act as great
info storage bins…
Over time it is believed RNA evolved into a more
stable DNA…
Evidence for #4: Protobiont Formation
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Experiments show that lipids and other molecules
can form membranes (cell)…
Over millions of years they become prokaryotic
cells
Representation of a Protobionts
Question: In no more than three sentences, explain why the abiotic synthesis of the nucleic acids RNA and DNA was overall so essential to helping
Data Set Question (U1,D3)
Synthesis Question (U1, D3)
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Question: In no more than three sentences, explain why
the abiotic synthesis of the nucleic acids RNA and DNA
was overall so essential to helping generate life on
Earth? (5 Points)
1pt. Discussion of the ability to store molecular
information on the construction of molecule
1pt. Discussion of inheritance of information from one
generation to the next
1pt. Discussion of the long term stability of DNA
1pt. Correct use of scientific terms.
1pt. Answer has no more than three sentences.
(Following Directions.)