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Molecular biology explains living processes in terms of the chemical
substances involved
Most varied and complex molecules are nucleic acids and proteins;
 nucleic acids comprise DNA and RNA, they are chemicals used to
make genes
 proteins vary in structure and have a wide variety of roles inside of
the cell
 relationship between genes and proteins is the heart of molecular
biology
Molecular biology is quite reductionist, chooses to explain a complex whole
through its smaller and more simpler parts
 Some argue that it can’t tell everything, as there are emergent
properties that can only be observed when the structure works as a
whole

Syntheses of Urea

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Urea is a compound produced by living organisms but can also be
synthesized
Nitrogen containing compound with simple structure
First discovered in urine, it is a component of it
Produced when there is an excess of amino acids, and so the nitrogen is
removed from them
Comes from a cycle of reactions, catalyzed by enzymes, in the liver; then
it is transported to kidney for filteration and is passed out in urine
Artificially synthesized for nitrogen fertilizer:
 Ammonia + CO2  Ammonium Carbamate  Urea + Water

Carbon Compounds

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Carbon atoms can form four bonds allowing a diversity of
compounds to exist
Covalent bond- when two adjacent atoms share a pair of electrons, with
one electron contributed by each atom; strongest type of bond between
atoms
Carbon bonds can be with other carbons to form chains or rings; fatty
acids have chains up to 20 carbon atoms; bonds can also be with other
elements such as hydrogen, nitrogen, oxygen, and phosphorous
Can bound to one element or a group of elements (ethanol); can have
single or double bonds

Life is based on carbon compounds such as lipids, carbohydrates,
proteins, and nucleic acids
Carbohydrates- composed by carbon, hydrogen, and oxygen; with
hydrogen and oxygen in the 2:1 ratio
Lipids- broad class of molecules that are insoluble in water such as
steroids, waxes, fatty acids, and triglycerides;
 Triglycerides are fats if they are solid at room temperature or oils
if they are liquid at room temperature
Proteins- Composed of one or more chains of amino acids; all of the
amino acids in the chain include oxygen, hydrogen, carbon, and nitrogen,
but two of the 20 amino acids also have sulfur
Nucleic Acids- chains of subunits called nucleotides, which have carbon,
hydrogen, oxygen, nitrogen, and phosphorus; two types: RNA and DNA

Drawing and Identifying Molecules

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Drawing
Ribose
 C5 H10 O5
 Five membered ring with side chain
 Four carbon atoms in the ring; one forms chain
 Carbon atoms can be numbered starting with 1 on the right
 Hydroxyl groups on carbon atoms 1,2, and 3 go up, down, and
down
Glucose
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C6 H12 O6
Six membered ring with side chain
Five carbon atoms in the ring; one forms chain
Carbon atoms can be numbered starting with 1 on the right
Hydroxyl groups on carbon atoms 1,2, 3, and 4 go down, down,
up, and down
In a form of glucose used by plants to make cellulose, the
hydroxyl group on carbon atom 1 points upwards

Saturated Fatty Acid
 Carbon atoms form an unbranched chain
 Bonded by single bonds
 Number of carbon atoms is commonly 14-20
 At the end of the chain, the carbon is bonded to carboxyl group
 At the other end, it is bonded to three hydrogens
 All other carbons are bonded to two hydrogens
Amino Acids
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Carbon atom in middle is bonded to four different things
o Amine group
o Carboxyl group, making it an acid
o Hydrogen atom
o The “R” group, the variable part

Identifying
 Proteins have C, H, N, and O; whereas carbohydrates and lipids
have all but N
Proteins also have sulfur, which carbs and lipids don’t

 Carbs have H and O in ration of 2:1
Lipids have less oxygen than carbs

Hydrogen Bonding in Water

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Metabolism is the web of all the enzyme catalyzed reactions in a
cell or organism
 Most reactions occur in the cytoplasm, some are extracellular
 Metabolism= sum of all reactions that occur in an organism
 Made up of pathways; one molecule is transformed to another, in
series of small steps
 Most are chain reactions, some are cycles
 Even in prokaryotes, metabolism is made up of 1000 different
reactions
Anabolism is the synthesis of complex molecules from simpler
molecules including the formation of macromolecules from
monomers by condensation reactions
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It is one of the parts of metabolism
This is the part that builds up larger molecules from smaller ones
Eg: anabolic steroids are the ones that help build muscle
Requires energy; in the form of ATP
Anabolism examples:
o
o
o
o

Protein synthesis through ribosomes
DNA synthesis through replication
Photosynthesis
Synthesis of complex carbohydrates such as starch,
cellulose, and glycogen
...

Cations and anions attract each other and form an ionic bond; in water,
the molecules have only partial charges, so the attraction is less but is
still enough to have effects
Water molecules’ attraction is called hydrogen bond; it is more an
intermolecular force than a bond; hydrogen atoms in one molecule is
slightly attracted to oxygen molecule in another
Hydrogen bonds and the properties of water
It is still a theory that hydrogen bonds form between water molecules;
they aren’t directly visible
They still explain the cohesive, adhesive, thermal, and solvent properties
of water
We can base our understanding of natural world on something that hasn’t
been proven to exist; if a theory has evidence, if it helps to predict
behavior, if it has not been falsified, and if it helps to explain a
phenomenon, then it works
...

The loss of an OH from one molecule and an H from another molecule,
which form H2O; involves combination of subunits and yields water
Condensation is anabolic and requires energy; ATP supplies energy to
monosaccharaides and this energy is used for condensation

Polysaccharides

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Different polysaccharides have different structure and functions because
of the type of glucose used to make them and the links between them
Glucose
 Has five OH groups
 Only three of them are actually use to link to make
polysaccharides
 Most common link is between OH on C#1 and OH on C#4
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The OH on C#6 is used to form side branches sometimes
The OH group on C#1 can be pointing up or down
o Alpha Glucose- OH is pointing downwards
o Beta Glucose- OH is pointing upwards

Cellulose
 Made up of beta glucose molecules
 Condensation leads to linking C#1 to C#4
 OH groups on C#1 and C#4 point opposite directions
 To add more glucose molecules, each molecule must be
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positioned at 180 degrees to add on
Glucose subunits are oriented up and down alternatively
Thus, cellulose is straight chain instead of curved
They are unbranched chains, so they can form bundles (called
cellulose microfibils) with hydrogen bonds linking to cellulose
The bundles have high tensile strength and are used as basis of
plant cell walls; prevents bursting, even due to osmosis

Starch
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Made up of alpha glucose molecules
Condensation leads to C#1 and C#4 linking
Both the OH groups point downwards, all glucose molecules are
oriented the same way
Starch molecule is curved instead of straight
Two forms of starch (branched globular and unbranched helix)
o Globular eg: amylopectin
o Helix eg: amylose
Made only by plant cells

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Both types of starch are hydrophilic but are too large to be water
soluble
Useful in cells where large amounts of glucose is needed but
concentrated glucose would lead to osmosis
Used as a store of glucose and energy in seeds and storage
organs such as potato cells
Used as temporary store in leaf cells when glucose is made by
photosynthesis than it can be exported to other parts in the plant
Easy to add or remove extra glucose molecules

Glycogen
 Similar to branched form of starch
 but there is more branching, making it more compact
 Made by animals and some fungi
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Stored in liver and some muscles in humans
Has same function as starch in plants
Easy to add or remove extra glucose molecules

Lipids

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Triglycerides are formed by condensation from three fatty acids
and one glycerol
Lipids are diverse group but share property of being water insoluble; one
of the main ones is triglycerides (sunflower seed oil, fat in humans)
Fats are liquid at body temperature but solid at room temperature; oils
are liquid at both temperature
Triglyceride
 Used as energy stores; energy can be released in aerobic cell
respiration
 Also used as heat insulators
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Each fatty acid linked to glycerol by condensation; link is called
ester bond
Leads to three water molecules
Ester bonds form when acid reacts with OH group in an alcohol
Here, the reaction is between COOH group on fatty acid and OH
group on glycerol leads to ester bond

Energy Storage

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Lipids are more suitable for long term energy storage than
carbohydrates
Lipids and carbs are both energy stores, but lipids are for long term
Lipids used are fats that are stored in adipose tissue
Adipose tissue is right under skin and around some organs (kidneys)
Reasons for Lipid>Carb for Long Term
 Amount of energy released in cell respiration per gram of lipids is
twice that of carbs; same amount stored as lipid rather than
carb,it would add half as much to body mass
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Fats form from pure droplets in cells with no water; but glycogen
(carbs) have 2g of water for every 1g of glycogen; so lipids are
six time more efficient in storage
Stored lipids have extra secondary roles; can be used as heat
insulators; this is the reason for much of our stored fat being in
sub cutaneous adipose tissue next to the skin
Also act as shock abosrbers since fat is liquid at body
temperature

Glycogen is used for short term storage, it is the carb for energy storage
Glycogen can be broken down to glucose rapidly and easily transported;
adipose fats are not as easily mobilized
Glucose can be used either in anaerobic or aerobic cell respiration
whereas fat is used only in aerobic cell respiration
Liver stores upto 150 grams of glycogen and some muscles store up to
2% glycogen by mass

Body Mass Index

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The BMI requires: mass of person in kg and their height in meters
BMI= mass in kg/ (height in meters)^2
Can also be found using chart called nomogram
The BMI is used to assess whether a person’s body mass is healthy or too
low or high
In some parts, world food supplies are insufficient or are unevenly
distributed  underweight
Anorexia nervosa  underweight
Obesity; excessive food intake and lack of exercise causes accumulation
of fat in adipose tissue, can lead to coronary heart disease and type 2
diabetes  low life expectancy and raises overall costs of health care

Fatty Acids

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Fatty acids can be saturated, monounsaturated or
polyunsaturated
Fatty acids- chain of carbon atoms, hydrogen atoms linked by single
covalent bonds; hydrocarbon chain
 One end of the chain is the acid part called the carboxyl group (COOH)
 Length of chain is variable but most have 14-20 carbon atoms
 Some fatty acids are linked by only single covalent bonds; other
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times the carbon bonds have double bonds
If there is a single covalent bond between carbons, then it can
bond to two hydrogens
If there is a double covalent bond between carbons, then it can
only bond with one other hydrogen
If a fatty acid has all single bonds, then it is a saturated fatty
acid
If a fatty acid has one (monounsaturated) or more double bonds
(polyunsaturated), then it is an unsaturated fatty acid

Unsaturated Fatty Acids can be cis or trans isomers
In unsaturated fatty acids in living organisms, the hydrogen atoms are
always on the same side of the two carbon atoms that are double bonded
(cis)
Hydrogens on the opposite sides are called trans-fatty acids
In cis, there is a bend in the chain at the double bond, making them less
good at packing together in regular arrays, which lowers the melting
point; usually liquid at room temperature (oils)
Trans fatty acids don’t have a bend at the double bond, so they have a
higher melting point and are solid at room temperature; produced
artificially by partial hydrogenation of vegetable or fish oils

Health risks of fats

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Main concern: coronary heart disease (CHD); coronary arteries
become partially blocked by fatty deposits  blood clots and heart attacks
A positive correlation has been found between saturated fatty acid intake
and rates of CHD; but it doesn’t mean it’s the cause; it could be another
factor in relation to saturated fatty acid intake that could cause CHD
The Maasai of Kenya have a lot of saturated fatty acids but they don’t
have many CHDs
Many say that olive oil (cis-monounsaturated fatty acid) is the cause of
low CHD rates; but genetic factors or use of tomatoes could explain low
CHD rates
Another positive correlation is trans-fats and CHDs; other factors have
been tested and none other factors have great effect; trans-fats probably
cause CHDs

Evaluating Health Risks of Foods

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There are many health claims made; some say that certain foods are
good and some are not
It is easy to test claims about effects on diet on health using lab animals;
genetically uniform animals can be bred and groups of them with same
characteristics can be used; other variables (temperature and diet) can
be controlled
Animal experiments don’t always give certainty of health effects on
humans; difficult to carry out controlled experiments with humans
Can find humans with similar characteristics but will always be genetically
different; also other variables wouldn’t be easily controlled
Researchers then must use epidemiological studies; involves finding a
large cohort of people and measuring their food intake and health over
the years
Then you can used statistics to find factors in the diet associated with
increased frequency of a disease; other effects of the factors will have to
be eliminated by the analysts
____

Amino Acids and Polypeptides

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Evaluation- assessment of implications and limitations; evidence for
health claims comes from scientific research
 Implications: Do the results of research support claim strongly,
moderately, or not at all?
 Limitations- Were the methods used rigorous, or was there
weakness that can be reflected in the conclusions
Answer to first question through analysis of research; analysis is easiest if
results are graphical or other visual form
 Correlation between intake of lipid being investigated and rate of
disease or health benefit? Could be positive or negative
correlations
 How large is the difference between average rates of disease

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with different levels of lipid intake? Small differences may be
insignificant
How widely spread is the data? The more wide spread, the less
likely is it that mean differences are significant
Do statistical tests show significant differences?

Second question is answered by assessing methods used
 How large was the sample size? Surveys should have thousands
of people to get reliable results
 How even was the sex, age, state of health and life style? The
more even , the less other factors can affect
 If sample was uneven, were the results adjusted to eliminate
effects of other factors?
 Were measurements of lipid intake and disease rates reliable?
Amino acids are linked together by condensation to form
polypeptides
Polypeptides chains of amino acids made by linking through condensation
reactions
 happens in ribosomes in a process called translation
 are main component of proteins and in many proteins they are
the only component;
o some have one polypeptide and others have two or more

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can have any number of amino acids
though, chains of less than 20 are called oligopeptides

Condensation reaction involves amine group (NH2) of one amino acid and
the carboxyl (-COOH), loss of water, and formation of peptide bond
Dipeptide- two amino acids linked by a peptide bond; polypeptide- many
amino acids linked by peptide bonds
Insulin is a protein with two polypeptides (21 amino acids and 30 amino
acids)
Largest polypeptide ever discovered is titin, part of our muscles; 34, 350
amino acids
There are twenty different amino acids in polypeptides
synthesized on ribosomes
All amino acids have some identical features: carbon atom in center
bonded to amine group, carboxyl group, hydrogen atom, and R group
20 different kinds of amino acids are used by ribosomes to make
polypeptides; R groups gives each polypeptide its character
Stock of R groups give wide range of proteins
Some proteins have amino acids that aren’t from the 20
Mostly due to one of 20 being modified after synthesis of polypeptide
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Eg: collagen (structural protein for tensile strength in skin,
vessels, tendons, ligaments); contains proline which can be
modified into hydroxproline making it more stable

Polypeptides

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Amino acids can be linked together in any sequence giving a huge
range of possible polypeptides
Ribosomes link amino acids until it forms the chain; ribosomes can make
bonds between any two amino acids
A polypeptide of n amino acids has 20^n possible sequences
The amino acid sequence of polypeptides is coded for by genes
The number of possible sequences is immense, but organisms only
produce small fraction of them
Amino acid sequence of each polypeptide is stored in a coded form in the
base sequence of a gene
Some genes have other roles; most genes store amino acid sequence
using genetic code; three bases of the gene are needed to code for each
amino acid in the polypeptide,
so a 400 amino acid polypeptide should need 1200 bases; in reality, there
are bases needed at end, beginning, and some points in the middle
open reading frame- base sequence that actually codes for a polypeptide
A protein may consist of a single polypeptide or more than one
polypeptide linked together
Integrin- membrane protein with 2 polypeptides, each of which has a
hydrophobic section embedded in the membrane ;The two polypeptides
act as blade and handle of folding knife
Collagen- three long polypeptides wound together to form rope like
molecule; great tensile strength than if they were separate; winding
allows for some stretching and not snapping

Hemo globin- four polypeptides with other non polypeptide structures;
four parts interact to transport oxygen more effectively together rather
than separate

Enzymes

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Amino acid sequence determines the 3D conformation of a protein
Conformation of a protein is its 3D structure; determined by amino acid
sequence in protein and its constituent polypeptides
Fibrous proteins (eg: collagen) are elongated, with repeating structure;
many are globular with parts that are helical or sheet like; amino acid
sequence doesn’t allow folding up
In globular proteins, the polypeptides gradually fold up to develop final
conformation, stabilized by bonds between R groups that have brought
together
Soluble, globular proteins have hydrophilic R groups on the outside and
hydrophobic ones on the inside; in membrane proteins, the hydrophobic R
groups are attracted to the center

Living organisms synthesize many different proteins with a wide
range of functions
Catalysis- there are thousands of enzymes to catalyze specific chemical
reactions in and out of the cell
Muscle Contraction- actin and myosin together cause the muscle
contractions used in locomotion and transport around body
Cytoskeletons- tubulin is subunit of mictrobules that give animal cell
shape and pull on chromosomes in mitosis
Tensile Strengthening- fibrous proteins give tensile strength for skin,
tendons, ligaments, and vessels
Blood Clotting- plasma proteins; blood from liquid to gel
Gas and Nutrient Transport- proteins in blood transport stuff

Cell Adhesion- membrane proteins;
Membrane Transport- factiliated diffusion, active transport, and
electron transport
Hormones- insulin, FSH and LH
Receptors- binding sites for hormones, neurotransmitters, tastes and
smells, and also light
Packing of DNA- histones; help chromosomes condense
Immunity- act as antibodies; but the most diverse group of proteins

Enzymes have an active site to which specific substrates bind
Enzymes- globular proteins acting as catalysts; called biological catalysts
because they are made by living cells and speed up biochemical reactions
Enzymes convert substrates into products
They are found in some cells and are also secreted by some cells to work
outside
Enzyme-substrate specificity- enzymes only catalyse one biochemical
reaction and thousands of reactions take place
Substrates bind to a special region on the surface called the active site;
shape and chemical properties match each other, allowing for binding
Substrates are converted into products when bound to the site, then
release freeing the active site for another reaction
...
Since water is in
liquid state, its molecules and all the particles dissolved in it are contact
with each other and are in continual motion
Both substrates and enzymes move around randomly, but substrates
move faster since they’re smaller
Collisions occurs due to random movement; successful one are in which
the substrate and active site allow binding to take place

Factors Affecting Enzyme Activity

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Temperature, pH and substrate concentration affect the rate of
activity of enzymes
Temperature
 In liquids, particles are in continuous random motion; when
heated, kinetic energy ups; enzyme and substrate move faster
and collider more and so enzyme activity is up
 When enzymes are heated, bonds in enzymes vibrate more and
chance of breaking increases; when bonds break, structure of

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enzyme changes along with active site; it is a permanent change
called denaturation
When denatured, the enzyme can’t catalyze; as more enzymes
become denatured, enzyme activity falls; eventually its
completely stops
As temperature ups, there are reasons for increase and decrease
in enzyme activity

pH
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Acidity is due to the presence of hydrogen ions, so lower pH,
higher hydrogen ion concentration
pH scale is logarithmic
Most enzymes have an optimum pH at which activity is highest
If pH level is too high or low than normal, then enzyme structure

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could alter also changing active site
Severe change could lead to irreversible denaturation
They don’t all have the same pH optimum- there is a wide range
Eg: Bacillus licheniformis has a pH optimum between 9 and 10

Substrate Concentration
 If substrate concentration is high, more chances of collision
 After binding of substrate to active site, the active site is
occupied and unavailable to others until products have been
formed and released
 As concentration rises, more and more enzymes are occupied
 Greater and greater proportion of collisions are therefore blocked
 Thus, increased in rate at which enzymes catalyse reactions gets
smaller and smaller (like a square root graph)
Denaturation
 Can cause enzymes dissolved in water to become insoluble and
form a precipitate

Immobilized Enzyme

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They are widely used in the industry
1897- Buchner brothers, Hans and Eduard, showed that an extract of
yeast with no yeast cells would change sucrose into alcohol
Beginning of a new area of using enzymes to catalyse reactions outside of
cells
Pasteur claimed that fermentation of sugars to alcohol would only be
present if there were living cells; this was part of theory of vitalism
Buchner theory provided more falsification for vitalism
More than 500 enzymes have commercial uses ; some are used in more
than one type of industry
Enzymes used in industry are immobilized; it is an attachment of the
enzymes to another material or into aggregations, so that movement of
the enzyme is restricted
You can stick enzymes to a glass surface, trap them in an alginate gel, or
bond them together to form enzyme aggregates of up 0
...
and pH,
reducing rate at which they are degraded and have to be
replaced
Can be exposed to higher enzyme concentration than with
dissolved enzymes, speeding up reaction rates

Nucleic acids and nucleotides

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Enzyme lactase can break down lactose into glucose and galactose
It is obtained from Kluveromyces lactis, a type of yeast that grows in milk
The yeast is cultured and the enzymes is extracted and sold to food
companies
The food companies use it for
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Reducing lactose from milk products for lactose intolerants
Galactose and glucose are sweeter than lactose, so less sugar
needs to be added to milk products
Lactose crystallizes during ice cream production, giving a gritty
texture; glucose and galactose are more soluble than lactose and
so they remain dissolved, with smooth texture
Fermentation of glucose and galactose is faster than lactose, so
production of yoghurt and cottage cheese is faster

Nucleic acids DNA and RNA are polymers of nucleotides
Nucleic acids first discovered in nuclei of cells; very large molecules linked
by nucleotides
Two types: DNA and RA
Consist of three parts:
 Sugar, 5 carbon atoms, pentose sugar
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Phosphate group, acidic
Base, contains nitrogen and has either one or two rings of atoms
in the structure

Base and phosphate are linked by covalent bonds to pentose sugar
(carbon)
Nucleotides are put in a chain or polymer by covalent bonds between
phosphate of one and pentose sugar of another; creates strong backbone
with alternating sugar and phosphate

Four different bases in both DNA and RNA, so there are four different
nucleotides; nucleotides can be linked together in any order
Base sequence is the store of info

DNA and RNA

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DNA differs from RNA in the number of strands, the base
composition, and the type of pentose
Three important differences:
 Sugar
o DNA: deoxyribose; RNA: ribose
o Deoxyribose has one fewer oxygen atom than ribose
 DNA: double stranded; RNA: single stranded
 Bases
o DNA: adenine, cytosine, guanine, and thymine
o RNA: adenine, cytosine, guanine, and uracil
DNA is a double helix with two antiparallel strands of nucleotides
linked by hydrogen bonding between complementary base pairs
Each strand has a chain of nucleotides linked by covalent bonds
They’re antiparallel strands since they run in opposite directions; one is 5’
to 3’ and the other is 3’ to 5’
They’re wound together to form a double helix
Strands are held together by hydrogen bonds; Adenine with Thymine and
Guanine with Cytosine; its called complementary base pairing

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Semi-Conservative Replication of DNA 6/11/2016 7:37:00
PM

Success in discovering structure of DNA was based on using evidence to
develop possible structures and testing it
First model was a triple helix, with bases on the outside and magnesium
holding strands together with ionic bonds to phosphates on each strand
The helical structure and spacing fit the patter obtained by Rosalind
Franklin; but he rejected it since there wouldn’t be enough magnesium to
form cross links between strands
...

The bases were cut out from cardboard and stuck together to show base
pairing; each was equal in length; then they used antiparallel strands and
finally built they’re second model with correct angles and lengths

Replication of DNA is semi-conservative and depends on
complementary base pairing
When cell prepares to divide, two strands separate; they are then guides
for the creation of a new strand
New strands made by adding nucleotides, one by one, and linking them;
thus, there are two new strands made up of the old and new strand; so, it
is semi conservative
Base sequence of template determines base sequence of new strand
Complementary bases form hydrogen bonds to stabilize; wrong base
pairing wouldn’t lead to hydrogen bonding and the new nucleotide would

be rejected; the rule that there are specific base pairs is : complementary
base pairing
Ensures identical replication from parental molecules

Obtaining Evidence on Theory of Semi
Conservative Replication
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This scientific theory seemed intuitively right, but required evidence
1958, Matthew Meselson and Franklin Stahl published results that
supported evidence for this theory; used an isotope of Nitrogen (15
atomic mass)
The devised a method of separating DNA containing 15N in the bases
from DNA with 14N through a technique called “ceesium chloride density
gradient centrifugation”
 Cesium chloride is spun at 45,000 rpm for 20 hours
 Cesium ions move to bottom of tube with the greatest
concentration and density at the bottom
 Anything along with it gets centrifuged and can be found at a
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level corresponding with the density
They cultivated E
...
Each of the two
strands act as template for formation of a new strand
DNA polymerase (enzyme) carries out assembly of new strands
DNA polymerase moves along template strand in the same direction,
adding nucleotide at a time; free nucleotides are around in the area
where DNA is replicated
Once a correct nucleotide has been brought into position and hydrogen
bonds form; DNA polymerase links it to end of the new strand
Covalent bond is made between phosphate and sugar

Pentose sugar is 3’ terminal and phosphate is 5’ terminal; DNA
polymerase adds on 5’ terminal to 3’ terminal of existing strand
DNA polymerase moves along template, assembling new strand, with high
degree of fidelity

PCR- the Polymerase Chain Reaction

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PM

The PCR is a technique used to make many copies of a selected DNa
sequence; very small quantity is needed to start
DNA is loaded into PCR machine in which steps double the quantity of
selected DNA
The stages include separation and combining to form double stranded
DNA
The two strands have hydrogen bonds that maybe be weak, but in
numbers they are stable enough to hold the two strands together at
temperatures that cells encounter
Hydrogen bonds break eventually, but if they are cooled then they can
reform,which is called re-annealing
For 15 seconds DNA is heated to 95 degrees celcius, then cooled to 54
degrees; it allows for re-annelaing but there are still short sections of
single stranded DNA present (called primers)
The primers bind to target sequences and prevent re annealing; copying
of single parent strands then starts from primers
Taq DNA polymerase is found from hot spring bacterium; the bacterium
can work in 50-80 degrees temperatures and survives the 95 degree heat
up
Then, the Taq DNA polymerase, at 72 degrees, can add about 1000
nucleotides per minute
When replication finishes, the next cycle can be started at 95 degrees, the
cycle can finish within two minutes; thirty cycles which make factor of a
billion, take less than an hour

Transcription and Translation

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Transcription is the synthesis of mRNA copied from the DNA base
sequences by RNA polymerase
The sequence of bases in a gene, don’t, on their own , give the organism
any observable characteristics
Most genes specify sequence of amino acids for polypeptides; the proteins
are what determine the observable characteristics
Transcription synthesizes RNA using DNA as a template; the transcription
occurs on only one strand of the DNA since RNA is a single strand
Process:






RNA polymerase binds to site on DNA at the start of the gene
RNA polymerase separates DNA and starts pairing RNA to one
strand of the DNA (uracil replaces thymine)
RNA polymerase forms covalent bonds between the RNA
nucleotides
RNA separates from DNA strand, the DNA’s helix is reformed
At the end of the gene, transcription stops, and the RNA
molecule is sent off

The RNA strand created has a base sequence identical to the DNA strand;
except for thymine  uracil
The strand that acts as the template is called  antisense strand
The strand that has the same sequence as the RNA  sense strand
Translation is the synthesis of polypeptides on ribosomes
The RNA molecule’s base sequence determines sequence of amino acids
for polypeptide production
Takes place on ribosomes; ribosomes have a small and large subunit,
both with binding sites

Part of the larger subunit is where peptide bonds are formed between
amino acids to form polypeptides

mRNA & Genetic Code and Codons &
Anticodons
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Amino acid sequence of polypeptides is determined by mRNA
according to genetic code
mRNA is the RNA that carries information needed to synthesize a
polypeptide
length of mRNA depends on the number of amino acids but on average,
for mammals, it is 2,000 amino acids
many different genes, within the genome, have information to make
polypeptides with specific gene formation; however, a cell, at a time, will

only need a few polypeptides
...
coli; since then method has developed to include yeast cells and
safflower plants
Each of these species has received the gene for making human insulin;
insulin produced is exactly the same as human production
All three species use the same genetic code as humans

Cell respiration is the controlled release of energy from organic
compounds to produce ATP
All living cells perform; organic compounds broken down to release
energy to be used by cell
Energy is released in muscle fibers by breaking glucose into CO2 and
water; the energy can be used for muscle contraction

Human, source of organic compounds is food we eat; carbs and lipids are
often used, by amino acids may be used if more than needed protein is
eaten; plants use carbs or lipid made by photosynthesis
It is carried out by enzyme in controlled fashion, so most energy is
retained in usable form; the form is ATP
ATP, made of phosphate group linked to ADP; requires energy for this
reaction, energy come from breakdown of organic compounds
ATP is not transferred from cell to cell, and cells require continuous
supply, making cellular respiration essential to all lives
ATP from cell respiration is available as a source of energy in the
cell
Cells require energy for 3 activities:
 Synthesis of large molecules like DNA, RNA, and proteins
 Pumping molecules or ions across membranes


Moving stuff around the cell

Energy is found in ATP, and is immediately available simply by splitting
ATP into ADP and phosphate, which can be reconverted
When energy from ATP is used, it turns to heat; it makes it unreusuable
and it is lost to environment; so, cell requires constant source of ATP

Yeast and its Uses

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Yeast is unicellular fungus occurring in habitats where glucose or other
sugars are available (fruits)
Can respire aerobically or anaerobically; anaerobic cell respiration is
bases for production of foods, drinks, and renewable energy
Bread is made by adding water to flour, kneading, then baking; yeast is
added to the bread to create bubbles of gas so that baked bread has a
lighter texture
After kneading, the dough is kept warm to encourage respiration in the
yeast; yeast uses up oxygen and then moves on to anaerobic cell
respiration where it creates CO2 that doesn’t escape the dough causing
bubbling
Ethanol is made too, but during baking it evaporates
Bioethanol is ethanol made by living organisms, for use as a renewable
energy source
Most comes from sugar can and corn using yeast; yeast converts sugars
into ethanol in large fermenters thru anaerobic respiration
Only sugars can be converted so starch and cellulose are broken into
sugars using enzymes
The ethanol produced is distilled from water to improve combustion; can
be used as fuel and can be mixed with petrol too

Anaerobic Respiration in Humans

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Humans used to maximize the power of muscle contraction
Maximally powerful muscles were used for survival before; now it is used
for sport
It involves production of lactate, so when it is being used to supply ATP,
the concentration of lactate in a muscle increases
There is a limit at how much the body can tolerate and this is the limit for
how much anaerobic respiration can occur
After vigorous contractions, the lactate must be broken down which uses
oxygen; can take several minutes for enough oxygen to be absorbed to
break lactate
Demand for oxygen that builds up during anaerobic respiration is called
oxygen debt

Metabolism, Anabolism, Catabolism

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Anaerobic cell respiration gives a small yield of ATP from glucose
Glucose is broken in anaerobic cell respiration without using any oxygen;
yield is small, but ATP can be produced quickly, making it useful in 3
situations:
 When short and rapid burst of ATP is needed
 When oxygen supplies run out
 When the environment lacks oxygen
Products of anaerobic respiration aren’t all the same in every organism;
glucose is converted into lactic acid (aka lactate) in humans; in yeast and
plans, glucose is converted to ethanol and CO2 (both of which are toxic in
excess)
Aerobic cell respiration requires oxygen and gives a large yield of
ATP from glucose
If oxygen is available to a cell, glucose can be more fully broken down to
release greater quantity of energy than in anaerobic
2 molecules per glucose with anaerobic; more than 30 per glucose with
aerobic
Involves chemical reactions; CO2 and water are produced; CO2 is a waste
product in most organisms and water is considered useful
In eukaryotes most reactions of aerobic cell respiration including all that
produce CO2 happen in the mitochondrion



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