BIO206 Notes

Cells are small membrane bound units filled with concentrated aqueous solution o
f chemicals and given the ability of reproducing itself by dividing. Thus for th
is purpose the cells are the fundamental unit of life.
If cells are modified to specific specialization they cause the cell to lose its
ability to reproduce, as a result they end up depending on other cells for the
basic needs.
In all living things genes are stored in the DNA molecule, encoded in the same c
hemical code, constructed out of the same chemical compounds, interpreted by the
same chemical machinery and reproduce in the same way.
DNA, RNA and proteins are the three main group of macromolecules which are impor
tant for the function of the cell.
Cell can function properly only if it has the correct set of proteins within the
cell.
Genetic continuity is the ability of the cell to renew it self and cont. living
through the next generation.
Central Dogma states that the DNA is transcribed into RNA which gets translated
into proteins. Proteins dominates the behavior of the cell. This is the one idea
which unifies all the cells, let it be prokaryotic or eukaryotic.
Proteins are made up of amino acid which are attached to each other in different
sequence giving the proteins its unique 3D structure (conformation).
DNA polymerase not only synthesis the DNA, but it also checks to make sure that
it is reading it correctly. It proof reads what it makes, to ensure that there a
re minimal mistakes in the copying of DNA during DNA replication.
The characteristics of life includes: ability to grow, the process of metabolism
, the reproduce, to respond to stimuli, and the ability of movement (only possib
le in certain species).
The cell theory states that the cell is the smallest unit of life, all the livin
g things are made up of cells and new cell arise only from pre-existing cells.
The first cell was created long time ago based on the Earth s condition which allo
wed the chemical compounds to create an organism that is able to reproduce itsel
f.
Mutation can create offspring in which they change for worse, better or neutral.
After mutation they go through different pressures exerted by natural selection
where the genes of the next generation will be of those of that survived.
The cells have the ability to transform the environment they live in. Ex. Cyanob
acteria transformed the earth s atmosphere by carrying out oxygenic photosynthesis
which resulted in oxidizing environment from reducing environment. This cell al
lowed for the evolution of the anaerobic life.
To estimate relatedness one method is to compare the nucleotide sequence encodin
g the 16s or 18srRNA (if these RNA are defective then the organism will die)
the
more diff the sequence the more distantly related the organisms.
Since the recent technology allows for the genome to be analyzed, we compare mor
e than one genes to estimate relatedness.
The nucleotide sequence of chips and human is greater than 99% in terms of simil
arity.
Using the method of relatedness, we can organize the organisms into tree of life
which is based on relatedness. It states that all the organisms we see today ar
ose from one ancestral specie.
The diversity in organism results from difference in pattern of expression of ge
nes temporally and spatially.
Evolution is the process by which the cells are modified and adapted to suit the
ir environment better. Evolutionary process is random, it doesn t have a purpose a
nd goal. This is based on selection pressure in the environment which selects ce
rtain traits that benefits the organism to be passed down.
During the evolution, in addition to vertical gene transmission, there is large
scale horizontal gene transmission. Ex. The mitochondria is an archaea which was
eaten by ancestral eukaryotic cell and started to live within the cell. This tr
ansfer of genes from that bacteria resulted in horizontal gene transmission. Ano
ther example of horizontal gene transfer is the evolution of chloroplast. Modern

day example can be seen in bacteria that is capable of transferring genes which
are capable of fighting antibiotics.
Genome is all the information stored in the DNA of the cell.
DNA is the structure which holds the genetic information of the cell. It codes f
or proteins and occasionally codes for RNA. It has 4 main properties to it:
Complementarity
Polarity
DNA is directional
Fidelity
the ability to be passed down to next generation in almost perfect sequ
ence identity (accuracy)
Stability
needs to be stable, structured. Must be able to resist the rapidly cha
nging environments in the cell.
Cells can be classified into 2 types:
Prokaryotes: cells with no defined nucleus - No nuclei, lack membrane-bound orga
nelles, and smaller than eukaryotes.
Eubacteria (Bacteria)
include many photosynthetic organism.
Archaebacteria (Archea)
grow in unusual environment.
Eukaryotes: cell with a true nucleus. - They are complex, have nuclei, abundant
and diverse organelles that compartmentalize biochemical reactions (separate com
partment for different set of reaction), larger than prokaryotes.
Includes protista, fungi, animals, plants
Cytoplasm is a transparent substance crammed with concentrated chemicals.
Mitochondria is thought to be evolved from aerobic bacteria that started to live
inside the eukaryotic cell. Similarly, chloroplast is thought to have evolved f
rom photosynthetic bacteria which started to live inside plant cell.
Nucleus is the essential structure in the eukaryotic cell. It holds the DNA whic
h are separated from the rest of the cell by surrounding it with Nuclear Membran
e. . This is the place where DNA are replicated and separated, and transcription
occurs. It houses the chromosome (condensed DNA strands) during the cell divisi
on.
Nucleoplasm contains DNA (genetic info) and chromatin (DNA + histones complex)
Nucleolus has condensed DNA and genetic info for synthesis of ribosome.
Mitochondria are present in all the eukaryotic cell, they are the powerhouse of
the cell. They have double membranes. Each has its own DNA and they reproduce by
dividing in half.
Chloroplast are the large green organelles found in the plant cells. They are re
sponsible for conversion of sunlight into food for the cells to use. They are li
ke mitochondria in sense that they have their own set of DNA and reproduce by di
viding in half and also that they have double layered membranes.
Plant cells are autotrophic, meaning they can capture sunlight and use it to pro
duce its own food. However, animal cells are heterotrophic, meaning they need to
have constant input of food and nutrients for survival.
Endoplasmic Reticulum is an irregular maze flattened membranes which houses the
space for production of materials which are destined to exported from the cell.
Golgi apparatus receives the modified materials and are responsible for the tran
sportation to the specific location inside or the outside the cell.
Lysosomes are small irregular structure which are responsible for breaking down
of the unwanted molecules.
Peroxisomes are closed space for very dangerous reactions to take place within t
he cell.
Endocytosis is the process of engulfing large molecules, while exocytosis is the
fusion of vesicle inside the cell to the external cell membrane.
Ribosomes are the machines required during the process of protein synthesis. The
y are found in cytoplasm, RER, chloroplast and mitochondria.
Cytoskeleton is the fine filaments of proteins which are anchored from the cell
membrane to the nuclear membrane. Their main function is to provide cell with st
ructural support and assist the cell in transportation of materials inside the c
ell and transportation of the cell itself. Consist of thee filaments:
Thinnest are the actin filaments, which are associated with production of contra
ctile forces.

Thickest are the microtubules, which plays a role in cell division when the chro
mosomes needs to be separated.
Intermediate filaments serve to strengthen the cell.
The proteins that are formed must be maturated and processed (post-transcription
al modifications) before they can be used and targeted to final destination.
Structure of DNA predicts the function. This structure allows us to predict how
it can be replicated.
Structure of proteins allows to predict the function of protein, such as which i
t binds to, what does it do.
DNA and RNA are polymers which are synthesized from a small set of repeatedly ut
ilized monomers.
Nucleotide are involved in more than just being a structural component. They pro
vide genetic info (DNA) and protein synthesis info (RNA), they are used in signa
ling (cAMP) and also function as coenzymes (NADH).
Chemical of life is based on 4 points:
Based a lot on carbon compounds
Chemical reaction that take place in aqueous solution with taking in the earths
atmospheric temperature into consideration
Very complex
Dominated and coordinated by collection of polymeric molecules which controls th
e growth and the reproduction of cells.
Atom is the smallest particle of an element which still retains its chemical pro
perties.
Atom is made up of electrons (negatively charged) revolving around nucleus (dens
e center of the atom) which consist of protons (positively charged) and neutrons
(neutral).
The electrons in the outermost shell determines how the atom behaves during chem
ical bonding.
There are two types of chemical bonds:
Covalent bonds: formed when electrons are being shared by equally strong atoms.
The sharing of electrons result because none of the atoms are strong enough to p
ull the electron away from the other.
Ionic bonds: formed when there is an exchange of electrons between a strong and
weak atom. This type of bonding results in generally between metal and non-metal
. It results in formation of ions. This type of bond is held together by electro
static attraction between the positively and negatively charged atoms.
Bonds vary in strength depending on the type of bonds. The strength of the bond
is determined by the amount of energy required to break that bond.
70% of the cells weight consist of water. Without water life as we know it would
not exist. Water is held together in the liquid state by hydrogen bonding (when
H binds to O or N of other molecule). Hydrogen bonding in water results in wate
rs boiling point and freezing point.
Substances that give hydronium ion when dissolved in water is known to be acid.
The stronger the acid the greater the number of hydronium ions produced.
Base is a substance that gives hydroxide ion when dissolved in water. The strong
er the base the greater the number of hydroxide ions produced.
Buffers are usually substances that are weak acids and bases. Their function is
to maintain the pH of the solution within the cell / extracellular liquid betwee
n specific ranges for the cells to function.
Simplest sugars are called monosaccharides which can be linked together by coval
ent bonds (glycosidic bonds) to form larger carbohydrates. The covalent bond is
formed between the OH of two diff monosaccharides, in this process a water molecu
le is produced, thus this reaction is known as condensation reaction.
The complex carbohydrates can be broken down into smaller sugar by breaking the
covalent bonds through a reaction known as hydrolysis, in which water molecule i
s consumed.
Fatty acids are long molecules which has 2 distinct regions. The long hydrophobi
c chain made up of hydrocarbon and the small hydrophilic head. This type of mole
cules is known as amphipathic since it contains both hydrophobic / hydrophilic p

roperties.
Amino acids are varied class of molecules with one defining property: they have
central C atom which has H, amino group and carboxylic acid attached to it. Thes
e are the building blocks of the proteins. AA has isomers but only the L-form ar
e found in the proteins.
Nucleotides are the building blocks of DNA and RNA. They can be grouped into two
type purines are (guanine and adenine) and pyrimidine (cytosine, thymine and ur
acil).
ATP provides the energy for most of the cellular activities. It has 3 phosphate
groups attached to it, and when those phosphate bonds are broken they release la
rge amount of energy to power the cell. The phosphates are linked by phosphoanhy
dride bonds.
Macromolecules are formed by linking simple organic molecules via covalent bond.
DNA

RNA
Double stranded and in form of helical structure due to H bonds between nucleoti

des
Made using Deoxyriboses sugar, contains one less oxygen than ribose
It consist of A, T, G and C
More stable, doesn t react often.
Stores genetic information and remains within the nucleus all the time.
Single stranded, has no helical structure, however nucleotides bind to itself.
Made from ribose sugar, which contains 6 oxygen.
Made up of A, U, G, C
Due to its structure, it reacts very often.
It codes for proteins. They are found within nucleus and cytoplasm.
Lecture 3
DNA has 4 main themes:
Complementarity: knowing how one set of nucleotide binds to other set.
Polarity: this is based on the chemical polarity (5 and 3 end). It has a direction
.
Fidelity: it has ability to accurately copy DNA from one generation to other.
Stability: has to have long term chemical stability. It should be able to last i
n variety of environment.
DNA is made from repeating sequences of nucleotides. They play many different ro
le in cell: protein synthesis, energy, signaling and coenzymes.
A single nucleotide is composed of pentose sugar (5C
deoxyribose) + nitrogenous
base (A, G, C, T) + phosphate.
The nitrogenous base is linked to pentose sugar by a N-glycosidic bond on the C1
and the phosphate group on C5 and on the C1 for pyrimidine and C9 for purine.
Purine are the nitrogenous base that have 2 ringed structure includes (A and G),
while pyrimidine are nitrogenous base with single ringed structure (C and T).
N to N
4 describes where the double bonds are found.
The ribose differ from deoxy in sense that on the second carbon ribose has OH wh
ile deoxy has H. Thus, the second carbon on ribose is chiral and the one on deox
y is achiral.
The prime , indicates that the carbon is part of the sugar.
Nucleoside differ from nucleotide in sense that nucleoside doesn t have a phosphat
e group and nucleotides have phosphate group.
The phosphate in ATP have a property, the one attached to C is alpha, the one se
cond further down C is beta and the one furthest from C is theta. Note that the
phosphate groups are always attached to the 5 C.
Nucleoside structure:
Pentose sugar (ribose or deoxyribose) + nitrogenous base (A,C, G, T/U)
phosphate
1909-1929
Levene DNA consist of equal proportions of Deoxyribose, nitroge
nous base, phosphate
1950s Chargaff
Number of A = T and G = C
Early 1950s
Franklin and Wilkins
X-ray diffraction shows DNA structure is
double helix

1953

Watson and Crick

Deduced the double helical structure of DNA
The two numbers that caught the eye was:
0.34nm
thickness of one of the nucleotide incorporated into the DNA
3.4
the distance the helix travel one complete rotation.
The polymerization of two nucleotides to form dinucleotide cost 2 ATP molecules.
The polymerization starts at the 5 and goes towards the 3 end. As the polymerizat
ion conts, it form 3 -5 phosphodiaster bonds.
By convention the DNA is written in format where it starts at 5 ? 3 , and only give
n one strand.
The native structure of DNA is cell is two antiparallel polynucleotide chains. L
ook diagram below.
For DNA is a double strand of nucleotides twisted into helical form at every 10
nucleotides (3.4nm), groves, hydrogen bonds between nitrogenous bases.
Complementary base pairing in DNA simplifies that one purine bonds to one pyrimi
dine. G-C base pairs are stabilized by 3 H bonds and A-T base pair by 2 H bonds.
Thus, when trying to break the structure, more energy is required when breaking
G-C bonds, as breaking A-T bonds. (apx temp at 90 can separate the strands apar
t). It is hard to break apart since, there are hydrophobic area which are stacke
d on top of each other.
Watson Crick predicted how the DNA could be replicated, based on the complementa
ry pairing.
A-DNA (associated with chromatin that isn t transcribed)
B-DNA (what is believed
to be in cell) Z-DNA (note known)
Right handed
Short and broad
<75% humidity
Right handed
Longer and thinner
Physiological condition
Left hand
Elongated and thin
Function unknown
Groves are noticed on the surface of the DNA. Major is followed by minor and acr
oss the major is minor. This is important when it comes to access the nucleotide
s in the DNA, the major groves allows easier access as compared to minor. And ma
jor grove is the place where the proteins are associated with during the transcr
iption / replication process.
DNA binding proteins bind to specific recognition sites on major or minor groove
.
RNA has structure like DNA, but in this the Uracil is used instead of Thymine. A
lso, it uses the sugar ribose as compared to deoxyribose in DNA. Furthermore, RN
A is much more reactive as compared to DNA. They exist as single stranded polynu
cleotide chain.
RNA can form secondary structure by folding back on to itself, by forming H bond
s between the complementary bases. The region where nucleotide base pair occurs
is called stem, and a region where there is no complementary base pairing forms
a loop.
RNA has many functions:
Can hold information like DNA but for short period of time
It is a catalytic molecule (ribozymes)
Regulatory molecule
ATP ? indicates that it uses ribose sugar as sugar molecule, while dATP ? indica
tes that deoxyriboses is used.
DNA has unique topology to it. It has bites in the DNA, either major or minor gr
oup which are the access for the proteins to form H bonds with the nucleotide sp
aces within the DNA itself.
Nucleotides aren t at 90 degrees to sugar phosphate backbone, they are 51.5 degree
s.
Gibson et al was the first biologist that were able to sequence the genome of th
e bacteria and were able to chemically synthesis all the nucleotide in the test

tubes. Then the artificial chromosome that was created was injected into the bac
teria and it was able to grow and reproduce. This was an experiment to show that
we are able to synthesis DNA.
Proteins are the molecules that do most of the work within the cell. They have m
any function, such as enzymes, structural protein, signaling, receptors, motor p
roteins, transport, gene regulation, immune system antibodies, and storage.
Proteins are so diverse in their function is due to the enormous diversity in th
eir shape.
Proteins are linear, unbranched polymers of amino acids.
There are 20 different amino acids.
Central C atom has amino group, carboxyl group, hydrogen, and side chain (R ).
There are optical isomers of amino acids, the D and L form. They are optically a
ctive (they rotate the plane polarized light). However, only the L form are foun
d in the cell. Proteins are stereospecific, meaning they are able to distinguish
between the L or D form.
Glycine is the only amino acid that doesn t have optical isomer because the R grou
p is an H atom.
The linking of amino acids results in formation of peptide bonds between the two
AA.
The R groups determines the chemistry (reactivity, solubility, polarity) of the
individual amino acids.
We have 10 side groups that are polar in nature. (5 charged and 5 uncharged). Th
e charged groups are either acidic or basic in nature.
Polar Side Group
interact with water
Aspartic acid and glutamic acid differ only by the extra methyl-amine group. Thu
s, glutamic acid is able to stick a little further out to the back bone of the a
mino acid.
Lysine, arginine, and histidine are three basic amino acids due to the slightly
positive charge at the end of the side chain. However, histidine is different fr
om the other two in sense that it has only slightly positive charge or it can ex
ist as non-charged molecule.
In the side chain, each carbon has a specific Greek alphabetical letter associat
ed with it.
Polar uncharged amino acids differ slightly: which includes serine, threonine an
d tyrosine. Syrine and threonine are important in sense that they can be phospho
rylated or methalyted at the end because of the OH group. However tyrosine is dif
ferent in sense that it has a phenyl group which makes it slightly hydrophobic.
Asparagine and glutamine differ in sense that rather than having a carboxylic ac
id, one of the O is replaced by amide group.

Non-polar Side Groups

don t interact with water
In this case the side groups are made up of either hydrocarbon or other uncharge
d group. They tend to associate with other hydrocarbons or lipids but not water.
The group of 5 amino acids above has side group made up of hydrocarbons. They ar
e allosteric amino acids, which have linear chains of hydrocarbons that are bran
ched. This includes the amino acids alanine, valine, leucine, isoleucine, and me
thionine.
The other non-polar amino acids are made up from other uncharged groups includes
prodine, phenylalanine and tryptophan. These three are different from glycine a
nd cysteine in sense that the side chain is bulky and made up of rings or cyclic
structure. Also, the ring structure can absorb the ultraviolet light and emit t
hat as florescence in UV region (only phenylalanine, and tryptophan).
Glycine has H group as the side chain making it non-polar. While cysteine has SH

as the terminal group giving it hydrophobic properties, however under certain co

ndition cysteine can lose the H atom and can become charged. In this S- state, cy
steine is very reactive and is very sensitive to oxidation. In this state cystei
ne can form disulfide bonds.
Synthesis of protein is directional, it starts at N terminus and ends at carboxy
lic terminus.
N-C-C is the backbone of the protein. Each chain has a chemical direction where
N terminus is positively charged (H-end) and C terminus is negatively charged (COOH end).
Proteins can form many conformation, however only 1-2 of them work. The structur
e that forms is determined by many functions: the linear sequence of amino acid,
the number polar and non-polar amino acids, the stable form determined by low e
nergy.
Sequence of amino acids will determine how a protein will fold. The folding proc
ess is assisted by protein chaperones.
Proteins can be organized into 4 levels:
Primary
the amino acid sequence of polypeptide chain.
Secondary
folding patterns created by intramolecular hydrogen bonds within the p
eptide chain. Can form one of the two forms: a-helix or b-pleated sheet
Tertiary
the 3D arrangement of polypeptide. Result from other type of bonding in
cluding intramolecular bonds, disulfide bonds and H bonds.
Quaternary
the 3D arrangement of multiple polypeptide chains.
The two regular protein folding patterns formed due to hydrogen bonding between
the N-H and C=O groups. The two patterns are:
a-helix
first found in a-keratin. Resembles a regular structure of spiral stairc
ase. Formed when single peptide chain turns around itself to form structurally r
igid cylinder and H bonds are made between every fourth amino acid. Found normal
ly associated with transport proteins and receptors.
Sometimes two or three a-helix will wrap around one another to stable structure
known as coiled-coil. Results when a-helix have most of their nonpolar side chai
ns on one side.
B sheet
first find in fibroin. These are formed when H bonds occurs between seg
ments of chains lying beside each other. They result in very rigid, pleated stru
cture.
Parallel b-sheet
when peptide chains runs in the same orientation
Antiparallel b-sheet
when peptide chains run in opposite direction
The peptide chain is very flexible since the bonds allow rotation of the atoms t
hey join. This rotation can allow them to fold in number of ways and as they sta
rt folding the flexibility starts to decrease. Once the proteins folds, the stru
cture is held together by hydrogen bonds, electrostatic attraction and van der w
aals interactions.
Protein domain is any structure that is capable of folding itself into stable st
ructure by itself. Main unit from which many larger proteins are made from.
Protein families are the ones that have similar amino acid sequence and 3D shape
, however the slight differences make these structure adapt to different functio
ns.
Binding site is the surface on protein which allows covalently bond interaction
with other molecules.
Two identically folded polypeptide chains form a symmetrical complex of two prot
ein subunits which is held together by interaction between two identical binding
sites.