BIOCHEMISTRY
Prepared by: Reuelle Kesha Anne A. Margate
TOPIC 1: BIOCHEMISTRY AND THE
ORGANIZATION OF CELLS
1. Definition of Biochemistry
2. The Cell
a.
b.
Types of Cells: Prokaryotic
and Eukaryotic Cells
Cell Structures and
Functions
3. Overview of the
Biomolecules
a.
b.
c.
d.
Amino acids and Proteins
Carbohydrates and Glucose
Nucleotides and Nucleic
Acids
Lipids and Fatty Acids
organic chemistry the study of compounds of
carbon, especially of carbon and hydrogen
and their derivatives
Amino Acids
The simplest compounds are the amino acids.
Under physiological conditions both the
carboxyl group and amino group are ionized (COO2 and –NH3+, respectively). Amino acids
can be shown in various ways, including a
structural formula or a ball and stick formula.
Amino acids have a basic structure where a
central carbon atom is bonded to a carboxyl
group, an amino group, a hydrogen, and a
variable group, called
Prokaryotes have nuclear region for DNA,
ribosomes (for protein synthesis), cell
membrane but do not have an internal
membrane system.
Biochemistry describes the molecular nature of life processes. In living
cells, many chemical reactions take place simultaneously. Cells of all types have so
many fundamental features in common that it is reasonable to say that they all had
a common origin. Life is based on compounds of carbon. This is the subject matter
of organic chemistry. The reactions of organic compounds are those of their
functional groups, which are specifically linked atoms that react in similar ways
under many different conditions.
How did living things originate?
Both molecules and cells must have arisen ultimately from very simple molecules,
such as water, methane, carbon dioxide, ammonia, nitrogen, and hydrogen.
Levels of structural organization in the human body
Atoms > Molecules or Chemicals > Macromolecules > Organelles > Cell > Tissue >
Organ > Organ System
Essential Amino acids the
body cannot make, and that
is needed in the diet.
Nucleic Acids: DNA and RNA
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The strand of DNA is composed of amino acids, it has a
purine base backbone and a carbohydrate.
DNA is a combination of carbohydrate, proteins, and amino
acids.
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A simple Glucose is C6H12O6, two glucose is
called disaccharide, and
only glucose can enter the cell, all other
carbohydrates cannot enter the cell.
All carbohydrate needs to be converted to into
glucose (ex. Fructose to Glucose)
Only glucose can be converted into energy.
(sugar + sugar= polysaccharide,
amino acid+ acid= polypeptide)
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Glucose is converted into a pyruvate, whose
byproduct will be NADH (Nicotinamide adenine
dinucleotide) plus hydrogen.
Glycolysis is the breaking down of glucose in the
cell membrane.
When NADH is produced in the inner membrane,
it will be converted into NAD+ + H+, Hydrogen exits
the intermembrane space and accumulates.
Hydrogen will create electron charges (electron
transport chain process). It will increase electron
charges in the intermembrane, thus forcing the H
to go back in the inner membrane though ATP
synthase.
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The muscle is shortened
through to the act of myosin
and tropomyosin by pulling it in
both directions.
ATP is needed in order for the
myosin to pull the tropomyosin
going backwards with the
muscle fiber and shortening or
contracting the muscles.
ATP (adenosine triphosphate)
will be used as an energy
resulting to ADP (adenosine
diphosphate) + Pi (inorganic
phosphate).
ATP can be recycled, as long
as there is hydrogen which is abundant in the
glucose.
High ATP signifies high energy state, and low ATP
signifies low energy state. Thus, having a directly
proportional relationship.
Topic 2: WATER: THE SOLVENT FOR
BIOCHEMICAL REACTION
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The partial negative charge of water is attracted to positively charged ions.
Like-wise, the partial positive charge on the other end of the water
molecule is attracted to negatively charged ions.
PROPERTIES OF WATER
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Water is composed of two hydrogen (positively charged), and a hydrogen
(negatively charged ion) which means water is a dipole.
Water is polar, with partial positive charges on the hydrogens, partial
negative charge on the oxygen, and a bent overall structure (104.3
degrees).
104.3 is the angle of one hydrogen to another hydrogen in relation to the
position of the oxygen.
Fats in the body are non-polar, they do not bind easily with water. All the substances in
our body are polar, an important characteristic for the body to cleanse the body in the
form of urine.
Important fat-soluble vitamins: Vitamin A, D, E, K that should not be taken too much as
it could overdose that body due to its non-polarity that can cause toxicity. Vitamin C
technically has no overdosage as the water could dissolve it, but could be crystalized
(kidney stones) if the liver fails to do its part.
Thus, water is needed to eliminate substances.
electronegativity -measure of the tendency of an atom to attract electrons to it in a
chemical bond
polar bonds -in which two atoms have an unequal share in the bonding electrons
polar bonds- can bind to water
nonpolar -refers to a bond in which two atoms share electrons evenly, cannot bind to
water
dipoles molecules- with positive and negative ends due to an uneven distribution of
electrons in bonds
salt bridge- an interaction that depends on the attraction of unlike charges
Electrostatic attraction between like charges:
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Hydration shells surrounding ions in solution
Unlike charges attract
van der Waals radius- the distance between an atom’s nucleus and its effective
electronic surface
WATER AND OIL- The oil will aggregate itself into a micelle, thus oil with bind
together leaving the water around.
Sodium palmitate, an amphiphilic molecule:
Amphiphilic molecules are frequently symbolized by a ball and zigzag line structure,
where the ball represents the hydrophilic polar head and the zigzag line represents the
nonpolar hydrophobic hydrocarbon tail.
They are said to be immiscible. This is because water is a polar molecule – its structure
means that is has a positive charge one end and a negative charge the other end. Water
molecules stick together because the positive end of one water molecule is attracted to
the negative end of another.
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(hydro)phobic- loving
(hydro)phylic- hating
Tail of the fats are non-polar, therefore oil is NON-POLAR molecule. Forces of
attraction only exist between the unlike charges.
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They are said to be immiscible. This is because water is a polar molecule –
its structure means that is has a positive charge one end and a negative
charge the other end. Water molecules stick together because the positive
end of one water molecule is attracted to the negative end of another.
Water can be a donor or acceptor, it can influence the structure of a molecule and it
can alter the structure of molecule (proton donor or proton acceptor).
Carbohydrate- composed of carbon, hydrogen, oxygen (CH2O)
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Water can alternate the structure of a compound by giving or receiving a H
molecule.
CONCEPT OF pH
Phenolphthalein pH indicator is the widely used indicator in measuring the unknown
substance through the addition of base as the known substance.
Water is Neutral (it can donate hydrogen or accept hydrogen)
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Acid is a proton donor
Base is a proton acceptor
conjugate- means added
Acid strength is the amount of hydrogen ion released when dissolved in water
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the Neutral value of pH (7) as the base cut-off is derived from the
Henderson- Hasselbalch equation
Rule of thumb- the greater the Ka (dissociation constant), the stronger the acid.
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+acid= +hydrogen (increase of acid is increase of hydrogen directly
proportional)
If an acid will dissociate, it will become a conjugate base.
If a base will dissociate, it will become a conjugate acid.
The greater the dissociation constant, the greater the acid.
Hydroxyl is equal to O+H, then Water is hydroxyl + hydrogen
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when water dissociates, equal number of OH- and H+ will cancel out and
free Hydrogen (H+) ions will no longer be present thus the process of
hydration of hydrogen occurs.
water has a neutral pH because once it dissociates, into a H+O- + H+ , high
likely it will for water again leaving no free H+ ions in the solution, thus
making it neutral (since higher number of hydrogen implies higher acid
strength).
Characteristics of acid
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Buffering- acid is added to the two beakers on the left. The pH of
unbuffered H2O drops dramatically while that of the buffer remains stable.
Base is added to the two beakers on the right. The pH of the unbuffered
water rises drastically while that of the buffer remains stable.
The most common buffer is phosphate buffer.
No matter how much volume of neutral substances, there will be a
resistance of change to pH.
Hydrochloric acid is acid, and Sodium hydroxide is a basic.
Carbohydrate general molecular formula Cn(H2O)n is metabolized and have a
byproduct of ATP’s, water, and carbon dioxide.
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CHO  ATP + H2O + CO2
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Bicarbonate also known as HC03 is the byproduct of the body’s
metabolism.
When humans respire, we produce a byproduct of carbon dioxide, and we
do not want CO2 to bind with water in our body.
carbon dioxide + water= carbonic acid (pH is below 7, with an acidity of
6 pH, the blood will have acidosis if there is too much carbonic acid in the
blood .
With homeostasis, carbon dioxide should be eliminated through
exhalation.
The natural buffer in the blood is bicarbonate buffer system or bicarbonate
carbonic acid system.
The Carbonic Acid-Bicarbonate buffer system or the Bicarbonate- Carbonic
Acid System is the most important buffer for maintaining the pH homeostasis of
blood. In this system, gaseous metabolic waste carbon dioxide reacts with water
to form carbonic acid, which quickly dissociates into a hydrogen ion and
bicarbonate.
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Blood should be slightly alkaline, otherwise it will be too acidic.
Topic 3: THE FLOW OF GENETIC
INFORMATION IN THE CELL
Prepared by: Reuelle Kesha Anne A. Margate
Topic Outline
1.
2.
Central Dogma of Life
a.
Replication
b.
Transcription
c.
Translation
RNA Synthesis and the Genetic Code
a.
RNA Synthesis and Regulation
b.
Basics of gene expression and gene regulation
Albumin- most abundant protein in the body that serves as transport protein, and
delivers important nutrients needed that is created from the liver. Cells in the liver create
these protein replications to produce albumin through protein synthesis.
Protein is used for muscle building that is why we should know its synthesis on how it is
done within our bodies.
Reverse transcription mostly exist in virus cells present in the body.
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Before cells divide they must synthesize a new copy of DNA though
replication.
When the DNA is used as a template to synthesize RNA, this process is
called transcription.
The RNA sequence of messenger RNA (mRNA) is used to direct the
synthesis of proteins in a process called translation. It happens in the
cytoplasm, specifically in the ribosome.
CENTRAL DOGMA OF LIFE
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When carbonic acid (H2CO3) is dissociated by the buffer system, it will
produce a HCO3 + H+, leaving a free hydrogen in the RBC which is a
waste product of the body eliminated through urination.
If there too much carbonate (CO2), it means there is a high pH then we
need the free hydrogen to bind into the carbonate to form bicarbonate.
Therefore, in order to achieve normal pH of the body, such system is used
for the equilibrium of acid and alkaline.
DNA REPLICATION
Deoxyribonucleic acid (DNA) helix strands will be separated first through an enzyme
called helicase to speed up the process. The DNA will be then transcribed into a mRNA
through the help of participating enzymes DNA polymerase I (which binds the
nucleotides Adenine, Thymine, Cytosine, and Guanine together). When a molecule of
DNA is replicated, each of two strands is used as a template to create a complementary
strand.
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When a cell divides into two, each of the two cells has one of the original
template strands and one of the new strands called semiconservative
replication.
When DNA molecules are replicated, the strands are separated at origins
of replications.
Synthesis occurs in both directions from the origin along replication forks.
origin of replication- the point at which the DNA double helix begins to unwind at the
start of replication
replication forks in DNA replication- the points at which new DNA strands are formed
DNA ligase- the enzyme that links separate stretches of DNA
DNA polymerase- the enzyme that forms DNA from deoxyribonucleotides on a DNA
template
primase- the enzyme that makes a short section
Challenges in DNA replication
1.
2.
3.
Separating DNA into 2 DNA strands- from a G0,G0 into two pairs: G0,G1 and
G1,G0 which are both a semiconservative replication; then into a second
replication with G0,G2 & G2, G1 and G1, G2 & G2, G0.
Synthesize DNA from 5’ to 3’ end -the polymerase should be able to identify
the prime ends to prevent mutation in the gene also known as insults.
Guard against errors in replication- to prevent congenital defect caused by
mutation in the information of the gene.
Replication Proof Reading
proofreading- the process of removing incorrect nucleotides when DNA replication is
in progress
repair- the enzymatic removal of incorrect nucleotides from DNA and their replacement
by correct ones
mutations- changes in DNA, causing subsequent changes in an organism that can be
transmitted genetically
DNA polymerase proofreading wherein the 3’ to 5’ (template strand) exonuclease activity
of DNA polymerase I removes nucleotides from the 3’ end of the growing DNA chain.
1.
2.
3.
Prevents Mutations- error in replication
Removal of incorrect nucleotides immediately after they are added to the
growing DNA during the replication process
DNA polymerase I
DNA polymerase removes the mismatch bases of nucleotides through the enzyme
exonuclease in the exonuclease site to correct the coding in the DNA.
The basics of transcription, RNA polymerase uses the template strand of DNA to make
an RNA transcript that has the same sequence as the non-template DNA strand, with
the exception that T is replaced by U. If this RNA is mRNA, it can later be translated to
protein.
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Transcription is the process of using a DNA template to produce RNA
Many types of RNA are produced such as messenger RNA (mRNA),
transfer RNA (mRNA), ribosomal RNA (rRNA), micro-RNA, small inferring
RNA, and small nuclear RNA
A primer is not needed for RNA synthesis
As does all polynucleotide synthesis, the reaction proceeds in the 5’ to 3’
direction.
CODING STRAND- 5’ to 3’
TEMPLATE STRAND- 3’ to 5’
mRNA strand- 5’ to 3’
DNA Polymerase I
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1.
Klenow Fragment- Polymerase and Proof-Reading Activity
2.
Repair Activity
DNA polymerase I uses 3’ exonuclease activity to remove the incorrect
nucleotide.
Replication resumes when the correct nucleotide is added, also by DNA
polymerase I
The 5’  3’ exonuclease activity of DNA polymerase I can remove up to 10
nucleotides in the 5’ direction downstream from a 3’-OH (3 prime hydroxyl group)
single- strand nick.
nick translation a type of DNA repair that involves polymerase I using its 5' to 3'
exonuclease activity to remove primers or replace damaged nucleotides.
DNA polymerase I uses its 3' exonuclease activity to remove the incorrect
nucleotide. Replication resumes when the correct nucleotide is added, also by
DNA polymerase I.
Note that DNA will not undergo Transcription to convert into mRNA if its main goal
is to duplicate itself alone. Instead, it will only undergo replication by producing a
complementary strand.
DNA TRANSCRIPTION
If genes do not undergo transcription, it cannot produce proteins.
General features of RNA Synthesis
1.
2.
This transcription process is the synthesis of RNA through a DNA template,
wherein the enzyme to catalyze the process is called DNA- dependent
RNA.
All four ribonucleic triphosphates: ATP (adenosine triphosphate), GTP
(guanosine triphosphate), CTP (cytidine triphosphate), and UTP (uridine
triphosphate) are required, as is Mg2+.
Note than Magnesium is a cofactor of enzymes. Therefore, if a person has
Hypomagnesemia, also known as magnesium deficiency, the enzymes will be inactive
and the cells will be unable to have metabolic processes. It happens when you have a
lower-than-normal level of magnesium in your blood. It can be mild or severe.
Magnesium is an electrolyte that's a key part of many bodily reactions that affect cellular
function, nerve conduction and more.
3.
4.
5.
6.
A primer is not needed in NA synthesis, but a DNA template is required.
Same case with DNA biosynthesis, the RNA chain grows from 5’  3’ end.
The nucleotide at the 5’ end of the chain retains its triphosphate group
(abbreviated as PPP).
The enzyme uses one strand of the DNA as the template for RNA synthesis.
The base sequence of the DNA contains signals for initiation and
termination of RNA synthesis. The enzyme binds to the template and moves
along it in the 3’  5’ direction.
The template is unchanged.
EUKARYOTIC TRANSLATION
Steps in Translation
1.
Chain Initiation- eIF (eukaryotic initiation factors)
2.
Chain Elongation- peptidyl transferase and ribosome translocation
3.
Chain Termination- encounter of Stop Codons (by-passed by suppressor
RNA)
mRNA- AUG (start codon) |UUC|CGA (stop codon: UAA, UGA, UAG)
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mRNA trinucleotides: AUG, UUC, CGA
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Methionine (UAC) pairs with AUG, Phenylalanine (AAG) pairs with UUC,
Arginine (GCU) pairs with CGA.
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The decision on what amino acid the tRNA carries will be based on the
trinucleotide sequence of the mRNA.
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Elongation will continue if there is a suppressor RNA.
Link: https://www.youtube.com/watch?v=7cn10wayDug
STEP 1: Chain Initiation- eIF (eukaryotic initiation factors)
Translation occurs after mRNA formed in the nucleus and is transported out of the
nucleus and into the cytoplasm where it attaches to the ribosomes. Proteins are
assembled on the ribosomes using the mRNA nucleotide sequence as a guide. Thus,
mRNA carries a “message” from the nucleus to the cytoplasm.
In the Ribosomes in human cells after the mRNA is sent out in the cytoplasm have a
ribosomal unit of (S stands for sub unit) 80S  60S 40S. Prokaryotes have 70S and
30 S.
1.
Assembly of a 43S preinitiation complex. Methionine- initial amino acid
attached to tRNAi
The 60S and 40S will be activated by the initiation factors: eIF1A along with IF3
which will activate the 80S into a 43S. IF3 activates 40S that will form the preinitiation complex through the initial Met-tRNA (amino acid Methionine). The
ribosome has two structures, overall, it is called 80S, bigger portion is called 60S
and smaller portion is 40’. When added together it becomes the 80S complex. The
43S complex therefore contains Met-tRNA, GTP for energy, through eIF2.
2.
mRNA is recruited. Scanning Mechanism- 5’ cap orients ribosome to the
correct AUG.
The presence of the 43S pre-initiation complex triggers the mRNA to do from 48S
pre-initiation complex, then proceeds to 60S will be bound and finally turn into a
80S initiation complex. The ribosome will then select the start codon of the
trinucleotide sequency which is AUG because of the start codon amino acid
Methionine that should start on the 5’ end of the mRNA [at 59:00 on the LECVID].
RNA SYNTHESIS AND GENETIC CODE
Summary: 80S is divided into portions 60S and 40S eIF1A and eIF3 initiation
factors binds with 40S, forming 43S  eIF2 and GTP initiates for the Met-tRNAi
(referred as the ternary complex) 43S initiation complexmRNA is initiated
with eIF4E,eIF4G,eIF4A,and eIF4B 48S binds with mRNA complex (48S
initiation complex)  60S binds with 48S initiation complex with eIFS (eIF3, GDP
and eIF2) 80S initiation complex.
Enhancer- allows continuous elongation
Initiator- used in translation of mRNA to tRNA and synthesis of protein
TATA protein- stops the translation, mostly used in mutation of gene otherwise gene
will dissolve through a process called sequestration.
protein- is a sequence of amino acids
peptide-is a short chain of amino acids
P (peptidyl) site- the binding site on a ribosome for the tRNA that carries the growing
peptide chain
What is the function of peptidyl transferase in the ribosome?
The ribosomal peptidyl transferase center (PTC) resides in the large ribosomal subunit
and catalyzes the two principal chemical reactions of protein synthesis: peptide
bond formation and peptide release.
Note that you should know the complementary base pairs of the trinucleotide sequence of the mRNA.
STEP 2: Chain Elongation
peptide bond- an amide bond between amino acids in a protein
translocation- in protein synthesis, the motion of the ribosome along the mRNA as the
genetic message is being read
2 Eukaryotic Elongation Factors:
a.
eEF1
b.
eEF2
1.
Codon Recognition
2.
Peptide Bond Formation
3.
Translocation
Step 3: Chain Termination
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Encounter of Stop Codons:
1.
UAA
2.
UAG
3.
UGA
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No tRNA binds to stop codon, Hydrolysis and dissociation of ribosome large
and small subunit
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Suppressor tRNA allows translation to continue resisting the stop codons
by inserting selenocysteine residue to the amino acids present in mRNA.
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Found in mutated genes, cancer cells.
chromatin- a complex of DNA and protein found in eukaryotic nuclei
histones- basic proteins found complexed to eukaryotic DNA
nucleosome- a globular structure in chromatin in which DNA is wrapped around an
aggregate of histone molecules
Note that:
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darker color in the nucleus means inactive and unexpressed genes, lighter
portion in the nucleus contains active gene.
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All cells in our body contains similar chromosomes, however the expression
of the gene depends because of the selective expression of gene.
In order to prevent the gene from being expressed randomly there are 4 ways:
1.
Transcription control
2.
RNA processing control
3.
RNA transport control
4.
Translation control
Whenever there is methylation or methyl groups attach to the DNA, the DNA will
therefore not be expressed. Otherwise, Methyl group will not be found on places
that require the gene.
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Sugar is linked to heterocyclic base by a beta-N-glycosidic bond,
almost always to the N-1 of a pyrimidine and to the N-9 of a
purine.
Video link kay nahurot na akoang ATP:
Nucleic acids - DNA and RNA structure
https://www.youtube.com/watch?v=0lZRAShqft0
How mRNA Vaccines Work - Simply Explained
https://www.youtube.com/watch?v=WOvvyqJ-vwo
Cancer Gene Therapy - Aiming Gene Technology at Cancer Specific
Molecular Targets
https://www.youtube.com/watch?v=DNf2GsjfRQk
Topic 4: NUCLEOTIDES AND
NUCLEOSIDES
Nucleosides
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Derivatives of purines and pyrimidines that have a sugar lilnked to
a ring N
Sugar in Ribonucleoside is D-ribose
Sugar in Deoxyribonucleoside is 2-deoxy-D-ribose
Gout pathophysiology/ Uric Acid Formation
https://www.youtube.com/watch?v=2r95ZVqAysQ
https://www.youtube.com/watch?v=bznoU5bke4U