CHM123_P6_LIPIDS - Ex: energy storage lipids,membrane lipids,

‘Lipids/AKA Fats: body’s petroleum industry protective coating lipids

- Contains hydrocarbon (organic compounds) that 2. Non-saponification lipids - Cannot be broken
can dissolve in organic solvents. into smaller units since they do not react with water
- Stores chemical energy, - Ex: emulsification lipids, messenger lipids.
- Provides carbon atom in body CHOLESTEROL IS NON
- Has efficient way to store excess calorie in the SAPONIFIABLE
body, plays integral role in cell membrane
- Funct: thermal regulation, protect body from Classification by structure
mechanical shocks? 1. Simple lipids (fats and waxes)
- Defining parameter: solubility instead of 2. Complex lipids
structure cuz its structure is diverse. 3. Steroids
- Marginally soluble to water 4. Eicosanoids: Prostaglandins, thromboxanes,
- Soluble to organic solvent leukotrienes
- Dual row: carbon hydrogen bonds.
Lipid Types
Characteristics
- Fatty acids
- Occur frequently in nature - Triacylglycerols
- Solubility: marginally soluble in water, soluble in - Phosphoacylglycerols (phospholipids)
organic solvents - Waxes
Classification - Sphingolipids
- Glycolipids
- Steroids
- Open-chain compounds with polar head ❖ Fatty acids - simplest lipid based on structure
groups and long nonpolar tails: makes lipid - Simple linear chain
amphipathic:5 (fatty acids, - Naturally occurring monocarboxylic acid
triacylglycerols,sphingolipids, - -COOH
phosphoacylglycerols, glycolipids) - Carboxyl group at the polar end (makes it
- Fused-ring compounds (steroids e.g. amphipathic) and a hydrocarbon chain at the
cholesterol) nonpolar tail
- Amphipathic
Classification by function

1. Energy storage lipids- adipocyte- stores energy Degree of Saturation: determined by number of double
bonds
- TAG(triglycerides/triacylglycerols: most
abundant lipid - SFA:Saturated fatty acids – single bond
2. Membrane lipids - 2nd most abundant lipids - UFA:Unsaturated fatty acids – double bond
- sphingoglycolipids,phospholipids,cholesterol - Monounsaturated – has single double
3. Emulsification lipids - bile acids: emulsify fats bond
4. Messenger lipids - steroid,hormones, - Polyunsaturated – 2 or more double
eicosanoids bonds
5. Protective-coating lipids- biological waxes(ex:
floor wax) *aside from degree of saturation they can be also
classified based on type of chain where the # of C
Saponification Classification atoms is determined.
Saponification: Ability of lipid to be converted into - Fatty acids are nearly always contain an
smaller molecules when hydrolysis occurs as they rx. even number of carbon atoms and have a
w/water carbon chain that is unbranched
- Characterized as:
1. Saponification lipids - Converted into smaller
- Long-chain-more than 12 C atoms
molecules when hydrolysis occurs
- Medium-chain - 8-10 C atom
 - Short-chain - 2-6 C atom MAin funct:
***the size of chain of F.A is INDIRECTLY 1. Building block for triglyceride and glycolipid???
PROPORTIONAL to the water solubility [33min]
- Ex. as carbon chain length increases, water 2. Sources of metabolic energy
solubility decreases. - F.A is not commonly found in nature, found in diet.
★ Dietary F.A - straight chain compounds and - unsaturated is more healthy cuz it could still be
have even # C atoms from 4-24 C atoms. broken down. Unsaturated from plants ,
while SFA from animals.
Saturated Fatty acids - solid phase @roomtemp
Unsaturated fatty acids will be converted to saturated fatty
*#C atoms and melting points is DIRECTLY acids through hydrogenation
proportional with each other = for LINEAR
BONDS/SINGLE CHAIN/SATURATED F.A - Once hydrogenated it will be broken down.
- Unsaturated F.A- we use cis and trans
configuration

Unsaturated Fatty Acids - liq phase @roomtemp

*as the # of DOUBLE BOND which determines the degree

of saturation increases the melting point decreases. ❖ TRIGLYCERIDES AKA triacylglycerol
INVERSELY PROPORTIONAL - Animal fats and plant oils
- Triester of glycerol and long chain of carboxylic
acids called fatty acids.
- Triacylglycerol: Glycerol + 3 F.A
- Type of bond: ester bond/linkage
- Plays a role in cell membrane and STORAGE
FORM OF LIPID
- Most has cis UFA
- Has no charge grp which is why it is known
as neutral lipid: which means it has no
polar hydrophilic grp. So it is INSOLUBLE
- Delta- specifies location of double bond
- *use comma to separate the loc of
double bond
- We ALWAYS assume that the -COOH is the
C#1
- OLEIC has higher melting point compared to
PALMITOLEIC cuz Oleic has longer chain

FATTY ACID in general plays a role in decreasing lipid

storage and lower tendency to block blood flow in arteries
(Saturated fatty acid.) ❖ Phosphoacylglycerols (phospholipids)
- Two fatty acids are esterified to the glycerol
Unsaturated- decreases cholesterol, and heart disease molecules → phosphatidic acid
 - Component of biological membrane ➔ Ceramides- consist of one fatty acid
- Most abundant type of membrane lipids(80% of linked to the amino group of sphingosine
mass of cell membrane is phospholipid) by an amide bond
- Amphipathic: phosphate grp can interact with - Amino group of sphingosine can from an amide
water bond with a FA carboxyl

➔ Sphingomyelin
- Common constituents of plasma membranes

- One phosphoric acid can form ester bonds

both to glycerol and to some alcohol
- Esterification: alcohol and acid rxn

❖ Glycolipids
- Carbohydrate is bound to an alcohol group of a
lipid by a glycosidic linkage
- Cerebroside:simplest glycolipid (primary
alcohol of ceramide + sugar residue)
Phosphatidylinositol- minor constituent of cell mem, - Gangliosides – glycolipids with complex sugars
????process of animal plant - Often found as markers on cell membranes
and play a large role in tissue and organ
specificity
❖ Glycosphingolipids
➔ Cerebroside - single unit of monosaccharides
◆ Galactose or glucose are mostly CHO
that are linked to cerebroside.
◆ Beta glycosidic linkage
◆ 7% of dry mass of brain are
❖ Waxes cerebroside
- Lipid that is a monoester of long-chain ◆ Also present in myelin sheath of nerves
carboxylic acids and long chain alcohols → *ganglioside: 7 monosaccharide units
- Protective coatings for both plants and animals
- Seen on the gray matter of brain and myelin
- SFA: 14-36 C atom and alcohol that is
sheath of nerve
saturated or unsat C16-30
-
❖ Sphingolipids
- Do not contain glycerol but contain long-chain
amino alcohol sphingosine
- Abundant in nervous system:brain , nerve cells,
nerve
 ❖ Steroids - OH group of cholesterol forms H bond with the
- A fused-ring containing 3 six membered rings and polar phospholipid head groups.
1 five membered ring
★ *fused ring is AKA STEROID NUCLEUS Lipid Soluble Vitamins
➔ Cholesterol - Unsaturated steroid alcohol - Vitamin A
- Most abundant steroid in body
- Vitamin D
- hydrophilic group – OH (single)
- Vitamin E
- Hydrophobic
- Vitamin K
- Precursor of other steroids and of Vitamin
Vitamin A
D3 however it is best known for its harmful
➔ Β carotene - has red-orange pigment
effects
- unsaturated hydrocarbon
- Ester bond, esterification forms at 1 F.A
- Precursor of vitamin A (retinol)
- Found almost exclusively synbthesized in
ANIMALS, there are derivatives from A derivative of Vit A plays a crucial role in vision when it
plants. is bound to a protein called opsin.
- ALSO NOT CHARGED, so it is also
classified as neutral lipid OPSIN- universal photoreceptor molecule
- Appearance: waxy material forms plate - Light sensitive
like crystal - Found in retina
- Plays a role in forming plaque: Vitamin D
deposition of fats found in B.Vlining, - Major role in regulation of calcium and
which blocks blood flow that can form phosphorus metabolism
heart damage. (atherosclerosis) - Active form:Vitamin D3 (cholecalciferol) formed
Funx: from cholesterol by the action of UV from the sun
- Manufacture and repair of cell membrane - Further processed in the body to
- Synthesis of bile acid and vitamin D. hydroxylated derivatives
- Precursor of other steroid hormones (sex - Presence of Vit D3 leads to increase
hormones: androgen,estrogen; synthesis of a Ca2+ binding protein,
glucocortocoids,nineralocorticoids,progestins) increases absorption of dietary calcium in
- Important constituents of cell the intestines → inc calcium
membranes. Vitamin E
- α-tocopherol is the active form
- Antioxidant – good reducing agent
- It reacts with oxidizing agents before they can
attack other biomolecules
- Reacts with free radicals
Vitamin K
- Comes from the German word “Koagulation”
C27 steroid molecule, alcohol grp found in C#3 of steroid
because it is an important factor in the blood-
nucleus.
clotting process:hemostasis
- Decreases the mobility of hydrocarbon tails of - vit.K dependent clotting factors: II, VII, IX,
phospholipids X [they need vit K to be activated]
- Interferes with the closely packing of FA tails in - Prior to fibrin clotting, we need to activate
the crystalline state thus inhibits transition to the the factor II before factor I so we can form
crystal state fibrin or fibrin clot
- Phospholipid membranes with high conc. of - Requirement to modify prothrombin and other
cholesterol have a fluidity intermediate proteins involved in the clotting process
between crystal and crystal state
- Hydroxyl group on the aqueous side while the
ring is towards the FA chains of phospholipids.
Eicosanoids - Fibrin clot forms when
- Messenger lipid; oxygenated C20 fatty acid bleeding is matagal na, and
derivative when 1 hemostasis can’t
- Metabolic precursor is arachidonic acid stop itl.
- Almost all cells produce eicosanoids EXCEPT Ex: A patient suffers from clot na mabilis ma form, and
RBC suffers from heart attack and takes aspirin. Aspirin is a
- Physiological effects of eicosanoids include blood thinner. Aspirin acts to the Thromboxane A2 so that
mediation of: platelets would not aggregate.
- Regulation of blood pressure This is also the reason why dengue patients does not take
- Production of pain and fever ASPIRIN cuz you prevent the individual from forming clot.
- Inflammatory response
- Induction of blood clotting
- Control of reproductive functions
- Regulation of sleep/wake cycle
➔ Prostaglandins - CYCLOPENTANE; O2
containing fx. grp
- Metabolic precursor is arachidonic acid
- Dense tubular system of platelets
- Functions:
- Control of blood pressure
- Stimulation of smooth muscle
contraction
- Induction of inflammation
- Raise body temperature
- Responsible for the pain
- Inhibit the secretion of gastric juices
➔ Leukotrienes
- Found in leukocytes and have 3 conjugated
double bonds
- Has -OH grp
- Constriction of smooth muscle
- Inflammatory properties,
- hypersensitivity: allergic rxn=type 1
hypersensitivity
- Released if may allergens or inflammation
whether acute or chronic
- Maybe involved in rheumatoid arthritis
➔ Thromboxane
- Derivative of arachidonic acid
- Contains cyclic ethers as part of its structure and
O2 containing funx grp.
- Thromboxane A2 is the most widely studied, is
known to induce platelet aggregation and smooth
muscle contraction
- Hemostasis: there are 2 types:
- Primary: forms platelet plug
- One step to form platelet
plug is platelet aggregation
- Secondary: Vit-K dependent
clotting factors = forms fibrin clot
CHEM123_P7_NUCLEIC ACID
- 1869: Friedrich Miescher- Discovered while
studying the nuclei of WBC
- cell nucleus is acidic: nucleic acid
contributes to this
❖ Types of Nucleic Acid
➔ DNA (deoxyribonucleic Acid)
- Found within the cell nucleus (chromosome) Deoxyribose: H @C#2: absence of oxygen
and small amounts in mitochondria
What projection: alpha or beta? Dextro or levo????
- Primary funx:Storage and transfer of genetic
information to new cell during cell division. Nitrogen-containing heterocyclic base
- Structure: double stranded, double helix,spiral
➔ RNA (ribonucleic acid) - Base cuz of funx grp in structure: AMINE-
- Occurs in all parts of a cell. [RNH2]accepts the protons or hydrogen ions
- 90% in cytoplasm (cuz we have free ribosomes and whenever a rx occurs.
ribosomes attached on RER) and 10% on nucleolus ➔ Purine – a bicyclic base with fused five and six-
- Synthesis of proteins membered rings [Adenince Guanine] “-OSIN”
- Structure: single stranded ➔ Pyrimidine – a monocyclic base with a
★ Viruses are classified acc. To the nucleic acid: six-membered ring “-IDINE”
- Ex: CORONA- single stranded RNA ★ Only 4 bases is applicable for each type of
nucleic acid
Nucleic acids ★ DNA and RNA: Adenine, Guanine, Cytosine
★ Uracil only found at RNA
- Unbranched polymer in which a monomer unit is a ★ Thymine only found in DNA
nucleotide ★ MEMORIZE THE STRUCTURE OF THESE!!!
- Nucleotide- is a three subunit molecule in
which a pentose sugar is bonded to both
phosphate group and nitrogen-containing
heterocyclic base
- -PREFIX of nucleotide represents the pentose
sugar unit found in its structure. Ex. DNA-
deoxyribose; RNA- ribose

Cytosine: only pyrimidine with amide (NH2) in side

chain

Uracil: AKA unmethylated thymine- cuz it has same

structure with thymine except from the methyl
5 types of nitrogenous base, not all are applicable to a OXO- prefix used if Oxygen is just a side chain
specific nucleic acid

Pentose Sugar

- The sugar unit of nucleotide is either pentose

ribose or pentose 2’-deoxyribose
 3rd sub unit of nucleotide: Phosphate Ex: in adenine: once paired with sugar unit it is called
- Phosphoric acid loses its hydrogen, giving off the adenosine since it is a purine
hydrogen phosphate ion under cellular pH ***if the sugar unit is deoxyribose use the prefix deoxy.
condition. Phosphates grp will bond to sugar unit IF ribose NO PREFIX USED
or carbohydrate to form nucleotide
Ex: deoxycytidine ,

Nucleotide Formation

1. Condensation, with formation of water molecule

between sugar-base and sugar-phosphate

● Condensation Is the rx involved

2. Base – bond at C-1’ of sugar. For purine base (N-9), Answer this:
pyrimidine (N-1); through (β-N) glycosidic linkage Uracil + ribose = uridine
3.Phosphate to sugar (C-5’) phosphate-ester linkage Guanine + deoxyribose = deoxyguanosine
★ Before nucleotide is formed, nucleoside is first Nucleotide formed: when phosphate is attached to
formed: nucleoside , nucleotide is formed
★ Nucleoside: has 2 subunit molecule-pentose sugar
and nitrogenous base 5’ monophosphate
★ Nitrogenous base attached at C1
★ In naming: name the nucleoside first based on sugar
and nitrogenous base:
○ LEFT side example-sugar: ribose
■ Check the C2: ribose has -OH
grp
○ LEFT side example-nitrogenous base:
adenine
■ Adenine is the only one with
NH2
○ RIGHT side example-sugar:
deoxyribose
■ Check the C2:deoxyribose none
attached
○ RIGHT side example-nitrogenous
base-Cytosine - NAME THE STRUCTURE FOUND (IMAGE ABOVE)
■ Cytosine is Monocyclic with - First structure: deoxyuridine
NH2 - Second : deoxyadenosine
- Third: deoxyadenosine
Naming: base’s suffix: if pyrimidine yung base use
-idine. If purine: -osine Mononucleotides are nucleosides in which a single
monophosphate group is attached to the hydroxyl group
of the pentose sugar.
Ex. AMP= adenine + ribose + phosphate

- Adenosine monophosphate
- Use mono as prefix is only one
phosphate grp.

2 phosphate groups = nucleoside diphosphate 3

phosphate groups = nucleoside triphosphate

ADENOSINE TRIPHOSPHATE (ATP):

BACKBONE OF NUCLEIC ACID: 5’ is ALWAYS the

starting point of structure of nucleic acid ,

- therefore: 5’ → 3’
- IN PROTEIN YUNG KATUMBAS NITO IS: 5’
amino grp, 3’ found at left -COOH/carboxyl grp
- 5’ = phosphate found at left
Ex: if the sugar is deoxyribose, name it as: - 3’= sugar
deoxyadenosine triphosphate (dATP) DNA Structure and Function
Ribose+uracil +2 phosphate grp- uridine diphosphate ❖ Serves as genetic material for cells both
(UDP) prokaryotes and eukaryotes
➔ In eukaryotes
Deoxyribose+thymine+3 =deoxythymidine triphosphate
- Located in the nucleus separated from the
(dTTP)
cytoplasm by the nuclear membrane.
MEMORIZE THIS!! NOT INCLUDED IN ANKI!!! ➔ In prokaryotes
- DNA is not separated from the rest of the
cellular contents
➔ Chromatin
- Complex of eukaryotic DNA bound to proteins

Structure of DNA

- DNA is a very long, thread like macromolecule

made up of a large number of deoxyribonucleotides
(N+S+P) :nitrogenous base + sugar unit
+phosphate grp
- Base of DNA molecule
- Carry genetic info
- Purine (A and G)
- Pyrimidine (T and C)
SUMMARY OF NAMING: - Sugar and phosphate groups
- Structural role
- Purine (-osin)- A,G - Deoxyribose
- Pyrimidine (-idine) - C,U,T
- Ribose if has -OH
- Use deoxy as prefix if it is deoxyribose sugar
 • Under physiologic conditions, almost entirely B-DNA.

Chargaff’s Rule

- Erwin Chargaff

• In DNA structure, the content of A is equal to that of T

and the contents of G equals to that of C.

- %A=%T ; %C=%G
- If: 30% A= 30% T ; 20%C=20%G

• Watson and Crick deduced that A must pair with T and G

to C because of stearic and hydrogen bonding factors.

• Thus, one member of a base pair in a DNA must

always be a purine and the other a pyrimidine.
Bond responsible for linkage of strands is hydrogen bond • Ratio of bases are always 1

- C-A: 1 hydrogen bond between em’

- T-G: 1 hydrogen bond
- In base pairing: Hydrogen bond is stronger in A-T
(2 hydrogen bonds) and G-C (3 hydrogen bonds)
complementary bases.

***the broken lines in the image above represents the

hydrogen bonds Functions of DNA
How to write DNA strand base on the sequential order:
- store genetic information
5’ → 3’ = leading strand - source of information for the synthesis of
all protein molecule of the cell
5’ A-G-T-A-C-G 3’ - provides the information inherited by
3’ T-C-A-T-G-C 5’ daughter cells or offsprings
★ DNA synthesised at INTERPHASE-S PHASE
Watson-Crick DNA Double-Helical Structure
Comparison of DNA and
- Francis Crick and James Watson RNA Unlike double-stranded DNA, RNA is a
❖ Hydrogen bonds single-stranded molecule
- held the chains - While DNA contains deoxyribose, RNA
➔ adenine and thymine contains ribose
- 2 H bonds - Complementary base to adenine is not
➔ Guanine and cytosine
thymine, as it is in DNA, but rather uracil,
- 3 H bonds
which is an unmethylated form of thymine
• In DNA structure, the content of A is equal to that of T Flow of Biologic Information: (Central Dogma)
and the contents of G equals to that of C. (Chargaff’s Rule) - Backbone of molecular biology
- DNA contains the genes that encode the
• B form of DNA (B-DNA) which is a right handed helix
information for the synthesis of a protein
of 10 base pairs per turn, containing grooves of alternate - Sequence of the bases in the DNA codes for the
size known as major and minor grooves. sequence of the amino acids in proteins
• A-DNA and Z-DNA [Z- zigzag pattern: - However, the DNA does not direct protein
phosphodiester backbone- responsible for DNA’s synthesis. mRNA is the one responsible to
structure] form monomers of protein which is amino acid, the
sequence of bases of amino acid codes the protein.
 - The genetic information in the DNA is decoded in Replication
the form of messenger RNA, which is then
translated to A.A. sequence of a protein DNA replication
- The doubling/duplication of DNA & occurs
during the interphase period of mitosis (S)
- Replicated only once
- If replicated from a single ori, with same rate as
bacteria, this would take over 150 hours
- DNA to be copied is fed through the proteins of
the replication factory
- The duplex DNA to be copied is first split into
single strands
- Each of the two template strands is copied and
becomes half of a new DNA double helix
Central Dogma (semi-conservative)
• Function
- 1st: DNA replication
- 2nd: transcription producing mRNA - Provision of progeny with the genetic
- 3rd: translation which produces the proteins information possessed by the parent

According to Francis Crick, this information cannot be Replication Enzymes

transferred from protein to either protein or nucleic acid

- This dogma also includes the replication of

DNA
- •It may start from RNA to DNA, and RNA can
also be replicated
- backbone of molecular biology

Three Major Stages in Central Dogma

1. DNA Replication
- Produces two identical molecules
- Regardless of what cell division involved there
will ALWAYS BE ONE DNA replication which ★ Topoisomerase -relaxes strands to facilitate
happens at S phase of interphase unwinding of DNA through help of enzyme helicase
★ Polymerization : elongates the building block
2. Transcription - from thymine it will change monomer unit , here the DNA is elongated
to URACIL
General Steps in DNA Replication in Prokaryotes
- Genetic information in the DNA is copied in
mRNA. 1. DNA Helicase
- Sequence of the mRNA bases is the same as that - Break the hydrogen bonds between bases of the
of the DNA two anti-parallel strands resulting in the
3. Translation unwinding of the helix
- Unzips the geans
- Codons in the mRNA direct the sequence of aa in
the protein • Origin of replication [ORI]

- Region in the chromosome which is the

initiation point for DNA replication
- Form a structure known as replication fork
 ★ DNA helicase unwinds the helix with the help of
Topoisomerase which relaxes the strand

2. Primase
- Binds the initiation point of the 5’-3’ parent
chain and synthesizes the RNA primer
• RNA primer

- Has the required 3’-OH end for the addition of a

new nucleotide

3. DNA Polymerase
- Elongates the new DNA strand at a 5’-3’ ***end of lecture for today
direction using the 3’-5’ template RNA (transcription and translation involve na
- 5’-3’ strand that proceeds to the direction of the RNA)
replication fork (leading strand)
- New strand using the 5’-3’ template is synthesize in - Another type of nucleic acid
a discontinuous manner (lagging strand) - Made up of unbranched chain of nucleotides as
- Okazaki fragment are the short DNA in DNA (straight chain polymer)
fragments added. - D-ribose, U instead of T and single stranded.
- Nick - found when okazaki fragment is
Transcription
formed, responsible for the discontinuity
or notch in the strands
- Process of copying of a DNA template in the
4. DNA Polymerase I form of RNA with the use of RNA polymerase.
RNA polymerase will catalyze to form mRNA
- Removes the primer in the lagging strand - All RNA’s are synthesized using DNA template
and fill the gap with appropriate nucleotides - Process requires the enzyme RNA polymerase.
5. DNA Ligase (access sa DNA- RNA polymerase)- complement
the bases that are found on DNA
- Gaps between the Okazaki fragments are - TRANSCRIPTION AS TWO STEP PROCESS
sealed by DNA ligase - Synthesis of hnRNA
- Editing hnRNA to yield mRNA molecule

Alignment of free nucleotides forms base pairs- how we

form mRNA
 ● a gene- segment of DNA base sequence responsible - Ribosomes known to be physical site of protein
na makapagproduce ng Hrna or mRNA synthesis 3million of molecular???
● Human genes have 20,000-25,000 genes that
make up the genome- (completes set of ***mRNA is being delivered to ribosomes by tRNA
genes)totality sum of all genes that are found in
an organism. ● tRNA – delivers amino acids to the site for
● 1,000 – 3,500 nucleotide (most each human protein synthesis transfer (transports/delivers
genes) amino acid to ribosomes ) smallest type of RNA
(75-90 nucleotides)
DNA is a double stranded molecule - acts as anti-codon to deliver a.a to protein
synthesis site.
❖ Sense strand
- Codes for the sequence of the gene (bases of
Post transcription processing
nucleotides are responsible for sequencing of gene)
- 5’-3’ = sense strand ***Involves conversion hRNA → mRN
❖ Anti-sense strand
- Starts at 3’- 5’
- Opposite complementary strand that is used
as the template for RNA synthesis (kaya
anti kasi opposuite ang pag run ng bases)
- In pairing, Adenine pairs w/ Uracil here
- RNA base sequence is identical with that of
the sense strand except for the presence of
U and T

Types of RNA Molecules 75 to few thousand

nucleotides in RNA molecules
Splicing
- RNA molec. are smaller than DNA molecule. *First thing needed is the unwinded DNA’s leading
● hnRNA (heterogeneous nuclear RNA) –(1st strand.
synthesized) - formed directly by DNA
transcription, during post transcription it will be - We have leading strand from DNA
converted to mRNA through splicing - Leading strand (5’to 3’)
● mRNA – carries instructions for protein - Bases typically makikita sa sequence
synthesis - hnRNA- mRNA
○ Depending on length of protein, - splicing – leading strand will be
varies… paired.???[diba anti-sense yung
- Responsible for possible amino acid template strand?]
sequence that will be coded which will - hnRNA will act as complementary strand
determine the protein to be produced of leading strand which comes from DNA
➔ snRNA – facilitates the conversion of hnRNA - we have to identify the exons and introns
to mRNA.It contains little amounts of
nucleotides.(100-200 nucleotides in 1 snRNA) Transcriptome
● rRNA - Structural component of the ribosomes - All of the mRNA molecules that can be
(sites of protein synthesis) ribosomal RNA generated from the genetic material in a
combines with specific protein =to form genome.
ribosomes. - Transcriptome is different from a genome
- Responsible for the biochemical complexity
→ rRNA + protein= ribosomes created by splice variants obtained by hnRNA.
Genetic Code 1966 (page 838)

● Marshall Nirenberg
● Har Gobind Khorana
- Scientist are now able to predict characteristics by
studying DNA.
- Genetic code is the assignment of the 64 mRNA
codons to specific amino acids.
- Out of 64, 61 lang nag proporduce ng
A.A , the 3 left UAG,UGA,UAA are
STOP/TERMINATING codons. Once stop
codons appear on codon sequence, the
translation for a.a will stop.
- Start codon - AUG (Methionine)
Anticodons and tRNA Molecules
- Synonyms- codons that specify the same
- During protein synthesis amino acids do not
amino acid.
directly interact with the codons of an mRNA
- Ex: Serine has synonyms of
molecule.
AGU,AGC,UCU,UCC,UCA,UCG
- tRNA molecules as intermediaries deliver
- Synonyms usually fall under a
amino acids to mRNA.
single box, unless they are more
- Two important features of the tRNA structure
than 4.
- The 3’ end of tRNA is where an amino
- The first two bases in a single
acid is covalently bonded to the tRNA.
box are the same, except for
- The loop opposite to the open end of tRNA
tryptophan and methionine cuz
is the site for a sequence of three bases
they only have 1 codon that
called an anticodon.
translates them.
-Anticodon - a three-nucleotide sequence on a tRNA
- Same codon specifies the same
molecule that is complementary to a codon on an mRNA
amino acid whether the cell is
molecule.
bacteria,human, or plant.
Translation
- Leads to genetic engineering, genetic
- Protein synthesis
counseling.
- Process by which the sequence of nucleotides in an
- In 1968 Marshall Nirenberg and Har Gobind
mRNA molecule directs the incorporation of amino
Khorana was awarded with NOBEL prize cuz
acid into protein
they discovered how protein was coded.They
Ribosomes- aka ribosomal rna protect complex
were able to illuminate how mRNA codes
- 65 % ribosomal rna by mass
proteins.
- 35 % protein by mass (ribosom-rRNA-protein
complex
• REFERENCE
• Stoker, S.H. General, Organic, and Biological
Chemistry, 6th edition, 2013, (pp. 734-771), Brooks/COLE
Cengage Learning
 • Common names of digestion enzymes still use “–in”
CHEM123_P10_ENZYMES ***enzymes found in GI tract use “-in”
Enzymes - pepsin, trypsin
• Catalyst that speeds up chemical reactions in our cells by • Identification of the substrate is often noted in
lowering the energy required for the reaction. addition to the type of reaction
- Most enzymes are specialized proteins that - glucose oxidase, succinate dehydrogenase
funx. As a biological catalyst.
• They are extremely effective, up to 1020 times faster Classification and Names of Enzymes
• Specific ***Classes or classification are based on type of rx
• 1,500- 3,000 different enzymes they catalyze
- Most enzymes are globular proteins, thus, they can Oxidoreductase - is a linked process
undergo DENATURATION which can affect its - Requires a COENZYME- Ex:NAD
activity. (nicotinamide adenine dinucleotide)
• Catalyst - Ex:Succinate dehydrogenase,glucose
• Substance that lowers the activation energy of a oxidase,LDH(Lactate
reaction without being changed itself are not dehydrogenase)=removes hydrogen from
consumed during the rx. the lactate
• Hydrolysis of protein in our diet (trypsin or pepsin) Transferase - transfer a funx grp from one molecule to
• Carbonic anhydrase in blood another
• 35M reactants in a minute - Ex: Transaminase - amino grp is transferred
Enzyme Structure - SGOT(serum glutamic oxaloacetic
2 General Structural Classes: transaminase)this is the old
1.Simple Enzyme name/AST(aspartate aminotransferase)
- An enzyme composed an only one protein - SGPT(serum glutamic-pyruvic
2.Conjugated Enzyme transaminase)this is the old
-An enzyme that has a non protein part in addition to name/ALT(alanine aminotransferase)
protein part - Kinase - phosphate group is transferred
➔ Apoenzyme - protein part - Ex: ATP → ADP
◆ Responsible to determine specificity of Hydrolase - water is added during the rxn.This will cause
enzyme to a substrate. Cofactors bind to bond breakage.
apoenzyme for it to be active and be able - Hydrolysis is the usual process involved in
to bind to the substrate digestion.
➔ Cofactor or prosthetic grp- non-protein part - In protein synthesis , condensation rxn occurs to
◆ Coenzyme/ co subtrate - small organic yield water, in order to break the peptide bond in
molecule (cofactor). Derived from dietary lipids, hydrolysis occurs.
vitamins - Proteases - protein,peptide bond
◆ Inorganic ions of cofactor: derived from - Lipase-lipid, ester bond
dietary minerals - Carbohydrases- -CHO , glycosidic
● Metal-ions:Zinc,Magnesium,Mn
- Phosphatases - Phosphate, phosphodiester
2+,Fe2
- Nucleases - N.A , phosphodiester
● Non metal ions: Cl-
➔ Holoenzyme(biochemically active conjugated
enzyme) - apoenzyme + cofactor

Nomenclature and Classification of Enzymes

• Most of the enzyme End in “–ase”
• Identifies a reacting substance
- sucrase – reacts sucrose; lipase - reacts lipid
• Describes function of enzyme
- oxidase – catalyzes oxidation; hydrolase –
catalyzes hydrolysis
 ENZYME ACTION MODELS
Enzyme Action : Lock and Key Model
- Active site in the enzyme has the fixed, rigid
geometrical conformation.(hindi nababgo yung
conformation ng active site)
- Substrates with a complementary geometry can
be accommodated. Not only the geometrical
shape but also the CHEMICAL NATURE are
COMPLEMENTARY
Lyase -catalyzes the addition of grp to a double bond or - The substrate and active site complements each
removal of grp to double bond WITHOUT using other.
hydrolysis or oxidation - Enzyme has predetermined sahep for active site,
- Decarboxylase - carboxyl only substrate of specific shape and chemical
- Deaminase - amino or amine grp nature could bind sa active site.
- Dehydratase - removes water
- Hydratases- adds water
Isomerase - rearrange mol to form isomer.
Ligase-Forms bond bet mol. Using ATP. Once ATP
is used up, ADP is left

Models of Enzyme Action

***there's ALWAYS a SUBSTRATE that will act

Enzyme active site
• Small part of an enzyme’s structure that is actually
involved in catalysis.
- place where substrate binds to the enzyme
- Formed due to folding and bending of protein
- APPEARANCE: crevice like = slow narrow
opening of enzyme
- Some enzyme has more than one active sites
• A three – dimensional entity formed by groups that
come from different parts of the protein chains
Once substrate binds sa enzyme it forms the enzyme
substrate complex
Enzyme – Substrate Complex
• The intermediate reaction species that is formed
when a substrate binds to the active site of an
enzyme.
- The orientation and proximity is favorable to
form a product therefore hastening the rx,
Induced – Fit Model Factors Influencing Enzyme Activity
• Enzyme’s active site is not rigid and static. • Enzyme and substrate concentration
• There’s a constant change in shape ***enzymes are not consumed in the rx they catalyze, so if
- Once substrate comes in contact to the enzyme it there is an increase in enzyme conx while the substrate conx
can change the shape of active site. ACTIVE SITE is constant = enzyme activity will increase
ADJUSTS itself for substrate.
• Allows for changes in the shape or geometry of the active
site of an enzyme to accommodate a substrate.
• Result of the enzyme’s flexibility; it adapts the • Temperature
incoming substrate. - Changes the conformation of the enzyme
- Higher temp, higher kinetic energy,increase
energy in reactant collison, higher activity of
enzyme
- Optimum temp - maximum enzyme activity
- For human enzymes - 37C
- Normal body temp: 37C
**once optimum temp is surpassed the enzyme activity
goes down. So pag super hot na the enzyme activity
decreases which is why life threatening if body temp
exceeds 40C
INCREASE TEMP leads to DECREASE ENZYME
ACTIVITY
- Cuz enzyme is denatured due to excess heat
• pH
- Optimum pH -pH at which the enzyme…
- Body has buffers that help maintain optimum pH
for the enzyme.
- Most enzymes are specific
- Blood:buffer = bicarbonate-carbonic
- Absolute - is the most restrictive and it is NOT
acid
COMMON. Stick to one lang sa isang substrate.
- Urease - only rx with UREA - Optimum pH: 7.0- 7.5
- 7.35- 7.45 blood pH
- Catalase - H202 (hydrogen peroxide) Digestive Enzyme: pepsin: stomach pH 2.0 Trypsin: S.I
-Group - same fx grp pH 8.0
- hexokinase - a transferase class of enzyme, rx to - R groups of amino acids have proper charge;
hexose, specifically glucose: variation of pH can affect the ions of groups on the
- carboxypeptidase - rx with protein, specifically at substrate
the carboxyl group of the peptide chain of protein (C
terminal end).
Linkage -for a particular chem bond. most GENERAL
ENZYME SPECIFICITY
-Lipase - ester
-Phosphatase -phosphodiester
Stereochemical- can distinguish stereo isomers
(CHIRALITY). Example, it will only rx with Levo A.A
 • Has effect reversed by increasing substrate
concentration, therefore no rx occurs when
competitive inhibitor binds sa active site
- Noncompetitive Inhibition
A noncompetitive inhibitor
• Does not have a structure like substrate
• Binds to the enzyme but not active site
- Binds at the ALLOSTERIC site of enzyme
- No rx occurs when the non competitive
inhibitor binds sa allosteric site ng enzyme
- Once it bind sa allosteric site nabbago nya
yung structure ng enzyme and enzyme site
kaya nagbago yung enzyme activity.
- Ex: heavy metal ions: Pg2 (lead), Ag+,Hg2+
• Changes the shape of enzyme and active site
• Substrate cannot fit altered active site
Substrate Conx. • No reaction occurs
As conx substrate increases, enzyme activity increases. But • Effect is not reversed by adding substrate
if the saturation curve is reached IT REMAINS
CONSTANT - Irreversible Inhibition
Saturation curve - enzyme increases up to a certain conx, A irreversible inhibitor
and therefore remain constant. oOnce it reached max rate • Inactivates enzymes by forming a strong covalent
and all active sites of enzyme is puno na Turnover bond to an amino acid side-chain group at the
number enzyme’s active site
• Number of substrate molecules transformed per minute • Does not reverse the inhibition process
by one molecule of enzyme under optimum conditions • Enzyme is permanently deactivated
of temperature, pH and saturation of the substrate. - Cuz strong covalent bond is formed by the
- Ex. Catalase: 5,600,000 irreversible inhibitor to the ACTIVE SITE
- Lactate dehydrogenase: 60,000 • Effect is not reversed by adding substrate Ex:
- Rx with lactate through the help of Chemical warfare agents (nerve gases);
enzyme NAD by oxidation organophosphate (insecticide)
- DNA Polymerase I: 900
Enzyme Inhibition
Inhibitors
• any substance that Slows or stops the normal
catalytic activity of the enzyme
• Change the protein structure of an enzyme
• May be competitive or noncompetitive
• Some effects are irreversible
- noncompetitive Inhibition and irreversible
inhibition
A competitive inhibitor
- Competes w/substrate with same active site cuz
they have similar structure and same charge
• Has a structure similar to substrate
• Occupies active site
• Competes with substrate for active site
Feedback Regulation
- Cellular process forms large amount of
enzymes and products which need to be
regulated
Negative feedback – pathway is inhibited by accumulation
of final product
Positive feedback – a regulatory molecule stimulates the
activity of the enzyme, usually between 2 pathways
- ADP levels cause the activation of the
glycolysis pathway to make more ATP
Medical Uses of Enzymes
• Used to diagnose certain diseases.
- SGOT/AST - liver marker
- SGPT/ALT -liver marker
- Lipase: pancreas
- LDH - cardiac marker
- CK (creatine kinase):
MM(muscle);MB(heart);BB(brain)
- Acute myocardial infarction (AMI) uses LDH
and CK MB to diagnose
• Appearance of these enzymes in the blood often indicates
that there is tissue damage in an organ and that cellular
contents are spilling out into the bloodstream.
- SERUM is used
• Used in the treatment of disease.