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LIPIDS
LIPIDS
 Are compounds that occur frequently in nature.
 They are found in places as diverse as egg yolk, the human nervous system, and other parts of the body
and some important components of plant, animal, and microbial membrane like carbohydrates.
 Commonly referred as FATS
 Family of substances that are insoluble in water but soluble in non-polar solvent and solvents of low
polarity. (Solubility is our basis)
 Examples of Non-polar solvents and solvents of low polarity:
- Diethyl-ether
- Benzene
- Hot alcohol
- Chloroform
- Acetone
Function of lipids
 storage of energy: with the absence of glucose
o Energy in the form of fats has greater importance because when we burn fats, they produce more
energy twice as much energy as the burning of an equal weight of carbohydrates
 membrane components:
o Separation of various components due its insolubility
 messenger
- Examples:
A. Steroids
 Deliver signals from one part of the body to another
 E.g. hormones
B. Prostaglandins and thromboxane
 Mediate hormonal response
 Act as surfactants, detergents, and emulsifying agents 
 Act as electric insulators in neurons
 Provide insulation against changes in external temperature
 Gives shape and contour to the body
 It protects internal organs by providing a cushioning effect 
 Help in absorption of fat soluble vitamins

Classified according to their chemical nature:

A. Open chain compounds

- Has a polar head and long nonpolar tails
- E.g. fatty acids, triacylglycerols (triglyceride), sphingolipids, phosphoacylglycerol, and glycolipids
B. Fused ring compounds
- In nature they are composed of benzene rings (furan
and pyran)
- E.g. steroids and waxes (cholesterol)

Main types of lipids:

1. Triglycerides— Most insoluble lipid
- Main storage lipid in man (adipose tissue) —95%
- Fasting: 12 hours
2. Phospholipids—Most abundant lipid
- Amphipathic: polar (hydrophilic head) and nonpolar (hydrophobic side chain)
- 70% Lecithin/Phosphatidyl choline
- 20% Sphingomyelin
- 10% Cephalin
3. Steroids and waxes
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Classification of Lipids:
Based on Structures: 4 groups

1. Simple Lipids
- Esters of fatty acids with glycerol or other higher alcohols.
- COMPONENTS: fatty acids with glycerol backbone or other higher alcohols in its backbone
2. Complex Lipids
- fatty acids esterified with alcohol and contain other groups such as phosphate.
- Example of complex lipids:
a. Phospholipids – have fat
b. Non-phosphorylated lipids
3. Steroids— Adrenal cortex (major site)
4. Prostaglandins, thromboxanes, leukotrienes

CLASSIFICATION:

1. FATTY ACIDS
- Examples of chains of fatty acids

NOTES ON THE PIC: 

 18 Carbons single bond—Stearic acid, saturated
 18 carbons, double bond—Oleic acid, unsaturated

Fatty acids
- a carboxyl group (blue) at the polar end and a
hydrocarbon chain (red) in the nonpolar tail.
o Note: the reason why lipids are insoluble to water is because of its hydrocarbon
tail.
- Amphipathic – compounds are both hydrophilic (carboxyl group)  and hydrophobic
(hydrocarbon tail) portions.
- The general formula of fatty acids: R-CO-OH
o R: hydrocarbon chain (unbranched)
 where variation occurs in the physical properties of a fatty acid.
 Changes that will happen:
 Different numbers of carbons
 Fatty acids will have either a double bond or  have 2 double bonds.
o CO- OH: carboxylic group, which represents the functional group.

NOTES:
 Normally, contains an even number of carbon atoms.
 Hydrocarbon chain is usually unbranched
 Do not normally have a conjugated double bond system.

To Further classify a fatty acid:

Based on the number of carbon atoms

EVEN CHAIN Seen in most of the naturally occurring lipids.

ODD CHAIN Seen in microbial cell walls.

Also present in milk

Based on the length of Hydrocarbon chains

SHORT CHAIN 2-6 Carbon atoms

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MEDIUM CHAIN 8-14 Carbon atoms

LONG CHAIN 16-22 Carbon atoms

VERY LONG CHAIN More than 24 Carbon atoms

Classification Based on Nature of Hydrocarbon Chain

Picture on hydrocarbon chain:

 Butyric Acid – Saturated Fatty Acid
 Oleic Acid – Monounsaturated Fatty Acid
 Linoleic Acid – Polyunsaturated Fatty Acid

 Saturated: single bond

- Saturated fatty acids are solid in room temperature
- Single bond
- SSS (SOLID, SINGLE, SATURATED)
 Unsaturated: double bond (carbon-carbon)
- The more double bonds it contain the lower the
melting point
- In room temperature they are liquid
- Monosaturated or polyunsaturated
- Cis double bond or trans double bond
o Trans- H atoms opposite
o Cis- H atoms same side
 bent configuration
(Simplified structure)

NOTE: increase in the number of cis double bonds in a

fatty acid leads to a variety of possible spatial
configurations of the molecule 

 The position of the double bond results from the

way the unsaturated fatty acids are synthesized in
the organism. (In cis and trans double bonds)

NOMENCLATURE OF FATTY ACIDS

 Genevan system
- naming the fatty acids
- Names the fatty acid after hydrocarbon
with the same number and arrangement
of carbon atoms
- Suffix: -anoic (saturated) or -enoic
(unsaturated)
- Genevan system: the carbon atoms are numbered from the carboxyl atom (COOH)
- Carbon atoms adjacent to the carboxyl carbon atoms are the alpha, beta, gamma carbons and the
terminal carbon is known as the omega- or n-1 carbon
- 🔺triangle indicates the number and position of the double bonds
- 18:1(denotes an 18-carbon fatty acid with one double bond)
- 🔺9 (indicates a double bond between carbons 9 and 10)
 Omega fatty acid
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- Classification is based on the location of the closest double bond in the methyl end (CH3) of the carbon
chain furthest from the carboxyl group.
- Starts with methyl end
- 𝜔9 or omega 9- indicates that a double bond on the 9th carbon counting from the 𝜔 carbon.

NOTES:
 𝜔 carbon is the last carbon.
 Omega fatty acid is done by
examining the formula of the fatty
acid. Examining how long it is and
counting the number of carbon
atoms starting from the methyl
group.

EXAMPLES OF FATTY ACIDS THAT ARE PART OF OMEGA FATTY ACIDS

Fatty acids Numbers of Carbon Atoms Family

Palmitoleic 16 Omega-7

Oleic 18 Omega 9

Linoleic 18 Omega-6

Linolenic 18 Omega-3

Some naturally occuring saturated fatty acids: structure, properties and nomenclature
Carbon Structure Systematic Common Melting Water Benzene
skeleton name name point (ºC) Solubility Solubility
(derivation) at 30 ºC at 30 ºC
(mg/g (mg/g
solvent) solvent
12:0 CH3(CH2)10COOH n- Dodecanoic Lauric acid 44.2 0.063 2,600
acid (Latin
laurus,
laurel plant)
14:0 CH3(CH2)12COOH n- Tetradecanoic Myristic acid 53.9 0.024 874
acid (Latin
Myristica,
nutmeg
genus)
16:0 CH3(CH2)14COOH n- Hexadecanoic Palmitic acid 63.1 0.0083 348
acid (Latin
palma, palm
tree)
18:0 CH3(CH2)16COOH n- Octadecanoic Stearic acid ( 69.6 0.0034 124
acid Greek stear,
hard fat)
20:0 CH3(CH2)18COOH n- Eicosanoic Arachidic 76.5
acid acid (Latin
Arachis,
legume
genus)
24:0 CH3(CH2)22COOH n- Tetrasanoic Lignoceric. 86.0
acid Acid (Latin
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lignum,
wood +cera,
wax

NOTES ON THE TABLE:

 The table is saturated.
 The more carbon, the higher the melting point.
 Kapag makapal yung solid, mas matagal uminit.

some naturally occuring unsaturated fatty acids: structure, properties, and nomenclature
Carbon Structure Systematic name Common Meltin Water Benzene
skeleto name g point Solubilit Solubilit
n (derivation (ºC) y at 30 y at 30
) ºC (mg/g ºC (mg/g
solvent) solvent
16:1 (∆ CH3 (CH2)5 cis-9- Palmitoleic 1-0.5
9) CH=CH(CH2)7COOH hexadecenoic acid
acid
18:1 CH3 (CH2)7 cis-9- Oleic acid 13.4
(∆9) CH=CH(CH2)7COOH octadecenoic (latin
acid oleum, oil)
18:2 CH3 (CH2)4 cis-, cis-9,12- Linoleic 1-5
(∆9, 12) CH=CHCH2CH=CH(CH2)7COO octadecadiecinoi acid
H c acid ( Greek
linon, flax)
18:3 CH3CH2 cis-, cis-, cis-9, Alpha- -11
(∆9, 12, CH=CHCH2CH=CH(CH2)7COO 12, 15- Linolenic
15) H octadecatrienoic acid
acid
20:4 CH3 (CH2)4CH=CHCH2CH Cis-, cis-, cis-, cis- Arachidonic -49.5
(∆5, =CHCH2CH= 5,8,11,14- acid
8,11, CHCH2CH=CH(CH2)3COOH Icosatetraenoic
14) acid

NOTES:
 The table is Unsaturated fatty acids
 Liquid at room temperature and the more carbon bond, the lower the melting point.
 The more it contains double bonds, the more liquidy it is

CLASSIFICATION OF FATTY ACIDS

1. Essential Fatty Acids

- If a fatty acid can only be obtained from the diet or from what we eat
- Examples are Linoleic and linolenic acid
2. Nonessential Fatty Acids
- If a fatty acid can be made by the human body.
- At some point, there is metabolism in the body that forms fatty acids.
- Made from carbohydrates and proteins or other forms of fatty acids.
- Carbohydrates and fatty acids chemical composition: carbon, hydrogen and oxygen,
- Proteins: carbon, hydrogen, oxygen and nitrogen.
- Thus, carbohydrates and protein can donate C,H,O to form fatty acids.

Glycerol + 3 fatty acid chains= Triglyceride + 3 water molecules

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TRIACYLGLYCEROL/ TRIGLYCERIDE
 Has 3 fatty acid chains and glycerol backbone
 Most common lipid material
 The alcohol of triglyceride is glycerol
 Triesters of glycerol and long chain fatty acids
 Triglycerol do not occur as component of cell membranes.
o the main storage forms of fatty  acids and stored in adipocytes
 Accumulate in adipose tissue, providing a means of storing fatty acid

Fatty acid component of triacylglycerol

 Any number of fatty acid and have certain things in common
 All are unbranched carboxylic acids so they are LINEAR 
 Range: about 10-20 carbons atoms
 Contain an EVEN NUMBER of carbon atoms
 Apart from the carboxyl group (-COOH), they have no functional groups except that some do have double
bonds
 In most fatty acids that have double bond, the cis isomer predominate.
o Meaning if there is a double bond there is a bending in the structure of fatty acids

Triacylglycerol Properties
 Physical state:
- Structural difference between fat and oil is the degree of
unsaturation

FAT OIL – double bonds

Comes from animals Comes from plants or fish

Contains a high proportion of Contains a high proportion of long

long chain, saturated fatty chain, unsaturated fatty acids or
acids short chain, saturated fatty acids

Solid at room temp Liquid at room temp 

 If fats and oills are PURE:  odorless, colorless, tasteless

 Fats and oils are mixture of triglycerides
 They are different in physical properties because of the difference of fatty acid components

SATURATED UNSATURATED
Lauric Myristic Palmitic Stearic Oleic Linoleic Linolenic Other
ANIMAL FATS
Beef tallow — 6.3 27.4 14.1 49.6 2.5 — 0.1
Butter 2.5 11.1 29.0 9.2 26.7 3.6 — 17.9
Human — 2.7 24.0 8.4 46.9 10.2 — 7.8
Lard — 1.3 28.3 11.9 47.5 6 — 5
VEGETABLE OILS
Coconut 45.4 18 10.5 2.3 7.5 — — 16.3
Corn — 1.4 10.2 3 49.6 34.3 — 1.5
Cottonseed — 1.4 23.4 1.1 22.9 47.8 — 3.4
Linseed — — 6.3 2.5 19 24.1 47.4 0.7
Olive — — 6.9 2.3 84.4 4.6 — 1.8
Peanut — — 8.3 3.1 56 26 — 6.6
Safflower — — 6.8 — 18.6 70.1 3.4 1.1
Soybean — — 6.1 2.6 25.1 66.2 — —
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Unsaturated fatty acids (oil): there are spaces to prevent close-packing and lowers the melting point and
increase in fluidity due to double bonds and bending of cis
Coconut: majority is composed of Lauric acid
Olive oil- mostly oleic acid, unsaturated
Animals fats—mostly are unsaturated oleic acid
Hydrogenation:

Oleic acid. Linoleic acid. Linoleic acid. Stearic acid.

 A process where carbon-carbon double bonds are reduced to single bonds by treating them with hydrogen
and catalyst; help in the speeding of reaction (e.g. enzyme)
 Add H2 to break double bonds
 Source of trans fatty acids
 It is not difficult to convert unsaturated liquid oil to solid or saturated

Saponification: 
 Oldest known chemical reaction
 based-promoted hydrolysis of fats and oils
 Produces glyceril and a SOAP (mixture of fatty acid
salts)
 Triglycerides undergo hydrolysis through acid and bases
 If an organisms uses fatty acids, linkages are hydrolyzed
by different enzymes (lipase), it takes place inside the
organism.
 While saponification takes place OUTSIDE the organism
and we use acids and bases. (E.g. bases are sodium or potassium hydroxide)
on pic: triglyceride+3NaOH—>1,2,3-propanetriol (glycerol;
Glycerin)+ Sodium soaps
COMPLEX LIPIDS
 Other kinds of lipids and a very important lipids because
they constitute the main components of the membrane of
the cell
 The picture is an example of a phospholipid:
- Composed of the hydrophilic head and hydrophobic
tails
DIAGRAM OF SIMPLE AND COMPLEX LIPIDS

Simple and complex lipids

simple complex lipids

phospholipids glycolipid

Glycerophospholipids Spingolipid
Glycerol and 3 fatty acids Glycerol SphingosineSphingosine
2 fatty acids Fatty acidglucose/galactose
PO4( phosphate) Phosphatefatty acid
Alcohol choline
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COMPLEX LIPIDS
 Are further classified into phospholipids and glycolipids

Phospholipids
 Can be glycerophospholipids or sphingolipids
 Glycerophospholipids and sphingolipids differ in their backbone
 Glycerophospholipids are composed of:  Sphingolipids are composed of:
- Glycerol: 3 carbon alcohol (choline, serine, - Sphingosine: more complex alcohol
ethanolamine, inositol)
- Phosphate - Phosphate
- 2 fatty acids - 1 fatty acid
 Phosphate has alcohol which can be choline, serine, ethanolamine, inositol or other compounds
 Phospholipids derived from glycerol are called phosphoglycerides or glycerophospholipids

Glycolipids
 like sphingolipids in a sense that it has sphingosine backbone but instead of phosphate and choline, sugar
(glucose or galactose) are attached to the backbone
 It still has 1 fatty acid component
 Composed of:
- Sphingosine
- 1 fatty acid
- Sugar (glucose or galactose)

PHOSPHOLIPIDS
 Like fatty acids, they are amphipathic which means it
has both hydrophilic and hydrophobic parts
 Polar “head”
- Glycerol (alcohol) along with the phosphoric acid
(phosphate group) and choline
 Nonpolar “tail”
- Hydrocarbon chains of the fatty acids
- Any form of saturated and unsaturated fatty acids
o Unsaturated fatty acids: important
components of the lipid bilayer to prevent
tight packing of the hydrophobic chain
 Liquid-like character of the
membrane

PHOSPHOLIPID: Glycerophospholipid
 Composed of:
- Glycerol (alcohol)
- 2 fatty acids (with or without double bonds); can be saturated or unsaturated fatty acids
- Phosphate group (esterified to another alcohol “x”)
 Also called phosphoglycerides
 The “x” or the third group is a head group substituent and can be in the form of different groups
preferably amino alcohol
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Glycerophospholipid (general structure)
NAME OF THE GLYCEROPHOSPHOLIPID X-ATTACHED IN THE PHOSPHATE GROUP
Phosphatidic acid (no x attached)
Phosphatidylethanolamine (cephalin) Ethanolamine
Phosphatidylcholine (lecithin) Choline
Phosphatidylserine Serine
Phosphatidylglycerol Glycerol
Diphosphatidyl glycerol Cardiolipin

 The naming of glycerophospholids depends on the x or third group attached/esterified in the phosphate
group.
 The classification of the phosphatidyl ester depends on the nature of the second alcohol esterified to the
phosphoric acid (third group)

A. Phosphatidylcholine
- The most abundant phospholipids of the cell membrane
- Represents a large proportion of the body’s store of choline
- Common name: lecithin
- Choline is important in nervous transmission as acetylcholine and as a store of labile methyl group

Choline phosphoric diester stearic acid, linoleic acid, A lecithin

 Structure of phosphatidylcholine
-
-
-
-
Glycerol
- Stearic acid
- Linoleic acid
- Attached to the phosphate
group is the amino alcohol
(choline)

- The “R”— depending upon on

the amount of hydrocarbons
attached on fatty acid

NOTE: Phosphatidylserine contains

oleic and arachidonic acid

B. Phosphatidylinositol
- Minor component of the
cell membrane
- Plays an important part
in cell signaling and
membrane trafficking
- Inositol is a naturally
occurring sugar alcohol
(looks like pyran)
- Myoinositol
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C. Diphosphatidylglycerol
- Clinical significance: decreased
level or alteration in its structure
or metabolism causes
mitochondrial dysfunction in
aging and in pathological
conditions such as heart failure,
hypothyroidism, and Barth
syndrome (a cardioskeletal
myopathy)
- This phospholipid is found
Phosphatidic acid phosphatidylglycerol
only in mitochondria and is
essential for mitochondrial
function
o So if there is a decreased level of diphosphatidylglycerol, an altered structure, or problems occur
in its metabolism, there will be a mitochondrial dysfunction

PHOSPHOLIPID: Sphingolipid
 Composed of:
- one molecule of a long chain amino alcohol (sphingosine)
- one long chain fatty acid (connected to the NH2 group by an
amide bond
- and a polar head group (esterified by phosphorylcholine)

Note:
 The combination of a fatty acid and sphingosine is called Ceramide
 Johann Thudichum – discovered sphingolipid
 Sphingolipid difference with glycerol lipid- NO GLYCEROL but it has CERAMIDE which is the combination of
fatty acid and sphingosine
 SPHINGOMYELIN – combination of ceramide and phosphorylcholine

Name of the Sphingolipid X Attached in the phosphate group

Ceramide —
Sphingomyelin Phosphocoline
Glucosylcerebroside Glucose
Lactosylceramide Di-, tri-, or tetrasaccharide
Ganglioside Complex Oligosaccharide

A. Sphingomyelin
- discovered by Johann Thudichum in 1874
- contain phosphocholine or phosphoethanolamine as their polar head group
- present in the plasma membranes of animal cells and are especially prominent in myelin sheaths of
nerve cells. Myelin sheaths is a membrane sheath that surrounds and insulates the axons of some
neurons
- associated with diseases like multiple sclerosis

GLYCOLIPID
 Difference of sphingolipid and Glycolipid: sphingolipid has phosphate group or glucose
 Glycolipid is a complex lipids that contain carbohydrates and ceramides.
 no phosphate group instead it has ceramide and carbohydrates + fatty acids
I. Cerebrosides
- consists of ceramide mono- or oligosaccharides (glucose or galactose carbohydrate units)
- occur primarily in the brain and a nerve synapses

Note: Those with galactose , they are characteristically found in the plasma membrane of cells in neural tissue
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Those with glucose, they are found in the plasma membrane of cells in non-neural tissues

II. Gangliosides
- contain a more complex carbohydrate structure
- function in cell to cell recognition and communication and as receptors for hormones and bacterial
toxin

Galactosylceramide structure:

Note: Di sya katulad nung sphingolipid na may

ceramide at glucose dahil ang ating glycolipid
wala kang makikitang phosphate group na
attached. Sphingolypid-may sugar sa X group

Galactosylceramide structure

Glycolipid
 prominent in the plasma membranes of neurons and some are
clearly recognition sites of the cell surface
 Note: Carbohydrate moieties of certain sphingolipids define
the human blood groups and therefore determine the
individual’s type of blood

Picture:
 O antigen, A antigen and B antigen- different carbohydrate units
RBC’s cell membrane
 A antigen – may galnac
 B antigen – may galactose
 O antigen- no attached carbohydrate
 Entire structure – has ceramide (Glycolipid). Nakaattach sila sa
membrane and then that membrane is may lipid in which your lipid na yung ceramide and your carbon
units which is complex.

Complex lipids in the cell membrane

LIPID BILAYER
 Two rows/ layers of complex lipid
molecules that are arranged tail to tail:
- Hydrophobic Tail – water fearing.
Point towards each other which
enable them to get them as far away
from the water
- Hydrophilic Head – water loving.
Project in inner portion and outer
surface of membrane
 serves as a barrier of movement of ions or
polar compounds in and out of the cells
 Membranes are made up of lipid bilayer
 Lipid bilayer – many phospholipids lined up together
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Important Attributes of Biological Membranes:
 Membranes are sheet-like structures, only two molecules thick, that form closed boundaries between
different compartments.
 The mass ratio of lipids to proteins ranges from 1:4 to 4:1, with carbohydrates
 Membrane lipids are small molecules that have both hydrophilic and hydrophobic moieties.
 Specific proteins mediate distinctive functions of membrane.
 Membranes are noncovalent assemblies.
 Membranes are asymmetric.
 Membranes are fluid structures.
 Most cell membranes are electrically polarized, such that the inside is negative.
NOTE:
 lipid component for regulation.
 Protein— transport system
 Membrane lipids are small molecules. This lipids
spontaneously form closed by molecular sheets in aqueous
media. And this lipid bilayers are barriers to the flow of polar
molecules.
 Specific proteins mediate distinctive functions of membrane.
So proteins may serve as pumps, channels, receptors,
enzymes and they can be in a form of membrane proteins so
pwede silang for cell recognition.
 Membranes are noncovalent assemblies. The constituent
proteins and lipid molecules are held together by many
noncovalent interactions which acts cooperatively.
 Membranes are asymmetric which means the two faces of
biological membranes always differ from each other .
 Membranes are fluid structures. Lipid molecules diffuse rapidly
in the plane of the membrane as the proteins unless they are
anchored by specific interactions. So, the presence of
unsaturated fatty acids makes it fluid like.
 Most cell membranes are electrically polarized, such that the
inside is negative or negatively charged.
 Take note: this shapes may also form bilayer sphere that are
structural basis for vesicles lysosomes which are subcellular
components that play a role in numerous physiological
functions.
 lipid bilayer may become component of vesicles and lysosomes.

LIPID BILAYER COMPOSITION

A. Phosphoglycerides
- Principal lipid components of the membranes
B. Glycolipids
C. Unsaturated fatty acids
- Prevent the tight packing of the hydrophobic chains,
thereby providing a liquid-like character.
D. Saturated fatty acids
E. Cholesterol
- Enhance order and rigidity
NOTES:
 It has Sphingomyelin, Ganglioside, Cerebroside,
Phosphoacylglycerol and Cholesterol.
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 Actually yung unsaturated fatty acids, nagkakaroon sya ng bending or yung kink. Eto is nagkakaroon sya ng
disorder dun sa packing mismo ng chains natin which makes for a more open structure that would be
possible for
 straight saturated chains—more open structure for packing of chains

FLUID MOSAIC MODEL

 “Fluid” – free lateral motion in the bilayers makes
membrane liquid-like; “mosaic”- refers to the topography
of the bilayers.
 Allows the passages of nonpolar compounds (soluble in
the lipid membrane) by diffusion.
NOTES:
 Sa lipid storage disease, nagkakaroon ng lipid
accumulation dahil meron tayong problema o meron
tayong defective na enzyme. Kasi etong enzyme na to,
their function is for the metabolism of the lipids. And since
hindi sya namemetabolize instead nag-aacumulate sya.
On picture: oligosaccharide, hydrophobic alpha helix, glycolipid, cholestero, integral protein, phospholipid
Name Accumulating lipid Missing or defective enzyme type
Gaucher’s disease Glucocerebroside B-glucosidase
Krabbe’s leukodystrophy Sphingolipids galactocylceramide/ Galactocerebrosidase
psychosire
Fabry’s disease Glycosphingolipids Galactosidase A
Tay-sachs disease Ganglioside GM2 B-N-Acetyl hexosaminidase
Niemann-pick disease Sphingomyelin sphingomyelinase

STEROIDS
 The difference of steroids compared to simple and complex lipids is that it
is composed of fused rings.
 Definition: Steroid consists of four fused rings (3 six carbons and 1 with
five carbons)
 Function: they serve as precursors for a variety of products with specific
biological activities (cholesterol, hormones: progesterone, cortisol,
testosterone, cortisone and estradiol)
- They almost have the same structure except for its side chain
CHOLESTEROL
 Most abundant steroid in the human body
 Formula: C27H46O
 Structure: steroid nucleus, hydroxyl group and the hydrocarbon side
chains
 Exists both in free form and esterified with fatty acids (bound
cholesterol)
 Needs a WATER-SOLUBLE CARRIER to circulate in the aqueous medium
of blood
 Take note that there are different substances in the human body or
metabolites, one of this is cholesterol wherein they travel from one
area to another area. For example, nasynthesized sila at one point and kailangan nilang pumunta sa ibang
organ, madistribute throughout the body in the blood vessel (medium of distribution) with a carrier
(kailangan ng carrier para makapaglakbay especially sa mga hindi soluble). These carriers are protein in
nature.
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Function
 A plasma membrane component in all animal cell (e.g. Red Blood Cell)
 Raw material for the synthesis of other steroids (sex and adrenocorticoid hormones) and bile salts
 Serve as the raw material (similarity with other steroids) to synthesize other hormones
Regulation
 The cholesterol in the body is in a dynamic state so it constantly
circulates in the blood because it has different functions
 Synthesis in the liver is reduced to half the normal rate of production
if blood level exceeds 150 mg/100 mL.
 As shown in the diagram, may minemaintain na serum cholesterol
level sa katawan which depends on the gender of a person.
 When the serum cholesterol level increases = synthesis decreases
 serum cholesterol level decreases = synthesis increases
 serum cholesterol and synthesis are inversely proportional
Note: EXCESS cholesterol level, rather than presence, is associated with disease.

Cholesterol Carriers
 Lipoproteins (VLDL, LDL, HDL, Chylomicron)
o Not the cholesterol itself , but the carrier of cholesterol
 Contain a core of hydrophobic lipid molecules surrounded by a shell of hydrophilic molecules
 In lipoproteins, there are embedded apolipoprotein (protein portion of lipoprotein), phospholipid
(serve as barrier), cholesterol (free cholesterol), cholesteryl ester (esterified with a fatty acids
(at the core) /bound cholesterol) and triglycerides.
 Therefore, lipoprotein is a spherical shaped cluster which contains both lipid and protein
molecules.
 Majority in the core are Triglycerides, compare to bound cholesterol
Composition of Lipoproteins

LIPOPROTEINS COMPOSITION (%)

CORE SURFACE
Cholesterol TAG Phospholipids Proteins
HDL 30 8 29 33
LDL 50 4 21 25
VLDL 22 50 18 10
Chylomicrons 8 84 7 1-2

 Majority of Chylomicrons are Triacylglycerol; Majority of HDL are Proteins and it’s structure constitutes of
the apolipoprotein
 For LDL, its major component is Cholesterol; while VLDL is composed primarily of TAG
 HDL – “Good Cholesterol”
 LDL – “Bad Cholesterol”

CHYLOMICRONS
 are produced in the intestine; packaged with dietary lipids
 Delivers dietary Lipids (lipids that are taken from the food we eat) to the liver (hepatic) and peripheral cells
 Largest and least dense among the Lipoproteins

LOW DENSITIY LIPOPROTEIN (LDL)

 Carries cholesterol to cells with specific LDL receptors
 Cells with LDL receptors includes Hepatocytes (Liver cells)
 Need to enter the cell to decrease the plasma concentration of the LDL; If not, the cholesterol will be
deposited to the arterial or inner surfaces of the arteries and blood vessels

Inside cell Plasma

Cell surface
LDL is metabolized (LDL enters LDL is removed from the
Sufficient number
the cell thru the receptor), and circulation (plasma
of LDL receptors
cholesterol is liberated. concentration decreases)
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 There must be a sufficient number of LDL receptor, where LDL binds

 Inside the cell (Hepatocytes), LDL is metabolized: it enters the cell thru the receptor on the cell surface
and cholesterol is liberated (Cholesterol inside the LDL separates from its carrier)
 As a result, LDL is removed from the circulation; plasma concentration of LDL decreases.
Take note: Excess cholesterol is associated with a disease.

 Liberated cholesterol can be used as a part of the membrane of Hepatocytes/other cells.

 If LDL has no surface LDL receptor or has a disease wherein the receptor is defective = LDL can’t penetrate
in the cell and travels in plasma/blood vessel = will result to increase in concentration of LDL

 High level of LDL = High level of cholesterol in the plasma

 Lipids are insoluble in water
 Wandering LDL will be deposited in the walls of arteries; diameter of the blood vessel will narrow =
pressure is more stronger = assoc. with High blood pressure as well as Atherosclerosis

HIGH DENSITY LIPOPROTEIN

 HDL transports cholesterol from peripheral tissues to deliver and transport cholesterol to LDL
 Transfers free cholesterol to LDL or liver
 Carry Cholesterol from plaques deposited in the arteries
 It is desirable to have High levels of HDL (Good Cholesterol) than LDL in the bloodstream.
 We can increase our HDL through exercise, weight loss, etc.

Take note: HDL is higher in pre-menopausal women than men

 Liver cell surface = HDL binds to the cell and transfers its cholesteryl ester to the cell
 As a result, HDL reenters the circulation

APOLIPOPROTEINS MAJOR LIPOPROTEIN LOCATION FUNCTION

Apo A-1 HDL Structural, LCAT activator, ABCA1 lipid acceptor
Apo A-2 HDL Structural
Apo A-4 Chylos, VLDL, HDL Structural
Apo B-100 LDL,VLDL Structural, LDL receptor ligand
Apo B-48 Chylos Structural, remnant receptor ligand
Apo C-1 Chylos, VLDL, HDL Structural
Apo C-2 Chylos, VLDL, HDL Structural, LPL cofactor
Apo C-3 Chylos, VLDL, HDL Structural, LPL inhibitor
Apo E VLDL, HDL Structural, LDL receptor ligand
Apo (a) Lp(a) Structural, plasminogen inhibitor

Apolipoproteins
 Can be seen/located in the surface of lipoprotein particles. It is the protein portion of cholesterol carrier or
lipoprotein.
 They help and maintain the structural integrity of lipoproteins
 Serves as ligands for cell receptor. When the ligands bind, there’s a transfer
 Serves as activators and inhibitors of various enzymes that can modify lipoprotein particles
 Among the Apolipoproteins, the Apo A-1 is the major protein of HDL.

Steroid Hormones
 Cholesterol is the starting material for the synthesis of the
steroid hormones such as testosterone, estradiol (sex
hormones) and cortisol, aldosterone, cortisone
(adrenocorticoid hormones)
 Can be sex hormones or adrenocorticoid
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BIOCHEMISTRY MIDTERMS
 The synthesis of the steroid hormones produced progesterone serves as a starting compound for both sex
hormones or adrenocorticoid

A. Adrenocorticoid Hormones
- Products of the secretion of adrenal gland
- “Adrenal” meaning adjacent to the renal, “corticoid” indicates the cortex of the gland as its secretion

Classification (According Example Function

to function)
Mineralocorticoid Aldosterone Enhances the reabsorption of sodium and chloride ions in
the kidneys
Glucocorticoids Cortisol Increases the glucose and glycogen concentration in the
body

 Aldosterone enhances the reabsorption of sodium and chloride ions in the kidneys. When hormones are
secreted to reabsorb sodium and chloride ions in the kidneys. When our body needs sodium and chloride,
kidney cannot bring out the sodium and chloride because our body needs it, therefore the aldosterone
instead in secreted in the adrenal gland do that the sodium and chloride instead it will go out outside of
the body through urine, the kidney will reabsorb sodium and chlorides

B. Sex Hormones
a. Testosterone
- Most important male sex hormone synthesized from cholesterol
- Function:
o Promotes the normal growth of the male genital organs
o Promotes secondary male sexual characteristics (deep voice and facial and body hair)
b. Estradiol
- Most important female sex hormone
c. Progesterone
- Essential for the implantation of the fertilized ovum

Function of Estradiol and Progesterone:

 Regulates the cyclic changes occurring in the uterus and ovaries
(menstrual cycle)
 Promote further preparation of the uterine lining to receive the
fertilized ovum (through sexual intercourse and will be implanted
in uterus). The location of the fetus must be suitable for the fetus
to be alive. The uterine lining will be thickened also to protect it
 Regulates secondary female sex characteristics (growth of breasts)
1. Proliferative phase 0-5 days—estrogen increase
- Endometrium thickens Proliferative phase (follicle growth)—
2. Secretory phase surge of estrogen stimulates surge of LH,
- Endometrium continues to thickens and glands secrete a which stimulates ovulation
material in preparation to receive the embryo 14 day- ovulation
3. Menstrual Phase/ period 14-28 days estrogen and progesterone
- Layers of the endometrium disintegrate and blood vessels increases
rupture
o The uterine lining must not be always thick, it will
disintegrate, the blood vessels will rupture
(menstrual flow will occur). The uterine lining will
now be thin. (28 days cycle)

Bile Acid/Bile Salts

 Looks like steroid
 Oxidation products of cholesterol
o Cholesterol is oxidized to hydroxy derivative. The
end of the aliphatic chain of hydrocarbon is
oxidized to carboxylic acids. Carboxylic acid forms
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now an amide bond with either glycine or taurine. It can now be formed into Glycocholate and
Taurocholate which are bile salt
 Function: Emulsify all kinds of lipids and facilitates digestion

Arachidonic Acid Derivatives

 Examples: Prostaglandins, thromboxane and glucotains
 Have wide variety of effects on body
 In general, they mediate hormone action

A. Prostaglandins
- Fatty acid-like substances
- Discovered by Kurzrok and Leib (1930s)
- First isolated from human semen by Ulf von Euler
- From the word itself, it came from prostaglandin
gland/prostate gland, that’s why it was named prostaglandin
- Used as a decongestant that opens nasal passages by constricting blood vessels
- Lowers blood pressure by relaxing muscles around blood vessels
- Have 2 types: PGE and PGF
- Prostaglandin is synthesized in the body by ring closure between carbon 8 and 12. These reaction is
catalyzed by an enzyme called Cycloxygenase (COX)

PGE PGF
Has carbonyl group at carbon 9 Has 2 hydroxyl group on the ring at carbons 9 and
11
Used as a decongestant (PGE1)
Lowers blood pressure (PGE2)
Both stimulates uterine contraction and induce labor

 Difference in the structure of PGE and PGF

 Prostaglandins are synthesized by a ring closer
between carbon 8 and 12
o This reaction is catalyzed by cycloxygenase
 PGG2 is a common precursor of PGE and PGF
 Cycloxygenase (COX)
- Catalyzes the synthesis of prostaglandins from
arachidonic acid
- Comes in two forms:
1. COX-1
- Catalyzes the normal physiological production of prostaglandins
2. COX-2
- Responsible for the production of prostaglandins in inflammation

B. Thromboxanes
- Substance derived from PGH2
- Known to induce platelet aggregation

Thromboxane A2
o Causes other platelets to clump, resulting to an
increase size of blood clot
o Other name for platelets: thrombocyte, kaya thromboxane

C. Leukotrienes
- Acts to mediate hormonal responses
- Occurs mainly in white blood cell, and called leukocytes
in WBC
- Found in other tissues of the body like lungs and cause
asthma-like attacks
- Derived from arachidonic acid by an oxidative mechanism (no ring closure)
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- Produce long-lasting muscle contractions especially in the lungs
- It’s difference to thromboxane and prostaglandins is that THERE’S NO RING CLOSURE

PROTEINS*
PROTEINS
 One of the important biomolecule or
macromolecule in the human body
 It has many activities in the body
 Across the cell membrane, we have proteins such as
the peripheral proteins or integral proteins, of which
they have many functions such as carrier, receptor,
and other serves as enzymes
 Proteins are made up of amino acids
 The most important of all biological compounds
 Derived from the Greek “proteios”, loosely means
“of first importance”
- Proteins regulate the life machine
- Regulates different processes which include
metabolism, cell growth and neurotransmission
 Large organic molecule constructed of a chain of
amino acids linked by amide bonds
- For example: cellulose is a chain of glucose units; while protein is a chain of amino acids
- Amino acids have carbon, hydrogen, oxygen, and nitrogen (major components)
- CHO is also a chemical formula of carbohydrates and lipids
- Protein is unique because it has nitrogen
- Some proteins contain sulfur and phosphorus (minor constituents)
- Nitrogen is a characteristic component of protein
- Nitrogen is mga nasa 16% of the weight of the entire protein structure
 All proteins are polymers of amino acids

FUNCTIONS OF PROTEINS:

1. STRUCTURE
- Structural proteins are constituents of
the skin, bones, hair, and nails:
o Collagen
o Keratin
- Collagen and keratin are proteins in
nature (they are also structural proteins)
- Structural proteins are the chief
constituents of the different parts of the
body
- The main structural material for plants is
cellulose

2. CATALYSIS
- All reactions that takes place in living
organism are catalyzed by proteins called
“enzymes” (enzymes are made up of
proteins)
- Without enzymes, the reaction would
takes place slowly
o For example: the glucose metabolism, when this process is done outside the body, it would take
most likely 2 hours before changes are visible
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o Whereas, pag sa loob ng katawan nangyari yung process, mas mabilis because we have enzymes
inside the body
o So mas mabilis if there is a presence of an enzyme compared to those of without enzymes
o Normally, enzymes are found inside the cell
o When the cells are damaged or the tissues are damage, the enzymes are release from the inside
to the plasma (or to the blood)
- One the activities of the enzymes is catalysis of which pinapabilis niya yung reaction sa katawan
- Catalysis means pinapablilis

3. MOVEMENT
- Muscles are made up of proteins:
o Actin
o Myosin
- Muscles contract and its function is for movement (involved in every movement that we make)

4. TRANSPORT
- Proteins transport molecules across cell membrane
- Hemoglobin (protein in the blood) carries oxygen from the lungs to the cells
- Ex: integral proteins in the cell membrane

5. HORMONES
- Ex: insulin (glucose metabolism), erythropoietin (helps in production of RBC), and human growth
hormone
- Not all hormones are made up of lipids because some are made up of proteins

6. PROTECTION
- Antibodies are produced to counteract the foreign proteins (antigens)
- Fibrinogen carries blood clotting (protein in nature)

7. STORAGE
- There are proteins which store substances in our body
- Ex: Ferritin (protein in the liver) stores iron
- Iron is seen in the RBC and also needed for RBC production
- Kapag madaming iron, iniistore ng body for future use
- After 20 days, RBC eventually die kasi kailangang mapalitan. After mamatay, yung iron component ay
hindi natatapon kundi nirerecycle lang ng katawan.

8. REGULATION
- Proteins can control the expression of genes
- So nagkakaroon ng regulation sa kind ng protein na nasysynthesized sa particular cell

CLASSIFICATION OF PROTEINS

FIBROUS GLOBULAR
SHAPE Long and narrow Round or spherical
(helix) (bend)
PURPOSE Structural Non-structural
SOLUBILITY Insoluble in water Soluble in water
EXAMPLES Collagen, myosin, Enzymes, hemoglobin,
fibrin, keratin, actin, insulin,
elastin immunoglobulin

AMINO ACIDS
- Monomer of proteins
- Composition is made of amino acids
- Is an organic compound containing an amino
group and a carboxyl group
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BIOCHEMISTRY MIDTERMS
- There are 20 common amino acids (amino group + carboxyl group + R group)

- The alpha carbon is bonded to hydrogen with side chains or R groups (R groups determine the identity
of the particular amino acids)
- Amino acids differs in terms its side chains

 Has the following roles:

- Polymerizes to form peptides (peptide = chains = protein)
- Serves as precursors for other small biomolecules (purines and pyrimidine found in our DNA)
- Oxidizes to serve as an energy source for the cell
o meron tayong procedure in which ang body natin kinoconvert ang biomolecules natin into
glucose, ang biomolecules natin ang nagcocompensate kapag mababa na ang glucose natin
o Examples: lipid and proteins. May process din in which our lipids and proteins can be converted
into energy

AMINO ACID NOMENCLATURE:

 Common names are assigned
 3 letter abbreviations  widely used for naming
 1 letter symbol  commonly used for comparing amino acid sequences
- when more than 1 amino acid contains the same first letter, yung amino acid na pinakamarami or
pinakaabundant ang makakakuha ng 1 letter symbol na yun..for example, arganine, alanine, etc.

NAMING AMINO ACIDS BASED ON OUR CARBONS

2 Conventions in Identifying Carbon Atoms:

1. A-Carbon is where the amino group, carboxyl group and side chains are bonded. Additional carbons in the
R group are commonly designated β (beta), γ (gamma), δ (delta), ε (epsilon) and so forth proceeding out
from the a-Carbon and terminal carbon is ω (omega).

2. Carbon atoms are simply numbered from one end, giving highest priority (C-1) to the carbon with the
substituent containing the atom of highest atomic number (carboxyl carbon).

NOTES:
 pag greek letter ang basehan = walang designation si carboxyl, ang alpha carbon natin ay kung saan
nakabond si R group. Kapag numbering, yung carbon na may carboxyl ang number one
 Greek lettering is ambiguous. More commonly used ang numbering method natin. Kasi may mga amino
acids tayo na may ring, or heterocyclic, in which di natin magagamit ang greek letter naming natin. That is
why numbering is more conventional in naming our amino acids.

Side Chains (R-group)

 Determines the function of amino acids and their polymers (proteins)
 Vary in size and electric charge
 Influences the solubility of amino acids in water
 Basis of classification depending on:
- Polarity
- Presence of acidic or basic group
- Presence of functional groups (and their nature) other than basic or acidic ones

NOTES:
 these are the only differences found in amino acids, lahat sila may Carboxyl at may amino group at
hydrogen
 Take note: we have 4 classifications of amino acids and nakabase siya sa polarity ng ating R-group

CLASSIFICATION BASED ON THE SIDE CHAINS (R-GROUP):

1. Non-polar Amino Acids
2. Polar (Uncharged Amino Acids)
3. Acidic Amino Acids
4. Basic Amino Acids
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NON-POLAR:
 Are hydrophobic (water repellant) and lipophilic
 Contains methyl and methylene groups
- made up of hydrocarbons, mainly hydrogen and carbon, which makes them nonpolar. Kagaya ng lipids
natin since they are made up of hydrocarbons they are nonpolar/hydrophobic
 Includes:
- Alanine
- Isoleucine
- Leucine
- Methionine
- Proline
- Phenylalanine
- Tryptophan
- Valine
- Glycine

POLAR, UNCHARGED:
 Are more soluble in water (hydrophilic)
 Contains functional groups (hydroxyl, sulfhydryl and mine) that from hydrogen bonds with water
 Includes:
- Asparagine
- Cysteine
- Glutamine
- Serine
- Threonine
- Tyrosine

ACID:
 Has a net negative charge at pH at 7.0
 Contains carboxyl group in their side chains
 Includes:
- Aspartate and glutamate

BASIC:
 Has a net positive charge at pH 7.0
 Includes:
- Arginine, histidine, and lysine

Note: Methionine = may Sulfur, Phenylalanine/Tryptophan/Proline = may ring

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CLASSIFICATION BASED ON STRUCTURE:

1. Aliphatic Amino Acids
a. Mono amino mono carboxylic acids
b. Mono amino dicarboxylic acids
c. Dibasic mono carboxylic acids
2. Aromatic Amino Acids
3. Heterocyclic Amino Acids
4. Imino Amino Acids
5. Derived Amino Acids
a. Found in proteins
b. Not seen in proteins
c. Non-alpha Amino Acids

CLASSIFICATION BASED ON NUTRITIONAL REQUIREMENTS:

1. Essential Amino Acids
- Indispensable
- Their carbon skeleton cannot be synthesized by human beings (kelangan natin kunin from our food)
2. Partially Essential Amino Acids
- Growing children require them in food
3. Non-essential Amino Acids
- Carbon skeleton can be synthesized by the body

Pneumonic: Any Help In Learning These Little Molecules Proves Truly Valuable
Semi: Any Help = Arginine Histidine
Essential: In Learning These Little Molecules Proves Truly Valuable = Isoleucine Leucine Threonine Lysine
Methionine Phenyalanine Tryptophan Valine

PEPTIDE FORMATION
 Amino Acid + Amino Acid = dipeptide
 Amino Acid + Amino Acid + Amino Acid = tripeptide
 Peptide bond - bond that combines amino acids together
 When amino acids are joined they form and contain: an amino (n-terminal) end and a carboxyl (c-terminal)
end

Peptides:
 Are compounds formed by linking small numbers (two to several dozens) of amino acids
 Formed by combining the – COO - group of one amino acid with the - NH 3+ group of a second amino acid
molecule

NOTES:
 Dito sa ating structure we have
here two amino acids which
includes your glycine and alanine.
Yung carboxyl group ng glycine can
combine with the amino group of
the second molecule which is the
alanine. And yung kanyang
pangalan since it is composed of glycine and alanine therefore, ang kanyang name ay glycylalanine. Take
note kapag pinagbaliktad natin to nauna si alanine and sumunod si glycine, magkaiba sila na dipeptide
kaya hindi sila pareho. Therefore, magkaiba si alanineglycine kay glycylalanine. Since these are 2 amino
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BIOCHEMISTRY MIDTERMS
acids joined together by a peptide bond (C-N) therefore the product is dipeptide. Dun sa formation ng
amino acid or dun sa combination ng 2 amino acids nagkakaroon ng release ng water molecule.

Peptide Bond
 An amide bond between amino acids in a protein

Polypeptide Chain
 It is formed by linking amino acids by peptide (amide) bonds

Residue
 An amino acid unit in a peptide
 Includes glycine and alanine (see figure)

NOTES:
 POLYPEPTIDE CHAIN – nafoform when amino acids usually more than a hundred are linked by a peptide or
amine bond

PEPTIDE FORMATION NO. 1

How to form a dipeptide? (See figure as a basis)
 Draw the two amino acid with the orientation of an amino group (from the left), alpha carbon, and
carboxyl group (to the right).
 Draw the reaction between the first amino acid’s carboxyl group and the second amino acid’s group to give
peptide bond
 The result is a dipeptide and water molecule

NOTES:
 For example, draw the dipeptide glyclalanine. Yung bond ay nafoform between your carboxyl and amino
group.
 Draw the reaction between the first amino acid’s carboxyl group and the second amino acid’s group to give
peptide bond. Idadraw natin yung orientation of which nagkakaroon ng bond with the first na amino acid
yung carboxyl group and yung carboxyl group ng ating una and yung amino group nung pangalawang
amino acid to give now the peptide bond.
 Magkakaroon ng release of water molecule therefore, mawawala yung isa nating oxygen plus yung
dalawang hydrogen sa part ng second amino group. Bali yung naiwan na lang e ito sa carboxyl (C=O) tsaka
eto naman sa amino group (N-H). Therefore, the result is a dipeptide and water molecule.
 San nanggaling yung water molecule? Yung kanyang dalawang hydrogen ay nanggaling kay amino group
nung second amino acid plus one oxygen group dun sa first na amino acid.

How do we name a peptide?

AMINO ACYL RESIDUES
 Referred to by replacing the suffixes of free amino acid (-ate and –ine) with vyl. Yung ine at ate papalitan
ng vyl
NOTES:
 Like for example, yung sa glycine, which ends in ine papalitan natin to ng vyl or yl. So bali yung pangalan na
nung unang amino acid is glycyl then idudugtong si alanine so yun yung ating dipeptide.
 Kunware maging tatlo like glycine+alanine+lysine so tripeptide sya. Ang mangyayare is that si alanine
papalitan natin ng yl yung ine. Bale ang magiging pangalan na is GLYCYLALANYLLYSINE. Therefore yung ine
ending sa second amino acid indicates that it is the last amino acid or ito yung may carboxyl end and itong
carboxyl end ay di na involve in a peptide bond which means sya na yung free na carboxyl end nung ating
tripeptide bond.

PEPTIDE FORMATION NO. 2

 Alanine + Glycine  Alanylglycine
(Ala-Gly)
- This is a dipeptide.
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PEPTIDE FORMATION NO. 3

How to form a tripeptide?
 Continue the process by adding a third amino
acid on the carboxyl end.

NOTES:
 Same lang yung ng tripeptide sa naming ng
dipeptide guys. OKIEE? Bali yung pangalan nung
nasa figure is ALANYLGLYCYLLYSINE.

How to form a tripeptide?

 Like the dipeptide
 we continue the process by adding a third amino acid
in the carboxyl end
 Pic: carboxyl end (yung gitna)—third unit is lysine—
magcocombine ang carboxyl at amino group to form
your tripeptide-another water molecule ulit ang
mawawala
 (C-N) first peptide bond, (C-N) second peptide bond
 3 peptides in the pic (tripeptides) Sa gitna nug
dalawang (C-N)
 Since meron syang lysine ang pangalan nya is
(Alanine, glycine lysine)

PEPTIDE FORMATION
 Meron tayong tinatawag na “End”,
may dalwang end ng peptide chain
 Amino Terminal- amino acid
residue at the end with a free a-
amino group
 In pic: Amino terminal is the H3N
 Carboxyl Terminal- amino acid
residue at the end with a free
carboxyl group
 Tinawag syang amino terminal-
kasi meron syang amino and carboxyl terminal kasi carboxyl yung kanyang free group dun sad ulo
 Other names:
- Amino Terminal  N terminal residue – meaning meron syang nitrogen end
- Carboxyl Terminal C-terminal residue – may carboxyl end
 6 Amino acids in peptide chain
 Kung irereview yung name nung peptide, peptides are named beginning in the amino terminal residue.

PEPTIDE FORMATION ASSOCIATED WITH TWO PEPTIDE HORMONES

OXYTOCIN
 Oxytocin and vasopressin is halos magkamukha
sila ng structure except that meron silang
difference in the 3rd and 8th amino acid residue
 These are peptide in nature which has 9 amino
acid residue
 Dahil magkaiba na sila ng amino acid sa
dalwang position magkaiba na sila ng name at
function
 Includes labor in pregnant women and controls
contraction of uterine muscle (more on buntis)
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 Plays a role in stimulating the flow of milk in nursing mother (yung mga may baby , ang nangyayari si
oxytocin trinitrigger ang release niya sa utak. Pag ang baby is sinusuck ang breast ni mother, yung process
ng sucking ng baby ,tinitriiger yung brain na magrelease ng oxytocin. Pag narelease ang oxytocin
iniistimulate nya yung mammary gland na magrelease ng milk.

ARGININE VASOPRESSIN (AVP)

 Merong Phenylalanine and Arginine
 Vasopressin
- Plays a role in the control of blood pressure by regulating contraction of smooth muscle
- Stimulates reabsorption of water by the kidneys, thus having an antidiuretic effect
- wala siyang kinalaman sa mga buntis; controls blood pressure
- kapag narereabsorb si water by kidneys, nagkakaroon tayo ng “anti-diuretic effect – hindi ka niya
pinapaihi
- may anti-diuretic effect kasi si water hindi muna kailangang ilabas ng katawan; kailangan ng body ng
water

PROPERTIES OF PROTEINS
 Are based on:
- Properties of the peptide backbone
- Properties of the side chains

Physical and chemical properties are determined by the 20 different amino acid side chains
 Ex. Acid-base behavior
- Acidic groups are provided by the side chains of glutamic and aspartic acids
o Ang side chains ng glutamic at aspartic acid ay negatively charged
- Basic groups are provided by the side chains of lysine and arginine
o If entire protein, majority ng amino acid constituent niya ay acidic, basic, polar, or non-polar;
ifollow ang property nay un

1. Isoelectric point
- Ang tinitignan natin dito ay yung charge ng isang amino acid – at yung pH scale (they’re associated)
- Ang basis sa properties ay yung amino acid constituent niya
- Isoelectric point is a point along the pH scale which an amino acid exists in a neutral form with a zero
charge
- Eto yung pH ng ating solution of which there is an equal number of + and – charge of an amino acid

- A n g a m i n o a c i d m a y
positive at negative naman ang carboxyl group
- Side chain ang magdidikta kung ano ang kanyang Isoelectric point

 Amino group = they are proton acceptor, basic, and (+) charged
 Carboxyl group = proton donor, acidic, and (-) charged
 Iso = equal
- Every amino acid has different Isoelecteric point; magkakaiba ng pH

 Zwitterion – from German word “Zwitter” = Hybrid

- A molecule that has an positive and negative charges
- Protein ay inilagay sa isang solution at nagkaroon ng positively and negatively charge; sya ay zwitterion.

 Isoelectric Point (pI)

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BIOCHEMISTRY MIDTERMS
- E.g. pH=1.0 (acidic)
o If the solution is acidic, ex: pH=1.0, so if the solution is acidic (like 1.0 pH) and you mix it with amino
acid, the net charge will be positive so the protein molecule will now have a net positive charge. An
acidic solution has an excess proton or hydrogen ions. What will happen? The Zwitterion (example
only of amino acid which have an equal negative and negative charge) when put in acidic solution,
the positively charge (excess hydrogen) will bond to carboxyl.
o The carboxylic group gains the proton (-COOH) and loses
its negative charge
o The amino group remains at positive charge
o Acidic solution will always have an excess hydrogen
atoms. And the hydrogen atom bonds to carboxyl and
amino acid.
o Therefore, in an acidic solution, the amino acid have net
positive charge because the negatively charge was
neutralize with excess hydrogen of acidic solution

- E.g. pH=12.0 (alkaline/basic solution)

o If the amino acid is placed in a alkaline solution, the protein molecule will have net negative charge
o The carboxylic group remains at negative charge
o If the alkaline solution have excess hydroxyl (which is a
negative charge)
o The amino group has removed a proton (-NH2) and
loses its positive charge
o The excess hydrogen will combine with OH na nasa
alkaline solution. OH causes the amino group to
donate its proton which is hydrogen to OH

 Isoelectric Point examples:

- Hemoglobin
o Isoelectric point is at pH 6.8 (have equal net charge)
- Serum Albumin
o Isoelectric point is at pH 4.9 (not equal net charge)

The isoelectric point of protein molecule is affected by the R or

functional group component of their side chains and also the
conformation of protein is affected depending on the pH of the
solution.

2. Water Solubility
- Depends upon the repulsive forces between like charges on surfaces.
o When protein molecules are at a pH at which they are (all) net positive (or net negative charge),
protein molecules repel each other. Like charges repel, opposite charges attract – protein
molecules would be soluble. But if our protein molecules have net positive charge and net negative
charge, there would be attraction and coagulation.
o At isoelectric point (net charges is zero), there are no repulsive forces, causing the protein molecule
to clump together and form aggregates (reduces solubility of protein in water) – mas nagiging
insoluble.

NUCLEIC ACIDS
Nucleic Acids
 Each cell of our bodies contains thousands of protein molecules. These protein molecules have their own
function. These protein molecules are made up of the same 20 amino acids and arranged in different
sequences.
 Take note: same species, those who are in the same species they have some differences in their proteins
but these variations are more obvious to those with diseases.
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BIOCHEMISTRY MIDTERMS
 The amino acid sequence of every protein in the cell is dictated by the sequence of the nucleotide.
 Therefore, every amino acids in the cell is dictated by the sequence of the DNA.
 The difference of protein to nucleic acid is that
o protein may primary, secondary, tertiary, and quaternary
o nucleic acid has primary, secondary, and higher order structures.

Gene
 Unit of heredity
o Heredity: transfer of characteristics from one generation to another generation.
o These characteristics are maybe ANATOMICAL(structure of the body) or BIOCHEMICAL(functions
or the processes at molecular level, genetic disorders).

 controls the manufacture of one protein and that it expresses external or internal characteristics (George
Beadle and Edward Tatum).
 A segment of DNA molecule that contains the information required for the synthesis of a functional
biological product, whether protein or RNA.
o Gene codes for one protein or another type of RNA.
 The information therefore, that tells the cell which protein to manufacture is carried to the molecules of
the DNA.
 Nucleus- where transfer of hereditary information from one generation to
another took place
o chemical analysis of nuclei shows that the nucleus is made up of
special basic proteins (histones) and surrounded by nucleic acids
 " only DNA carries the hereditary information" - Oswald Avery

Nucleic acids
 Consist of a large number of linked nucleotides
 Nucleotides is the building block (monomer) of nucleic acid
o Composes of sugar, phosphate and nitrogenous base
o Sugars and phosphates are alternating and they form the backbone. They play as a structural role
 the sequence of nitrogenous bases along nucleic acid strands carries the genetic information. The genetic
information depends on the sequence of nitrogenous bases.

Nucleotides
 Composed of 3 simpler units (base, monosaccharide, phosphate)
 Two types of nucleic acids found in the cell the DNA and RNA—both are polymers
DNA RNA
Present in the chromosomes of the nuclei Located elsewhere in the nucleus and cytoplasm
A, G, C , T bases A, G, C , U bases
2-deoxy-D-ribose (sugar) — deoxygenated at D-ribose (sugar)
carbon 2
Almost always double stranded Single stranded
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BIOCHEMISTRY MIDTERMS

FUNCTIONS OF NUCLEOTIDES
1. Basic for sources of energy
Take note: the basis of sources of energy is our Adenosine triphosphate
(ATP).
2. It is an important constituent of several coenzymes
3. It is a building blocks of the nucleic acids

NITROGEN BASE OR NITROGENOUS BASE

 It is a heterocyclic aromatic amines:
 AROMATIC – it is a cyclic structure with alternating single and double
bonds. Therefore, nitrogenous bases are alkaline in nature.

NITROGENOUS BASE CAN BE:

1. PYRIMIDINE
- consists of a cyclic structure with alternating single and double
bonds (aromatic)
- It is a single ring aromatic compound.
- Includes: cytosine, uracil (found in RNA), thymine (found in DNA).
2. PURINE
- consist of 2 nitrogen rings, it is a double ring aromatic
compound
- The 2 nitrogen rings are pyrimidine (6 carbon) like and an
imidazole ring (5 carbon)
- Includes: adenine and guanine

TAKE NOTE:
 If both purine and pyrimidine are linked or attached with the sugar or a monosaccharide, the hydrogens at
some parts of the structure are lost.
 For purine: Nitrogen at 9th position is missing
 For pyrimidine: Hydrogen at the 1st nitrogen position
 In these areas the monosaccharides are attached

NOTE:
 Our Nucleic acid bases are nitrogen containing aromatic
compounds that make up the coding portion of the nucleic
acid.
 The 5 Nitrogenous bases are the compositions of the codes of
a nucleic acid.
o Deoxyribose vs ribose

MONOSACCHARIDES
 Can be a D- ribose (RNA) or 2-deoxy-D-ribose (DNA)
- Full name of ribose(green): beta D- ribofuranose
 It is a ribose in a furan form or 2-deoxy-D- ribose (DNA)
- Full name of Deoxyribose (blue): beta 2-Deoxy D-
ribofuranose

NUCLEOSIDE
- Sugar + base= water
- When sugar or monosaccharides and nitrogenous base
are combined.

NOTES ON PIC: Adenosine

 At purine: Nitrogenous bases are linked at the 9th nitrogen
position so they are linked to the carbon 1 of our
monosaccharide through beta-N-glycosidic bond.
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BIOCHEMISTRY MIDTERMS
 During this process, water molecules are removed or there is dehydration.

NUCLEOSIDE VS. NUCLEOTIDE

This table is for DNA

BASE NUCLEOSIDE NUCLEOTIDE (base + sugar + phosphate)
(base + sugar)
Adenine Deoxyadenine Deoxyadenosine 5’- monophosphate (dAMP)
Guanine Deoxyguanosine Deoxyguanosine 5’- monophosphate (dGMP)
Thymine Deoxythymine Deoxythymidine 5’- monophosphate (dTMP)
Cytosine Deoxycytidine Deoxycytidine 5’- monophosphate (dCMP)

This table is for RNA

BASE NUCLEOSIDE NUCLEOTIDE (base + sugar + phosphate)
(base + sugar)
Adenine Adenine Adenosine 5’- monophosphate (AMP)
Guanine Guanosine Guanosine 5’- monophosphate (GMP)
Uracil Uridine Uridine 5’- monophosphate (TMP)
Cytosine Cytidine Cytidine 5’- monophosphate (CMP)
NUCLEOTIDES
PHOSPHATE
 PHOSPHORIC ACID – the third component of nucleic acid.

NOTES ON PIC:
 In the picture it is shown that a three
phosphate is fine to form ATP.
 Adenosine Triphosphate serves as a common
currency into which the energy gain from
food is converted and stored.
 For ATP, there are more than 1 phosphate (3
phosphate)
- ANHYDRIDE, ESTER, AMP, ADP, ATP

THIS IS THE COMPLETE STRUCTURE OF NUCLEOTIDES

DNA AND RNA STRUCTURE

 Nucleic acids are chains of monomers and have

different structures: primary, secondary, higher order structure
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BIOCHEMISTRY MIDTERMS

PRIMARY STRUCTURE
 It is the sequence of nucleotides

DIVIDED INTO 2 PARTS:

1. Backbone of the molecule
- Which consist the alternating sugar and phosphate group
- Each phosphate is linked at the 3’ position and another at the 5’
position of our sugar.
- Provides structural stability for the DNA and RNA molecules.
2. Bases that are the side chain groups
- They carry all necessary information for protein synthesis
- The order of bases provides the primary structure. The 4 bases of each
nucleic acid are arranged in different or in various specific sequences,
and that is our primary structure.

NOTE:
The primary structure of RNA is the same with DNA, except that the
sugar is a ribose. And the base in RNA is Uracil instead of Thymine.
 The first thing to look at in a nucleotide is the sugar, if it's
deoxygenated or ribose because at:
- Carbon 2 and deoxygenated – the nucleotide is found in the
DNA

 The backbone of the DNA and RNA chains has 2 ends:

- 3’- OH end (terminus)
- 5’- OH end
 each phosphate is linked at the Carbon 3’ position of the first
monosaccharide and another at the Carbon 5’ position of the
second monosaccharide
 2 ends of the structure have a rule similar to those of the C
terminal and N terminal ends in protein.

SECONDARY STRUCTURE
 Two strands have opposite polarity (antiparallel)

On the video:
 Double stranded DNA intertwined to form the double helix
 B-form DNA—the most common form of the DNA double helix
 The nitrogenous base is always attached at the one prime of the sugar
 Nucleotides attached to each other at the DNA strand by phosphodiester bonds
o the phosphate group of one nucleotides binds to 3’ oxygen of the neighbouring nucleotides
 The carbon membrane is key to describing the directionality of the DNA strand: 5’ to 3’ (Watson)
 Bottom strand: 3’ to 5’ (Crick)
 The two DNA strands interact thru non-covalent hydrogen bonds between the bases
o Contributes to specificity of base-pairing
o Thymine-adenine—2 hydrogen bonds
o Cytosine-guanine—3 hydrogen bonds
 Each turn of the helix measures approximately 10 base-pairs, regular
 Pi-pi interactions- formed when the aromatic rings of the bases stuck next to each other and share
electron probabilities
 Major (base-pair specific information) and minor grooves ( base-pair non specific information) due to
pattern of hydrogen bonds acceptors and donors that proteins can interrupt with in the grooves
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BIOCHEMISTRY MIDTERMS

James Watson and Francis Crick

- Their work became the cornerstone in the history of biochemistry
Established the 3-dimensional structure of DNA based on two pieces of information:
1. Chargaff Rule
- Base pairing; compatibility
- Complementary/Compatible base pairing occurs because of the stability of hydrogen bonds
2. X-ray diffraction photographs by Rosalind Franklin and Maurice Wilkins
- Rosalind is a British Scientist and known for her contribution in discovering to the molecular structure
of the DNA
- Maurice Wilkins is the third man
3-dimensional structure of DNA
 DNA is composed of 2 strands entwined around each other in a
double helix

DNA double helix

 Arrangement which 2 strands of DNA are coiled around each other
in screw-like fashion.

Note:
 The 2 polynucleotide chains run in opposite direction.
 The first strand is at the 5’ -3’ direction, whereas the second strand
runs from 3’-5’ direction.
 Based on the structure, the sugar-phosphate backbone is exposed to the aqueous environment, and the
bases point inward (hydrophobic).
o The hydrophobic interactions of the bases stabilises the double helix.

DNA double helix

 Are not equally spaced
 Backbone is located outside
 Bases located inside and paired according to Chargaff’s rule

 Major group and Minor Group = 1 complete turn

 1 turn = 10 base pairs
 Chargaff’s rule: kung ano ba yung compatible na base-pairing
natin

In the picture:
 Adenine and Thymine (A-T) = 2 hydrogen bonds
 Guanine and Cytosine (G-C) = 3 hydrogen bonds
 The entire action of the DNA and the hereditary mechanism
depends on base pairing
- Because it is the only base that fits and forms strong
hydrogen bonds (stabilizer)
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BIOCHEMISTRY MIDTERMS
- The entire heredity mechanism rests on this alignment of hydrogen bonds

T-G
/ C-A  The bases of DNA cannot stack properly in the
 There’s only one hydrogen bond double helix if a purine is in the opposite of a
 These combinations are not found in DNA purine or a pyrimidine is the opposite of the
pyrimidine
Purine - Purine  In the secondary structure, 3D model and the
 There would be a gap between the pyrimidines base-pairing and the hydrogen bonds that
stabilises the structure
Pyrimidine - Pyrimidine
 There would be an overlap of 2 Purines NOTE: Same as with protein, hydrogen bond
stabilises the structure
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BIOCHEMISTRY MIDTERMS
Higher-Order Structure of DNA
- histones: specialised proteins in the nucleus, where the DNA coiled
 Superstructure: chromosome
 Highlights the packing of Higher-Order Structure of DNA
 DNA Helix/ DNA molecules
- It may seem to be stretch out but they are not but rather they are
coiled around a basic protein molecules called histones.

 Nucleosome
- A unit formed when the DNA (acidic) and histone (basic) attract each
other by electrostatic or ionic forces.
- Further condensed into chromatin.

 Chromatin
- Formed when nucleosomes are
further condensed and wound
in a solenoid fashion
- Chromatin fiber is a pack of
nucleosome

 Solenoid
- A coil wound in the form of a
helix with 6 nucleosomes forming a repeating
unit
- As it forms helix, chromatin fibers organised
further into loops which are arranged into
bands which provides the super structure of
the chromosome

Short region of DNA double helix 2 nm

Beads on a string form of chromatin 11 nm
30-nm chromatin fibre of packed nucleosomes 30 nm
Section of chromosome in an extended form 300 nm
Condensed section of chromosomes 700 nm
Entire mitotic chromosomes 1400 nm

Classes of RNA
 Have several kinds but none of them have repetitive double stranded structure like the DNA
 They are single-stranded although base pairing can occur within the chain and when it does, the adenine
pairs with uracil because thymine in not present in RNA
 Participate in protein synthesis

VIDEO PRESENTED BY YOUTUBE:

 Cell is the basic unit of all living tissue
 Nucleus contains the genome. In humans, the genome is split between 23 pairs of chromosomes.
 Each chromosome contains a long strand of DNA which are tightly packaged around protein called
histones.
 Within the DNA are sections called genes. These genes contain the instruction of making proteins. When a
gene is switch on, an enzyme called RNA polymerase attaches to the start of the gene, it moves along the
DNA making a strand of messenger RNA out of free bases on the nucleus.
 The DNA code determines the order in which the free bases are added to the mRNA. This process is called
TRANSCRIPTION
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BIOCHEMISTRY MIDTERMS
 Before the mRNA can be used as a template to produce proteins, it needs to be processed, which involves
removing and adding sections of RNA.
 The mRNA moves out of the nucleus into the cytoplasm. Protein factories in the cytoplasm called
ribosomes binds to mRNA. The ribosomes read the code in the mRNA to produce a chain made of amino
acids.
 There are 20 types of amino acids. Transfer RNA carry the amino acids to the ribosome. The mRNA read
three bases at a time. As each triplets are read, a tRNA delivers a corresponding amino acid which are
added to growing chain of amino acid. Once the last amino acid has been added, the chain folds into a
complex 3D shape to form protein

Information Transfer in Cells

 The various kinds of RNA participate in the synthesis of protein.
 In series of reaction, they are ultimately directed by the basic
cells of DNA
 On all types of RNA and the amino acid that will be attached on
growing peptide chain is determined by the basic quench found
in the DNA
 Involves how protein are being synthesized
 Two process:
1. Transcription of nucleotide sequence of DNA
- Information is encoded in the nucleotide sequence of
the DNA which are located in the base pair ,
transcribed through synthesis of an RNA molecule
whose sequence is dictated by DNA sequence.
- base sequence is transcribed into mRNA
2. Translation of RNA nucleotide sequence into amino acid
sequence
- mRNA sequence are read as groups of 3 consecutive
nucleotides known as codons
- codons are translated into the sequence of amino acids in a protein
2 LANGUANGES: mRNA language and language of the protein which the sequence of the amino acids

Replication
 DNA replication yield 2 DNA molecules identical to the original one
 Replication is a process that ensures transmission of genetic information to the daughter cells with
exceptional fidelity (identical to the original)

Transcription
 the sequence of bases is recorded as a sequence of complementary bases in a single stranded mRNA
molecule
 DNA—>mRNA (both nucleotides)
 Uracil—Adenine pairing

Translation
 3-base codons on the mRNA corresponding to the specific amino acids direct the sequence of building a
protein dito natin malalaman kung ano ang pagkakasunod sunod ng ating mga amino acids
 Nucleotides—>amino acids
 3 types of RNAs that are present in our translation process:
- mRNA
- tRNA – recognizes the codons, which carries the appropriate amino acid
- ribosomal RNA.
NOTE: occur in the ribosomes—machinery of protein synthesis

Classes of RNAs:
Messenger RNA (mRNA)
 Carries genetic information from DNA to the ribosome and acts as a template for protein synthesis
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BIOCHEMISTRY MIDTERMS
 Consists of a chain of nucleotides whose sequence is exactly complementary to that of one of the strands
of the DNA
 MRNA DO NOT LIVE LONG, they are synthesized as needed and are degraded
o Their concentration at any given time is very low
o Produced in a process called transcription

Transfer RNA (tRNA)

 Transports amino acids to the site of protein synthesis in ribosomes
 Can be L-shaped (3-dimensional) or clover leaf (2-dimensional) in structure (usually used)
 Contains not only cytosine, guanine, adenine, and uracil but also several other modified nucleotides such
as 1-methylguanosine

Ribosomal RNA (rRNA)

 The RNA complexed with proteins
 Found in ribosomes:
- Small spherical bodies located in the cell but outside the nuclei
- Site of protein synthesis
- Contains subunits:
o Larger
 Prokaryotes = 2 RNA molecule 35 different proteins
 Eukaryotes = 3 RNA molecule and 50 different proteins
 Where we can find our tRNA docking sites
o Smaller
 Consists of one large RNA molecule and 20 different
proteins
 Where we can find our mRNA binding sites

Small Nuclear RNA (snRNA)

 Found in the nucleus of eukaryotic cells
 Complexed with proteins to form snRNPs (small nuclear
ribonucleoprotein particles)
 Prepare the mRNA before proceeding to transcription
 Helps with splicing reaction
- process that helps with the processing of the initial mRNA transcribed from DNA into a mature form
that is ready to export out of the nucleus

Micro RNA (miRNA)

 Type of small RNA
 Has a role in cancer, stress responses, and viral infections
 Inhibit translation of mRNA into protein and promote the degradation of mRNA
 Stimulate protein production in cells when the cell cycle has been arrested or stop.

Small Interfering RNA (siRNA)

 Used to eliminate expression of an undesirable gene (one that causes uncontrolled cell growth or one that
came from a virus)
 Lead to degradation of specific mRNA molecule

RNA TYPE FUNCTION

tRNA Transports amino acids to site of protein synthesis
rRNA Transports amino acids to site of protein synthesis
mRNA Directs amino acid sequence of proteins
snRNA Processes initial mRNA to its mature form in
eukaryotes
siRNA Affects gene expression: used by scientists to knock
out a gene being studied
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BIOCHEMISTRY MIDTERMS
miRNA Affects gene expression; important in growth and
development

DNA REPLICATION

YOUTUBE VIDEO:
 DNA is a molecule made up of two strands twisted around each other in a double helix shape.
 Each strand is made up of a sequence of four chemical bases represented by the letters A,C, G, T.
 The two strands are complementary. This means that wherever there’s a T in one strand there will be an A
in the opposite strand, and wherever there’s a C there will be a G in the other strand.
 Each strand has a 5’ end and a 3’ end. The two strands run in opposite directions
 This determines how each strand of DNA is replicated.

STEPS:
 The first step in DNA replication is to
separate the two strands. This
unzipping is done by an enzyme
called helicase, and results in the
formation of a replication fork.
- The separated strand each
provide a template for creating
a new strand of DNA
 An enzyme called primase starts the process. This
enzyme makes a small piece of RNA called a
primer. This marks the starting point for the
construction of the new strand of DNA.
 An enzyme called DNA polymerase binds to the
primer and will make the new strand of DNA.
 DNA polymerase can only add bases in one
direction from the 5’ end to the 3’ end.
 One of the new strands of DNA, leading strand is
made continuously, the DNA polymerase adding
bases one by one in the 5’ to 3’ direction.

 The other strand, the lagging strand,

cannot be made in the continuous way
because it runs in the opposite
direction.

 The DNA polymerase can therefore only

make this strand in a series of small
chunks called Okazaki fragments.
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BIOCHEMISTRY MIDTERMS
 Each fragment is started with an RNA primer.
 DNA polymerase then adds a short row of DNA bases in the 5’ to 3’ direction.
 The next primer is then added further down the lagging strand.
 Another Okazaki fragment is then made and the process is repeated again.
 Once the new DNA has been made. The enzyme exonuclease removes all the RNA primers from both
strands of DNA.
 Another DNA polymerase enzyme the fill in the gap that are left behind with DNA
 Finally, the enzyme DNA ligases seal up the fragment of DNA in both strands to form a continuous double
strand.
 DNA replication is described as semi-conservative. Because each DNA is made up of one old, Conserved
strand of DNA and one new one

DNA in the chromosome carries out 2 function

1. It produces itself/ REPLICATION processes
- The process by which copies of DNA are made during cell division.
- supplies the information necessary to make the RNA and proteins to the body, including your enzymes
2. Synthesis of products such as protein and RNA
molecules

OVERVIEW OF THE REPLICATION PROCESS

1. double helix of DNA
- composes of sugar phosphate backbone (outer
line) and nitrogenous bases ( horizontal lines)
2. Before replication, parent strands must split
-
double
helix
separates forming 2
strand
3. 2 strands act as a
template which is the
basis of the new strand that
will be copied and formed.
4. Complementary base
pairing, Chargaff’s Rule
o Percentages of
Adenine and
Thymine bases are
almost equal in any
sample of DNA
5. 2 Daughter strands
(semi-conservative- combination of old and new DNA strand
NAME FUNCTION
HELICASE Unwinds parental double helix
DNA POLYMERASE Forms new strands
 enzymes that create DNA molecules by
assembling nucleotides
 enzyme involves in the elongation process
DNA polymerase 1 (exonuclease) removes RNA
primer and inserts the correct bases
PRIMASE Adds a short primer to template strand
LIGASE Joins Okazaki fragments and seals gaps in sugar-
phosphate backbone
TOPOISOMERASE catalyse and guide the unknotting or unlinking of
DNA by creating transient breaks in the DNA using a
conserved tyrosine as the catalytic residue.
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BIOCHEMISTRY MIDTERMS

 The 2 strands run in antiparallel or opposite

directions
 The DNA polymerase only adds a nucleotide at
the 3 end of pre-existing chain to synthesize the
new complementary strand of the DNA thus all
synthesis of the nucleotide occurs in the 5’ to 3’
direction

STEPS OF DNA REPLICATION (ppt)

1. OPENING UP THE SUPER STRUCTURE

a) The very condensed super structure of
chromosome must be opened so that it
becomes accessible to enzymes and other proteins.
b) Diba yung DNA natin is makikita siya sa chromosome. Then yung structure ng chromosome
napapalibutan ng histones yung DNA so kailangan yung chromosome must be open. So that it’s
accessible to the different enzyme that will
participate in the process as well as yung other
proteins natin.

2. RELAXATION HIGHER-ORDER STRUCTURES OF

DNA
a) Facilitated by topoisomerases (gyrases)
b) So, the gyrases are enzymes that facilitated
the relaxation of the supercoiling in DNA by
temporarily introducing either single or double
strand in the DNA
NOTE: Once the supercoiling is relaxed,
topoisomerases diffuses from the location of the
replication fork.

3. UNZIPPING OF THE DNA HELIX

a) The helicase acts on the hydrogen bond
between the base pairs which leads to the
opening of the helix and creation of the
replication forks.
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BIOCHEMISTRY MIDTERMS
SINGLE STRAND BINDING PROTEIN (SSB)
- Reacts with the single stranded regions of the unwound DNA to hold the strands aparts and stabilize
them.

4. FORMATION OF PRIMER
a) Required to initiate the synthesis of the new nucleotide sequence
b) Catalyzed by the enzyme primase
- DNA polymerase cannot initiate the synthesis of the complementary base pair of the daughter strand,
thus, it needs a primer

PRIMER
o short RNA oligonucleotides synthesized from ribonucleoside triosphate
o Sequence of 10 nucleotides complementary to the parent DNA
o After elongation, primer must be removed because it is RNA in nature

5. ELONGATION
a) Performs by the enzyme DNA polymerase
b) Addition of new nucleotides (adenine, cytosine, guanine and thymine) to the 3’ end of the growing
chain)

Their difference first is the direction.

LEADING STRAND LAGGING STRAND
Runs in 3’ to 5’ direction (same direction as the Runs in 5’ to 3’ direction (opposite direction as the
helicase opening the helix) helicase opening the helix)
Continuous synthesis Discontinuous synthesis (formation of short
fragments)
NOTE: formation of short fragments in lagging strand which are okazaki fragments.

Take note:
Synthesis of DNA strand— from 5’ to 3’ direction
6. LIGATION
a) Performs by the enzyme DNA ligase
b) Okazaki fragments and any nicks remaining are joined together by enzyme ligase (

GENE EXPRESSION AND PROTEIN SYNTHESIS

Central Dogma of Molecular Biology states that

“The information contained in DNA molecule is transferred to RNA molecules,and then from the RNA
molecules, the information is expressed in the structure of proteins’’

Transcription and translation represents the

general cases, from DNA to RNA to PROTEIN.
But, we have a reverse transcription represents
special cases in RNA Viruses .
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BIOCHEMISTRY MIDTERMS
Gene Expression – is a process by which functional product (protein or another type of DNA) are made from
genes
a) The activation of a gene to produce a specific protein or other functional products
b) Involves:
1. Transcription – production of RNA from a gene
2. Translation – production of proteins by the ribosomes using now the RNA from the transcription
process

1. TRANSCRIPTION
a. The process in which information encoded in a DNA molecule is copied into and mRNA
molecule
b. Occur in the nucleus
 mRNA – carries the information from the nucleus to the site of protein synthesis
 rRNA – forms the ribosomes
 tRNA – required to carried out the translation into protein language

Take note: The information in the DNA , thus it is in the nucleus of the cell, and the amino acid are assembled
outside the nucleus. So with this, the information from the DNA must be carried out of the nucleus.

TRANSCRIPTION
 Starts when the DNA double helix begins to unwind at a point near the gene that is to be transcribed.
 The start of transcription process: DNA unwinding

TEMPLATE STRAND CODING STRAND

(-) strand, antisense strand (+) strand, sense strand

Strand that serves as a template for the formation of Strand with a sequence that matches the RNA that
RNA will be produced during transcription

The difference between the coding strand and mRNA

- Sugar and uracil and thymine bases
Nucleosome – DNA coiled to histone

Specific binding proteins binds to the nucleosome making the DNA become less dense and more accessible,
then, the helicase which is a ring shape complex of a six protein subunits, unwind the double helix.

Only one strand of DNA molecule is transcribe and that is the template strand. The coding strand will now be
used as a template.

3 TYPES OF RNA POLYMERASE

 Pol 1- formation of most of the rRNA
 Pol 2- formation of mRNA
 Pol 3- formation of tRNA as well as one ribosomal subunit and other small regulatory RNA types (snRNA)
2. TRANSLATION
- Happens in the ribosome
- The process in which the genetic information preserved in the DNA and transcribed into mRNA is
converted to the language of proteins(amino acid sequence)
- The information encoded in the mRNA molecule is used (yung nakuha ni mRNA from DNA is ginagamit
to assemble a specific protein
- The protein synthesis takes place in the ribosome (ang nangyayari dito is that
-
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BIOCHEMISTRY MIDTERMS
- The mRNA is attached to the ribosomal body specifically in the small subunit (mRNA binding site) and
amino acids are brought to the site which are carried by tRNA molecule

- Ribosome has two parts: (1) larger subunit (2)smaller subunit and has also different sites.
a) mRNA binding site – where the mRNA enters
b) Aminoacyl site
c) Peptidyl site—attachment of amino acid to growing polypeptide chain
d) E site- exit

3 BINDING SITES:
1. A site = where the incoming
aminoacyl-tRNAs enter the
ribosome (dito pumapasok yung
tRNA na may amino acid)
2. P site = where the peptidyl-tRNA
carrying the growing polypeptide
chain is held
3. E site = holds the empty tRNA just
before they exit the ribosome

3 PHASES OF TRANSLATION:
1. Initiation
- the ribosome assembles around
the target mRNA and the first
tRNA is attached at the START CODON (these are three bases of the mRNA, initiates translation
process)
- Codon = these are triplets of bases in the mRNA
2. Elongation – the tRNA transfers an aminoacid to the tRNA corresponding to the next codon and the
ribosome moves to the next mRNA codon to continue the process (addition of amino acid in the growing
polypeptide chain)
3. Termination – a peptidyl tRNA encounters a STOP CODON and the ribosome folds the polypeptide units
into its final structure
PICTURE of the process of translation

NOTE: Entire process of gene expression and protein synthesis is summarized in this picture.
1. DNA. In nucleus serves as a template.
2. mRNA is processed before leaving the nucleus
3. When mRNA is formed it has codons
4. mRNA moves into cytoplasm and becomes associated with ribosomes
5. tRNA with anticodon carries amino acid to mRNA
6. Anticodon-codon complementary base pairing occurs
7. Peptide chain is transferred from resident tRNA to incoming tRNA
8. tRNA departs and will soon pick up another amino acid.
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BIOCHEMISTRY MIDTERMS

GENETIC CODE
 Is the sequence of triplets of nucleotides (codons) that determines the sequence of amino acid in a
protein.
 The order of bases in a DNA molecule corresponds to the order of amino acid in a particular protein
 Marshall Nuremberg— attempted to break the code
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BIOCHEMISTRY MIDTERMS
U C A G
U UUU Phenylalanine UCU Serine UAU Tyrosine UGU Cysteine U
UUC Phe UCC Ser UAC Tyr UGC Cys C
UUA Leu UCA Ser UAA Stop UGA Stop A
UUG Leu UCG Ser UAG Stop UGG Trp G
C CUU Leucine CCU Proline CAU Histidine CGU Arginine U
CUC CCC CAC His CGC C
CUA CCA CAA Glutamine CGA A
CUG CCG CAG Gln CGG G
A AUU Isoleucine ACU Threonine AAU Asparagin AGU Serine U
AUC Ile ACC Thr AAC e AGC Ser C
AUA Ile ACA AAA Asn AGA Arginine A
AUG Methionine ACG AAG Lysine AGG arg G
Lys
G GUU Valine GCU Alanine GAU Aspartic GGU Glycine U
GUC Val GCC Ala GAC Asp GGC Gly C
GUA GCA GAA Glutamic GGA A
GUG GCG GAG Glu GGG G

AUG = serve as the principal initiation codon, corresponding amino acid is methionine
UGA,UAA,UAG= STOP codon

Genetic code example:

Codon:
 CGU (5’-3’)
Amino acid:
 Arginine
Anticodon:
 GCA (3’-5’)