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Biomolecules
Biomolecules
Biomolecules
- Of the ~92 natural elements, about 20– 25% - Valence electrons - are those in the outermost
required for life (essential elements) shell, or valence shell
- Carbon, Hydrogen, Oxygen, and Nitrogen make • Octet rule – to become stable, atoms
up 96% of living matter combine to fill the outer valence shell.
- Most of the remaining 4% consists of calcium, • Elements with a full valence shell are
phosphorus, potassium, and sulfur chemically inert (Nobel gases- He, Ne, Ar, Kr, Xe,
- Trace elements are required by an organism in Rn)
only minute quantities
Atoms
- smallest constituent of ordinary matter
• Proton – a positively charged (+1)
subatomic particle found in the nucleus.
• Electron – a negatively charged (-1)
subatomic particle that orbit the nucleus.
• Neutron – another subatomic particle
found in the nucleus. Has no charge
Note: Neutron mass and proton mass are almost
identical and are measured in Dalton • An orbital is the three-dimensional space
where an electron is found 90% of the time
- Atoms of the various elements differ in • Each electron shell consists of a specific
number of subatomic particles number of orbitals
- Atomic number - number of protons in its
nucleus
- Atomic Charge – number of electrons
- Mass number - sum of protons + neutrons
in the nucleus
- Atomic mass - atom’s total mass, can be
approximated by the mass number
Molecular Shape
Chemical Reactions
Note: The most electronegative element is
Fluorine. - making and breaking of chemical bonds
Types of Bonding - The starting molecules of a chemical reaction are
called reactants
1. Ionic Bond - The final molecules of a chemical reaction are
- This bonding requires the transfer one electron to called products
the other. Thus, one atom
gains an e- while the other loses it.
- Involves two atoms of opposing charges, a
positive (cation) and a negative (anion) atom. Properties of Water
- Usually involves a metallic and a nonmetallic
atoms. Water
• Compounds formed by ionic bonds are called - transparent, odorless, tasteless, and nearly
ionic compounds, or salts colorless substance that covers around 71% of the
Example: NaCl Earth’s surface.
- Only 0.3% are available for consumption
2. Covalent Bond - Consists of 2 Hydrogen and 1 Oxygen
- A bond that shares, rather than donates, atoms
an electron to its pair. - This substance is crucial to the development
• Nonpolar covalent bond – the atoms and sustainment of life.
share the electron equally
• Polar covalent bond – one atom is more 1. Water has a high surface tension
electronegative, and the atoms do not share the Surface tension – elastic tendency of the
electron equally surface of liquids which makes it acquire the least
- Due to a slight positivity or negativity of either possible surface area
atom, the bond will produce a dipole moment - Due to the hydrogen bonds created by water;
Two types:
3. Hydrogen Bond Cohesion – attraction of liquid molecules,
- is a relatively weak bond particularly water, to attract each other.
- A bond that greatly relies on the element Adhesion – attraction of liquid molecules to
Hydrogen [H+] for bonding. other substances aside from its own.
- Due to its highly positive nature, H+ can bind to a
highly electronegative atom in a different molecule 2. Water has a high temperature range
(such as O, F, N) - Water remains liquid at (0-100oC); it freezes at
0C and boils at 100C
4. Van der Waals - Due to its hydrogen bond, it requires high energy
to break apart, allowing it to stay liquid, allowing
life to prosper.
• Play an important role in the formation of the
3. Water has a High Specific heat macromolecules
Specific heat – amount of energy required
to change the temperature of a substance
(compare to heat capacity C)
- Water takes or loses massive amount of energy
before it warms up or cools down, respectively
Macromolecules
- A very large molecule created by the
polymerization of smaller subunits (monomers).
These are extremely important in the maintenance
of life.
- Monomers can be chemically connected through
dehydration reaction or disassembled through
5. Neutral pH
• Water is neither acidic or basics. In its
purest form, it is neutral; 7
• When substances are introduced, that is when
water can change its pH hydrolysis.
Macromol Monomer Polymer Linkage
• Acids – substances that gives up hydrogen ecule
ions. Has a pH of below 7.0 Carbohydr Monosacch Polysaccha Glycosidic
• Bases – substances that gives hydroxyl ate aride ride bond/linkag
ions. Has a pH of above 7.0 e
pH = - log10([H+]) or log10(1/[H+]) Lipid Fatty acids Not a Ester bonds
and polymer
pOH = - log10([OH-]) or log10(1/[OH-]) glycerols
Protein Amino Polypeptid Peptide
6. It has a high polarity acids e bonds
- Its polarity is due to the oxygen and the two Nucleic Nucleotides Polynucleo Phosphodie
hydrogen atoms in its molecule. Acid tide ster bonds
- Because of this, water can dissolve a high number
of substances. 1. Carbohydrates (C H O)
• Thus, it is called the Universal Solvent • polyhydroxy aldehyde or polyhydroxy ketones or
Rule of thumb: like dissolves like – a polar complex substances which on hydrolysis yield
molecule dissolves a polar molecule while a polyhydroxy aldehyde or polyhydroxy ketone
nonpolar molecule dissolves a nonpolarmolecule o aldehyde(-CHO)
o ketone(-CO-)
Macromolecules: The functional groups - contains C, H, and O, which usually has a formula
• The most important list you need to know in of - Cm(H2O)m
Biochemistry - hence, Hydrated carbon compounds
• A specific group of atoms that have a very
- Carbon atoms are linked to the hydrogen atom and
particular set of characteristics and behavior,
-
regardless of the atoms present a hydroxyl (OH ) group.
- Deoxygenated sugars:
• Example: Deoxyribose (C H O ) • Carboxyl head(-COOH)
5 10 4
• Hydrocarbon tail
(compare to ribose C5H10O5)
-However, all lipids are hydrophobic due to the
hydrophobic tail being relatively longer than the
A. Types of Carbohydrates
head.
1. Monosaccharides
- The simplest sugars
A. Types of Lipids
- monomer (subunit) for carbohydrates
1. Saturated fatty acids
- Most common types are pentose (5-carbon) and
- These are fatty acids that doesn’t have any
hexose (6-carbon)
double or triple bonds in its fatty acids
- Other Examples: Triose and Tetrose
- solidifies at room temperature
- Examples: Glucose
Galactose
2. Unsaturated fatty acids
Fructose
- These are fatty acids that have double and or
triple bonded carbons
2. Disaccharides
-liquid at room temperature
- two monosaccharides.
- Examples
• Sucrose – Glucose + Fructose
3. Trans-fatty acids
• Lactose – Galactose + Glucose
- are a form of unsaturated fat.
• Maltose – Glucose + Glucose
- formed when a unsaturated fat( normally liquid at
room temp) is hydrogenated
3. Oligosaccharides
Hydrogenation - is a chemical reaction that
- These are carbohydrates that are made-up of three
adds hydrogen to a molecule.
to ten monosaccharides.
- this process removes double/triple bonds. Note:
- Used in many biological processes.
When Double/Triple bonds are removed, this
- Can bound to proteins as Glycoprotein or Lipids
increases the melting point of a fat. Thus, trans fats
as Glycolipids
are unsaturated fats that are solid at room
-Functions for Cell Recognition and Cell Adhesion
temperature.
4. Polysaccharides
- These are long polymers of monosaccharides that
are linked together.
- The nature of polysaccharides are not only
dependent to its composition, but also the way they
are bounded.
- Example: Starch and Cellulose
Glycogen
Chitin
B. Type of Molecular Bond
- Glycosidic bond/linkage – a type of covalent
bond that links carbohydrates from each other
- Dehydration or condensation- linking of the - Cis-trans isomerism
monosaccharides involves the removal of the OH - Happens when a pair of molecules, having the
group of monosaccharide and a hydrogen atom same formula, have different orientation.
from the other (reaction. - Happens when a carbon creates a double-bond to
2. Lipids (C H O)_ another carbon
- Naturally occurring compounds that include fats, - Cis – Same Side
waxes, sterols, fat-soluble vitamins(Vitamins A, - Trans – Opposite side
D, E, K), etc. -Triglycerides
- Monomer: Fatty acids - Free fatty acids are relatively rare, they are
- Has a polar head and a nonpolar tail normally esterified to glycerols
- When bounded to each other, the molecule is
called Triglycerides or triacylglycerides (TAG).
Lipids: Phospholipids
- These are one of the most important lipids in a cell
because they are the major components of the cell
membrane.
• Amphiphilic – a molecule that possesses
both hydrophobic and hydrophilic properties
• Hydrophilic head – due to a phosphate Lipids: Waxes
group - Complex and varying mixtures of lipids with long
• Two Hydrophobic tail – fatty acids fatty acid tails. These are used as a water repellant,
prevent water loss, or as a lubricant.
Phospholipid Aggregation: How are
phospholipid bilayers formed? Lipids: Steroids
- Lipids with a rigid backbone of four carbon
Phospholipids rings with no fatty acid tails. The functional group
- are the basic components of all present-day that is attached to the steroid defines if.
biological membranes, including the plasma - Example: Testosterone and Progesterone
membranes of both prokaryotic and eukaryotic
cells.
- the key characteristic of the phospholipids that
form membranes is that they are amphipathic
molecules, meaning that one portion of the
molecule is soluble in water and another portion is
not.
- long, water-insoluble (hydrophobic) hydrocarbon 3. Proteins (C, H, O, N for amine group)
chains joined to water-soluble (hydrophilic) head - The most diverse macromolecule
groups that contain phosphate. - Responsible for numerous bodily or biological
- When placed in water, phospholipids functions
spontaneously aggregate into a bilayer with their - Proteins are made-up of amino acids, its
phosphate-containing head groups on the outside in monomer.
contact with water and their hydrocarbon tails in the
interior in contact with each other. A. Proteins: Monomer
-Such a phospholipid bilayer forms a stable barrier Amino acids – an organic compound with
between two aqueous compartments—for example, an amine group(-NH2) and a carboxyl (-COOH)
separating the interior of the cell from its external group. Variations of amino acids are determined by
environment. its R side chain.
- Naturally, proteins have 20 distinct amino acids.
Micelle – lipid molecules that arranges itself in a Each amino acids have different functionality
aqueous solution
B. Proteins: Bonding
Phospholipid bilayer • Cell membrane - Amino acids are linked together by a peptide
bond
Peptide bond – a bond that is formed
between carboxyl group of one molecule (amino
acid) and an amino group of another.
- Continuous bonding will create a polypeptide
Polypeptide - A linear polymer consisting - Bonding: side chain interactions/intramolecular
of numerous amino acids forces
- Proteins normally consists of a hundred to • Hydrogen bond
thousands of amino acids that are commonly linked • Polarity (hydrophobic interaction)
via peptide bonding • Disulfide bridges
• N terminus – start, NH2 group side • Ionic bond
• C terminus – end, COOH side • VanderWaals
D. Proteins: Enzymes
- REVIEW: Chemical reactions can take years to
3. Tertiary Structure perform. To increase the rate, there are three general
- These are polypeptides that folds and refolds itself ways:
to assume a three dimensional. 1. Increasing the temperature and pressure
2. Increasing the concentration of the - Always follow a 5’ to 3’ configuration
substances
3. Introduce a catalyst
b. tRNA – “transfer”
- Adaptor molecule that links the mRNA to the
amino acid sequence
c. rRNA – “ribosomal”
- RNA component of the ribosomes