L2 Cell Biology

🧠 Concepts Introduced

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Learning Objectives

• Define atom and its properties

• Discuss the different chemicals bonds found in biological molecules

• Explain the four macromolecules and how are they important to living organisms

Chemical composition of cells

Elements form the basic building block of all matters

Atom is the smallest particle of an element that still retain the properties of element.

A molecule forms when an atom bonds with other atoms; this includes atoms of the same element or atoms from different elements. (Molecules have a defined size. The reason why graphite and diamond are only considered element is because they don't have a defined size and more carbon atoms can be added to it. )

Atom

Atoms are made up of a dense nucleus (protons + neutrons) orbited by a cloud of electrons

Atomic number - total number of protons in nucleus

Examples:

• Hydrogen (Z = 1): 1 proton, 0 neutrons, 1 electron
• Carbon (Z = 6): 6 protons, 6 neutrons, 6 electrons
• Oxygen (Z = 8): 8 protons, 8 neutrons, 8 electrons

Positively charged nucleus contains most of the atomic mass or atomic weight.

Much lighter and negatively charged electrons occupy space around the nucleus, they do not contribute to the atomic weight.

Electrons are held to the nucleus by electrostatic attraction

Electronic Shell

Electrons in an atom are grouped around the nucleus into shells. (Electrons are in orbit)

The first shell (closest to the nucleus) can hold two electrons. The second shell can hold 8 electrons. The third shell can hold 18 electrons. The fourth shell can hold 32 electrons, and so on…

The number of electrons in the outer most shell tend to form chemical bonds with other atoms.

This outer most shell is known as valence shell, and the electrons found in it are called valence electrons.

A neutral or STABLE atom has a same number of protons and electrons

Periodic Table

Elements are organized by atomic number (number of protons), it also shows how its electrons are arranged

Different number of electron shells is grouped vertically in Periodic Table

The periodic table continues to grow as scientists discovered more elements

At the end of 2018, chemists confirmed four more elements bringing up the number of known elements to 118 and completed the 7th row of the table

Avogadro's number

Atoms are in pico-scale size

An individual carbon atom is roughly 0.2 nm in diameter

One proton or neutron weighs approximately 1/(6 x10^23) gram

eg. hydrogen has one proton, hence 1 gram of hydrogen contains 6 x 10^23 atoms eg. carbon has 6 protons and 6 neutrons, and atomic mass of 12. Hence, 12 grams of carbon contain 6 x 10^23 atoms

6 x 1023 atoms is called Avogadro's number, it is also called one mole of substance (ie. 1 mole = gram/molecular mass)

!!!!! remember no. of atom calculation using no. of mol x 6 x 10^23

Intramolecule Forces

Intramolecular force = inside the molecule Intermolecular forces = outside the molecule (between cell and cel)

H2O between H and O is intramolecular force NaCl and NaCl is intermolecular forces Na and Cl is intramolecular force

Ionics Bonds vs Covalent

Unfilled electron shell is not stable, atom with incomplete outer shells tend to interact with other atoms

The electron exchange occurs either by transferring electrons from one atom to another or by sharing electrons between two atoms.

Ionic bond is formed when electrons are donated by one atom to another

Covalent bond is formed when two atoms share a pair of electrons.

Sharing of electrons is unequal with a partial transfer between two atoms - one more electronegative than the other.

Formation of Ionic bond: 1 metal + 1 non-metal

Sodium has 3 shells and a total of 11 electrons, with an electrical configuration of 2, 8, and 1. It is in the process of losing one electron from its outermost shell to form a positively charged ion i.e., sodium cation, Nat.

There are 17 electrons among the three shells of the chlorine atom. Its electronic configuration is 2, 8, 7. During the formation of sodium chloride, it is in the process of gaining one electron and forms the chloride ion Cl.

Thus, one electron from the sodium atom's outermost shell is donated, which the chlorine atom gains, resulting in the formation of sodium chloride

Formation of covalent bonds: 2 non-metal

The chemical reactivity of an atom depends on the presence of unpaired electrons (valence electrons) in the outer electron shell.

The formation of a covalent bond between 2 atoms is governed by the fundamental principle that an atom is most stable when its outermost electron shell is filled.

These strong bonds (C-C and C-H bonds, 400 kJ mol-¹) DO NOT dissociate spontaneously at body temperatures and pressures or even at finite concentrations in the body

Condition for the formation of a Covalent bond

1. Elements should be nonmetals eg. H, B, C, N, O, F, etc.

2. Elements should belong to p-block (colored yellow in periodic table)

3. The electronegativity difference between atoms should be less than 1.7.

Electronegativity Difference and Covalent Bonding

Check AUSMAT organic chem -> covalent bonding

Electronegativity is defined as the attraction for electrons in a covalent bond.

High electronegativity depends on (1) nuclear charge (number of protons) (more protons more electronegativity cuz can attact more electrons), (2) atomic radius (shorter radius), and (3) shielding effect from inner electrons (smaller electron shell more electronegativity)

Summary:

• Nuclear Charge: More protons mean a stronger positive charge in the nucleus. This creates a more powerful pull on both its own valence electrons and the shared electrons in a bond.

• Atomic Radius: A smaller distance between the nucleus and the outermost shell means the attractive force is much stronger, following Coulomb's law (forces are stronger when objects are closer).

• Shielding Effect: Fewer inner electron shells mean less interference. The positive pull of the nucleus can reach the bonding electrons directly without being blocked by layers of core electrons.

The more electronegative an atom, the more strongly it pulls the shared electrons towards itself.

Nonpolar Covalent Bonds: If the electronegativity difference between two atoms is between 0.0 and 0.5, then the electrons are shared almost equally, resulting in a nonpolar covalent bond.

Polar Covalent Bonds: If the electronegativity difference is between 0.5 and 1.7, the electrons are shared unequally, resulting in a polar covalent bond. The atom with the higher electronegativity will attract the shared electrons more strongly.

Ionic Bonds: If the electronegativity difference is greater than 1.7, the electrons are transferred from one atom to another, resulting in an ionic bond. This typically occurs between a metal and a nonmetal. pulling it totally into its orbit

Polar vs Non-Polar

Oxygen is more electronegative than hydrogen as it has higher atomic number (=number of protons) and attracts more electrons.

As the electrons move towards the more electronegative atom, the concentration of electrons develops a partially negative charge over the more electronegative molecule (-5).

The less electronegative molecule has an electron depletion and thus develops a partial positive charge (+5).

Intermolecular Forces

Check AUSMAT organic chem -> intermolecular forces

Weaker interactions (2.5-40 kJ mol-1) compared to covalent bonds (400 kJ mol-1)

DO NOT depend on shared electron but rather on attractive forces (electrostatic attraction) between atoms (of different molecules) having an opposite charge

Responsible for folding macromolecules into their active conformations and to hold the molecules together in the cells

THREE basic types of intermolecular force:

• hydrogen bond (12-29 kJ mol¹)

• dipole-dipole attraction (5-20 kJ mol-1)

• van der Waals force (< 5 kJ mol-¹)

Hydrogen Bond

12-29 kJ mol-1

The attraction between a partially positively charged H atom attached to a highly electronegative atom (such as N, O, F)

Occur in inorganic molecules such as water, organic molecules such as DNA and proteins

Important in the stabilisation of secondary structures of proteins, such as a-helices and B-sheets and in the base pairing of DNA (A&T, C&G) and RNA

!!! why hydrogen bond and not covalent cuz protein need to be flexible and break the bonds to reconstruct as the structure can change. If use covalent bond, the force will be too strong and structure cannot be changed

H atom attracted to F/O/N attracted to lone pair of electrons on F/O/N from another molecule

Dipole-dipole Attraction

Partially positively charged part of a molecule interacts with the partially negatively charged part of the neighbouring molecule.

In hydrogen chloride (HCI), the hydrogen atom of one molecule is attracted to the & chlorine atom of another molecule.

These dipoles can interact with each other in an attractive fashion, which will also increase the boiling point.

Dipole-dipole interactions help stabilize protein tertiary structures by forming attractions between polar side chains.

They also play a role in enzyme-substrate recognition, allowing molecules to fit and bind in specific orientations.

Van der Waals or London Dispersion Force

(weak, temporary dipoles due to uneven distribution of electrons at any instant whch causes an attraction between atoms) <-

A distance-dependent interaction between atoms or molecules

Occur when adjacent atoms come close enough (5nm or less) that their outer electron clouds just barely touch

This action induces charge fluctuations that result in a nonspecific and nondirectional attractions

The force is caused by temporary attractions between electron-rich regions of one molecule and electron- poor regions of another

The weakest intermolecular interaction

Carbon is the Backbone of Life

Carbon is the basic building block for nucleotides, amino acids, carbohydrates and fatty acids. They are also known as organic molecules

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules.

The backbone of carbon compound is hydrocarbon, saturated and unsaturated.

Carbon-containing backbones may be linear, branched, or cyclic.

Biological Macromolecules

Carbohydrates

It is also able to form large, complex molecules eg. testosterone, progesterone, estrogen, etc

Biological Macromolecules

Four biological macromolecules: nucleotides, amino acids, carbohydrates and fatty acids.

Macromolecules are basically polymers, long chains of molecular sub- units called monomers.

Monomers undergo dehydration/condensation to form polymer and release H2O.

Polymers can be broken down to monomer via hydrolysis.

Carbohydrates

A source of energy for the body eg. glucose, and a store of energy eg. starch in plants

Building blocks for polysaccharides (giant carbohydrates) eg. cellulose in plants and glycogen in the human body

Components of other molecules eg. DNA, RNA, glycolipids, glycoproteins, ATP

C, H and O in carbohydrates are held together by covalent bonds

General formula (CH2O), n = 3 to 7 (cellular metabolism)

3-carbon sugar - trioses 4-carbon sugar - tetroses 5-carbon sugar - pentoses 6-carbon sugar - hexoses 7-carbon sugar - heptoses

Monosaccharides

The simplest form of carbohydrates is monosaccharide eg. glucose, fructose and galactose (CH1O).

Monosaccharides can exist as a linear chain or as ring-shaped molecules.

Glucose, galactose and fructose are isomer

Glucose and galactose are aldoses, and fructose is a ketose ie. carbonyl group in different form or position

Disaccharides

3 common types of carbohydrates:

• Monosaccharides
• Disaccharide
• Polysaccharides

A disaccharide is formed when a dehydration reaction joins two monosaccharides

Two monosaccharides joined to one another by glycosidic bond (a type of covalent bond)

Common disaccharides include: Sucrose - table sugar, major component of plant sap (glucose + fructose) Lactose - milk in most mammals (glucose + galactose) Maltose (malt sugar) - found in starchy grains, vegetables and fruits (glucose + glucose)

Polysaccharides

Known as polymers of sugars for (1) energy storage and (2) structural component

Structure and function determined by its sugar monomers and the position of glycosidic bond

Common polysaccharides - Glycogen, Starch, Cellulose, Chitin

Smaller oligosaccharides can also be covalently linked to proteins to form glycoproteins or to lipids (glycolipids), both found on cell membrane, to protect the cell surface and cell adhesion

Nucleic Acid

Macromolecules constructed of long chains (strands) of monomers called nucleotides

A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen- containing base.

Nucleotide is the monomer of nucleic acid

Sugar-phosphate groups are joined by 3'- 5' phosphodiester bonds (joining between hydroxyl group (-OH) and carboxyl group (-COOH))

Two types of nucleic acid:

• deoxyribonucleic acids (DNA)
• ribonucleic acids (RNA)

Base pairing rules:

• Purine (double ring structure) (A and G) pairs with pyrimidine (single ring structure) (T and C)
• A pair with T (or U) G pair with C
• A forms 2 hydrogen bonds G forms 3 hydrogen bonds

Protein

Proteins are macromolecules that carry out all of a cell's activities.

Examples:

• Enzyme - accelerate rate of metabolic reaction (eg. pepsin)
• Structural cables - provide mechanical support both within cells and outside
• their perimeters (eg. collagen, actin, myosin)
• Hormones (eg. insulin)
• Defensive (eg. antibodies)
• Transport (eg. haemoglobin)
• Membrane receptor (eg. nerve cell receptors)
• Serve as toxins, form blood clots, absorb or refract light…the list goes on…

N-terminal is amino group C - terminal is carboxyl group

Protein is made of amino acids (as monomers) Each protein has unique sequence of amino acids that gives the molecule its unique properties. During protein synthesis, each amino acid becomes joined to another amino acid forming polypeptide chain.

Amino acid are joined by peptide bonds, that results from linkage of carboxyl group of one amino acid to the amino group of its neighbour, with elimination of a water molecule.

Peptide bond connect amino acids into polypeptide chain (polymer).

Different levels of protein structure

A functional protein consists of either one or more polypeptides precisely twisted, folded, and coiled into a unique shape

The sequence of amino acids determines a protein's 3-dimensional structure

A protein's structure determines its function

Protein structure can be described in 4 levels

• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

Primary Structure

Directly translate DNA triplet/ codon (eg. CUU, CCA, GUU, GAU) into amino acids

Primary structure is a specific linear sequence of amino acids

The linked series of Carbon, Nitrogen and Oxygen makes up the protein backbone.

Held by peptide or polypeptide bonds

Amino acid sequence provide information required to determine protein's 3D shape, and thus its function.

Secondary Structure

Secondary proteins consists of alpha (a) helix, beta (ẞ) strand and loop & turn.

Structure of a helices can be stabilized by hydrogen bonds.

Right-handed spiral structure. Side chain extend outwards.

12 residues have approximately ~3 helical turns.

Common functional roles of a-helix include DNA-binding, membrane insertion.

• B-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation

• Beta (B)-sheet is two or more ẞ-strands lining up side-by-side

• They are stabilized by hydrogen bond between N-H and carbonyl groups of adjacent chains.

• Loops connect two regular secondary structures.

• give flexibility to structure. without it the protein structure will be very rigid

• Loops cause a change in direction of the polypeptide

• chain allowing it to fold back on itself to create a more compact structure.

• Loops that have only 4 or 5 amino acid residues are called turns when they have internal hydrogen bonds

Tertiary Structure

Protein contains more folding in the 3D shape of functional protein

Stabilized by array of weak noncovalent bonds between diverse side chain of the protein.

Including hydrogen bonds, electrostatic bonds, hydrophobic interaction, van der waals

Strong covalent bond (disulfide bonds) can reinforce protein structure.

Quaternary Structure

Proteins can exist as single polypeptide chain (monomer) OR multiple polypeptide chains (dimer, trimer, tetramer, etc).

Each polypeptide chain forms one subunit or monomer

Each subunit interact with one another through covalent disulfide bond, noncovalent bonds and/or hydrophobic interactions

Lipids

Diverse group of nonpolar biological molecules

Dissolved in organic solvents such as chloroform or benzene. Inability to be dissolved in water

Energy storage (stores more calories than glycogen).

• Humans and mammals store fat in adipose cells
• Adipose cells cushions vital organs and insulate body

Precursor of hormones, lubrication, cell membranes

Important lipids in cellular function include

• Fats/Triglycerides
• Phospholipids
• Steroids
• Waxes

Fats or Triglycerides

The main form of stored energy in animals.

Consists of glycerol molecule linked by ester bond to 3 fatty acids.

Scientific name = tri acyl glycerol (= triglyceride)

Saturated vs Unsaturated Fatty Acids

Carbons in fatty acid are bonded with hydrogen or make double bonds to other group of atoms

Saturated Fatty Acids

• Having the maximum number of hydrogen atoms possible and no double bonds
• Fats are solid at room temperature
• Most animal fats are saturated eg. poultry skin, fatty meat, butter, full cream dairy
• Increased risk of heart disease

Unsaturated Fatty Acids

• Having one or more double bonds
• Unsaturated fats or oils, and are liquid at room temperature
• Plant fats and fish fats are usually unsaturated eg. olive oil, sunflower oil, peanut oil, etc
• Can be divided into mono and poly unsaturated fat

Phospholipids

Phospholipids are the major component of all cell membranes

Two fatty acids and a phosphate group are attached to glycerol

The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head - amphipathic molecule

Hydrophobicity of Phospholipids When phospholipids are added to water, they self-assemble into liposomes, micelles or bilayers, with the polar heads facing the water. This results in a bilayer arrangement found in cell membranes.

Two major types of phospholipids The presence of glycerophospholipids and sphingolipids in all mammalian cells.

Steroids

Steroids are characterized by a carbon skeleton consisting of four fused rings

Cholesterol, an important steroid, is a component in animal cell membranes

• the precursor for the synthesis of many steroid hormones.
• It is also found in cell membrane to give fluidity and stabilize the membrane

Waxes

A long chain of non-polar/ neutral lipids

Completely water-insoluble and solid at room temperature

Function as water repellents on leaves, feathers, cuticles of insects, ear, honeycombs

Also serve as energy-storage substances in zooplankton (oil sac)