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Molecular biology- Macromolecules chapter 2




Molecular biology- Macromolecules chapter 2












Matter is any substance that takes up space and has mass, and is composed of elements

elements have distinct chemical and physical properties

atom is the smallest unit of matter that still retains the chemical properties of an element

molecule is when 2 or more atoms combine

organic vs. inorganic molecules

Organic molecules are molecules that contain carbon atoms and are arranged in long chains or rings

To note: the carbon (C) usually bonds with Nitrogen, Oxygen and hydrogen atoms. (NOH)

Inorganic molecules are molecules that do not contain Carbon atom.

Intramolecular vs. intermolecular forces

  1. Intramolecular forces : strong, attractive forces, that hold atoms within the molecule.

  2. Intermolecular forces: forces that exist between molecules and determine physical properties (boiling point, melting point, ...). Weaker than intramolecular forces.

monomers vs. polymers

Monomers are single units that can form polymers by binding together

Polymers are made up of monomers through a process called polymerization.

A monosaccharide is a monomer of sugar, and its polymer is a polysaccharide.

Carbohydrates

- macromolecules that contain carbon, oxygen and hydrogen

  • various types of carbohydrates; monosaccharides, disaccharides, polysaccharides


Monosaccharides

  • one sugar molecules

  • (CH2O)n = molecular formula for monosaccharides; n= number of carbons

  • number of carbons will range from 3-7; most notable ones are pentoses; 5 carbon molecule, and hexoses which are 6 carbon molecules

  • pentose and hexose monosaccharides can both form linear molecules or rings;

  • stereoisomers are defined as sugar rings that have differential positions of functional groups; describes the position of functional groups of the sugar rings within the plane of the ring structure below vs. above: alpha vs. beta

  • alpha pentose/ hexose - refers to the position of hydroxyl OH group located below the plane

  • beta pentose/hexose - refers to OH group of sugar pointing above the plane

  • alpha -- below plane, beta -- above plane

  • ribose sugar= 5 carbons

  • glucose sugar = 6 carbons

  • fructose sugar = 6 carbons

  • fructose and glucose are isomers of one another

  • isomer = same atoms but different arrangements

disaccharides

  • 2-sugar = di-saccharide

  • formed through dehydration or condensation reactions

  • sucrose = glucose + fructose

  • lactose = galactose + glucose

  • maltose = glucose + glucose

polysaccharides

  • polysaccharides are long polymers of monosaccharides

  • may be branching or linear (dependent on monomers and their physiological function; storage, structure)

  • starch

    • function: storage in plants

    • glucose monomers (linear and branched)

    • linear starch = amylose, alpha 1,4 glycosidic linkage

    • branched starch = amylopectin, alpha- 1,6 glycosidic linkage

  • glycogen

    • function: storage in humans

    • glucose monomers (branching only)

    • found in liver and muscle cells

    • contains alpha-1,4 and alpha-1,6 glycosidic linkage

  • cellulose

    • function: structural component in plant cell walls, wood.

    • glucose monomers

    • linear structure with beta-1,4-glycosidic linkage

    • lots of hydrogen bonding in between the linear strand; packed tightly together

  • chitin

    • function: structural component in fungi cell wall

    • contains nitrogen as a functional group instead of OH in the glucose molecule

    • N-acetylglucosamine monomers are formed

    • beta-1,4 glycosidic linkage



Proteins

- proteins can be dissected in to polypeptides which are polymers of amino acids

- amino acids have a distinct structure with a central alpha carbon that has 4 functional groups attached, starting with the amino group (NH2), Hydrogen atom (H), Carboxyl group (COOH) and R-group which is variable in each AA giving the AA unique characteristics; forming 20 different AAs with differing properties such as acidity, basicity, polarity and non-polarity.

  • amino acids are attached via peptide bonds/amide bonds which is bonding of amino group of one AA to the next AA's carboxylic acid group.

  • peptide bonds can be formed with help of enzymes called peptidyl transferases.

  • peptidyl transferases are part of aminoacyl transferase enzymes

  • amino N-terminus refers to the NH2 group end of a polypeptide (NH2)

  • carboxyl C-terminus refers to the COOH end of a polypeptide (COOH)

Protein structure and function

  1. Primary structure: specific order of a peptide determined by DNA genes

  2. Secondary structure: occurs through hydrogen bonding, creating 2 different shapes alpha-helices or beta sheets. H-bonding between amino or carboxyl groups only (no involvement of R-group atoms).

  3. Tertiary structure: 3D structure of the polypeptide chain due to R-group interactions; which can include dipole-dipole forces,van der Waal forces, hydrophobic interaction (non-polar AA fold inward and polar AA are on the surface and come in contact with aqueous environment) and disulfide bonds which occur with amino acid cysteine which contains sulfur.

  4. Quaternary structure are multiple polypeptide chains such as hemoglobin molecule which is a tetramer protein.

Protein function

  • structure, transport, storage, immunity, receptors, enzymes, motion

Protein denaturation refers to a process where the functional protein loses its structure which leads to loss of protein function. Note: retains primary structure

  • excess temperature, pH changes, chemicals and radiation can lead to denaturation (can be reversible or irreversible).



Lipids

  • hydrophobic, non-polar molecules

  • long hydrocarbon chains

  • energy storage, insulation, structural elements in cell membrane, synthesis of hormones

  • fats have glycerol backbone that is attached to three fatty acids via an ester linkage

    • glycerol an organic alcohol with 3 hydroxyl group and 3 carbons

    • fatty acid is a long hydrocarbon chain attached to a carboxylic acid

saturated, monounsaturated, polyunsaturated

  • if a fatty acid tail has no double bonds = saturated

  • if a fatty acid tail has one double bond= monounsaturated

  • if a fatty acid tail has more than one double bond= polyunsaturated

  • cis-unsaturated fatty acids have kinks in their structure, as the hydrogen atoms remain on one side of the carbon double creating kinks and packed less tight --> liquid at room temperature

  • Trans-unsaturated fatty acids have hydrogens on opposite sides of the double bond, thus pack tight--> solid at room temperature.

phospholipids

  • amphipathic lipids that contribute to cell membranes

  • 3 carbon glycerol backbone with one phosphate group and 2 fatty acid tails

  • amphipathic lipid= phosphate group is polar and hydrophilic and fatty acid group is non-polar and hydrophobic

  • Phospholipids can form a bilayer due to being amphipathic, polar heads sticking outward and non-polar tails sticking inward; self-assemble into a lipid bilayer in the cell membrane.

cholesterol

  • a type of lipid that contains 4 fused hydrocarbon ring

  • precursor to hormones such as estrogen and testosterone

  • found in the cell membrane of eukaryotes

  • contributes to fluidity and rigidity of eukaryotic cell membrane

    • factors that influence fluidity of the cell membrane: temperature, cholesterol and degree of saturation of phospholipids

    • temperature: with increasing temperature, phospholipids pack loosely together and with decreasing temperature phospholipids pack tightly

    • cholesterol, stabilizes the cell membrane increasing its flexibility and retaining the cell integrity and structure.

    • degree of saturation of phospholipids are variable and dependent on temperature, when temperature is decreasing there is increasing level of unsaturation to decrease rigidity.

    • liver synthesizes cholesterol, also present in the diet

    • it is a precursor to bile acids and vitamin D



Nucleic Acids

  • primary structure contains Carbon, Hydrogen, Nitrogen, Phosphorous

  • responsible for continuity of life, passing on genetic information

  • Deoxyribonucleic acid DNA, Ribonucleic Acid RNA are the two forms of Nucleic acids, they are synthesized from nucleotide monomers, that build into polymers.

  • Nucleosides are five-carbon sugar rings with a nitrogenous base, and Nucleotides are five-carbon sugar rings with a nitrogenous base attached to a phosphate group.

  • Deoxyribonuleotide has an oxygen removed from the five carbon sugar ring on the 2' carbon group, hence called deoxy. whilst the ribonucleotide has a hydroxyl group at the 2' carbon group.

  • There are four 4 nucleotides Adenine Guanine Cytosine Thymine

    • adenine and guanine are purine

    • cytosine and thymine are pyrimidines

    • nucleotides are connect via phospho-diester bonds which a re linkages that connect the phosphate group of one nucleotide at the 5' end to the hydroxyl group of another nucleotide at the 3' end .

    • the process of adding nucleotides to the 3' end of a growing chain is called polymerization

    • Deoxyribonucleic acid, is a double stranded antiparallel helix, containing genetic information. the strands are complementary to one another, where Adenine only hydrogen bonds to thymine via two hydrogen bonds, and guanine only hydrogen bond to cytosine via three hydrogen bonds. there AG bonds are much bulkier than AT bonds, and harder to break.

    • Ribonulceic acid is a single stranded nucleic acid, containing Adenine, guanine, cytosine, and uracil (in place of thymine). During transcription the same pairing of GC/AU applies.

    • The cell theory

  1. ALL CELLS COME FROM PRE-EXISTING CELLS

  2. ALL LIFE FORM CONTAINS ONE OR MORE CELLS.

  3. CELL IS THE BASIC STRUCTURAL, FUNCTIONAL, AND ORGANIZATIONAL UNIT OF LIFE.

  4. AN ORGANISM'S ACTIVITY IS DEPENDENT ON THE TOTAL ACTIVITY OF ITS CELLS.

  5. ALL CELLS ARE SIMILAR IN NATURE IN TERMS OF THEIR CHEMICAL COMPOSITION IN A SPECIFIC SPECIES.

  6. ENERGY FLOW, THE PROCESS OF METABOLISM AND BIOCHEMISTRY OCCURS WITHIN CELLS.

  7. GENETIC INFORMATION IS STORED IN THE CELL IN FORM OF DNA AND PASSED DOWN TO OTHER CELLS.

  • The central dogma of genetics states that genetic information flow from DNA-->RNA--> Proteins, there is no reversal from proteins to RNA or DNA however there can be a reversal form RNA to DNA through Reverse transcriptase enzymes.

  • RNA world hypothesis states that the primary existing units of life were RNA. RNA developed self replicating mechanisms that allows re-synthesis of the RNA and ability to catalyze reactions, and further synthesize important macromolecules such as proteins.

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