Biology 1050: Introduction to Cell & Molecular Biology - Topic 2 Notes (2024) PDF

Biology 1050 Introduction to Cell & Molecular Biology Topic 2 The Molecules of Life  Topic 2 The Molecules of Life  Atoms and Elements Atoms consist of protons, neutrons, and electrons. The atom’s nucleus is formed by protons and neutron...

Biology 1050 Introduction to Cell & Molecular Biology Topic 2 The Molecules of Life  Topic 2 The Molecules of Life  Atoms and Elements Atoms consist of protons, neutrons, and electrons. The atom’s nucleus is formed by protons and neutrons. The atom’s electrons move in orbitals around the nucleus. An element is a substance that cannot be decomposed into simpler substances by ordinary chemical processes. - Elements contain only one type of atom.  Atomic Mass The atomic number is specified by the number of protons. Atomic number of an atom defines the identity of the element. For example, an atom with six protons is always carbon. The atomic mass is the number of protons plus the number of neutrons.  Isotopes For isotopes of an element, the proton number stays the same, but the neutron number is different. Carbon Atom Carbon Isotopes  Energy Levels of an Atom Distribution of Electrons - The lower energy shells will be filled first. Then the higher energy shells. - From lower to higher energy levels: 1s, 2s, 2p, 3s, 3p etc… - The numbers are the principal energy levels (shells). The letters represent the sublevels (orbitals) of each principal level. Principal 2 principal 1 1  Electron Orbitals Electrons occupy regions of space called orbitals. Atoms with more than two electrons have at least two orbitals. 2p 2p 2S 2p 1S Principal Energy Levels (numerals) and Their Sub-Energy Levels or Orbitals (letters) Elements - An element is defined by its number of protons (i.e. atomic number) in the nucleus. - Atomic number of an element determines the chemical properties of the element.  Recurring, Periodic, Chemical Properties Reading Across the Rows - A periodic table arranges the elements in increasing order of their atomic numbers. - It also groups elements with similar properties in the same vertical column (or group).  Basic Information of an Element on the Periodic Table Example: Oxygen Atomic mass is expressed in dalton (symbol: Da), or mass of 1 proton (or 1 H atom), or unified atomic mass unit (u). 1Da = 1g/Avogadro number = 1.660538921 × 10 −24 g 1 molar mass of an atom or a molecule = atomic or molecular mass in grams. Why isn’t the atomic mass of C a whole number?  Recurring, Periodic, Chemical Properties Reading the Columns Group - Vertical columns are called groups, or families. - Elements in the same vertical column (group) have similar chemical properties. - Members of a group have the same number of electrons in their outermost shell (valence electrons). - For example, carbon, silicon and lead have the same number of valence electrons in their outermost shell. You discover an isotope of an element that has 6 electrons in its second and outermost shell, 8 protons, and 6 neutrons. What element is it? A. nitrogen (N) B. carbon (C) C. oxygen (O) D. fluorine (F) Which choice ranks the elements carbon, sodium, calcium, and iodine in order of decreasing number of valence electrons? A. I→C→Ca→Na B. I→Ca→Na→C C. C→Na→Ca→I D. C→Ca→Na→I  Chemical Bonds Atoms can combine with one another to form molecules, which are held together by chemical bonds. Molecule stability occurs when atoms of the molecule share enough electrons to occupy the outermost energy level. Usually with 2 electrons in the 1st row and 8 electrons on other rows. - The number of valence electrons affects the number of bonds that can be formed. - A valence electron can participate in the formation of a chemical bond if the outer shell is not filled already. - For example, C has 4 valence electrons. It can form 4 covalent bonds with other atoms. E.g. C bonds with 4 H atoms to form CH4. - N has 5 valence electrons but only 3 of its valence electrons can form covalent bonds with other atoms. It is because its outer shell is filled after 3 of its valence electrons form covalent bonds with other atoms. E.g. N bonds with 3 H atoms to form NH3.  Covalent Bonds - A covalent bond forms when two atoms share a pair of electrons in a molecular orbital. - The sharing of electrons most generally occurs in the outermost orbitals of the atoms. - A molecule forms when two atoms share their valence electrons with each other.  Polar Covalent Bonds Polar covalent bonds occur when electrons that are shared between two atoms are not equally shared. In a molecule of water, the electrons will be closer to the oxygen most of the time because the electronegativity of oxygen is greater than that of hydrogen. The unequal sharing of electrons results in partial negative charges on the oxygen and partial positive charges on the hydrogen. Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons. Factors Affecting Electronegativity of an element - Electronegativity increases as the number of an atom increases. - Electronegativity also increases as the distance between the nucleus and the valence electrons decreases. - For example, electronegativity of the following list of elements decreases from left to right: F > O > Cl > N > Br > I > S > C > H > Metals - The most electronegative element is Fluorine, and electronegativity must always increase towards Fluorine in the Periodic Table. Nonpolar covalent bonds form when atoms share electrons equally. Importance of Polar and Non-Polar Chemicals/Compounds - If the chemical/compound is a solvent, its polarity determines the property of the solvent: Like Dissolves Like. - If the chemical/compound is a solute, the polarity of the chemical often controls its solubilities in polar and non-polar solvents. Which option accurately describes a polar covalent bond? A. the unequal sharing of electrons between an atom with a partial positive charge and an atom with a partial negative charge B. the interaction of an atom with very high electronegativity and an atom with very low electronegativity C. the interaction of a hydrogen atom connected to an atom with a high electronegativity and an electronegative atom of another molecule D. the equal sharing of electrons between atoms of identical or similar electronegativities E. None of the other answer options is correct. The oxygen and hydrogen atoms of a water molecule contain what type of bond? A. polar covalent B. ionic C. hydrogen D. van der Waals interactions Consider the two molecules (A and B) shown here. Do either of these molecules have polar covalent bonds? Molecule A Molecule B A. Molecule A only B. Molecule B only C. Both molecules D. Neither molecule  Ionic Bonds The electronegativity of chlorine is much greater than sodium. When ionic bonds between the two form, the chlorine takes an electron from sodium, and the result is a negatively charged chlorine atom and a positively charged sodium atom. The interaction between the two occurs because opposite charges attract one another. Chemical reactions sometimes involve breaking and making chemical bonds. Example: Reaction between H2 & O2  Water is one of the most important chemicals in living organisms. - It accounts for about 70% of total cell mass and is essential for all living organisms. - It is an important solvent (also called universal solvent) that helps cells transport and use substances like oxygen or nutrients. - It is an essential medium for biochemical reactions to proceed. - It is also directly involved in many chemical reactions to build and break down important components of the cell. - It maintains the osmolarity and the pH of the body fluids. Why do salts dissolve in water? In water, the partial positive charge on the hydrogen ions associate with the negative charge on the chloride ions, and the partial negative charge on the oxygen ions associates with the positive charge on the sodium ions.  Water Chemistry Water is a polar molecule. Water is a good solvent. Molecules can be described as hydrophilic or hydrophobic depending on how they react with water. The pH of water is 7 (H+ = OH-). pH is a measurement of the concentration of protons (H+) in solution.  Hydrogen Bonds in Water: The Importance of Polar Covalent Bonds - A hydrogen bond is an interaction of a hydrogen atom and an electronegative atom (e.g. O or N). - For example, the partially +ve H of H2O attracts to the partially –ve O of another H2O to form a hydrogen bond. - The hydrogen bonds keep water molecules together in its liquid and solid forms. - These bonds also give water molecules the property of cohesion, the tendency of the molecules to stick to one another. - Hydrogen bonds are weaker than covalent and ionic bonds, but they do help stabilize biological molecules.  Water has unusual properties Water is less dense when solid (frozen) than when liquid. Water freezes at 0°C and its density is highest at 4°C. Water resists decreases or increases in its temperature because it has a high specific heat capacity (amount of heat requires to raise 1 g of a material by 1oC). In order for the water temperature to increase, hydrogen bonds between the water molecules must be broken. Since H bonds between water molecules are strong, a lot of heat is needed to break the H bonds and increase the water temperature. This property is important for living organisms because water resists temperature variations that would otherwise result from the numerous biochemical reactions taking place within them.  Carbon: Life’s Chemical Backbone The four major elements that make up the human body are: carbon oxygen hydrogen nitrogen Organic compounds are defined as covalently bonded compounds containing carbon, excluding carbonates and carbon oxides (e.g. CO2). Therefore, compounds such as carbon dioxide (CO2) and sodium carbonate (Na2CO3) are considered to be inorganic. Major Covalent Bonds of Carbon in Organic compounds 1. C-H bonds 2. C-C, C=C, C≡C bonds 3. C-O, C=O bonds 4. C-N, C=N bonds 5. C-S bonds  Major Organic Molecules in Cells (Biomolecules) There are four major types of biomolecules: 1. Proteins provide structural support and act as catalysts to facilitate chemical reactions. 2. Nucleic acids encode and transmit genetic information. 3. Carbohydrates provide structural support for many organisms and a source of energy. 4. Lipids make up cell membranes, store energy, and are important in cell communication. Proteins are made of amino acid subunits.  Proteins are also called polypeptides. When amino acids (figs. a and b) are linked together in a chain (fig. c), they form a protein. Amino acids are joined through a covalent bond called a peptide bond (fig. c). The carboxyl group releases the –OH, and the nitrogen loses the -H to form a molecule of water when peptide bonds are formed. Peptide Bond Formation Nucleotides have three main components and are the building blocks of nucleic acids. Ribonucleotides - Building blocks of RNA. A base A five-carbon containing One or more sugar nitrogen phosphate groups Deoxyribonucleotides - Building blocks of DNA. Nucleotide Bases This base is only This base is only found in DNA. found in RNA.  Bonds Between Nucleotides The phosphodiester bond joins two nucleotides together. The bond is formed between the phosphate group at the 5’ position of a nucleotide and the 3′-OH of the last nucleotide. Structure of DNA (Deoxyribonucleic acid) A=T G≡C - DNA is a double helix structure. - The 2 strands of the DNA are anti-parallel. - The nucleobase pairing of DNA follows the Chargaff's rules: - The amount of A equal to T - The amount of G equal to C - Total purine = Total pyrimidine  Carbohydrates - Carbohydrates are (bio)molecules consisting of carbon (C), hydrogen (H), and oxygen (O) atoms. They include sugars, starches and fibres. - Carbohydrates usually have a H:O atom ratio of 2:1 and thus with the empirical formula Cm(H2O)n.  Carbohydrates (Hexoses, C6H12O6) - These carbohydrates (sugars) are monosaccharides. They all have the same chemical formula, but they are isomers of each other, which means they are functionally different from one another. - Glucose and fructose are structural isomers (different functional groups). - Glucose and Galactose are stereoisomers (with one or more chiral carbons).  Types of carbohydrate Molecules Monosaccharide Polysaccharide 1. A monosaccharide contains one sugar molecule (e.g. glucose). It is often a subunit, or monomer, of more complex sugars. Virtually all monosaccharides in cells are in cyclic form. 2. Disaccharides contain two bonded monosaccharides (e.g. sucrose). 3. Polysaccharides contain more than two monosaccharide monomers and are formed through dehydration reactions. The monosaccharides are strung together by glycosidic linkages/bonds to form a polysaccharide. 4. Both mono- & di-saccharides are simple sugars/carbohydrates while starch and fiber are complex carbohydrates. Lipids: Fatty acids are examples of lipids (with 16C) Lipids are a class of organic compounds that are insoluble in water (or hydrophobic) but soluble in organic solvents. Therefore, they are a chemically diverse group of chemicals including many natural oils, waxes, and steroids. Lipids also include fatty acids or their derivatives. Fatty acids are long chains of carbon with a carboxyl group at the end.  Lipids: Structure Saturated versus unsaturated fatty acids have different structure based on the presence of C=C double bonds. Glycerol is a sugar alcohol not lipid but it is a component of some lipids such as triglycerides. Triacylglycerols (e.g. triglycerides) are or triglyceride uncharged and hydrophobic and can often form oil droplets within the cell. Van der Waals The hydrocarbon chains in Forces fatty acids have non-polar covalent bonds. Electrons are still moving around the atoms in the fatty acids, creating short- lived regions with slight negative charges. These are attracted to slight positive regions in another atom. The longer the hydrocarbon tail, the greater the strength of van der Waals forces. Saturated Fats Animal fats are saturated. Without double bonds causing kinks in the structure, animal fats can stack closely together and are stabilized by more van der Waals interactions than unsaturated fats. This also contributes to the quality of animal fats, where they are solid at room temperature.  Unsaturated fatty acids decrease the Van der Waals force or hydrophobic interactions between fatty acids (i.e. decrease the melting points of fats), and increase the fluidity of membranes  Lipids: Steroids Cholesterol is a steroid. It is found in the lipid bilayer of animal cell membranes. It maintains the structure of animal cell membranes. Cholesterol also serves as a precursor for the synthesis of steroid hormones such as estrogen and testosterone. Sometimes fatty acids line up next to each other. These associations can be very stable in the cell. Which of the interactions do you think helps stabilize the association of lipids? A. covalent bonds B. hydrogen bonds C. ionic bonds D. van der Waals interactions  Miller’s experiment to demonstrate the formation of building blocks of life under possible early pre-life earth conditions that only simple inorganic and organic chemicals are present Miller and later by other scientists conducted many variations of this experiment. They showed that amino acids, nucleotides, lipids, simple sugars and other biologically important molecules can be formed from simple inorganic and organic chemicals under primitive earth conditions (such as high temperature and lightning discharge). Formation of nucleic acids from nucleotides Clay minerals in volcanic rocks Leslie Orgel put can bind and stabilize short single- nucleotides on their surface and strand nucleic bring nucleotides close enough acids in a that small polymers could form. reaction chamber. The nucleotides formed the complementary sequence and a double-stranded nucleic acid.  Evolution of the last universal common ancestor (LUCA) from simple organic and inorganic chemicals. Studies of the origin of life on Earth help us to consider what would be required for life elsewhere in the universe. What is most likely to be true of extraterrestrial life if it exists? A. Carbon will act as the backbone for organic molecules. B. Light from a nearby star will make photosynthesis possible. C. Oxygen will be used to convert energy in cells. D. Water will not be required to sustain life.