ERTH 1040 - NSII Components of Life Part I: atoms, molecules, amino acids, and proteins J. D. Price
All life on Earth is composed of a combination of only a few chemical components. In this course, we’ve previously discussed some of the inorganic materials (e.g. minerals and fluids) of the Earth. We’ve also touched on the basic organic molecules: hydrocarbons
Q: What are the most common elements associated with life?
The chemical compounds associated with life on Earth are called organic compounds. Organic applies to most arrangements of carbon, oxygen, and hydrogen, with a few exceptions. CO and CO 2 are typically termed inorganic, as they are very abundant in the Earth, even in regions where life doesn’t exist.
Crystalline phases – seeking the lowest energy configuration for atoms. Complex organic molecules are not the lowest energy assembly of atoms at the surface of the Earth. They require (small amounts of) extra energy to become stable Life may use sources of energy: Sun’s radiaiton, Earth’s heat, gravitational potential, energy of chemical bonds, etc… Q: what is a source of additional energy used to make complex organic structures?
To understand the nature of the molecules of life, we must first understand how atoms are assembled into molecules Bonding Ionic Covalent Metallic Electrostatic
Metals (M) prefer to lose electrons
Ionic bonding Can only attract so far – “solid spheres”
Ionic compounds are formed by the mutual attraction of charged atoms, the ratio of which is determined by overall charge neutrality; e.g.: Na + + Cl - = NaCl Ca 2 + + + 2F - = CaF 2 Ionic compounds dissolve readily in water to form ionic solutions that conduct electricity. Ionic compounds formed from groups IA and IIA form colorless of white solids (e.g., salt) formed from transition elements (B families) often form colored compounds.
Covalent bonding Two atoms in close proximity can share their electrons so that each takes on an electronic structure similar to a noble gas. The diatomic H-H system: Most of the compounds affiliated with life are dominated by this type of bonding.
Q: What ultimately controls bonding in any compound?
Double bonding Two electron pairs are shared Triple bonding Three electron pairs are shared
Coordinate covalent bonds – the shared electron is donated by atom. Most carry an overall negative charge (CO 3 ) 2- , (OH) - , (HCO 3 ) - , (PO 4 ) 3-
F, � = 4 H, � = 2.1 Ionic-covalent character makes molecules dipolar
Acids There are a number of criteria used to define a substance as an acid. For our purposes, we will define an acid as that which when dissolved in water will produce more hydronium molecules than hydroxide (Arrhenius criteria). The opposite, we will call a base. An inorganic acid, HCl HCl + H 2 O � H 3 O + + Cl - Hydr. Chloride water hydronium chlorine Organic acids are typically very weak (not much hydronium produced in dissolution
E.B. Watson
Covalent compounds CO 2 carbon dioxide (Greek "di" for 2) CO carbon monoxide (Greek "mono" for 1) CCl 4 carbon tetrachloride (Greek "tetra" for 4) Empirical Formulas Always used in ionic compounds NaCl CaF 2 CH 2 O
Structural formulas show the geometry and bonding
Hydrocarbons C-H molecules. Methane (CH 4 ) to asphaltenes C n , n is 1 to 60, increasing n changes state. In CH 4 , n is 1. e.g. Straight-chain parafins n = 1-4 gas n = 5-16 liquid n > 16 solid
Oil is not very soluble in water (vice-versa) because of their different molecular structure. Water and oil are largely separate in nature – oil floats on water.
Straight Chain Organic Compounds Q: What is added to the hydrocarbon to make other straight-chain organic molecules?
2C 4 H 10 + 13 O 2 � 10H 2 O + 8CO 2 Hydrocarbon C 6 H 12 O 6 + 6 O 2 � 6H 2 O + 6CO 2 Carbohydrate Glucose
Carbohydrates Molecular formulas help to describe the structure of the molecule: While CH 2 O accurately describes the ratio of elements in glucose, it fails to characterize the whole molecule Q: why are there no carbon molecules shown on the diagram at right?
Carbohydrates – C H and O compounds that are organized in to pentagonal and hexagonal structures. Structural formula of glucose.
Glucose is a simple carbohydrate. More complicated molecules may be formed. Two carbohydrates have particular significance, not as sources of energy, but as a structural agent in the genetic and process portions of life. Q: What’s the difference in these two molecules?
Making carbohydrates Photosynthesis: energy consumption Carbohydrates require additional energy to form. Photosynthesis is one such way that energy is consumed to produce simple carbohydrates. These may be modified by further reactions. Q: can you briefly outline carbohydrate construction?
Using carbohydrates Recall that we’ve talked extensively about combustion Combustion is the oxidation of matter to produce energy You should be completely familiar with these diagrams of chemical reactions: or
The actual combustion process within cells is more complicated than the previous slides suggest. You need not memorize this process, but realize that the actual reaction pathway looks like this: The net result is the same: hydrolyzed carbohydrate and an enzyme ( acetyl CoA) are oxidized, yielding energy.
The act of respiration, as well as all of the actual work done by life, is accomplished by proteins, which are long, complex molecules built of amino acids. All life (and even some non-living things) require amino acids, therefore nitrogen is important. H O Carboxylic group (COOH) Amino functional group (NH 2 ) R C C OH Hydrocarbon group (C,H) NH 2 Some organisms can remove nitrogen from the nonlivng environment, others must consume other N-bearing lifeforms. Q: where do we find abundant nitrogen on Earth?
Amino Acids H O Carboxylic group (COOH) Amino functional group R C C OH (NH 2 ) NH 2 Hydrocarbon group (R) • Different amino acids are formed by adding hydrocarbon group as side chains Q: How many amino acids are there?
The 20 amino acids Ala Alamine Arg Arginine Asn Asparagine Asp Aspartic Acid Cys Cystine Gln Glutamine Glu Glutamic Acid Gly Glycine His Histidine Thr Threonine Ile Isoleucine Trp Tryptophan Leu Leucine Tyr Tyrosine Lys Lysine Val Valine Met Methionine Phe Phenylalanine Pre Proline Ser Serine
The 20 amino acids You and all other animals require all 20 to survive. Of the 20 your body is able to synthesize 12. The other 8 (boxes) you must acquire from diet. Eggs and milk are excellent sources for these. A vegetarian diet requires careful attention to amino acid intake
Proteins Macromolecules (chain of smaller molecules) of amino acids. Amino acids are joined by peptide bonds between the amino groups and carboxyl groups (polypeptides) The order of amino acids and the resulting shape determines its properties. With 20 amino acids combined by the hundreds in some cases, the diversity of proteins is staggering!
The peptide bond: holding amino acids together. Q: what requirement of life is needed for this?
The Role of Proteins • Enzymatic catalysis Enzymes exhibit enormous catalytic power by increasing the rate of the reaction at least a million fold • Transport and storage Many small molecules and ions are transported by specific proteins.
The Role of Proteins • Coordinated motion Proteins are the major component of muscle. Muscle contraction is accomplished by the sliding motion of two kinds of protein filaments (actin and myosin). • Mechanical support The high tensile strength of skin and bone is due to the presence of collagen, fibrous protein.
The Role of Proteins • Immune protection Antibodies are highly specific proteins that recognize and combine with such foreign substances as viruses, bacteria and cells from other organisms. • Generation and transmission of nerve impulses The response of nerve cells to specific stimuli is mediated by receptor proteins. Receptor proteins that can be triggered by specific small molecules are responsible for transmitting nerve impulses.
• Growth and differentiation Controlled sequential expression of genetic information is essential for the orderly growth and differentiation of cells. In higher organisms, growth and differentiation are controlled by growth factor proteins. For example, the activities of different cells in multicellular organisms are coordinated by hormones
Protein Structure Primary structure: exact sequence of the amino acids Secondary structure: Hydrogen bonding shape the protein into coils, helixes, spheres, blobs… Tertiary structure: cross-linking between amino acids brought together by folding. Quaternary structure: two or more separate long chains may be brought together. Q: do we know the exact shape taken by a given combination of amino acids?
Examples or proteins relevant to Homo sapiens Enzymes – catalyze metabolic reactions Hormones – regulate body activities Hemoglobin – transports oxygen in blood Antibodies – defend against infection
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