SLIDE 1 Components of Life
Part I: atoms, molecules, amino acids, and proteins
ERTH 1040 - NSII
SLIDE 2 All life on Earth is composed of a combination of only a few chemical components. In this course, we’ve previously discussed some
- f the inorganic materials
(e.g. minerals and fluids) of the Earth. We’ve also touched on the basic
hydrocarbons
SLIDE 3
Q: What are the most common elements associated with life?
SLIDE 4 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 CO2 are typically termed inorganic, as they are very abundant in the Earth, even in regions where life doesn’t exist.
SLIDE 5
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?
SLIDE 6
To understand the nature of the molecules of life, we must first understand how atoms are assembled into molecules Bonding Ionic Covalent Metallic Electrostatic
SLIDE 7
Metals (M) prefer to lose electrons
SLIDE 8
Can only attract so far – “solid spheres”
Ionic bonding
SLIDE 9 Ionic compounds are formed by the mutual attraction of charged atoms, the ratio of which is determined by
- verall charge neutrality; e.g.:
Na+ + Cl - = NaCl Ca2
+ + + 2F - = CaF2
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.
SLIDE 10
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.
SLIDE 11
Q: What ultimately controls bonding in any compound?
SLIDE 12 Double bonding
Two electron pairs are shared
Triple bonding
Three electron pairs are shared
SLIDE 13
Coordinate covalent bonds – the shared electron is donated by atom. Most carry an overall negative charge (CO3)2-, (OH)-, (HCO3)-, (PO4)3-
SLIDE 14
Ionic-covalent character makes molecules dipolar
F, = 4 H, = 2.1
SLIDE 15
SLIDE 16 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.
HCl + H2O H3O+ + Cl-
- Hydr. Chloride water hydronium chlorine
An inorganic acid, HCl
Organic acids are typically very weak (not much hydronium produced in dissolution
SLIDE 18
Covalent compounds CO2 carbon dioxide (Greek "di" for 2) CO carbon monoxide (Greek "mono" for 1) CCl4 carbon tetrachloride (Greek "tetra" for 4) Empirical Formulas Always used in ionic compounds NaCl CaF2 CH2O
SLIDE 19
Structural formulas show the geometry and bonding
SLIDE 20
Hydrocarbons C-H molecules. Methane (CH4) to asphaltenes Cn, n is 1 to 60, increasing n changes state. In CH4, n is 1. e.g. Straight-chain parafins n = 1-4 gas n = 5-16 liquid n > 16 solid
SLIDE 21
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.
SLIDE 22
Q: What is added to the hydrocarbon to make other straight-chain organic molecules?
Straight Chain Organic Compounds
SLIDE 23 2C4H10 + 13 O2 10H2O + 8CO2 C6H12O6 + 6 O2 6H2O + 6CO2
Glucose
Hydrocarbon Carbohydrate
SLIDE 24 Carbohydrates Molecular formulas help to describe the structure of the molecule: While CH2O accurately describes the ratio
- f elements in glucose, it fails to
characterize the whole molecule Q: why are there no carbon molecules shown on the diagram at right?
SLIDE 25 Carbohydrates – C H and O compounds that are
- rganized in to pentagonal and hexagonal
structures. Structural formula of glucose.
SLIDE 26 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? Glucose is a simple carbohydrate. More complicated molecules may be formed.
SLIDE 27
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?
SLIDE 28 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
SLIDE 29 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.
SLIDE 30 R C H C O OH NH2 Carboxylic group (COOH) Amino functional group (NH2) Hydrocarbon group (C,H)
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.
Q: where do we find abundant nitrogen on Earth?
Some organisms can remove nitrogen from the nonlivng environment, others must consume other N-bearing lifeforms.
SLIDE 31 Amino Acids
- Different amino acids are formed by adding
hydrocarbon group as side chains R C H C O OH NH2 Carboxylic group (COOH) Amino functional group (NH2) Hydrocarbon group (R) Q: How many amino acids are there?
SLIDE 32 The 20 amino acids
Ala Alamine Arg Arginine Asn Asparagine Asp Aspartic Acid Cys Cystine Gln Glutamine Glu Glutamic Acid Gly Glycine His Histidine Ile Isoleucine Leu Leucine Lys Lysine Met Methionine Phe Phenylalanine Pre Proline Ser Serine Thr Threonine Trp Tryptophan Tyr Tyrosine Val Valine
SLIDE 33 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
must acquire from diet.
Eggs and milk are excellent sources for these. A vegetarian diet requires careful attention to amino acid intake
SLIDE 34
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!
SLIDE 35
The peptide bond: holding amino acids together. Q: what requirement of life is needed for this?
SLIDE 36
SLIDE 37 The Role of Proteins
- Enzymatic catalysis Enzymes exhibit enormous catalytic
power by increasing the rate of the reaction at least a million fold
Many small molecules and ions are transported by specific proteins.
SLIDE 38 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.
SLIDE 39 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.
SLIDE 40
- 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
SLIDE 41 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.
Protein Structure
Q: do we know the exact shape taken by a given combination of amino acids?
SLIDE 42
Examples or proteins relevant to Homo sapiens Enzymes – catalyze metabolic reactions Hormones – regulate body activities Hemoglobin – transports oxygen in blood Antibodies – defend against infection
SLIDE 43 Male reproductive tract, secondary characteristics Entire body Testes, Adrenals Androgens Uterine contraction, lactation Breasts, uterus Pituitary Oxytocin Uterine processes, Maintains pregnancies Uterus, breasts Ovaries Progesterone Reproductive tract, secondary characteristics Entire body Testes Testosterone Reproductive tract, secondary characteristics Entire body Ovarian Follicle Estrogen Ovulation and sex hormone production Gonads Pituitary LH/ICH Gonad development Gonads Pituitary FSH Lactation Ovarian cycle Breast, Ovaries Pituitary Prolactin Function Target Gland Hormone
Hormones – proteins linked to growth and reproductive processes (examples for humans).
SLIDE 44 Summary of proteins: All life activity is accomplished through the chemistry of proteins. Complex life forms, such as ourselves, require a large number of different proteins.
Q: What determines the behavior
SLIDE 45 Lipids
Complex molecules that do not easily dissolve in water. This is a diagram
a molecule that composes much
structure in all life. Higher energy needed to make these!
Q: Which stores more energy, a fat or a sugar?
SLIDE 46 Fatty acids are lipids essential to diet. Those with no double C=C bonds are termed
produce cholesterol, and are an important molecule in cells Consuming too many saturated fats leads to deposits in bloodstream Those with C=C are
- unsaturated. (note kinks)
Watch out for hydrogenated polyunsaturated fats – they’re no better. Added hydrogen remove C=C bonds.
Q: What is hydrogenation? Why is it used?
SLIDE 47 Nucleotides
Q: What are the three components of any nucleotide?
Adenine Base
SLIDE 48
SLIDE 49 Purine Pyrimidine Q: What’s the difference between a purine and a pyrimidine?
Adenine Base
SLIDE 50 DNA molecules are composed of four components, with the same phosphate- sugar structure. Q: What pyrimidines are found in DNA?
Adenine Base
SLIDE 51 RNA molecules are composed of four components, with the same phosphate- sugar structure.
Q: What pyrimidines are found in RNA? Q: What problems could arise due to similar structures
Adenosine Base
SLIDE 52 DNA and RNA strands are chains
phosphate-sugar with purine and pyrimidine DNA – Deoxyribonucleic sugar and thymine RNA – Ribonucleic sugar and uracil
SLIDE 53 Q: What are the purine-pyramidine combinations in DNA?
Each purine may bond with one specific
- pyramidine. Guanine bonds with cytosine (GC), and
in DNA, adenine bonds with thymine (AT). Single strands may then couple in this way. DNA molecules are typically coupled when they are not being copied or bonded to RNA RNA may do the same, except adenosine bonds with uracil (AU). RNA molecules are coupled when bonded to other chains of RNA or DNA.
SLIDE 54 The forming of nucleoprotein
27-593 Figure 27.15
Q: Where is DNA found in cells from K. Monera?
SLIDE 55 DNA replication
27-594 Figure 27.16
SLIDE 56 DNA replication process
Q: What type of molecule is involved in duplicating DNA?
SLIDE 57 DNA replication in nucleus
27-596 Figure 27.18
SLIDE 58 Transcription
Q: What is transcription? How are the molecules linked?
SLIDE 59 Manufacture of mRNA in a eukaryotic cell
27-598 Figure 27.20
SLIDE 60 G Glycine Glutamic Acid Alanine Valine A Glycine Glutamic Acid Alanine Valine C Glycine Aspartic Acid Alanine Valine U Glycine Aspartic Acid Alanine Valine G G Arginine Lysine Threonine Methionine A Arginine Lysine Threonine Isoleucine C Serine Asparagine Threonine Isoleucine U Serine Asparagine Threonine Isoleucine A G Arginine Glutamine Proline Leucine A Arginine Glutamine Proline Leucine C Arginine Histidine Proline Leucine U Arginine Histidine Proline Leucine C G Tryptophan Stop Serine Leucine A Stop Stop Serine Leucine C Cystine Tyrosine Serine Phenylalanine U Cystine Tyrosine Serine Phenylalanine U G A C U Third Position Second Position First Position
SLIDE 61 So the mRNA codes for specific amino acids, which will be bonded together into a protein. Here is a strand of mature (buffer removed) mRNA. It contains the information need to encode a part of a particular protein (realize of course real mRNA is much, much longer).
SLIDE 62 The mRNA fits into a grove of a ribosome (an organelle made of protein and ribosomal RNA).
SLIDE 63 The second part of the ribosome, which aligns tRNA, comes together with the first. It attracts the appropriate RNA for assembly.
SLIDE 64 Because the mRNA is AUG, the tRNA is UAC and is bonded to the amino acid Tyrosine. The bases from both RNAs are bonded together.
SLIDE 65 The ribosome shifts to the next position, attracting the next appropriate tRNA sequence
SLIDE 66 When the bases are bonded, so are the adjacent amino
- acids. A polypetide chain is beginning to form.
The first tRNA sequence is unbonded at it bases, and is unbonded from its amino acid.
SLIDE 67 The sequence continues down the mRNA as the ribosome moves along.
SLIDE 68
SLIDE 69
SLIDE 70 This will continue until the ribosome hits an mRNA code for a stop (one of three possible sequences). Note that this short mRNA is coded to stop at the end of this chain.
SLIDE 71 Steps involved in protein synthesis
27-601 Figure 27.23
SLIDE 72 Result of a nucleotide substitution
27-599 Figure 27.21
Q: What happens in a mutation?
SLIDE 73 G Glycine Glutamic Acid Alanine Valine A Glycine Glutamic Acid Alanine Valine C Glycine Aspartic Acid Alanine Valine U Glycine Aspartic Acid Alanine Valine G G Arginine Lysine Threonine Methionine A Arginine Lysine Threonine Isoleucine C Serine Asparagine Threonine Isoleucine U Serine Asparagine Threonine Isoleucine A G Arginine Glutamine Proline Leucine A Arginine Glutamine Proline Leucine C Arginine Histidine Proline Leucine U Arginine Histidine Proline Leucine C G Tryptophan Stop Serine Leucine A Stop Stop Serine Leucine C Cystine Tyrosine Serine Phenylalanine U Cystine Tyrosine Serine Phenylalanine U G A C U Third Position Second Position First Position
