CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE1. An element is a substance that can’t be broken down into other substances by chemical reactions. A compound is a substance w/ two or more different elements. 2. ESSENTIAL ELEMENTS OF LIFE: 25 out of 92 natural elements are essential to life. Four elements that make up 96% of living matter: C (carbon), H (hydrogen), N (nitrogen), O (oxygen). 3. Trace elements: elements required by an organism only in small quantities. Ex: Fe, I (iodine) in vertebrates produced by thyroid. Iodine deficiency = goiter4. Atoms: Have subatomic particles, and different # of electrons and protons. 5.Helium has an atomic mass of 4 daltons, atomic number of 2 a. Neutron: electrically neutral. Proton: positive charge. Both are found in the nucleus, and are about the same mass. Have masses of 1 Dalton (atomic mass unit / amu). b. Atomic #: Number of protons in an element. Also tells number of electrons in an electrically neutral atom. (Ex: 2He says that helium has 2 protons in its nucleus.) Mass number: #protons + #neutrons in nucleus of an atom. It is an approximation ofthe total mass of an atom, which is the atomic mass (since protons and neutrons have mass of close to 1 dalton). 6. # of neutr ons in an atom = Ma ss nu mber – ato mic n umbe r7. Isotopes : Isotopic forms of an element have the same # of atoms (cuz they’re the same element). But, they have different number of neutrons, therefore different atomic masses. (Ex: Carbon-12 has 6 neutrons and mass number of 12. Takes up 99% of carbon in nature. The rest of 1% is Carbon-13 and has 7 neutrons. There’s also Carbon-14 which has 8 neutrons. They all have 6 protons). 8. Radioactive Isotopes: Not stable, nucleus decays spontaneously and releases particles and energy. APPLICATIONS IN BIOLOGY? Using measurement of radioactivity in fossils to date stuff. Can also be used as tracers to follow atoms through chemical processes of an organism. Cells use radioactive atoms just like nonradioactive isotopes of an element, but radioactive isotopes are easier to detect. Also used as diagnostic tools in medicine, PET scans that monitor chemical processes (lie cancerous growth). 9. Energy: Capacity to cause change by doing work. Potential energy: energy matter has because of its location or structure. Matter wants to move to the lowest state of potential energy (rock goes downhill). Electrons have potential energy due to their arrangement in relation w/ the nucleus. Negative charged electrons are attracted to positive ly charged nucleus. The first electron shell is
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1. An element is a substance that can’t be broken down into other substances by chemical reactions.
A compound is a substance w/ two or more different elements.
2. ESSENTIAL ELEMENTS OF LIFE : 25 out of 92 natural elements are essential to life.Four elements that make up 96% of living matter: C (carbon), H (hydrogen), N (nitrogen), O (oxygen).
3. Trace elements: elements required by an organism only in small quantities. Ex: Fe, I (iodine) in
vertebrates produced by thyroid. Iodine deficiency = goiter
4. Atoms: Have subatomic particles, and different # of electrons and protons.
5.Helium has an atomic mass of 4 daltons, atomic number of 2
a. Neutron: electrically neutral. Proton: positive charge. Both are found in the nucleus, and are
about the same mass. Have masses of 1 Dalton (atomic mass unit /
amu).
b. Atomic #: Number of protons in an element. Also tells
number of electrons in an electrically neutral atom. (Ex: 2He says that helium has 2 protons in its
nucleus.)
Mass number: #protons + #neutrons in nucleus of an atom. It is an approximation of the total mass
of an atom, which is the atomic mass (since protons and neutrons have mass of close to 1 dalton).
6. # of neutrons in an atom = Mass number – atomic number
7. Isotopes: Isotopic forms of an element have the same # of atoms (cuz they’re the same element). But,
they have different number of neutrons, therefore different atomic masses. (Ex: Carbon-12 has 6
neutrons and mass number of 12. Takes up 99% of carbon in nature. The rest of 1% is Carbon-13 and
has 7 neutrons. There’s also Carbon-14 which has 8 neutrons. They all have 6 protons).
8. Radioactive Isotopes: Not stable, nucleus decays spontaneously and releases particles and energy.
APPLICATIONS IN BIOLOGY ? Using measurement of radioactivity in fossils to date stuff. Can also
be used as tracers to follow atoms through chemical processes of an organism. Cells use radioactive
atoms just like nonradioactive isotopes of an element, but radioactive isotopes are easier to detect.
Also used as diagnostic tools in medicine, PET scans that monitor chemical processes (lie cancerous
growth).
9. Energy: Capacity to cause change by doing work . Potential energy: energy matter has because of its
location or structure. Matter wants to move to the lowest state of potential energy (rock goes
downhill). Electrons have potential energy due to their arrangement in relation w/ the nucleus.
Negative charged electrons are attracted to positively charged nucleus. The first electron shell is
closest to the nucleus and is under the influence of the nucleus’s pull more so it has less potential
energy.
10. CHEMICAL BONDS : attractions between atoms.
a. Covalent bond: Sharing of a pair of valence electrons. When two hydrogens come close enough for their
1s orbitals to overlap, they share electrons. 2 or more atoms held by covalent bonds are called molecules. The
more electronegative an atom, the more strongly it pulls shared electrons towards itself. In Nonpolarcovalent bonds, atoms are equally electronegative. In Polar covalent bonds, one atom is more
electronegative than another and the bond isn’t shared equally. Ex: H2O. O is a lot more electronegative.
b. Ionic Bonds: Attraction between oppositely charged ions. Two atoms are so unequal in their attraction for
valence electrons that the more electronegative atom takes the electron completely away from its partner.
ELECTRON TRANSFER takes place. Cation is positive charge (less electrons). Anion is negative (gain
electrons). Ionic compounds form salts. Yeahhh.
11. Strong covalent bonds link atoms to form a cell’s molecules. Weaker bonds also contribute to
emergent properties of life. For example, big biological molecules (proteins! Alpha helix + betasheets held by h-bonds) are held together in a functional form by weak bonds. When two molecules
make contact, they temporarily stick by weak bonds. They can come together, respond, then separate.
12. HYDROGEN BONDS: Form when hydrogen atom covalently bonded to an electronegative atom is
attracted to another electronegative atom… Electronegative partners are either Oxygen or Nitrogen.
Ex: H2O and NH3. Water molecules do hydrogen bonding!
VAN der WAALS interactions: Result of interactions of e-. Molecules w/ nonpolar covalent bonds have
+ and – regions. Forces are very weak. Occur when atoms and molecules are really close together. But
they can help gecko lizards walk up walls! There are many Van der Waals interaction between hair tip
molecules and molecules of wall’s surface that allow gecko’s to climb up walls.
13. MOLECULAR SHAPE AND FUNCTION: The shape of a molecule mirrors its function. A
molecule’s shape is determined by the position of the atom’s orbitals. When atoms form covalent
bonds, orbitals in its valence shells rearrange. Molecular shape determines how biological molecules
recognize and resond to one another. Molecules w/ complementary shapes form weak bonds and
bond w/ eachother.
14. Chemical equilibriumヽ(`д´)ノ is the point where reactions offset one another exactly. Reactions are
still going, but there is no net effect on the concentration of the reactants and products. (NOT thatreactants and products are equal concentration.) It means their concentrations have a stabilized ratio.
So, the forward and reverse reaction occur at the same rate and the relative concentrations of products
Compound: Thiol. Properties: 2 sulfhydryl groups form Cystein bonds in proteins. Cross-linking of cysteins
in hair protein keeps curly or straight hair. When you get a perm, you break and re-form cross-linking bonds.
f. Phosphate:
Properties: Provides backbone for phospholipids
g. Methyl -CH3
Properties: Adding Methyl to DNA or molecules bound to DNA affects gene expression. Arrangement of methyl group in male and female sex hormones affects their shape and function. Hydrophobic.
6.
ATP YEAHHHH BOII It’s an important source of energy!!!
7. When 3 phosphates are present in a series (like in ATP), one phosphate splits off when reacting with
water. This reaction releases energy that can be used by the cell.
P-P-P-Adenosine -----reacts with H2O-- Pi + P-P-Adenosine + Energy
THE MOLECULES OF LIFE.
8. Polymers are long molecules with many similar or identical units linked by covalent bonds.
Monomers are those units.
9. Condensation and Hydrolysis Reactions:
CARBOHYDRATES SERVE AS FUEL AND
BUILDING MATERIAL
10. Monosaccharide: “simple sugars”. Have a formula some multiple of CH2O. Example: Glucose
C6H12O6. Trademarks of sugar: Carbonyl group, multiple hydroxyl groups. Dpending on the
carbonyl group’s location, the sugar is an aldose or a ketose. Glucose is an aldose. Fructose, an
isomer of glucose, is a ketose.
Disaccharide: 2 monosaccharides joined by a glycosidic linkage (covalent bond formed between 2
monosaccharides by dehydration rxn). Ex: Maltose is formed by 2 glucose.