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chemistry of life
chemistry of life
elements
substances that cannot be broken down into simpler substances by chemical means
oxygen
essential element of life; found in all macromolecules
carbon
most essential element of life; found in all macromolecules
hydrogen
essential element of life; found in all macromolecules
nitrogen
essential element of life; found in proteins and nucleic acids
trace elements
required in very small quantities
atom
smallest unit of an element that retains its characteristic properties
protons
subatomic particle with a positive charge
neutrons
subatomic particle with no charge
electrons
smallest subatomic particle with negative charge
nucleus
the core of the atom where protons and neutrons are packed together
isotopes
same number of protons but differ in the number of neutrons in the nucleus
radiometric dating
examining the rate of decay of carbon-14 and other isotopes in an artifact can date it because some isotopes are radioactive and decay predictably over time
compound
two or more individual elements are combined in a fixed ratio
chemical reaction
the process by which one or more substances change to produce one or more different substances
• hydrogen atoms get together with oxygen atoms to form water
chemical bond
what atoms of a compound are held together by
ionic bond
formed between two atoms when one or more electrons are transferred from one atom to the other which causes one atom to lose electrons and become positively charged and the other to gain electrons and become negatively charged
covalent bond
formed when electrons are shared between atoms
hydrogen bond
type of chemical bond which is usually weak and happens with water molecules (4 hydrogen bonds per molecule) but they contribute to water's special properties
ions
charged forms of the atoms
nonpolar covalent
If electrons are shared equally between atoms
polar covalent
if electrons are shared unequally between atoms
polar molecule
molecules that have partially positive and partially negative charges
cohesion
water molecules have a strong tendency to stick together
adhesion
water molecules like to stick to other substances
surface tension
cohesion of water molecules creates tension on the surface of water which allows light things like leaves and water striders to sit atop the surface without sinking
heat capacity
water has a high heat capacity which means it's harder to increase the temperature which helps keep ocean temperatures stable and helps us keep a stable body temperature
expansion on freezing
water expands when freezing because liquid water is denser and solid water because the lattice structure of four water molecules together causes it to expand upon freezing which helps aquatic life survive because bodies of water freeze from top to bottom
capillary action
cohesion and adhesion help water rise up roots, trunks, and branches of trees
acidic
contains a lot of hydrogen ions (H+) and has a pH less than 7 like lemons which have citric acid in them
basic
contains a lot of hydroxide ions (OH-) and is said to be "alkaline" and has a slippery consistency like soap which is composed largely of bases
neutral
midpoint (7) on the pH scale
alkaline
fancy name for basic solutions
pH scale
measures acidity or alkalinity of a solution
organic compounds
chemical compounds that contain a skeleton of carbon atoms surrounded by hydrogen atoms and often other elements (CH4)
inorganic compounds
molecules that do not contain carbon atoms (NaCl)
polymer
chains of building blocks that make macromolecules
monomer
individual building blocks of a polymer (subunits)
carbohydrates
organic compounds that contain carbon, hydrogen, and oxygen
monosaccharides
simplest sugars like glucose, fructose, galactose, ribose, and deoxyribose that serve as an energy source for cells and a subunit for polysaccharides
disaccharides
two monosaccharides formed by removing hydrogen and hydroxide from each sugar molecule to form water (dehydration synthesis)
polysaccharides
many repeated units of monosaccharides that consist of branched or unbranched chains of monosaccharides such as starch, cellulose, and glycogen
glucose
most common monosaccharide, main source of energy for cells
fructose
second most common monosaccharide
dehydration synthesis (condensation)
hydrogen is removed from one molecule and hydroxide from the other to form a new joined molecule and water
glycosydic linkage
the bond formed between two monosaccharides
hydrolysis
breaking two substances by adding water and restoring the hydroxyl and hydrogen removed from dehydration synthesis
starch
sugar storage molecule in plants
cellulose
made of β-glucose and is a major part of the cell walls in plants
chitin
a polymer of β-glucose molecules that serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods
glycogen
sugar storage molecule in animals
amino acids
organic molecules that serve as the building blocks of proteins
amino groups
-NH2 part of the amino acid
carboxyl group
-COOH part of the amino acid
R-group
what differentiates amino acids
side chain
another name for R-group which differentiates amino acids
how do side chains differ?
• composition of elements (C, H, O, N, and S)
• polarity (polar, nonpolar) which affects whether an amino acid if more hydrophobic or more hydrophilic
• charge (neutral, positive, negative)
• shape (long-chain, short-chain, ring-shape)
dipeptide
two amino acids joined
peptide bond
the bond between two amino acids
polypeptide
group of amino acids joined together in a "string"
protein
three-dimensional structure after polypeptide chain twists and folds on itself
primary structure
linear sequence of amino acids (polypeptide chain)
secondary structure
polypeptide begins to twist, forming either a coil (alpha helix) of a zigzagging pattern (beta-pleated sheets)
tertiary structure
after secondary structure is formed the amino acids can interact with each other moving the hydrophilic amino acids outside and the hydrophobic amino acids inside minimizing the free energy of the molecule and locks it into a stable 3D shape
quaternary structure
several different polypeptide chains interacting with each other making the individual polypeptide chains called subunits of the final whole protein
chaperone proteins (chaperonins)
help the protein fold properly and make the process more efficient
lipids
consist of carbon, hydrogen, and oxygen atoms but not in the 1:2:1 ration typical of carbohydrates and example being triglycerides, phospholipids, and steroids that serve as insulation, signaling molecules, and a means of energy storage
triglycerides
bodies store fat in tissue called adipose which is made of cells called adipocytes which are filled with triglycerides made of a glycerol molecule (glycerol backbone) with three fatty acid chains attached to it (a long chain of carbons in which each carbon is covered in hydrogen and one end of the chain has a carboxyl group formed by dehydration synthesis
phospholipids
contain two fatty acid "tails" (hydrophobic) and one negatively charged "phosphate" head (hydrophilic) meaning it's an amphipathic molecule which contributes to the shape and structure of the cell membrane
steroids
four-ringed hydrophobic molecules that are used for the structure of the cell membrane and signaling hormones/molecules the most common being cholesterol and is the precursor to vitamin D, testosterone, estrogen, progesterone, aldosterone, cortisol, and bile salts.
glycerol
backbone of triglycerides
ester linkage
the linkage formed between the glycerol molecule and the fatty acids by dehydration synthesis
saturated
hydrogens along its long carbon chain
unsaturated
double bond in chain
polyunsaturated
many double bonds in the chain
hydrophobic
water hating and insoluble in water
hydrophilic
water loving and soluble in water
amphipathic molecule
has both a hydrophilic region and a hydrophobic region
cholesterol
four-ringed molecule found in membranes that increases membrane fluidity except at very high temperatures when it helps to hold things together instead and is important for making certain types of hormones and for making Vitamin D
nucleic acids
made of simple units called nucleotides that contain carbon, hydrogen, oxygen, and nitrogen, like proteins, but also contain phosphorus examples being deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
nucleotides
subunits of nucleic acids
deoxyribonucleic acid (DNA)
nucleic acid that contains the sugar deoxyribose and is a double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins
ribonucleic acid (RNA)
a single-stranded nucleic acid that contains the sugar ribose that is present in all living cells and that plays a role in protein synthesis