Ch. 1-5 Flashcards
Selective pressure
any phenomena which alters the behavior and fitness of living organisms within a given environment
Eukaryotes
Cells with membrane enclosed nuclei and membrane enclosed organelles
Archaea & Bacteria
are not more closely related to each other than eukaryotes
Prokaryotes
Cells without membrane enclosed nuclei or organelles
Populations
group of organisms within the same species with viable reproduction, within that group
Matter
anything that occupies space and has mass
Element
a substance that cannot be broken down into simpler substances by chemical means
Trace elements
a chemical element present in living organisms in very small amounts, typically less than 0.1% by volume
Compound
a substance made up of 2 or more different elements chemically combined in fixed proportions
Molecule
the smallest unit of a substance, composed of 2 or more atoms held together by chemical bonds which retains the chemical properties of that substance
subatomic particles
a particle that is smaller than an atom
neutrons
no charge
protons
positive charge
electrons
negative charge
atomic number
number of protons; unique to each element
mass number
number of protons + neutrons
isotopes
atomic forms of the same element; same number of protons, varied number of neutrons
valence electrons
refers to the electrons located in the outermost shell of an atom
chemical bonds
interactions that result in atoms being held together to form molecules by sharing/transferring electrons between them
covalent bonds
sharing of a pair of valence electrons
ionic bonds
when 2 atoms interact, the more electronegative atom strips a valence electron away from the less electronegative atom
hydrogen bonds
hydrogen atoms in a molecule that carry a partial positive charge are attracted to electronegative atoms to which they are not covalently bonded
electronegativity
the attraction of a given atom for the electrons in a covalent bond; O is the most electronegative, then N
anion
the more electronegative atom has one extra electron and carries a negative charge
cation
the less electronegative atom has one less electron and carries a positive charge
Photosynthesis
6 CO2 + 6 H20 —> C6 H12 O6 + 6 O2
(Aerobic) Cellular respiration
C6 H12 O6 + 6 O2 —> 6 CO2 + 6 H20
surface tension
a measure of how difficult it is to break the surface of a liquid
Water’s high specific heat
minimizes temperature fluctuations to within limits that permit life (heat is absorbed when hydrogen bonds break; heat is released when hydrogen bonds form)
Evaporation/vaporization
transformation of a substance from liquid to gas
heat of vaporization
the heat a liquid must absorb for 1g to be converted to gas
evaporative cooling
as a liquid evaporates, its remaining surface cools
floating of ice on liquid water
ice floats in liquid water because hydrogen bonds in ice are more “ordered”, making ice less dense than water
water’s greatest density
occurs at 4 degrees Celsius
aqueous solution
solution where water acts as the solvent
polarity of water molecules
makes them a powerful solvent, especially for salts
pH
a measure of hydrogen ion concentration equal to the negative log of the [H+] and ranging in value between 0 to 14
Acid
a substance that increases the hydrogen ion concentration of a solution
Base
a substance that reduces the hydrogen ion concentration
buffers
prevent a rapid change in pH when an acid or base is added to a solution; are compounds that readily accept or donate H+ ions
hydrophobic
water fearing; will not dissolve in water (oils)
hydrophilic
water loving; will dissolve in water (salts)
lipids
hydrophilic head, hydrophobic tail
kinetic energy
anything that moves has kinetic energy
thermal energy
kinetic energy associated with the random movement of atoms and molecules
temperature
average kinetic energy of molecules in a body of matter
adhesion
stickiness of a water molecule to another surface
cohesion
stickiness of a water molecule to another water molecule
carbon
basis for all biological molecules
carbon skeleton
refers to the chains of carbon atoms in a compound’s structure
isomers
compounds that have the same number of atoms of the same elements but with different structures and properties
structural isomers
differ in the covalent arrangement of their atoms
cis-tran isomers
cis=same side; trans=opposite side; must have a double bond in the compound; arrangement of atoms around the double bond differs between the isomers
enantiomers
isomers that are mirror images of each other; contains an asymmetric carbon
asymmetric carbon
a carbon that is bonded to 4 different atoms
functional groups
a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions
hydroxyl group
(-OH), alcohol; polar due to electronegative oxygen, forms hydrogen bonds with water
carbonyl group
(C=O), ketone (interior)/aldehyde (end)
carboxyl group
(-COOH), carboxylic acid or organic acid; acts as an acid
amino group
(-NH2), amine; acts as a base
sulfhydryl group
(-SH), thiol, least common
phosphate group
(-OPO3^2-), organic phosphate; high energy, ATP
methyl group
(-CH3), methylated compound
hydrocarbons
compounds that contain only carbon and hydrogen atoms
macromolecules
a giant molecule formed by the joining of smaller molecules, usually by a dehydration reaction
polymers
long molecules consisting of many similar or identical building blocks linked by covalent bonds (biological macromolecules are polymers)
monomers
the subunits from which polymers are built
dehydration reactions
chemical reaction when 2 monomers are covalently linked together and a water molecule is produced
hydrolysis
reverse of a dehydration reaction; water is used to break a covalent bond
carbohydrates
sugars; carbon chains containing hydroxyl groups and one carbonyl group
monosaccharides
the monomers from which carbohydrates are built
polysaccharides
a few hundred to a few thousand monosaccharides joined together; energy stores; structural material
disaccharides
consists of 2 monosaccharides joined by a dehydration reaction (glycosidic bond)
glycosidic bond
type of covalent bond that joins a carbohydrate molecule, or sugar, to another group
starch
polymers of glucose monomers; energy storage; plants use amylose and amylopectin
cellulose
plant structural polysaccharaide
chitin
animal and fungal structural polysaccharide
glycogen
animals store glucose as glycogen
fats
combination of glycerol and three fatty acids; also referred to as triacylglycerol or triglyceride
glycerol
an alcohol; contains 3 hydroxyls
fatty acids
- hydrocarbon chains of 16-18 carbons
- end carbon has a carboxyl group
- use a dehydration reaction to link fatty acids to glycerol
saturated fatty acids
(solid at room temperature) if all the carbons in the chain have the maximal amount of hydrogen covalently bonded, the molecule is saturated with hydrogen
unsaturated fatty acids
(liquid at room temperature) if two carbons in the chain are linked by covalent bonds, then the maximal amount of hydrogen is not covalently bonded and the molecule is unsaturated
hydration
refers to atoms of hydrogen
lipids
-not a true polymer
-don’t have repeating units of monomers
-smaller than macromolecules like starch
-common trait: hydrophobic
ester bond
a covalent bond between a hydroxyl group and a carboxyl group
phospholipids
only two hydrocarbon chains; third hydroxyl group on the glycerol subunit forms a covalent bond with a phosphate group
phosphate group
are negatively charged and hydrophilic; can attach other functional groups to the phosphate
amphipathic
both hydrophobic and hydrophilic
lipid bilayer
phospholipids self organize into bilayers:
-hydrophobic tails associate together
-hydrophilic heads associate with an aqueous environment
(all cell membranes and organelles have a lipid bilayer)
cholesterol
-depending on the cell type, cholesterol can account for 50% of the plasmic membrane
-orients with the hydroxyl group towards the aqueous solution
steroids
-do not have a glycerol subunit
-grouped with fats and phospholipids because they are hydrophobic
-contain a carbon skeleton with four fused ring
-cholesterol is a steroid
proteins
-work horse molecules of the cell
-the majority of functions in the cell are carried out by proteins
hormonal protein function
coordination of an organism’s activities
receptor protein function
response of cell to chemical stimuli
contractile and motor protein function
movement
structural protein function
support
enzymatic protein function
selective acceleration of chemical reactions
defensive protein function
protection against disease
storage protein function
storage of amino acids
transport protein function
transport of substances
enzymes
proteins that act as catalysts
catalysts
are chemical agents that speed up chemical reactions without being consumed by the reaction
amino acids
-monomers that are linked together by dehydration reactions to form polypeptides
-contain both an amino and carboxyl functional group
-also have “R” group or side chain
peptide bond
type of covalent bond
polypeptide
many peptides joined together
4 Levels of Proteins Structure
1) Primary- the sequence of amino acids in the polypeptide chain
2) Secondary- structures within regions of the polypeptide chain that are determined by the interactions of the atoms in the polypeptide backbone
3) Tertiary- 3D shape of a polypeptide that is determined by the interactions of the atoms in the side chains of the polypeptide
4) Quaternary- Interactions of multiple, individual polypeptides
Protein folding
-happens spontaneously; dependent on the chemical interactions within the protein itself
-cells have mechanisms to assist with protein folding
chaperonins
are other proteins that can provide a protective environment in which proteins can fold spontaneously
denaturation
the unfolding of a protein by disrupting the bonds that hold proteins together through changes in pH, salt concentration, or temperature
renaturation
proteins can refold once the correct environment is restored
nucleic acids
polymers of monomers called nucleotides
deoxyribonucleic acid (DNA)
stores the hereditary info of a cell; genes are discrete units of hereditary information consisting of a specific nucleotide sequence
ribonucleic acid (RNA)
- mRNA=messenger RNA
- rRNA=ribosomal RNA
- t RNA=transfer RNA
(these three essential for protein synthesis) - miRNA=microRNA
mRNA
RNA molecules that cary genetic information from the DNA to the ribosomes, where proteins are synthesized
rRNA
RNA molecules that complex with proteins to form the ribosomes
tRNA
RNA molecules that carry amino acids to the ribosomes where the amino acids will be incorporated into a protein
miRNA
small RNA molecules that regulate transcription
components of a nucleotide
-5 carbon sugar (a pentose)
-phosphate group
-nitrogenous base
pentose
the pentose in DNA differs from the pentose in RNA in that deoxyribose lacks a hydroxyl group on the 2nd carbon
nitrogenous bases
carbon rings that also contain nitrogen
Pyrimidines
-Cytosine
-Uracil (RNA)
-Thymine (DNA)
*think “CUT the Py”
Purines
-Adenine
-Guanine
*think “Pure As Gold”
Polynucleotides
dehydration reactions between the phosphate group on one nucleotide and the hydroxyl on the 3’ carbon of a 2nd nucleotide link monomers together in a phosphodiester bond
nucleic acid polymers
are held together by phosphodiester bonds
polynucleotide orientation
-phosphate is always linked to the 5’ carbon of the pentose
-new monomers are always added to the 3’ carbon of the last pentose in the chain
nucleotide
a phosphate group on a nucleoside creates a nucleotide
nucleoside
sugar and base combined
phosphate group
inorganic phosphate can form a covalent bond with the 5- carbon of a nucleoside by a dehydration reaction; forms a phosphate ester bond
carbon numbering
because nucleotides are complex, the sugar carbons are noted with ‘ (prime) to differentiate from carbons in the nitrogenous base
