Chapter 1: Chemistry Flashcards
atom/molecule
Neutrons, protons, and electrons/group of 2 or more atoms held together by chemical bonds (chemical bonds due to electron interactions)
electronegativity
Ability of an atom to attract electrons (determines kind of bond that forms)
bond types
- Ionic=transfer of electrons from one atom to another (different electronegativities)
- Covalent=sharing of electrons between atoms (similar EN-)
Nonpolar= equal sharing of electrons (identical EN)
Polar=unequal sharing of electrons (different EN and dipole formation) - Hydrogen=weak bond between molecules with a hydrogen attached to a highly EN atom and is attracted to a negative charge on another EN molecule (N,O,F)
excellent solvent/hydrophilic/hydrophobic
dipoles of H2O break up charged ionic molecules. Hydrophilic=water loving… dissolve in water. Hydrophobic= water fearing … do not dissolve in water.
high heat capacity
degree in which a substance changes temp in response to gain/loss of heat (changes temperature very slowly with changes in heat content). For example, the temperature of large water body are very stable in response to temp changes of surrounding air; must add large amount of energy to warm up water. High heat of vaporization as well.
ice floats
water expands as it freezes, become less dense than its liquid form (H-bonds become more rigid and form crystal that keeps molecules separated).
cohesion/surface tension
attraction between like substances due to H-bonds; strong cohesion between H2O molecules produces a high surface tension (water surface that is firm).
adhesion
attraction of unlike substances (wet finger and flip pages); capillary action: ability of liquid to flow without external forces (e.g. against gravity).
organic molecules
characterized by carbon atoms. Macromolecules form monomers (1 unit) which forms polymers (series of repeating monomers). 4 of carbon’s 6 electrons are available to form bond with other atoms.
functional groups
particular cluster of atoms, gives molecules unique properties such as acidity and polarity
hydroxyl (OH)
polar and hydrophilic
carboxyl (COOH)
polar, hydrophilic, weak acid
amino (NH2)
polar, hydrophilic, weak base
phosphate (PO3)
polar, hydrophilic, acid (sometimes shows as PO4)
carbonyl (C=O)
aldehyde (H-C=O)
ketone (R-C=O)
polar and hydrophilic
methyl (CH3)
nonpolar and hydrophobic
carbohydrates: monosaccharide
single sugar molecule (e.g. glucose and fructose). Alpha or beta based on position of H and OH on first (anomeric) carbon (OH down=alpha, OH up=beta).
disaccharide
two sugar molecules joined by a glycosidic linkage (joined by dehydration/condensation=loss of water). E.g. sucrose (glu+fru), lactose (glu+gal), maltose (glu+glu)
polysaccharide
series of connected monosaccharides; polymer. Bond via dehydration synthesis, breakdown via hydrolysis (addition of water).
starch
polymer of a-glucose molecules; store energy in plants
glycogen
polymer of a-glucose; store energy in animal cells
cellulose
polymer of b-glucose; structural molecules for cell walls in plants and wood
chitin
polymer similar to cellulose; but each b-glucose has a nitrogen-containing group attached to ring. Structural in fungal cell walls (also exoskeletons of insects)
lipids and their functions
hydrophobic molecules. Fxns: insulation, energy storage, structural (cholestrol and phospholipids in membranes), endocrine
triglycerides (triglycerols)
three fatty acid chains attached to a glycerol backbone
saturated triglycerides
no double bonds (bad for health, saturated=straight chain=stack densely and form fat plaques=solid at room temp)
unsaturated
double bonds (better for health, unsaturated=double bonds cause branching=stack less dense=liquid at room temp)
phospholipid
two fatty acids and a phosphate group (+R) attached to a glycerol backbone. Amphipathic=both hydrophilic and hydrophobic properties
steroids
three 6 membered rings and one 5 membered ring … hormones and cholesterol (membrane component)
lipid derivatives
- phospholipids (covered above)
- waxes
esters of fatty acids and monohydroxylic alcohols. Used as protective coating or exoskeleton (lanolin)
- steroids
(sex hormones, cholesterol, corticosteroids)—4 ringed structure
- carotenoids
fatty acid carbon chains w/ conjugated double bonds and six membered C-rings at each end. Pigments which produce colors in plants and animals due to high conjugation (carotenes and xanthophylls (subgroups)
- porphyrins (tetrapyrroles)
4 joined pyrrole rings. Often complex w/metal (e.g. porphyrin heme complexes with Fe in hemoglobin, chlorophyll w/Mg)
adipocytes
specialized fat cells
- white fat cells contain a large lipid droplet composed primarily of triglycerides with a small layer of cytoplasm around it
- brown fat cells have considerable cytoplasm, lipid droplets scattered throughout, and lots of mitochondria
glycolipids
like phospholipids but w/carb group instead of phospholipid
Note: lipids are insoluble so they are transported in blood via lipoproteins (lipid core surrounded by phospholipids and apolipoproteins)
lipid membranes and temperature
cell membranes need to maintain a certain degree of fluidity and are capable of changing membrane fatty acid composition to do so.
1. cold weather= to avoid rigidity, cells incorporate more mono and polyunsat. fatty acids into the membrane (lower melting pts. and are kinked to increase fluidity).
2. Warm weather climates show opposite trend.
Note: Usat. fatty acids have lower m.p. compared to sat. fatty acids due to less efficient packing from kinks. (Less efficient packing means less intermolecular interactions, so less heat is required to med the solid to liquid form. )
proteins
polymers if amino acids joined by peptide bonds
structure of proteins
H
NH2-C-COOH
R
major functions of proteins
- structural-keratin in hair and collagen in connective tissues
- storage-casein in milk, ovalbumin in egg whites, zein in corn seeds
- transport- hemoglobin to carry oxygen, cytochromes carry electrons
- defensive- antibodies
- enyzmes- regulated rate of chemical reactions (forward and reverse reactions) such as amylase in breaking down a-glycosidic bonds in starch.
* **Random: enzymes are almost always considered to be proteins, but sometimes RNA can act as an enzyme (e.g. ribozyme)
protein structure
- primary=sequence of amino acids ***(all proteins have this)
- secondary= 3D shape resulting from hydrogen bonding between amino and carboxyl groups of adjacent amino acids (alpha helix, beta sheet) ***most proteins have this structure)
- tertiary= 3D structure due to noncovalent interactions between R groups (subunit interactions) (factors: H-bond, ionic bonds, hydrophobic effect [R group push away from water center], disulfide bond, van der waals)
- quaternary= 3D shape of protein that is a group if two or more separate peptide chains
protein classifications
- simple= entirely amino acids
- albumins and globulins = functional and act as carriers or enzymes
- scleroproteins =fibrous, structural, e.g. collagen
- conjugated= simple + nonprotein
- lipoprotein=bound to lipid
- mucoprotein=bound to carb
- chromoprotein=bound to pigmented molecule
- metalloprotein= complexed around a metal
- nucleoprotein= contain histone or protamine, bound to nucleic acid
3 main protein categories
- globular proteins=somewhat water soluble, fxns=enzymes, hormones, inter and intracellular storage and transport, osmotic regulation, immune response, dominated by 3ary structure.
- fibrous/structural proteins= not water soluble, made from long polymers, maintain+add strength to cellular and matrix structure, mostly dominated by 2ndary structure
- membrane proteins= membrane pumps/channels/receptors
denaturation
- 2ndary and onward structure of proteins is removed, the peptide bonds are not broken down into individual amino acids.
- usually irreversible unless the denaturing agent is removed
nucleic acids
DNA is a polymer of nucleotides
nucleotides
nitrogen base, five carbon sugar-deoxyribose, and a phosphate group
AT=2 H-bonds and CG=3 H-bonds
purines
- two rings
2. A and G
pyrimidines
- one ring
2. C and U and T (Cut the Pi)
nucleoside
sugar and base
structure of DNA
two antiparallel strands=double helix
RNA
- polymer of nucleotides that contain ribose
- thymine replaced by uracil (paris with A)
- single-stranded
cell doctrine/theory 1
- all living organisms are composed of one ore more cells
- the cell is the basic unit of structure, function, and organization in all organisms
- all cells come from pre-existing cells
- cells carry the hereditary info
RNA world hypothesis
proposes that self-replicated RNA were precursors to DNA
- stores info
- catalyzes chemical rxns like enzyme protein (RNA was unstable compared to DNA … more likely to participate in chemical rxns due to extra OH group)
- role in evolution of life
central dogma of genetics
DNA to RNA to proteins
catalyst
lowers activation energy, accelerating the rate of rxn
metabolism
- catabolism=breakdown
- anabolism=formation
- energy transfer
What determines the net direction of metabolic reactions, whether it is forward or reverse?
the concentration of reactants and end products
equilibrium
rate of forward rxn=rate of reverse rxn
*** the net production is 0
What are the characteristics of an enzyme?
- globular proteins that act as catalysts
- substrate specific
- unchanged during rxn
- catalyzes both in forward and reverse directions
- temperature and pH affect enzyme fxn
- active site and induced fit is how enzyme binds
cofactors
nonprotein molecules that assist enzymes usually by donating or accepting some component of a rxn such as electrons
conenzymes
- organic cofactors
2. usually donate or accept electrons
inorganic cofactors
- usually metal ions (Fe2+ or Mg2+)
2. if binds tightly/covalently=prosthetic group
ATP
- common source of activation energy.
- phosphorylation=ATP formation … ADP + phosphate using energy from energy rich molecule like glucose
- ATP contains, but is not itself, potential energy (held in the phosphate bonds)
allosteric enzyme
both active site for substrate binding and allosteric site of an allosteric effector (activator or inhibitor)
competitive inhibition
substance that mimics the substrate inhibits the enzyme by binding at the active site. can overcome by increasing substrate concentration
noncompetitive inhibition
substance inhibits enzyme by binding elsewhere than active site, substrate still binds but reaction is prevented from completing.
uncompetitive/anticompetitive inhibition
enzyme inhibitor binds only to formed E-S complex, preventing formation of product
cooperativity
enzyme becomes more receptive to additional substrate molecules after one substrate attached to an active site (e.g. hemoglobin [not an enzyme] binding additional oxygen)
Km=Michaels constant
represents the substrate concentration at which the rate is half the maximum velocity (Vmax)
- high Km= substrate binding worse … need high substrate concentration for binding
- low Km=substrate binding better because need a less concentration for binding
