Chapter 1 - Molecules and Fundamentals of Biology Flashcards
Organic molecules contain what elements?
carbon, hydrogen, nitrogen, oxygen
Starch is a ____ polysaccharide in ____
storage; plants
Linear plant starch is called ____ and contains ____ bonds
amylose; alpha-1,4 glycosidic bonds
___ is a critical storage polysaccharide found in humans
glycogen
___ is the branched form of plant starch and forms ____ bonds
amylopectin; alpha 1,4 and alpha-1,6 glycosidic bonds
glycogen is mainly stores in:
liver and muscle cells
structural polysaccharide found in plant cell walls:
cellulose
cellulose contains what kind of bonds? what kind of structure results?
beta-1,4 bonds; linear strands that pack together in parallel, adjacent strands held together by H bonding
True or false: humans can digest cellulose
false: cannot digest cellulose, it passes through our digestive tracts as fiber
chitin is a _____ polysaccharide found in ____ cell walls and _____
structural; fungi cell walls; exoskeleton of insects
what kind of bonds does chitin have?
Beta-1,4 glycosidic bonds; however is a polymer of N-acetylglucosamine
True or false: chitin is a polymer of glucose molecules
false: made of N-acetylglucosamine molecules
proteome
all the proteins expressed in a cell under one set of conditions
at physiological pH, amino group in an amino acid is ____ and the carboxyl group is ____
protonated; deprotonated
unique enzymes called ____ ____ help peptide bond formation
peptidyl transferases (belong to broader class of enzymes called aminoacyl transferases)
primary structure
specific order of a peptide which is determined by DNA genes
secondary structure
folds that occur in polypeptide chain due to intermolecular interactions between atoms of the polypeptide backbone (not R group atoms)
two of the most common secondary protein structures
alpha helices; beta-pleated sheets
tertiary structure
3D structure of larger polypeptide chains which occurs due to R-group interactions
what R-group interactions can occur in tertiary structure?
- ionic bonding
- hydrogen bonding
- dipole-dipole interactions
- London dispersion forces
- hydrophobic interactions
- disulfide bonds between cysteines
True or false: tertiary structure interactions are usually not covalent
true; disulfide bonds are an exception to this
quaternary structure1
refers to large proteins that have multiple subunits which come together by the same general interactions used in creating tertiary structure
protein denaturation can occur by:
excess temperature, chemicals, pH changes, radiation
True or false: denatured proteins cannot fold back into their functional shapes
false: some can, which tells us that all of the information necessary for the folding of those proteins is contained directly within the amino acid sequence.
enzymes are:
globular (usually) protein catalysts that speed up specific forward and reverse reactions by lowering their activation energies
enzymes change the energy of:
the transition state
enzymes catalyze reactions by:
binding to reactant molecules called substrates
active site
location on enzymes where the substrate binds to
Because most enzymes are proteins, amino acids give the active site unique properties and ____ ___
substrate specificity
specificity constant
measures how efficient an enzyme is in converting substrate to product (high specificity constant means high efficiency)
true or false: some enzymes are not proteins
true: one example is ribozymes (RNA molecule capable of acting as enzyme)
cofactor
non-protein molecules that assist enzymes in the reactions they manipulate
coenzymes
organic cofactors (usually include things like vitamins)
inorganic cofactors
tend to be metal ions like Fe2+ or Mg2+
Holoenzymes
refer to enzymes that are bound to their cofactor
apoenzyme
enzyme not bound to its cofactor
prosthetic groups
cofactors that tightly/covalently bind to their enzyme in a holoenzyme
competitive inhibition
inhibitors compete with substrates for active sites
true or false: we can outcompete a competitive inhibitor
true: as we increase the amount of substrate, there is a higher chance that the substrate can bind to the active site
true or false: adding more substrate will continuously increase the speed of catalysis
false: this only occurs until all active sites are occupied (enzyme saturation). then catalysis plateaus
noncompetitive inhibition:
when an inhibitor binds to the allosteric site of an enzyme (dif location that is not the active site)
true or false: we can outcompete noncompetitive inhibitors
false: rate of enzyme catalysis is unaffected by increasing the substrate concentration
velocity (V)
rate at which reaction is occurring
Vmax
maximum reaction velocity
Michaelis constant (Km)
the substrate conc at which Vmax is at 50%
Small Km implies:
we only need a little bit of substrate bc enzyme ability/function is high
Large Km implies:
that we need many substrates for reaction progression because enzyme availability/function is low
If we add a competitive inhibitor:
Km increases while Vmax stays the same
If we add a noncompetitive inhibitor:
Km stays the same while Vmax decreases
Fat is also called
triacylglycerol or triglyceride
triglycerides are found in:
adipocytes
fats have __ unique parts which are:
2; glycerol backbone and 3 fatty acids
glycerol structure
3 carbons and 3 hydroxyl groups
fatty acid
long hydrocarbon tail attached to a carboxylic acid
fats are produced by ____ reactions
dehydration/condensation (just like for carbs and proteins)
fats have what kind of linkages?
ester
true or false: many fats contains fatty acids that are of different lengths and degrees of unsaturation
true
phospholipid structure
3-carbon glycerol backbone, 1 phosphate group, 2 fatty acid tails
glycolipid
looks virtually the same as a phospholipid, however these contain a carbohydrate molecule in place of the phosphate group
cholesterol makes up around __-__% of a eukaryotic cell membrane
30-50%
cholesterol contains _ hydrocarbon rings
4
true or false: cholesterol is hydrophobic
false: amphipathic
which organ makes cholesterol?
liver (but we can also get it from the diet)
Cholesterol is a starting material for:
steroid, vitamin D, bile acids
how do lipids travel through blood?
in lipoproteins
lipoproteins contain:
coat of phospholipids, cholesterol, proteins and a lipid core
LDL
considered to be unhealthy because they deliver cholesterol to peripheral tissues via the bloodstream. (bad cholesterol)
HDL
high density of proteins. They are generally considered to be healthy because they take cholesterol away from peripheral tissues and deliver it to the liver.
Other lipid derivatives (3)
- waxes
- carotenoids
- sphingolipids
Waxes
contain long fatty acids that are connected to monohydroxy alcohols by ester linkages., serve as hydrophobic protective coating
carotenoids
long carbon chains that have conjugated double bonds and six-membered rings at each end, function as pigments that provide color to plants and animals
carotenoid examples
carotenes and xanthophylls
sphingolipids
have a sphingoid base backbone composed of a set of aliphatic (non-aromatic) amino alcohols. They serve as structural integrity, signal transduction and cell recognition
sphingolipids examples
ceramides, sphingomyelin
purines
adenine and guanine
pyrimidines
cytosine, thymine, uracil
purines have _ rings
2
pyrimidine have how many rings?
1
A-T has how many H bonds?
2
G-C has how many H bonds?
3
modern cell theory statements:
- all life is composed of one or more cells, where cells are the basic structural, functional, and organizational unit of life
- all cells come from pre-existing, living cells via cell division
- genetic information (stored within cells) to pass onto new cells
- organism’s activity is dependent on the activity of its independent cells
- metabolism and biochemistry (energy flow) occur within cells, where all cells have the same chemical composition.
true or false: cell theory does not apply to viruses
true - viruses are not living cells
central dogma
dna–> rna –> protein
main implication of central dogma:
information cannot travel from protein to protein, or from proteins to nucleic acids
true or false: information cannot travel from rna to dna
false: they can
prions
example where info can travel from protein to protein. they are misfolded proteins that cause other proteins to misfold as well, destroying their function in the process
RNA world hypothesis
Earth’s “primordial soup” had a lot of RNA nucleoside triphosphates, which made phosphodiester bonds with each other to create short strands of RNAs. As the strands grew longer and longer, they became more and more stable. continued to evolve until they could replicate
