Exam 1 Flashcards
define hydroxyl group
C single bonded to OH
hydroxyl group
“alcohol”
hydroxyl group
define carbonyl group
C double bonded to O and to 2 other atoms
carbonyl group
“ketone/ketoses”
“aldehyde/aldoses”
carbonyl group
ketone vs aldehyde
ketone has C bonded to 2 C and double bonded to O
sugars & acetone have ______ groups
carbonyl
define carboxyl group
C double bonded to O, to OH, and to something else
carboxyl group
“organic acids”
carboxyl
ionized form of carboxyl group
H+ breaks off of the hydroxide, leaving O-
define amino group
N bound to 2 H and one C
amino group
ionized form of amino group
a H+ binds to N, making N+ (then N is bound to 3 H)
define sulfhydryl group
SH bound to chain
sulfhydryl group
“thiol”
sulfhydryl group
define phosphate group
P bound to 4 O with 3 single bonds and 1 double bond; 2 O- are included
phosphate group
allows molecules to react with water, releasing energy
phosphate groups
define methyl group
C bound to 3 H
methyl group
Affects expression of genes & sex hormones
methyl groups
elements that comprise 96% of living matter
carbon
hydrogen
oxygen
nitrogen
4 major properties of water
- cohesive behavior
- ability to moderate temperature (high specific heat)
- expansion upon freezing
- versatility as a solvent
why is cohesive behavior important in water?
allows water to flow against gravity in plants
define specific heat
amt of heat that must be absorbed/lost for 1 g of a substance to change temp by 1 degree C
2 properties of water that help organisms maintain stable temp
high specific heat
evaporative cooling
water reaches greatest density at ___ degrees C
4
if ice sank…
all bodies of water would eventually freeze
define hydration shell
when an ionic compound is dissolved, each ion is surrounded by a sphere of water molecules
(due to hydrogen bonds; hydrogens attracted to anions, oxygen attracted to cations)
explain dissociation of water
loses H+ — becomes OH- (hydroxide)
gains H+ — becomes H3O+ (hydronium)
______ protect organisms from extremes of pH
buffers
most biological fluids are between ___-___ pH
6-8
study of compounds containing carbon
organic chemistry
structure of carbon
protons
valence electrons
6
4
In molecules w/ multiple carbons, each carbon bonded for 4 other atoms has a _______ shape
tetrahedral
In molecules w/ 2 atoms joined by a double bond, the atoms joined are __________ as the carbon
in the same plane
define hydrocarbons
organic molecules only consisting of C and H
________ undergo reactions to release large amounts of energy
hydrocarbons
same molecular formula, but different structure & properties
isomers
3 types of isomers
structural
geometric/cis-trans
enantiomers
what are structural isomers?
different covalent arrangements - different shape
what are geometric isomers?
what do cis and trans mean?
- same covalent bonds, but different structural arrangement
- Cis - “x” atoms on same side
- Trans - “x” atoms on opposite sides
what are enantiomers?
isomers that are mirror images of one another
examples of enantiomers
S ibuprofen works, R ibuprofen does not
R albuterol works, S albuterol does not
components of organic molecules most involved in chemical reactions
functional groups
define polymers
long chains of monomers
macromolecules are made of…
polymers
only non-macromolecule biomolecule
lipids
explain synthesis of polymers
-
Dehydration reaction - 2 monomers bind through loss of a water molecule
- OH and H (on each monomer) bind to form water; water is released, and monomers are allowed to bind
explain breakdown of polymers
- Hydrolysis - disassembly of polymers with addition of water - reverse of dehydration reaction
lipids consist mainly of…
hydrocarbons
most biologically important lipids
fats
phospholipids
steroids
components of fats
glycerol
fatty acids
what is a glycerol?
3-carbon alcohol with hydroxyl group attached to each carbon
what is a fatty acid?
carboxyl group attached to long carbon skeleton
explain saturated fatty acids
shape?
state?
source?
every available area on C is linked to H (all single bonds)
straight shape
solid at room temp
most animal fats
explain unsaturated fatty acids
shape?
state?
source?
have 1+ double bonds between C - prevent saturation with H
bent shape
liquid at room temp (“oils”)
most plant and fish fats
major functions of fats
energy storage
cushioning
insulation
components of phospholipids
2 fatty acids & a phosphate group attached to a glycerol
natural arrangement of phospholipids
bilayer
components of steroids
Lipids with carbon skeleton consisting of 4 fused rings
functions of cholesterol
component of animal cell membranes & precursor from which all other steroids are synthesized
covalent bond unique to lipids
connects glycerol to fatty acids
ester linkage
most basic formula of monosaccharides
CH2O
monosaccharides classified by…
location of carbonyl group & number of carbons in skeleton
Glucose + glucose =
maltose
glucose + fructose =
sucrose
covalent bond between monosaccharides
glycosidic linkage
storage polysaccharide in plants
starch
starch is stored as…
granules in chloroplasts & other plastids
simplest starch
amylose
animal storage of polysaccharides
glycogen
major component of tough wall of plant cells
cellulose
how is cellulose structured differently from starch?
OH side of the glucose is flipped on every other one
where is chitin found?
exoskeleton of arthropods (embedded in proteins)
cell walls of fungi
in aqueous solutions, most sugars form…
rings
function of nucleic acids
Store, transmit & help express genetic information
monomers of nucleic acids
nucleotides
functions of DNA
includes directions for its own replication
directs synthesis of mRNA
controls protein synthesis (gene expression)
function of mRNA
interacts with ribosomes to direct production of a polypeptide
polymers of nucleic acids
polynucleotides
components of nucleotides
a nitrogenous base, a pentose sugar, and 1+ phosphate groups
what is a nucleoside?
portion of a nucleotide w/o the phosphate
pentose sugar in DNA & RNA
dna - deoxyribose
rna - ribose
2 families of nucleotides & their structures
- Pyrimidines - cytosine, thymine, uracil - single 6-membered ring (smaller)
- Purines - adenine, guanine - 6-membered ring fused to a 5-membered ring (larger)
linkages of nucleic acids
phosphodiester bonds
sugar-phosphate forms the _______ of DNA while the nitrogenous bases are ________
backbone
appendages
codon
3 bases coding for 1 amino acid
which directions are genes read in?
5 prime to 3 prime
basic structure of DNA
Double helix - 2 polynucleotides spiraling around an imaginary axis - backbones run in opposite directions (antiparallel)
__ hydrogen bonds between A & T
__ hydrogen bonds between C & G
2
3
define protein
biologically functional molecule consisting of 1+ polypeptides
define polypeptide
unbranched polymers built from amino acids
2 ends of a polypeptide
carboxyl end (c-terminus)
amino end (n-terminus)
structure of an amino acid
amino and carboxyl groups bound by an alpha carbon
unique R group
bonds used in proteins
peptide bonds
proteins account for >__% of dry mass of cells
50
major functions of proteins (8)
- Enzymes - catalyze chemical reactions
- Defense - ex antibodies
- Storage - store amino acids - ex casein, ovalbumin
- Transport - ex hemoglobin, transport proteins
- Cellular communication - ex hormones, receptor proteins
- Movement - contractile & motor proteins - ex cilia, flagella, actin, myosin
- Structural support - ex keratin, collagen, elastin
- Gene regulation
what is primary structure?
unique sequence of amino acids - determined by genetic info
what is secondary structure?
coils (helices) & folds (pleated sheets) in polypeptide chain
what is tertiary structure?
overall shape, resulting from interactions among various side chains (R groups) rather than backbone constituents
what is quaternary structure?
when a protein consists of multiple polypeptide chains folded together (does not occur in all proteins)
what allows hydrogen bonding in polypeptides?
Backbone of the chains have O bound to C (-) and H bound to O (+) at different spots
hydrogen bonding between repeating constituents of the polypeptide backbone
secondary structure
interactions among various side chains (R groups)
tertiary structure
tertiary structure includes which types of bonds?
hydrogen bonds
ionic bonds
hydrophobic interactions (cluster on the inside of the protein)
van der waals interactions
strong covalent bonds that reinforce protein’s structure
disulfide bridges
fibrous protein consisting of 3 polypeptides coiled like rope
collagen
hemoglobin consists of…
4 polypeptides (2 alpha and 2 beta subunits)
begins with a specific molecule (substrate) & ends with a product
metabolic pathway
energy is released by breaking down complex molecules
catabolic pathway
consumes energy in order to build complex molecules from simpler ones
anabolic pathway
study of how energy flows through living organisms
bioenergetics
define energy
capacity to cause change
define thermal energy
kinetic energy associated with random movement of atoms/molecules
define heat
thermal energy transfer between objects
define potential energy
energy that matter possesses because of its location or structure
define chemical energy
potential energy available for release in a chemical reaction
study of energy transformation
thermodynamics
energy of the universe is constant
1st law of TD
During every transfer of energy, some energy is unusable and “lost” as ______
thermal energy
every transfer of energy increases the entropy of the universe
2nd law of TD
define entropy
measure of randomness/molecular disorder
measure of thermal energy
not available to use in work
examples of entropy increasing
increases as water boils
as salt dissolves in water
as we digest complex molecules
define spontaneous processes
occur w/o energy input
energetically favorable
example of a spontaneous process
water running down a hill
processes that decrease entropy are _________; occur only if energy is provided
nonspontanteous
why don’t organisms violate 2nd law?
Entropy may decrease in a particular system, as long as the total entropy of the system’s surroundings (universe) increases
________________ of a reaction tells us whether or not the reaction occurs spontaneously
Free-energy change (ΔG)
energy that can do work
measure of a system’s instability
tendency to change to a more stable state
Gibbs free energy
ΔG =
ΔH - TΔS
ΔG is ________ for all spontaneous processes
0 or ______ ΔG requires energy
negative for spontaneous processes
0 or positive requires energy
define equilibrium
state of maximum stability
only an ______ system can reach equilibrium
isolated
define exergonic reactions
spontaneous
becomes more stable
net release of free energy
define endergonic reactions
nonspontaneous
becomes less stable
absorbs free energy from its surroundings
composition of ATP
ribose (sugar)
adenine (nitrogenous base)
3 phosphate groups
define phosphorylation
the 3rd phosphate is transferred to another molecule (the phosphorylated intermediate)
ATP powers cellular work by…
coupling exergonic reactions with endergonic reactions
overall, coupled reactions are…
exergonic (ΔG is negative)
exergonic = (-/+) ΔG
negative
endergonic = (-/+) ΔG
positive
3 main kinds of cellular work
- Chemical - pushing endergonic reactions
- Transport - pushing substances against direction of spontaneous movement (gradient)
- Mechanical - ex contraction of muscle cells
Energy to phosphorylate ADP comes from…
catabolic reactions in the cell
define enzymes
catalytic proteins that speed up a reaction w/o being changed by it, by lowering the activation energy of the reaction
define Free energy of activation (Ea)
energy required to begin a reaction
Ea is often supplied in the form of….
thermal energy absorbed from the reactants’ surroundings
define catalysis
lowering of the Ea barrier in order to speed up reactions
define induced fit
brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
define saturated enzyme
enzyme has all its active sites engaged
If an enzyme is saturated, the reaction can only be sped up by…
adding more enzymes
Why does each enzyme have optimal conditions for its functioning?
Optimal conditions favor the most active shape for an enzyme
define competitite inhibitors
bind to the active sites of enzymes, competing with substrate
define noncompetitive inhibitors
bind to another part of the enzyme, causing a conformational change that ↓ its activity
define allosteric regulation
when a regulatory molecule binds to a protein one one site, causing a change in function at another site
define activator (allosteric reg)
stabilizes the active form of the enzyme
define inhibitor (allosteric reg)
stabilizes the inactive form of the enzyme
define feedback inhibition
end product of a metabolic pathway shuts down the pathway
feedback inhibition prevents…
waste of chemical resources
define cofactors
inorganic “helpers” to enzymes - zinc, magnesium, iron, etc
define coenzymes
organic cofactors - vitamins
most allosterically regulated enzymes are made of…
polypeptide subunits, each with its own active site
requirements for activators/inhibitors
only requires 1
how does feedback inhibition work?
End product may bind to the first enzyme in a pathway, inactivating it
