biomolecules / macromolue - ANSWER any molecule present in living
organisms
-includes large macromolecules: very large molecules like a protein commonly
created by polymerization of smaller subunits (monomers, typically 1,000
atoms or more: (proteins, carbs, lipids, nucleic acids). Biomolecules can also be
small molecules (primary metabolites secondary metabolites, natural products)
-most are organic compounds created from (O, C, H, N, and some contain
phosphorous or sulfur) SPONCH
-biomolecules exhibit directionality + possess chirality (stereo specific)
-Why are biomolecules composed of SPONCH elements?
-More beneficial for organisms to have mol. with strong or weak bonds?
-Extremely strong covalent bond that must constantly be broken to sustain life?
- ANSWER -multiple bonds, mostly carbon
-low atomic weight stronger covalent bonds
-but organisms are dynamic and weak chem bonds are more easily broken and
rearranged to support life-sustaining processes. Need both strong and weak
bonds
-Triple bond in nitrogen gas must be fixed/ reduced for use
Proteins/ Nucleic acids/ lipids/ carbs - ANSWER Proteins-highly versatile
biomolecules
- AA--> AA sequence as a linear polymer--> protein native structure
-can be signal molecules, receptors for signal molecules and enzymes,
biological catalysts
NA- made of nucleotides, 2 types:
1- DNA: double helix of polymers made of deoxyribose, phosphate, and 4 bases
AGCT
2-RNA: single strand polymer made of ribose, phosphate, and AGCU
L- hydrophobic/philic properties
-form barriers (membranes) that allow compartmentalization
-can be fuel molecules and signal molecules
,C- fuels and informational molecules
-glucose is a common carb, stored as glycogen in animals, a branched polymer,
important signal molecules in cell-cell recognition
chemical bonding - ANSWER -bond forming: exothermic- energy released
-bond breaking- endothermic- energy needed to be absorbed
covalent/ ionic (electrostatic), H bonds/ van der waals interactions/ hydrophobic
interactions (effect) - ANSWER C-strong bond (200-1,000 KJ/mol), electrons
shared to form bond
-nonpolar- equal sharing
-polar- unequal sharing creating dipoles
I- (100-1,000 KJ/ mol), high electronegativity difference b/w atoms as one atom
strips electrons away from the other
-E transfer creates ions (charged atoms)
-ionic bonds can be found in salts (NaCl)
-cations=+ (e is lost)
-anions=- ( e gained)
H- relatively weak but abundance makes them important (4-20 KJ/mol)
-H atom covalently bonded to 1 electronegative atom is also attracted to another
electronegative atom (O or N).
-3D structures of many biomolecules and macromol structures are determined
by h bonds and hydrophobic interactions
VW- 0.3-20 KJ/mol, weak interactions from fluctuations in electronic charge
around atoms, can be substantial when summed over many atoms. have to be at
optimal distance-Van der waals contact distance
Hydrophobic interactions- molecules that have mutual fear of water, come
together in an aqueous environment, most important non covalent interactions
for proteins in aqueous environments, come into play at closer distances than
ionic interactions
vital properties of water - ANSWER -anomalous for a substance of rel low
molecular weight
, -high BP- liquid at rel high temperatures
-high MP- ice exists- climate stabilization
-large amounts of water in all 3 states of matter
-surface tension- cohesion- important for water transport in plants and blood
transport in animals
-ice less dense than water so lakes dont freeze over completely
-unique physical properties attributed to H bonding, derived from the presnece
of dipole/ polar covalent bonds derived from electronegativity/ molecular shape
Gibbs energy - ANSWER -Delta G= change in gibbs free energy, negative
spontaneous
-Delta H= change in enthalpy (heat)
-T- temp K, always>0
-Delta S- change of entropy, when + more disorder, when - increased order
H S. G.
- +. - -
+. +. +/- - at high temp
- - +/- - at low temp
+. - +. +
hydrophobic effect - ANSWER the aggregation of nonpolar groups in water
leads to increase in entropy owing to the release of water molecules into bulk
water
-large increase in entropy of released water molecules makes delta G more
negative favoring the clustering of hydrophobic groups
-membrane formation: phospholipids are amphipathic and exclude H2O, delta
S>>0, delta G<<0
-protein folding:
-each unfolded protein mol adopts unique conformation with high entropy (delta
S)
-during protein folding, hydrophobic AA cluster in sequence due to
hydrophobic effect
-protein mol are driven toward a common folded structure w minimal entropy,
while entropy of released water molecules is maximized
organisms
-includes large macromolecules: very large molecules like a protein commonly
created by polymerization of smaller subunits (monomers, typically 1,000
atoms or more: (proteins, carbs, lipids, nucleic acids). Biomolecules can also be
small molecules (primary metabolites secondary metabolites, natural products)
-most are organic compounds created from (O, C, H, N, and some contain
phosphorous or sulfur) SPONCH
-biomolecules exhibit directionality + possess chirality (stereo specific)
-Why are biomolecules composed of SPONCH elements?
-More beneficial for organisms to have mol. with strong or weak bonds?
-Extremely strong covalent bond that must constantly be broken to sustain life?
- ANSWER -multiple bonds, mostly carbon
-low atomic weight stronger covalent bonds
-but organisms are dynamic and weak chem bonds are more easily broken and
rearranged to support life-sustaining processes. Need both strong and weak
bonds
-Triple bond in nitrogen gas must be fixed/ reduced for use
Proteins/ Nucleic acids/ lipids/ carbs - ANSWER Proteins-highly versatile
biomolecules
- AA--> AA sequence as a linear polymer--> protein native structure
-can be signal molecules, receptors for signal molecules and enzymes,
biological catalysts
NA- made of nucleotides, 2 types:
1- DNA: double helix of polymers made of deoxyribose, phosphate, and 4 bases
AGCT
2-RNA: single strand polymer made of ribose, phosphate, and AGCU
L- hydrophobic/philic properties
-form barriers (membranes) that allow compartmentalization
-can be fuel molecules and signal molecules
,C- fuels and informational molecules
-glucose is a common carb, stored as glycogen in animals, a branched polymer,
important signal molecules in cell-cell recognition
chemical bonding - ANSWER -bond forming: exothermic- energy released
-bond breaking- endothermic- energy needed to be absorbed
covalent/ ionic (electrostatic), H bonds/ van der waals interactions/ hydrophobic
interactions (effect) - ANSWER C-strong bond (200-1,000 KJ/mol), electrons
shared to form bond
-nonpolar- equal sharing
-polar- unequal sharing creating dipoles
I- (100-1,000 KJ/ mol), high electronegativity difference b/w atoms as one atom
strips electrons away from the other
-E transfer creates ions (charged atoms)
-ionic bonds can be found in salts (NaCl)
-cations=+ (e is lost)
-anions=- ( e gained)
H- relatively weak but abundance makes them important (4-20 KJ/mol)
-H atom covalently bonded to 1 electronegative atom is also attracted to another
electronegative atom (O or N).
-3D structures of many biomolecules and macromol structures are determined
by h bonds and hydrophobic interactions
VW- 0.3-20 KJ/mol, weak interactions from fluctuations in electronic charge
around atoms, can be substantial when summed over many atoms. have to be at
optimal distance-Van der waals contact distance
Hydrophobic interactions- molecules that have mutual fear of water, come
together in an aqueous environment, most important non covalent interactions
for proteins in aqueous environments, come into play at closer distances than
ionic interactions
vital properties of water - ANSWER -anomalous for a substance of rel low
molecular weight
, -high BP- liquid at rel high temperatures
-high MP- ice exists- climate stabilization
-large amounts of water in all 3 states of matter
-surface tension- cohesion- important for water transport in plants and blood
transport in animals
-ice less dense than water so lakes dont freeze over completely
-unique physical properties attributed to H bonding, derived from the presnece
of dipole/ polar covalent bonds derived from electronegativity/ molecular shape
Gibbs energy - ANSWER -Delta G= change in gibbs free energy, negative
spontaneous
-Delta H= change in enthalpy (heat)
-T- temp K, always>0
-Delta S- change of entropy, when + more disorder, when - increased order
H S. G.
- +. - -
+. +. +/- - at high temp
- - +/- - at low temp
+. - +. +
hydrophobic effect - ANSWER the aggregation of nonpolar groups in water
leads to increase in entropy owing to the release of water molecules into bulk
water
-large increase in entropy of released water molecules makes delta G more
negative favoring the clustering of hydrophobic groups
-membrane formation: phospholipids are amphipathic and exclude H2O, delta
S>>0, delta G<<0
-protein folding:
-each unfolded protein mol adopts unique conformation with high entropy (delta
S)
-during protein folding, hydrophobic AA cluster in sequence due to
hydrophobic effect
-protein mol are driven toward a common folded structure w minimal entropy,
while entropy of released water molecules is maximized
