Chapter 1: Foundations of Biochemistry Flashcards
metabolites
- small organic molecules
- an intermediate or end product of metabolism
- intermediates in biosynthetic and degradative pathways
Molecular weight
- the mass of a molecule of a substance
- a.k.a molecular mass
- unit: atomic mass units (amu)
Molar mass
- the mass of one mole of a substance.
- units: grams per mole or g/mole
mole (mol)
- just a number
- 6.022x1023
- Avogadro’s number
macromolecules
- polymers with molecular weights above ∼5,000
- assembled from relatively simple precursors
- i.e. Proteins, nucleic acids, polysaccharides, etc.
oligomers
a polymer whose molecules consist of relatively few repeating units
stereoisomers
- compounds with the same exact molecular formula and connectivity (chemical bonds) but they differ in the arrangement of atoms in three-dimensional space (configuration)
- simplest forms of stereoisomers are cis and trans isomers, both of which are created by the restricted rotation about a double bond or ring system
configuration
- the fixed spatial arrangement of atoms
- relative position of the atoms in a molecule
- does not change when the molecule twists into another conformation
- can be changed exclusively by cleaving and forming new chemical bonds
the fixed spatial arrangement of atoms. Interactions between biomolecules are invariably ______, requiring specific _______ in the interacting molecules.
- stereospecific
- configurations
Conformations
the set of possible shapes a molecule can have by means of rotation about single bonds
stereochemistry
the 3D relationships between atoms in a molecule
isomers
compounds with different physical and chemical properties but the same molecular formula
two types of stereoisomers
- enantiomers: mirror images
- diastereoisomers: non-mirrow images
geometric isomer
each of two or more compounds which differ from each other in the arrangement of groups with respect to a double bond, ring, or other rigid structure.
when comparing compounds, if the bonds are the same, and there are double bonds or rings they are
geometric isomers
when comparing compounds, if the bonds are the same, and they are not superimposable, they are
stereoisomers
enantiomers
- compounds that are non-superimposable mirror images
- said to be chiral
chiral, asymmetric, stereogenic carbon atom, or stereocenter
a carbon w/4 different substituents
any molecule in which only one of its carbon atoms has 4 different groups attached will always be
chiral
max # of stereoisomers for a molecule with n chiral carbon is
\<= 2ⁿ n = # of chiral atoms
When a tetrahedral carbon has only three dissimilar groups (i.e., the same group occurs twice), only one configuration is possible and the molecule is _____, or _____
- symmetric
- achiral
racemix mixture / racemate
- when one enantiomer is combined w/the same amount of another
- solution does not rotate polarized light because the two compounds rotate the light equally in opposite directions
- displays different characteristics than a pure solution of either one
E and Z nomenclature
- Z = same side
- E = opposite sides
- Z & E are prefixes in parens, italicized, connecting to name with a hyphen: (Z)-4-Chloro-3-methil-2-betenoic acid
Cahn-Ingold-Prelog-Convention
priority of substituents for E and Z
- ↑ atomic # = ↑ priority
- if elements are isotopes of same element, the 1 w/↑ mass has ↑ priority
- unshared e- pair = lowest priority
- H has lowest priority
Cahn-Ingold-Prelog-Convention
example step 1: evaluate C1
- look @ atoms attached directly to C═C & assign priority to atom w/higher atomic #
- For C1
Cahn-Ingold-Prelog-Convention
example final step: name molecule
Cahn-Ingold-Prelog-Convention
example step 4: evaluate C2 expansion atomic #
- For C2: substituents have same atom → look @ next shell
- Next shell, aldehyde (CHO) has double bond which needs expansion
- Look at the expanded molecules
- list shell atoms in ↓ atomic #
- pick ↑ atomic # from 1st different atoms
Cahn-Ingold-Prelog-Convention
example step 3: evaluate C2 expansion
- For C2: substituents have same atom → look @ next shell
- Next shell, aldehyde (CHO) has double bond which needs expansion
- Look at the expanded molecules
Cahn-Ingold-Prelog-Convention
example step 2: evaluate C2
- For C2: substituents have same atom → look @ next shell
- Next shell, aldehyde (CHO) has double bond which needs expansion
dextrorotary
- optical activity of the substance
- rotates polarized light clockwise
- prefix: (+) or d
- (+)-2-butanol or d-2-butanol
levorotatory
- optical activity of the substance
- rotates polarized light counter-clockwise
- prefix: (−) or l
- (−)-2-butanol or l-2-butanol
The D-L system
- different from d (+) and l (−)
- configuration of a molecule, compared to enantiomers of glyceraldehyde
- Compounds with the same configuration as (+)-glyceraldehyde are assigned D, and those w/ configuration of (-)-glyceraldehyde are given L
In assigning D & L configurations look for the OH group of the bottom asymmetric carbon in the Fischer projection. If it’s located on the right → _____, located on left → _____
- label it D
- label it L
Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
when priority 4 group is pointing towards back
- attach priority to the substituents around the carbon atom
- turn the chiral carbon atom so that the priority four group is pointing towards the back
- designate R or S
Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
when priority 4 group is NOT pointing towards back
- attach priority to the substituents around the carbon atom
- if priority 4 group is not pointing towards back
- swap priority group 4 w/the one facing the back
- designate R or S
- then take the opposite of R or S
Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
S configuration
- substituents are arranged in ascending priority order counterclockwise
- chiral center has the (S) configuration
Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
R configuration
- substituents are arranged in ascending priority order clockwise
- chiral center has the (R) configuration
In living organisms, chiral molecules are usually present in only one of their _____ forms. For example, the amino acids in proteins occur only as their L isomers. If the binding site on a protein is complementary to one _____ of a chiral compound, it will not be complementary to the other isomer, for the same reason that a left glove does not fit a right hand
- chiral
- siomer
Molecular configuration can be changed only by
breaking covalent bonds
Lecture
system
- everything within a defined region of space
- all the constituent reactants and products, the solvent that contains them, and the immediate atmosphere
Lecture
system and its surroundings together constitute the
universe
Lecture
isolated system
If the system exchanges neither matter nor energy with its surroundings
Lecture
closed system
If the system exchanges energy but not matter with its surroundings
Lecture
open system
if it exchanges both energy and matter with its surroundings
Lecture
The first law of thermodynamics
formula
ΔU - Q - W
- ΔU: change in internal energy
- Q: heat added
- W: work done by the system
The first law of thermodynamics
- describes the principle of the conservation of energy
- in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change
Lecture
entropy
- The entropy of an object is a measure of the amount of energy which is unavailable to do work
- also a measure of the number of possible arrangements the atoms in a system can have
- it is a measure of uncertainty or randomness
- The higher the entropy of an object, the more uncertain we are about the states of the atoms making up that object because there are more states to decide from
Whenever a chemical reaction results in an increase in the number of _____—or when a solid substance is converted into _____ or _____ products, which allow more freedom of molecular movement than solids— molecular disorder, and thus _____, increases
- molecules
- liquid
- gaseous
- entropy
second law of thermodynamics
- the tendency in nature is toward ever-greater disorder in the universe
- randomness in the universe is constantly increasing
structural isomers, or constitutional isomers
molecules with identical chemical formulas but with different bonding arrangements of the atoms
3 types of constitutional isomers
skeletal, positional, and functional
skeletal isomers
constitutional isomers that have the same functional groups but differ from each other in the connectivity of the carbon skeleton
positional isomers
constitutional isomers that have the same carbon skeleton and the same functional groups but differ from each other in the location of the functional groups in the carbon chain
functional isomers
constitutional isomers bearing different functional groups
Lecture
vitalist statement:
The substances composing living matter are qualitatively different from those of the non-living world.
state scientific response
Experiment of Wöhler, the German chemist: made urea from ammonium cyanate. Urea was well known to be an “organic” chemical, i.e. one which is produced by living organisms. Ammonium cyanate was well known to be an inorganic chemical, i.e. not produced by living organisms, This experiment founded the discipline of organic chemistry.
Lecture
vitalist statement:
We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells.
state scientific response
- 1897, Edward and Hans Buchner, beer makers, showed that extracts of broken - & thus dead - yeast cells could conduct fermentation, converting sugar into ethanol.
- Opened the way to the study of reactions in vitro (“in glass”) rather than in vivo (“in life”)
- Meant that metabolic reactants and products as well as catalysts - enzymes, or “ferments” - could be studied individually.
Lecture
vitalist statement:
We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells.
state scientific response
- 1897, Edward and Hans Buchner, beer makers, showed that extracts of broken - & thus dead - yeast cells could conduct fermentation, converting sugar into ethanol.
- Opened the way to the study of reactions in vitro (“in glass”) rather than in vivo (“in life”)
- Meant that metabolic reactants and products as well as catalysts - enzymes, or “ferments” - could be studied individually.
Lecture
vitalist statement:
Living matter may be like non-living, but organisms arise from non-living matter by spontaneous generation through the intervention of the “vital force.”
state scientific response
Pasteur: Only living organisms produce other living organisms. No vital force needed. He also linked specific species, e.g. yeast, to specific processes, e.g. fermentation.
vitalist statement:
Structure of “ferments” is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible
state scientific response
- 1926: J. B. Sumner crystallized urease, an enzyme, just like any other organic compound
- Implies that structure and function are amenable to study like other organic compounds
- Led eventually to x-ray crystallography, which has elucidated the 3D structures of many enzymes and of DNA.
