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Biochemistry 403 > Chapter 1: Foundations of Biochemistry > Flashcards

Chapter 1: Foundations of Biochemistry Flashcards

1
Q

metabolites

A
  • small organic molecules
  • an intermediate or end product of metabolism
  • intermediates in biosynthetic and degradative pathways
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2
Q

Molecular weight

A
  • the mass of a molecule of a substance
  • a.k.a molecular mass
  • unit: atomic mass units (amu)
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3
Q

Molar mass

A
  • the mass of one mole of a substance.
  • units: grams per mole or g/mole
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4
Q

mole (mol)

A
  • just a number
  • 6.022x1023
  • Avogadro’s number
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5
Q

macromolecules

A
  • polymers with molecular weights above ∼5,000
  • assembled from relatively simple precursors
  • i.e. Proteins, nucleic acids, polysaccharides, etc.
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6
Q

oligomers

A

a polymer whose molecules consist of relatively few repeating units

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7
Q

stereoisomers

A
  • 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
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8
Q

configuration

A
  • 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
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9
Q

the fixed spatial arrangement of atoms. Interactions between biomolecules are invariably ______, requiring specific _______ in the interacting molecules.

A
  • stereospecific
  • configurations
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10
Q

Conformations

A

the set of possible shapes a molecule can have by means of rotation about single bonds

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11
Q

stereochemistry

A

the 3D relationships between atoms in a molecule

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12
Q

isomers

A

compounds with different physical and chemical properties but the same molecular formula

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13
Q

two types of stereoisomers

A
  • enantiomers: mirror images
  • diastereoisomers: non-mirrow images
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14
Q

geometric isomer

A

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.

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15
Q

when comparing compounds, if the bonds are the same, and there are double bonds or rings they are

A

geometric isomers

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16
Q

when comparing compounds, if the bonds are the same, and they are not superimposable, they are

A

stereoisomers

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17
Q

enantiomers

A
  • compounds that are non-superimposable mirror images
  • said to be chiral
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18
Q

chiral, asymmetric, stereogenic carbon atom, or stereocenter

A

a carbon w/4 different substituents

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19
Q

any molecule in which only one of its carbon atoms has 4 different groups attached will always be

A

chiral

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20
Q

max # of stereoisomers for a molecule with n chiral carbon is

A 
\<= 2ⁿ
n = # of chiral atoms
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21
Q

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 _____

A
  • symmetric
  • achiral
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22
Q

racemix mixture / racemate

A
  • 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
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23
Q

E and Z nomenclature

A
  • 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
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24
Q

Cahn-Ingold-Prelog-Convention

A

priority of substituents for E and Z

  1. ↑ atomic # = ↑ priority
  2. if elements are isotopes of same element, the 1 w/↑ mass has ↑ priority
  3. unshared e- pair = lowest priority
  4. H has lowest priority
25
Q

Cahn-Ingold-Prelog-Convention

example step 1: evaluate C1

A
  1. look @ atoms attached directly to C═C & assign priority to atom w/higher atomic #
  2. For C1
26
Q

Cahn-Ingold-Prelog-Convention

example final step: name molecule

A
27
Q

Cahn-Ingold-Prelog-Convention

example step 4: evaluate C2 expansion atomic #

A
  1. For C2: substituents have same atom → look @ next shell
  2. Next shell, aldehyde (CHO) has double bond which needs expansion
  3. Look at the expanded molecules
  4. list shell atoms in ↓ atomic #
  5. pick ↑ atomic # from 1st different atoms
28
Q

Cahn-Ingold-Prelog-Convention

example step 3: evaluate C2 expansion

A
  1. For C2: substituents have same atom → look @ next shell
  2. Next shell, aldehyde (CHO) has double bond which needs expansion
  3. Look at the expanded molecules
29
Q

Cahn-Ingold-Prelog-Convention

example step 2: evaluate C2

A
  1. For C2: substituents have same atom → look @ next shell
  2. Next shell, aldehyde (CHO) has double bond which needs expansion
30
Q

dextrorotary

A
  • optical activity of the substance
  • rotates polarized light clockwise
  • prefix: (+) or d
  • (+)-2-butanol or d-2-butanol
31
Q

levorotatory

A
  • optical activity of the substance
  • rotates polarized light counter-clockwise
  • prefix: (−) or l
  • (−)-2-butanol or l-2-butanol
32
Q

The D-L system

A
  • 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
33
Q

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 → _____

A
  • label it D
  • label it L
34
Q

Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms

when priority 4 group is pointing towards back

A
  • 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
35
Q

Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms

when priority 4 group is NOT pointing towards back

A
  • 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
36
Q

Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
S configuration

A
  • substituents are arranged in ascending priority order counterclockwise
  • chiral center has the (S) configuration
37
Q

Cahn-Ingold-Prelog-Convention
for Chiral Carbon Atoms
R configuration

A
  • substituents are arranged in ascending priority order clockwise
  • chiral center has the (R) configuration
38
Q

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

A
  • chiral
  • siomer
39
Q

Molecular configuration can be changed only by

A

breaking covalent bonds

40
Q

Lecture

system

A
  • everything within a defined region of space
  • all the constituent reactants and products, the solvent that contains them, and the immediate atmosphere
41
Q

Lecture

system and its surroundings together constitute the

A

universe

42
Q

Lecture

isolated system

A

If the system exchanges neither matter nor energy with its surroundings

43
Q

Lecture

closed system

A

If the system exchanges energy but not matter with its surroundings

44
Q

Lecture

open system

A

if it exchanges both energy and matter with its surroundings

45
Q

Lecture

The first law of thermodynamics

formula

A

ΔU - Q - W

  • ΔU: change in internal energy
  • Q: heat added
  • W: work done by the system
46
Q

The first law of thermodynamics

A
  • 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
47
Q

Lecture

entropy

A
  • 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
48
Q

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

A
  • molecules
  • liquid
  • gaseous
  • entropy
49
Q

second law of thermodynamics

A
  • the tendency in nature is toward ever-greater disorder in the universe
  • randomness in the universe is constantly increasing
50
Q

structural isomers, or constitutional isomers

A

molecules with identical chemical formulas but with different bonding arrangements of the atoms

51
Q

3 types of constitutional isomers

A

skeletal, positional, and functional

52
Q

skeletal isomers

A

constitutional isomers that have the same functional groups but differ from each other in the connectivity of the carbon skeleton

53
Q

positional isomers

A

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

54
Q

functional isomers

A

constitutional isomers bearing different functional groups

55
Q

Lecture

vitalist statement:

The substances composing living matter are qualitatively different from those of the non-living world.

state scientific response

A

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.

56
Q

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

A
  • 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.
57
Q

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

A
  • 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.
58
Q

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

A

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.

59
Q

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

A
  • 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.

Biochemistry 403 (12 decks)

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