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Biochemistry > Sec. 1: Biochemistry Helps Us Understand Our World > Flashcards

Sec. 1: Biochemistry Helps Us Understand Our World Flashcards

1
Q

What is the “unity of biochemistry?”

A

The observation that organisms are remarkably uniform at the molecular level.

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2
Q

What unity of biochemistry reveals what about Earth organisms?

A

A core of biochemical processes appeared in an early ancestor common to all organisms.

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3
Q

What three elements make up 98% of the atoms in an organism? (order from most to least abundant)

A
  1. Hydrogen
  2. Oxygen
  3. Carbon
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4
Q

What is the percent composition of Hydrogen in a human?

A

63%

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5
Q

What is the percent composition of Oxygen in a human?

A

25.5%

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6
Q

What is the percent composition of Carbon in a human?

A

9.5%

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7
Q

Biological fuel molecules are made entirely of what elements?

A

Carbon, hydrogen and oxygen.

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8
Q

What type of reaction provides energy to power the cell with a biological fuel?

A

Combustion

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9
Q

What is the % abundance of Carbon in the Earth’s crust?

A

0.19%

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10
Q

What is the % abundance of Silicon in the Earth’s crust?

A

28%

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11
Q

What are two (2) reasons carbon more suited for building life than Silicon?

A
  1. Carbon-to-carbon bonds are stronger than silicon-to-silicon bonds.
  2. After combustion, carbon dioxide can exist as a gas or be dissolved in water, remaining in biochemical circulation; silicon is essentially insoluble and after oxidation is permanently out of circulation.
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12
Q

What are two (2) consequences of carbon-to-carbon bonds being stronger than silicon-to-silicon bonds?

A
  1. More stable bonds allow carbon-carbon bonds to be a backbone for large molecules.
  2. More energy is released when carbon-carbon bonds undergo combustion.
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13
Q

What are the four (4) key classes of biomolecules?

A
  1. Proteins
  2. Nucleic Acids
  3. Lipids
  4. Carbohydrates
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14
Q

Describe the structure of proteins (4 components)

A
  1. unbranched polymers
  2. folded into 3D structures
  3. formed from amino acid monomers
  4. linked by peptide bonds.
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15
Q

Discuss the number of amino acids that exist (3 components)

A
  1. Over 200 amino acids
  2. 22 are known to be proteinogenic amino acids
  3. 20 are well-known proteinogenic amino acids
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16
Q

What are four (4) functions of proteins?

A
  1. Signal molecules
  2. Receptors for signal molecules
  3. Structural roles (ex. allow mobility, provide environmental defenses)
  4. Catalysis
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17
Q

What is the function of a receptor?

A

Receptors convey to the cell that a signal has been received and initiates the cellular response.

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18
Q

What are catalysts?

A

Agents that enhance the rate of a chemical reaction without being permanently affected themselves.

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19
Q

What is a protein catalyst called?

A

Enzyme

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20
Q

Describe the structure of nucleic acids (2 components)

A
  1. Linear polymer

2. constructed from four building blocks called nucleotides.

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21
Q

What are two types of nucleic acids?

A
  1. Deoxyribonucleic acid (DNA)

2. Ribonucleic acid (RNA)

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22
Q

Describe the structure of a nucleotide (3 components)

A
  1. Heterocyclic ring structure called a base
  2. five-carbon sugar [deoxyribose OR ribose]
  3. at least one phosphoryl group
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23
Q

What are the four deoxyribonucleotides used to make DNA?

A
  1. adenine (A)
  2. cytosine (C)
  3. guanine (G)
  4. thymine (T)
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24
Q

What are the four ribonucleotides used to make DNA?

A
  1. adenine (A)
  2. cytosine (C)
  3. guanine (G)
  4. uracil (U)
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25
Q

What holds nucleotides together in a strand of nucleic acid?

A

Phosphodiester linkages (bonds)

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26
Q

What are two (2) differences in the nucleotides of DNA and RNA?

A
  1. The base thymine (T) in DNA is replaced by the base uracil (U) in RNA
  2. The sugar component of the ribonucleotides [ribose] contains an additional hydroxyl (-OH) group.
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27
Q

What is the primary function of nucleic acids?

A

To store and transfer information.

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28
Q

How is the information content of DNA stored?

A

The sequence of nucleotides linked together by phosphodiester bonds.

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29
Q

Compare the size of lipids to proteins and nucleic acids

A

Proteins and Nucleic acids can have molecular weights of thousands to millions; a typical lipid has a molecular weight of 1300.

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30
Q

Explain the difference in the size between lipids and proteins & nucleic acids.

A

Lipids are not polymers like proteins and nucleic acids.

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31
Q

Describe a key structural characteristic of lipids (2 components)

A
  1. Hydrophilic head (water soluble)

2. Hydrophobic tail (hydrocarbon chain, insoluble in water)

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32
Q

The dual nature of lipids allows them to perform what important function?

A

Delineate the cell and cellular compartments; development of “inside” and “outside” at biochemical level.

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33
Q

How does the dual nature of lipids form membranes?

A

(1) Hydrophobic chains cannot interact with water, so (2) hydrocarbon chains of two lipid molecules interact with each other and form a barrier; (3) the water-soluble heads interact with the aqueous environment outside of this membrane.

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34
Q

What are three (3) functions of lipids?

A
  1. Form barriers/membranes
  2. Fuel from hydrophobic component
  3. Signal molecules
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35
Q

Describe the structure of carbohydrates

A

Polyhydroxy aldehydes or ketones

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36
Q

What are two (2) functions of carbohydrates?

A
  1. Fuel source

2. Cell-to-cell recognition and interaction

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37
Q

What is the most common carbohydrate fuel?

A

The simple sugar glucose.

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38
Q

How is glucose stored in animals? (2 components)

A

(1) Many glucose molecules linked end-to-end with occasional branches forming (2) glycogen.

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39
Q

How is glucose stored in plants?

A

Starch, which is similar to glycogen in molecular composition.

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40
Q

Life depends on the manipulation of ______ and ______.

A

Energy and information.

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41
Q

Who proposed the Central Dogma and when?

A

Francis Crick 1958

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42
Q

What does the Central Dogma describe?

A

The scheme that underlies information processing at the level of gene expression.

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43
Q

What are the steps of the Central Dogma?

A
  1. information flows from DNA to RNA and then to protein.

2. DNA can be replicated

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44
Q

Define genome

A

The complete set of inheritable genetic information in an organism

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45
Q

Define gene

A

A distinct sequence of nucleotides which contains information towards building a polymer.

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46
Q

Define DNA replication

A

The process of copying genetic information, i.e. the genome.

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47
Q

What catalyzes DNA replication?

A

A group of enzymes collectively referred to as DNA polymerase.

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48
Q

How is the information in genes made accessible, in order to be useful?

A

Transcription

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49
Q

Define transcription of RNA

A

the nucleic acid DNA is transcribed into RNA

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50
Q

What catalyzes transcription?

A

The enzyme RNA polymerase

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51
Q

What defines the function of a cell or tissue?

A

The selective expression of genes

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52
Q

What is a key aspect of selective expression of genetic information?

A

Transcription of genes into mRNA

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53
Q

What is the purpose of the process of translation?

A

To render the genetic information in mRNA into a functional form (protein).

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54
Q

Where does the process of translation occur?

A

Large macromolecular complexes called Ribosomes

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55
Q

What two biomolecules are ribosomes composed of?

A
  1. RNA

2. Protein

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56
Q

What is the basic unit of life?

A

The cell

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57
Q

The human body is composed of approximately how many cells? (3 components)

A

Depends on the metric:

  1. By volume, about 10 trillion.
  2. By weight, about 100 trillion.
  3. By cell/tissue type and volume/density analysis, about 37.2 trillion.
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58
Q

Describe the structure of a cell membrane

A

A lipid bilayer: two layers of lipids organized with their hydrophobic chains interacting with one another and the hydrophilic head groups interacting with the environment.

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59
Q

How is a cell delineated (how is a single cell defined)?

A

A cell is delineated by a membrane that separates the inside of the cell from its environment.

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60
Q

What are two (2) basic types of cells?

A
  1. Eukaryotic cells

2. Prokaryotic cells

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61
Q

What is the main difference between the two basic types of cells? (2 components)

A

(1) Eukaryotes have membrane-enclosed compartments (such as the nucleus), while (2) prokaryotes have an absence of such compartments.

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62
Q

Give an example of a prokaryotic cell in the human body

A

The human gut bacteria Escherichia coli

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63
Q

Describe the structure of a prokaryotic cell

A
  1. Inner and outer membrane separated by
  2. Periplasmic space and cell wall

[The order from Outside to Inside is Cytoplasm -> Inner (plasma) membrane -> Cell wall -> Periplasmic space -> Outer membrane]

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64
Q

What are two minimal cell features common to all cell types, prokaryotic and eukaryotic?

A
  1. a barrier that separates the cell from its environment

2. an inside that is chemically different from the environment and that accommodates the biochemistry of living

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65
Q

What is the name of the barrier that separates the cell from its environment?

A

Plasma membrane

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66
Q

What is the name of the intracellular chemical environment?

A

Cytoplasm

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67
Q

Describe the permeability of the plasma membrane

A

Impermeable to most substances, including fuels, building blocks and signal molecules (information) that must enter the cell.

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68
Q

In order to allow important substances to enter into the cell, what must be done to the plasma membrane?

A

Its barrier function must be mitigated through proteins.

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69
Q

What is selective permeability?

A

The mitigation of plasma membrane barrier function through the work of embedded and associated proteins.

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70
Q

What is a key structural difference between plant and animal cells?

A

The plant’s plasma membrane is surrounded by a cell wall.

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71
Q

How do some substances easily permeate the cell wall?

A

Plasmodesmata

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72
Q

What substance is the cell wall constructed from?

A

Cellulose

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73
Q

What are plasmodesmata?

A

microscopic holes/channels in the cell wall

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74
Q

What is cellulose?

A

A glucose polysaccharide

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75
Q

How has the concept of the cytoplasm changed?

A

It was once thought to be a “soup” of important biomolecules. Now it is thought to be highly organized by a network of structural filaments.

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76
Q

What is the cytoskeleton?

A

A network of structural filaments (protein fibers) that organizes the cytoplasm.

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77
Q

What are three (3) kinds of protein fibers that form the cytoskeleton in many eukaryotes?

A
  1. actin filaments
  2. intermediate filaments
  3. microtubules
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78
Q

What are three (3) functions of the cytoskeleton?

A
  1. Support the structure of the cell
  2. Help localize certain biochemical activities
  3. Serve as “molecular highways” by which molecules can be shuttled around the cell.
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79
Q

The structural difference between eukaryotes and prokaryotes leads to what key difference in their biochemistry?

A

In eukaryotes, biochemical functions are sequestered into cellular compartments.

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80
Q

What is an organelle?

A

Intracellular, membrane-bounded compartments found in eukaryotes

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81
Q

What are three (3) organelles that predominantly carry out unique biochemical functions?

A
  1. Nucleus
  2. Mitochondion
  3. Chloroplast
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82
Q

What are two (2) large organelles that process and sort proteins?

A
  1. Endoplasmic Reticulum (ER)

2. Golgi complex

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83
Q

What are four (4) organelles that are vesicles?

A
  1. Vacuoles (plant)
  2. Lysosomes
  3. Transport vesicles
  4. Secretory vesicles
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84
Q

What is the largest organelle?

A

Nucleus

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85
Q

Describe the structure of the nucleus (2 components)

A
  1. double-membrane-bounded

2. contains nuclear pores

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86
Q

What is the function of the nucleus?

A

Information center of the cell; Location of organisms’s genome.

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87
Q

What occurs within the nucleus? (2 components)

A

Genetic information is:

  1. Stored
  2. selectively expressed at the proper time and in the proper amount
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88
Q

Describe the structure of the mitochondrion (three components)

A
  1. Two membranes separated by inter membrane space:
    a. outer mitochondrial membrane, is in a bean shape
    b. inner mitochondrial membrane has invaginations and defines the matrix
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89
Q

What notable biochemistry occurs in the mitochondrion?

A

Fuel molecules undergo combustion into carbon dioxide and water with the generation of cellular energy in the form of adenosine triphosphate (ATP).

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90
Q

Approximately what % of energy used by the cell is produced in the mitochondrion?

A

90%

91
Q

What are two (2) poisons that can shut down the function of the mitochondrion?

A
  1. Cyanide

2. Carbon monoxide

92
Q

What cells contain chloroplasts and briefly describe their structure

A
  1. Found only in plants

2. Double-membrane bound

93
Q

What notable biochemistry occurs in the chloroplast?

A

The conversion of sunlight into chemical energy

94
Q

What is the name of the process that converts sunlight into chemical energy?

A

Photosynthesis

95
Q

Describe the general structure of the Endoplasmic Reticulum

A

Series of membranous sacs

96
Q

Name the two (2) surfaces of the sacs composing the ER

A
  1. cytoplasmic surface (exteriors)

2. lumens (interiors)

97
Q

What are the two (2) types of endoplasmic reticulum?

A
  1. smooth endoplasmic reticulum (SER)

2. rough endoplasmic reticulum (RER)

98
Q

What is an especially notable function of the SER?

A

The processing of exogenous chemicals, such as drugs.

99
Q

What gives the RER its rough appearance?

A

Ribosomes are attached to the cytoplasmic surface

100
Q

Where are two locations for ribosomes in the cell?

A
  1. Cytoplasm

2. Rough ER

101
Q

Ribosomes of the cytoplasm synthesize what sorts of proteins?

A

Proteins for use inside of the cell

102
Q

Ribosomes of the RER synthesize what sorts of proteins? (2 components)

A

Proteins that will either be (1) inserted into cellular membranes or (2) be secreted from the cell.

103
Q

Describe the process of protein synthesis in the RER (5 steps)

A
  1. Protein is transported into the lumen of ER during process of translation
  2. Inside the lumen, the protein folds into its 3D structure AND
  3. is modified in other ways (ex. by attachment of carbohydrates)
  4. protein is sequestered into region of RER that lacks ribosomes
  5. protein and the region of RER its attached to bud off and form transport vesicle

[Abridged: Lumen -> Modification -> Budding]

104
Q

What are the names of proteins that aid in the folding of a protein into its three-dimensional structure within the lumen of the RER?

A

Chaperone proteins

105
Q

What is a transport vesicle?

A

A membrane-bound protein carried from RER to Golgi Complex.

106
Q

Describe the structure of the Golgi complex

A

A series of stacked membranes

107
Q

What occurs at the Golgi complex?

A

Proteins arriving in transport vesicles from RER are processed, sorted and shipped.

108
Q

What processing occurs in the Golgi complex?

A

A different set of carbohydrates is added to the protein.

109
Q

How are proteins shipped out of the Golgi complex?

A

A vesicle filled with the proteins destined for secretion buds off of the Golgi complex.

110
Q

What are two (2) names for the vesicle that buds off of the Golgi complex?

A
  1. secretory granule/vesicle

2. zymogen granule

111
Q

What happens to a secretory granule?

A
  1. It is directed towards the cell membrane.

2. When signal is received, it fuses with plasma membrane and dumps proteins into the extracellular environment.

112
Q

What is the name of the process for when a secretory vesicle secretes proteins into the extracellular environment?

A

Exocytosis

113
Q

What is endocytosis?

A

When material is taken into the cell by the plasma membrane invaginating and budding into the cytoplasm.

114
Q

When are endosomes formed?

A

During endocytosis

115
Q

What is it called when very large amounts of material are taken into the cell by a process similar to endocytosis?

A

Phagocytosis

116
Q

What is a lysosome?

A

An vesicle that contains a wide array of digestive enzymes

117
Q

How are lysosomes formed?

A

A manner similar to the formation of secretory granules (budding from the Golgi complex).

118
Q

How do lysosomes and secretory granules differ? (2 components)

A
  1. Secretory granules fuse with cell membrane

2. Lysosomes fuse with endosomes.

119
Q

What are two functions of lysosomes?

A
  1. Digesting extracellular material

2. Digesting damaged intracellular organelles

120
Q

Describe the structure of a plant vacuole

A
  1. single-membrane bound

2. occupy as much as 80% of cell’s volume

121
Q

What is the function of a plant vacuole?

A

Storage:

  1. Water
  2. Ions
  3. Various nutrients
122
Q

How does material move across a plant vacuole membrane?

A

Transport proteins

123
Q

What types of bonds are responsible for the complex structure and function of cells?

A

Weak bonds; interactions with less strength than covalent bonds.

124
Q

What are two advantages that weak bonds provide for building complexity?

A
  1. Large numbers of weakly stabilizing bonds aggregate to be stable.
  2. Weak bonds break and reform quicker than strong bonds; this allows transient chemical reactions.
125
Q

What is an advantage of transient chemical reactions?

A

permit energy and information to move about the cell and organism quickly

126
Q

Define an angstrom (Å)

A

1 Å = 0.1 nm = 1 x 10-10 m = 100 picometers = one 10 billionth of a meter

127
Q

What are two characteristics of a transient chemical reaction?

A
  1. Weak bonds involved

2. Reversible

128
Q

Give an example of an important transient chemical reaction in biochemistry

A

The ionization of water and weak acids

129
Q

What is Brownian motion?

A

random movement of particles suspended in a fluid

130
Q

What is the cause of Brownian motion?

A

The random fluctuation of the energy content of the fluid (the environment)

131
Q

What is thermal noise?

A

Random fluctuation of the energy content of an environment

132
Q

In a cell, what is the most common environment responsible for Brownian motion?

A

Water

133
Q

What is the % water composition of a typical cell?

A

70%

134
Q

What is the % water composition of a human?

A

65%

135
Q

What is the chemical basis for water’s strong solvent ability?

A

The electronegative oxygen atom bonded with hydrogen creates a nonuniform charge distribution (polarity).

136
Q

What are hydrogen bonds?

A

Partially positive charged hydrogen atom interacts with a partially negative Nitrogen or Oxygen atom.

137
Q

How does water’s hydrogen bonding influence the structure of liquid water?

A

Cohesion; molecules of water interact through hydrogen bonding with each other.

138
Q

In liquid water, each molecule interacts with how many neighbors?

A

3.4 neighbors

139
Q

What consequence does water’s polarity have on the structure of aqueous solutions?

A

Water can solvate any charged or polar molecule.

140
Q

What is the name for the class of molecules that do not interact (form solutions) with water?

A

nonpolar or hydrophobic

141
Q

What is observed when a hydrophobic molecule is placed in an aqueous environment?

A

the molecules are sequestered (isolated)

142
Q

What is the name of the process that is observed when a hydrophobic molecule is placed with water?

A

the hydrophobic effect

143
Q

The hydrophobic effect is the chemical animus for what structures?

A

Cell and organelle membranes

144
Q

Weak interactions are synonymous to what what types of bonds?

A

Noncovalent bonds

145
Q

What are the three (3) fundamental noncovalent bonds?

A
  1. electrostatic interactions
  2. hydrogen bonds
  3. van der Waals interactions
146
Q

The fundamental noncovalent bonds differ in what three (3) aspects?

A
  1. geometry
  2. strength
  3. specificity
147
Q

What are two (2) other names for electrostatic interactions?

A
  1. ionic bonds

2. salt bridges

148
Q

Define electrostatic interactions

A

Interactions between distinct electrical charges on atoms (usually between completely positive and completely negative charges)

149
Q

The force of an electrostatic interaction is given by what law?

A

Coulomb’s law

150
Q

Mathematically express Coulomb’s law

A

F = (kq◘q•)/Dr^2

where:
F is the force
q• and q◘ are charges on the two atoms
r is the distance between the two atoms
D is the dielectric constant
k is the proportionality constant
151
Q

What is the purpose of the dielectric constant in Coulomb’s law?

A

it accounts for the effects of the intervening medium

152
Q

Qualitatively express Coulomb’s law (3 components)

A

The (force of the) electrostatic interaction (1) increases as the magnitude of charge of the atoms increases; (2) the interaction decreases quadratically as the distance between atoms increases; (3)the interaction also decreases as the dielectric constant of the medium increases.

153
Q

Electrostatic interactions are theoretically strongest in what medium?

A

Vacuum, where D = 1

154
Q

What is the dielectric constant of water?

A

80

155
Q

What is observed when crystalline Na+Cl- is put into water?

A

The salt dissolves.

156
Q

What is the chemical explanation for the observation of putting sodium chloride crystals in water? (4 components)

A
  1. NaCl crystal is a lattice formed by ions.
  2. Water is polar and can interact with ions.
  3. Water molecules interact with Na+ and Cl-
  4. Na+ and Cl- react less with each other, breaking crystal structure.
157
Q

What quantifies the chemical explanation for the observation of dissolving NaCl with water?

A

Dielectric constant

158
Q

What are the four most common Hydrogen-bond donor/acceptor interactions in Biochemistry?

A
  1. N-H ——- N
  2. N-H ——- O
  3. O-H ——- N
  4. O-H ——- O
159
Q

What is the typical energy range for hydrogen bonds?

A

8 to 20 kJ per mol (2 to 5 kcal per mol)

160
Q

What is the approximate energy of a carbon-hydrogen covalent bond?

A

418 kJ per mol (100 kcal per mol)

161
Q

What is the approximate bond length for the O-H or N-H bond?

A

0.9 Å to 1.0 Å

162
Q

Structurally, the hydrogen bond exists between what two atoms?

A

The hydrogen of the donator and the O or N of acceptor.

163
Q

What is the typical bond length of a hydrogen bond?

A

1.5-2.6 Å

164
Q

What is the approximate distance between the two nonhydrogen atoms of a donor/acceptor Hydrogen bonding interaction?

A

2.4Å to 3.5Å

(Distance of O-H/N-H bond) + (Distance of hydrogen bond) = (Distance between nonhydrogen atoms)

(0.9 Å) + (1.5 Å to 2.6Å) = [2.4Å to 3.5Å]

165
Q

Compare hydrogen bonding between between molecules of methanol (CH3OH) with and without water. (2 components)

A
  1. In water, there will be less hydrogen bonding between methanol molecules.
  2. Conversely, hydrogen bonding between two methanol molecules is stronger in the absence of water.
166
Q

Explain the disruption of hydrogen bonding when a substance (such as methanol) is placed in water?

A

Hydrogen bonds between two molecules will be disrupted by water because water itself will compete to form hydrogen bonds with the molecules.

167
Q

Explain how the van der Waals interaction originates

A

Transient asymmetry: The distribution of electron charge around an atom changes with time and thus at certain time intervals the charge is asymmetric

168
Q

How does transient asymmetry affect neighboring atoms or molecules?

A

Induces a complementary asymmetry in neighboring molecules that causes an attraction.

169
Q

Explain the van der Waal contact distance

A
  1. transient asymmetry induces complementary asymmetry in neighboring molecule
  2. transient polar molecules are attracted to each other
  3. energy decreases until a minimum at the contact distance, past which causes orbital overlap and electron-electron repulsion.
170
Q

What is the approximate contact distance for van der Waal interactions?

A

3-4 Å

171
Q

What are the approximate energies associated with van der Waal interactions per atom pair?

A

2 to 4 kJ per mol (0.5 to 1.0 kcal per mol)

172
Q

Explain the role that low bond energies of weak interactions (hydrogen bonds) play in the information function of DNA

A

Hydrogen bonds are:

  1. weak enough to allow access to the information under appropriate circumstances
  2. strong enough to stabilize and protect DNA
173
Q

What happens when a single nonpolar molecule is added to water? (4 components)

A
  1. The nonpolar molecule forms a cavity where it doesn’t interact with water.
  2. Water molecules at the edge of the nonpolar molecule orient themselves for maximum hydrogen bonding.
  3. There are fewer ways to arrange these water molecules for maximum hydrogen bonding than for molecules exposed on all sides.
  4. Entropy decreases.
174
Q

What happens when multiple nonpolar molecules are added to water?

A
  1. Entropy decreases for ordered water molecules.
  2. Association of nonpolar molecules (hydrophobic interactions) releases water molecules around each molecule (by “decreasing surface area”)
  3. Entropy increases.
  4. Thus association of nonpolar molecules happens spontaneously.
175
Q

What factor drives the hydrophobic effect?

A

Entropy

176
Q

What is the name for a molecule with two distinct chemical personalities (such as a lipid)?

A

Amphipathic or amphiphilic

177
Q

The hydrophobic effect powers what two processes?

A
  1. Membrane formation

2. Protein folding

178
Q

How does the hydrophobic effect power protein folding? (3 components)

A
  1. A folded protein has less entropy than an unfolded protein.
  2. For a protein to fold spontaneously, there must be an entropy increase somewhere.
  3. Nonpolar amino acids associate in a protein, increasing entropy of water.
179
Q

What role do weak interactions play in the process of protein folding?

A

Weak interactions stabilize the structure that is formed through the hydrophobic effect

180
Q

Explain how the following statement applies to biochemistry: Order can be generated by an increase in randomness (3 components)

A
  1. Creating order requires a decrease in entropy
  2. for this to be spontaneous there must be a greater increase in entropy elsewhere.
  3. Increasing randomness somewhere else in the system (e.g. water through hydrophobic effect) will allow order to be generated (e.g. protein folding).
181
Q

What are three (3) generalizations that make dealing with biochemistry manageable?

A
  1. All biomolecules interact through weak interactions and the hydrophobic effect.
  2. There are four classes of biomolecules.
  3. There are eight common functional groups.
182
Q

What are eight *8) common functional groups of Biochemistry?

A
  1. Hydrophobic (aliphatic and aromatic)
  2. Hydroxyl
  3. Aldehyde
  4. Keto
  5. Carboxyl
  6. Amino
  7. Phosphate
  8. Sulfhydryl
183
Q

What is the structure of a hydrophobic functional group?

A

R-CH3 or R-Phenyl

184
Q

What is the structure of a hydroxyl functional group?

A

R-OH

185
Q

What is the structure of an aldehyde functional group?

A

R-(C=O)-H

186
Q

What is the structure of a keto functional group?

A

R-(C=O)-R

187
Q

What is the structure of a carboxyl functional group?

A

R-(C=O)-OH

188
Q

What is the structure of an amino functional group?

A

R-NH2

189
Q

What is the structure of a phosphate functional group?

A 
O(-)
        |
R-O-P=O
        l
       O(-)
190
Q

What is the structure of a sulfhydryl functional group?

A

R-SH

191
Q

How is the concentration of hydrogen ions (protons) measured?

A

By pH, which ranges from 0-14.

192
Q

What is the pH of human blood?

A

About 7.4

193
Q

Why do changes in pH drastically affect the health of an organism? (3 components)

A

(1) Changes in concentration of protons affects (2) the internal electrostatic environment (3) which can alter the weak bonds that maintain biomolecule structures.

194
Q

What is chemical equilibrium?

A

The condition in which concentrations of reactions and products have no net change over time.

195
Q

Write the equilibrium constant Keq for the autoionization of H2O

A

Keq = [H+][OH-]/[H2O]

196
Q

What are the concentrations of H+ and OH- in pure water?

A

Both are 1.0 x 10^-7

197
Q

Define the ion product of water

A

define: Kw = Keq * [H2O]
simplify: Kw = [H+][OH-]

198
Q

What is the standard value for the ion product of water?

A

1.0 x 10^-14 @ 25 Celsius

199
Q

Define pH and pOH

A 
pH = -log [H+]
pOH = -log[OH-]
200
Q

Express the quantitative relationship between pH and pOH

A

pH + pOH = 14

201
Q

Write the ionization equilibrium for the weak acid HA

A

HA H(+) + A(-)

202
Q

Write the equilibrium constant Ka for the ionization of a weak acid

A

Ka = [H+][A-]/[HA]

203
Q

Relate the strength of a weak acid to its equilibrium constant Ka

A

The larger the value of Ka, the stronger the acid.

204
Q

What is an important use of the Henderson-Hasselbalch equation?

A

To determine how dissociated an acid will be at a particular pH.

205
Q

Starting with the equilibrium constant Ka for a weak acid, derive the Hendersen-Hasselbalch equation. (3 steps)

A

Start: Ka = [H+][A-]/[HA]
Divide both sides by [Ka][H+]
1. 1/[H+] = [A-]/[HA][Ka]
Take logarithm of both sides
2. log (1/[H+]) = log (1/Ka) + log ([A-][HA])
substitue pH and pKa for log (1/[H+]) and log (1/Ka)
3. pH = pKa + log([A-][HA]

206
Q

The Hendersen-Hasselbalch reveals what relationship between pH and pKa

A

pKa is the pH at which the acid is half dissociated.

207
Q

At pH below pKa, does [A-] or [HA] dominate?

A

[HA]

208
Q

At pH above pKa, does [A-] or [HA] dominate?

A

[A-]

209
Q

Why are most biochemical acids referred to by the name of the conjugate base (ex. pyruvic acid referred to as pyruvate)

A

Most biochemical acids are predominately dissociated at physiological pH (~7.4)

210
Q

What is a chemical buffer?

A

A solution (of an acid-base conjugate pair) that resists changes in the pH.

211
Q

What is a titration?

A

A technique where a known concentration of a solution is used to determine the concentration of an unknown solution (commonly the concentration of H+ or OH-)

212
Q

Describe a titration curve of buffer action

A

A plot of the pH of solution (y-axis) as acid or base is added (x-axis).

213
Q

In general, a weak acid is most effective in buffering against pH changes in what vicinity?

A

pH changes in the vicinity of its pKa

214
Q

Give two (2) reasons for why knowledge of buffer systems is important in the study of biochemistry.

A
  1. In vitro investigation of pH dependent biomolecules requires buffers to maintain proper pH
  2. The organism uses physiologically crucial buffers in vivo.
215
Q

What is compensatory respiratory alkalosis?

A

The mechanism of blood-pH control involving (1) H2CO3/HCO3- [bicarbonate buffer system] and (2) respiration.

216
Q

How is carbonic acid produced in the blood for the compensatory respiratory alkalosis buffer system?

A

Water reacts with CO2 produced from biochemical consumption of fuels.

217
Q

Write the two reactions involved in the bicarbonate buffering system

A

CO2 + H20 H2CO3 HCO3(-) + H(+)

218
Q

What catalyzes the reaction between carbon dioxide and water to form carbonic acid in the blood?

A

Carbonic anhydrase

219
Q

How does respiration maintain the ratio of HCO3(-) and H2CO3 in the blood? (3 components)

A

If acid is added to the blood:

  1. the dissociation of carbonic acid will be shifted to the left (more carbonic acid)
  2. the synthesis of CO2 and H2O will be pushed to the left (more CO2)
  3. [CO2] is decreased by respiration until the concentrations return to normal.
220
Q

What is chemical equilibrium?

A

The condition in which concentrations of reactions and products have no net change over time.

221
Q

What is the pKa of acetic acid?

A

4.76

222
Q

What is the pKa of ammonium ion?

A

9.25

223
Q

What is the pKa of the carboxyl hydrogen on Glycine?

A

2.34

224
Q

What is the pKa of the amino hydrogen on Glycine?

A

9.60

Biochemistry (7 decks)

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