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Biochemistry 1 > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

What are the 4 basic biomolecule compounds?

A

Lipids

Proteins

Carbohydrate

Nucleic Acid

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2
Q

What are the monomeric units of proteins and nucleic acids?

A

Proteins: amino acids

Nucleic acids: nucleotides

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3
Q

What is the parent sugar of most carbohydrates?

A

Glucose

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4
Q

What functional group links the membrane mimics and nucleotides?

A

Glycerol

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5
Q

Describe a monomer and a polymer

A

Monomer:The single units that make up a macromolecule

Polymer: multiple monomeric units joined together form a polymer

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6
Q

What are the organic elements?

A

C, H, O, N, P, S

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7
Q

Life is ______ based

A

Carbon

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8
Q

In terms of rotation what is the difference between a single and a double bond?

A

Single allows for rotation to occur

Double prevents rotation from occurring

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9
Q

What is a trace element?

A

Essential but do not require them in large amounts. Essential because our body cannot make them.

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10
Q

Define nucleoside and nucleotide

A

Phosphate, sugar and base = nucleotide

Sugar and a base = nucleoside

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11
Q

Describe purines and give examples

A

Dicyclic, ex: Adenosine, Guanine

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12
Q

Describe Pyrimidines and give examples

A

Monocyclic

Ex: Uracil, thymine, cytosine

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13
Q

What is the general path of energy transformations?

A

Potential energy -> energy transductions accomplish work resulting in Heat and simple compounds -> simple compounds polymerize to form information such as DNA, RNA, Protein.

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14
Q

________ predominate at pH values between the pka values of the amino and carboxyl groups

A

Zwitterions

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15
Q

When net charge is _______ when Zwitterions are present

A

Zero

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16
Q

What is the difference between primary vs secondary amino groups?

A

Primary amino groups are free and not connected to anything but the alpha carbon (ex: alanine)

Secondary amino groups are further bonded to a second carbon group (ex: proline)

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17
Q

Proline is not a typical amino acid because its amino group is a __________ amine and because of this feature, it is called an ________ acid

A

Secondary

Imino

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18
Q

________ binds to another _______ through their R groups to form disulfide bonds

A

Cysteine

Cysteine

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19
Q

What amino acids have negatively charged R groups?

A

Aspartate and Glutamate

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20
Q

A negative charge indicates the amino acid has donated a _______ at physiologic pH making it _______

A

Proton

Acidic

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21
Q

What are the amino acids that contain positively charged (basic) R groups?

A

Lysine (K)

Arginine (R)

Histidine (H)

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22
Q

Positive charge indicates the amino acids have _______ a proton at physiologic pH making it _______

A

Accepted

Basic

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23
Q

Polar in charged R groups side chains can form _______ bonds

A

Hydrogen bonds

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24
Q

What are the amino acids that have polar uncharged R groups

A

Serine

Threonine

Cysteine

Asparagine

Glutamine

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25
Q

What amino acids contain sites for phosphorylation?

A

Serine

Threonine

Tyrosine

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26
Q

What amino acids have aromatic R groups?

A

Phenylalanine

Tyrosine

Tryptophan

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27
Q

________ R groups absorb UV light at 270-280nm

A

Aromatic

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28
Q

What amino acids have nonpolar, aliphatic R groups?

A 
Glycine
Alanine
Proline 
Valine
Leucine
Isoleucine
Methionine
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29
Q

Polar uncharged, positively charged and negatively charged and 1 aromatic (tyrosine) are all ________ amino acids

A

Hydrophilic

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30
Q

Phenylalanine and tryptophan (aromatic R groups) and the non polar aliphatic amino acids are all ________ amino acids

A

Nonpolar, amino acids

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31
Q

Amino acids can act as buffers in two pH regimes pointed out via _______ and ______ on the graphs

A

Pk1 and pK2

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32
Q

When have an acidic amino acids, how do you find the isoelectric point?

A

Take pKr and pK1 and add them together then divide them by 2

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33
Q

If have a basic amino acid, how do you calculate the isoelectric point (pI)?

A

Take the pKR and the pK2 and add them together then divide them by 2.

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34
Q

Net charge is ______ when pI=pH

A

Zero

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35
Q

In any other case in finding the pI of an uncharged amino acid, what is the math?

A

take the pK1 and pKR and divide it by 2

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36
Q

In the hydropathy index, a large positive index indicates that the R group is very ___________

In the hydropathy Index, a very negative index indicates that the R group is very _________

A

Hydrophobic

Hydrophilic

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37
Q

Cysteine is generally classified as having a ________ R group despite having a positive hydropathy index

A

Polar

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38
Q

What does a small positive or negative index indicate?

A

That the R is neither very hydrophobic nor very hydrophilic

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39
Q

What is the most hydrophobic amino acid, most hydrophilic amino acid?

A

Most hydrophobic: Isoleucine

Most hydrophilic: Arginine

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40
Q

What are the hydrophobic amino acids and their ranking on the hydropathy index

A

1) isoleucine
2) Valine
3) Leucine
4) Phenylalanine
5) methionine
6) Alanine

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41
Q

What is the rank of the most hydrophilic R groups based on the hydropathy index

A

1) Arginine
2) Lysine
3) asparagine
4) glutamine
5) aspartate
6) Glutamate
7) Histidine

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42
Q

How is cysteine classified as having a polar R group despite having a positive hydropathy index?

A

Because of the ability of the sulhydryl group to act as a weak acid to form a H bond with oxygen or nitrogen

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43
Q

What is the smallest amino acid?

A

Glycine

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44
Q

What is the amino acid that is classified as an imino acid?

A

Proline

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45
Q

What are the branched chain amino acids?

A

Isoleucine
Leucine
Valine

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46
Q

What is an example of a branched chain ketogenic amino acid?

A

Leucine

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47
Q

What amino acids contain sulfur?

A

Cysteine

Methionine

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48
Q

What is the largest amino acid?

A

Tryptophan

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49
Q

What amino acid can serve as a biological buffer?

A

Histidine

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50
Q

What amino acid has the lowest pI?

A

Aspartate

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51
Q

Life is ______ based

A

Carbon

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52
Q

What is the definition of a trace element?

A

Essential elements but are not required in large amounts.

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53
Q 
What are the names of the following funcitonal groups?
R-CH3
R-CHO
R-SH
R1-CO-R2
R-OH
A 
Methyl 
Aldehyde 
Sulfhydryl 
Ketone
Hydroxyl
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54
Q 
What are the names of the following functional groups?
R-COOH
R1-S-S-R1
R1-COO-R2
R1-O-R2
R-O-PO3H
A 
Carboxylic acid
Disulfide
Ester
Ether
Phosphoryl
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55
Q

What qualifies as potential energy sources?

A

Nutrients in environment (complex molecules such as sugar, fats)

Sunlight

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56
Q

What qualifies as potential energy sources?

A

Nutrients in environment (complex molecules such as sugars and fats)

Sunlight

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57
Q

How can energy be wasted to surroundings in terms of enthalpy?

A

Heat is given off during reactions which is known as enthalpy
ATP can break down and heat can be a byproduct

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58
Q

Which form of potential energy is commonly generates by cells?

A

ATP

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59
Q

______ is the change in heat or enthalpy where the reaction either gives off heat or absorb heat (endothermic or exothermic)

A

Heat (enthalpy)

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60
Q

______ is equivalent to disorder or randomness. More entropic then the ________ the disorder. Less entropic then _________ disorder of the system

A

Entropy
Increases
Decreases

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61
Q

What is used to make predictions about direction and reaction feasibility?

A

The change in free energy

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62
Q

Why are standard conditions helpful when considering series of reactions?

A

Used to predict the direction and how far the reaction is from equillibrium

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63
Q

If Keq is positive then delta G is ________ and the reaction proceed ___________

A

Negative

Forward

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64
Q

If Keq is negative then the delta G is _______ and the reaction proceeds __________

A

In reverse

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65
Q

What is the delta G of the of a reaction when it reaches equilibrium?

A

Free energy is zero at equilibrium

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66
Q

What is the equation to find standard free energy?

A

-RT LnKeq

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67
Q

Endergonic vs exergonic reactions

A

Endergonic reactions require external energy

Exergonic reactions do not require external energy

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68
Q

What two ways do living organisms use to speed up a reaction and what are the barriers of the other two?

A 
Energy coupling (coupling ATP with endergonic reactions to make them exergonic)
Lower activation barrier by catalysis

Barriers of the other two are 1) with higher temperatures, the stability of macromolecules is limiting 2) higher concentration of reactants is costly bc it requires more valuable starting material

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69
Q

How do enzymes act as catalysts?

A

Enzymes act as catalysts via increasing the rate of a chemical reaction by
Accelerating under mild conditions, offer high specificity, a possibility for regulation

70
Q

Metabolic pathways ____________

Signal transduction ______________

A

Produces energy or useful byproducts

Transmits information

71
Q

What allows the DNA molecule to be more reliable in terms of making copies of code?

A

The semiconservative method of replication

The antiparallel strands and replication can occur in both strands. Have coding and noncoding DNA

72
Q

What is the central dogma?

A

Flow of genetic information from DNA transcribed to RNA translated to protein that perform specific cellular activity

73
Q

Chiral molecules have __________

A chiral center example is _____

A

Different substituent groups

Carbon as the center with all the substituents being different

74
Q

What are enantiomers?

A

Mirror images

75
Q

_________ have identical physical properties (except with regard to polarized light) and react identically with achiral molecules

A

Enantiomers

76
Q

________ is the process of converting genetic information from DNA to RNA

A

Transcription

77
Q

_______ the process of converting mRNA to proteins

A

Translation

78
Q

What are the 4 major functions of proteins?

A

Catalysis
Transport
Structure
Motion

79
Q

What are some of the attributes of amino acids which allow them to perform a variety of biological functions?

A

Capacity to polymerize
Useful acid base properties
Varied physical properties
Varied chemical functionality

80
Q

What is an alpha amino acid?

A

Carbon that is bound to the carboxylate group

81
Q

Naming of amino acid begins from the ______ carbon

A

Alpha

82
Q

Most of the amino acids exist in ______ form

A

L

83
Q

Amino acids are classified based on their __________

A

R substituent

84
Q

_________ is a nonpolar hydrophobic sulfur containing amino acid

A

Methionine

85
Q

________ is an imino acid which adds kinks to the protein structure

A

Proline

86
Q

______ is an aromatic amino acid which has a hydroxyl group

A

Tyrosine

87
Q

_________ is a sulfhydryl group containing amino acid

A

Cysteine

88
Q

______ is the biggest amino acid

A

Tryptophan

89
Q

______ is the smallest amino acid

A

Glycine

90
Q

In eukaryotes, this amino acid ___________ initiates protein synthesis

A

N-formyl-methionine

91
Q

Name the amino acids that can undergo phosphorylation

A

Tyrosine, threonine and serine

92
Q

Name the most hydrophobic and hydrophilic amino acid based on the hydropathy index

A

Most hydrophobic- Isoleucine

Most hydrophilic - Arginine

93
Q

What are essential amino acids and what are their names?

A

Essential amino acids are those required though diet

H, I,L,K,M,F,T,W,V

94
Q

Taurine is a _________ _______ amino acid and is a principle component of ______

A

Conditionally essential

Bile

95
Q

Name the branched chain amino acids

A

Isoleucine, leucine and valine

96
Q

Why are branched chain amino acids sold as supplements to boost muscle health?

A

While most amino acids are oxidized in the liver, branched chain amino acids are oxidized in muscles. This boosts muscle recovery and acts as a supplement

97
Q

Name the amino acid in beans, grains vegetables and corn

A

Methionine

98
Q

What are complementary foods?

A

Complementary foods are sources of the essential amino acids that are not created in the body

99
Q

________ are condensation products of amino acids linked by _____ bond.

A

Polypeptide

Peptide

100
Q

Long weak bonds that result in unique properties, are important in structure and function of proteins, DNA, etc.

A

Hydrogen bond

101
Q

H bonds are formed between H and __________ atom that have unshared electrons

A

Electronegative

102
Q

________ molecules are molecules that contain a hydrophobic and a hydrophilic region

A

Amphipathic

103
Q

______, oriented in a way to where hydrophobic regions are together and away from water while hydrophilic heads are oriented towards the water

A

Micelles

104
Q

___________ ______ play an important role in folding of proteins and hormone receptors and ligand binding

A

Hydrophobic interactions

105
Q

Van der Waals interactions:

  • ________ individually
  • ________ (occur btwn Andy two atoms that are near each other)
  • determines _______ complementarity
  • stabilizes _________ ________
  • faciliates binding of ______ _______
A 
Weak
Universal
Steric
Biological macromolecules 
Polarizable ligands
106
Q

When a cell is placed in a _______ solution the water moves out of the cell and shrinks to equalize osmolarity outside and inside the cell

A

Hypertonic solution

107
Q

In _________ the solute concentration is high externally. Since there is less water outside the water rushes out and the cell shrinks

A

Hypertonic

108
Q

In a ______ solution, water moves in creating outward pressure resulting in cell _______

A

Hypotonic solution

Lysis

109
Q

When salt concentraiton is too low outside compared to the inside where does the water go?

A

The water rushes in and the cells lyse due to the excess water pressure inside the cell

110
Q

_______ is the negative log of the hydrogen ion concentration

A

The pH

111
Q

In neutral solution, the concentration of H+ and OH- are equal and the pH is ____

A

7

112
Q

______ is a condition in which too much acid accumulates in the body causing the pH to fall below 7.35

A

Acidosis

113
Q

______ occurs when too many bases accumulate in the body, this causes the pH to rise above 7.45

A

Alkalosis

114
Q

Short hops of protons between a series of H bonded water molecules result in an extremely rapid net movement of a proton over a long distance

A

Proton hopping

115
Q

______ resist changes in pH

A

Buffers

116
Q

When pH=pKa, the mixture of acid and conjugate base is ______

A

50:50

117
Q

Buffering capacity of an acid/anion system is greatest at __________

A

pH=pKa

118
Q

Buffering capacity is lost when ________

A

The pH differed from pKa by more than 1 pH unit

119
Q

What amino acid can act as a buffer at neutral pH?

A

Histidine

120
Q

Water is a ______ molecule in which oxygen atom carries a _____ charge and hydrogen atoms have a ______ charge

A

Dipolar

Negative

Positive

121
Q

Water can serve as both a _________ ______ and _______ _______ due to ______ bonds

A

Hydrogen acceptor

Hydrogen donor

Hydrogen bonds

122
Q

Hydrogen bonds are shown as three lines that are _______ and ________ than covalent bonds

A

Longer and weaker

123
Q

The attraction between the partial electric charges are _________ when O-H-O atoms are aligned in a _________ (geometry)

A

Greatest

Straight

124
Q

Water is a good solvent for ________ and _____ molecules such as ______

A

Charged and polar

Amino acids and peptides, small alcohols and carbohydrates

125
Q

Water is a poor solvent for _______ molecules such as ______

A

Nonpolar molecules

Aromatic moieties, aliphatic chains and nonpolar gases

126
Q

What is an example of an amphipathic molecule?

A

Phosphatidylcholine

127
Q

High _______ _____ of water reduces attraction btwn oppositely charged ions allowing strong electrostatic interactions between ______ ions and water molecules. This inturn ______ entropy and weakens the crystal lattice

A

Dielectric constant

Solvated

Increases

128
Q

Van der Waals such interactions have two components __________ and _______

A

attractive (London Dispersion) and repulsive force (steric repulsion)

129
Q

Why are non polar molecules poorly soluble in water?

A

Because they are unable to form H-bonds due to their low entropy

130
Q

In structures called ________, the hydrophobic groups are sequestered from water and hydrophilic groups are oriented outward to interact with the aqueous medium. This results in _______ entropy

A

Micelles

Increased

131
Q

The concentration of [H+] in acidic solutions is _____ than neutral and basic solutions

A

Higher

132
Q

In neutral solutions [H+] is _______ to [OH-]

A

Equal

133
Q

In basic solutions [H+] is _____ than [OH-]

A

Lower

134
Q

What is the relationship between strength of an acid or base to its pKa?

A

The stronger the acid, the smaller its pKa value

The stronger the base, the larger its pKa value

135
Q

When is the buffering capacity of a buffer at its maximum?

A

Buffering capacity of can acid/anion system is greatest at pH=pka

136
Q

Why can some biomolecules act as buffers?

A

Because they carry charge and reactive R groups that can act as a proton donor or acceptor and have ionizable groups.

137
Q

Amino acids with ________, __________ R groups can form Hydrogen bonds

A

Polar uncharged

138
Q

_________ R groups can absorb UV light at 270-280nm

A

Aromatic

139
Q

A positive charge indicates that the amino acid have ________ a proton at physiology pH. AKA _______

A

Accepted

Basic

140
Q

Negative charge indicates the amino acid has _______ a proton at physiologic pH. AKA _______

A

Donated

Acidic

141
Q

Proline is not a typical amino acid because its amino group is a _______________ in contrast to the primary amine found in the other 19 protein amino acids.

It is also called an ______ acid due to this feature

A

Secondary amine

Imino

142
Q

_________ bonds are important in stabilizing proteins in nature

A

Disulfide bonds

143
Q

____________ predominate at pH values between the pKa values of the amino and carboxyl groups

A

Zwitterions

144
Q

What are the hydrophobic amino acids?

A 
Glycine
Alanine
Proline
Valine
Isoleucine
Leucine
Methionine
Phenylalanine 
Tryptophan
145
Q

What are the hydrophilic amino acids?

A 
Cysteine
Arginine
Glutamine
Asparagine
Serine
Threonine
Tyrosine
Glutamate
Aspartate
146
Q

What are the basic and acidic amino acids?

A

Basic: Histidine, Lysine, Arginine

Acidic: Aspartate and glutamate

147
Q

What amino acids contain sulfur?

A

Methionine

Cysteine

148
Q

What are the aliphatic amino acids

A 
Glycine
Alanine
Proline
Valine
Isoleucine
Leucine
Methionine
149
Q

What are the branched chain amino acids?

A

Valine, leucine and Isoleucine

150
Q

What are the essential amino acids

A 
Valine
Histidine
Methionine
Isoleucine
Leucine
Lysine
Phenylalanine 
Theronine
Tryptophan
151
Q

Conditionally essential

A 
Cysteine
Glutamine
Arginine
Glycine
Proline
Tyrosine
152
Q

Explain the difference between essential, nonessential and conditionally essential amino acids

A

Essential amino acids: acquires through the diet (the body cannot sybntheszie them form other precursors)

Nonessential: produced in human metabolism

Conditionally essential: when body is unable to make enough due to illness or stress

153
Q

With an uncharged R group the net charge of the amino acid at pH 1 is _______

A

+1

154
Q

What is the net charge of an uncharged R group at pH 7?

A

0

155
Q

What is the net charge of an uncharged R group at pH13

A

-1

156
Q

What is the net charge of a positively charged R group at pH 1

A

+2

157
Q

What is the net charge of a positively charged R group at pH 7

A

+1

158
Q

What is the net charge of a positively charged R group at pH 13

A

-1

159
Q

What is the net charge of a negatively charged R group at pH 1?

A

+1

160
Q

What is the net charge of a negatively charged R group at pH 7?

A

-1

161
Q

What is the net charge of a negatively charged R group at pH 13?

A

-2

162
Q

Keq has a ______ relationship with delta G. When Keq is greater than 1 delta G is ________. When Keq is less than 1 delta G is _______

A

Inverse

Negative

Positive

163
Q

How do you determine Keq?

A

(Products)/(reactants) = Keq

164
Q

________ is the difference between free energy content of the products and reactants under standard conditions

A

Delta G’o

165
Q

Explain isotonic

A

No net water movement

Ideal environment for cell function.

166
Q

In ______ environments, the concentration of molecules are equal inside and outside the cell

A

Isotonic

167
Q

What is the ionic product of water?

A

1x10^-14

168
Q

In pure water [H+] = [OH-]= _______

A

10^-7

169
Q

pH=pKa + log [A-]/ [HA] is what equation

A

The henderson Hasselbach equation

170
Q

Aggregation of non-polar groups in aquoues soltuion is called the _________________

A

Hydrophobic effect

171
Q

What is the driving force of protein folding, protein protein interactions, formaiton of micelles and hormone receptors and hormone receptor interactions

A

Hydrophobic effect

Biochemistry 1 (4 decks)

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