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Phase 1 Flashcards

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1
Q

Nonpolar, aliphatic R groups

A 
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine
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2
Q

Polar, uncharged R groups

A 
Serine
Threonine
Cysteine 
Asparagine
Glutamine
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3
Q

Negatively charged R groups

A

Aspartate

Glutamate

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4
Q

Positively charged R groups

A

Lysine
Arginine
Histidine

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5
Q

Aromatic R groups

A

Phenylalanine
Tyrosine
Tryptophan

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6
Q

Glycine

A

Nonpolar, aliphatic R group

Functional group: hydrogen

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7
Q

Alanine

A

Nonpolar, aliphatic R group

Functional group: methyl

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8
Q

Proline

A

Nonpolar, aliphatic R group
Functional group: three carbon propyl group fused to the nitrogen

*makes it an imine

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9
Q

Valine

A

Nonpolar, aliphatic R group

Functional group: isopropyl

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10
Q

Leucine

A

Nonpolar, aliphatic R group

Functional group: isobutyl

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11
Q

Isoleucine

A

Nonpolar, aliphatic R group

Functional group: sec-butyl

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12
Q

Methionine

A

Nonpolar, aliphatic R group

Functional group: thiomethyl

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13
Q

Serine

A

Polar, uncharged R group

Functional group: alcohol

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14
Q

Threonine

A

Polar, uncharged R group

Functional group: alcohol

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15
Q

Cysteine

A

Polar, uncharged R group

Functional group: thiol

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16
Q

Asparagine

A

Polar, uncharged R group

Functional group: Amide

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17
Q

Glutamine

A

Polar, uncharged R group

Functional group: amide

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18
Q

Phenylalanine

A

Aromatic R group

Functional group: phenyl

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19
Q

Tyrosine

A

Aromatic R group

Functional group: phenol

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20
Q

Tryptophan

A

Aromatic R group

Functional group: ?

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21
Q

Lysine

A

Positively charged R group

Functional group: primary amine

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22
Q

Arginine

A

Positively charged R groups

Functional group: imine

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23
Q

Histidine

A

Positively charged R group

Functional group: imidazole

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24
Q

Aspartate

A

Negatively charged R group

Functional group: carboxylic acid

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25
Q

Glutamate

A

Negatively charged R group

Functional group: Carboxylic acid

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26
Q

What is biochemistry?

A

The study of chemical processes in living organisms

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27
Q

What makes the cell and its organelles similar?

A

They are all surrounded by membranes that share the same basic composition: the phospholipid bilayer

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28
Q

What is the nuclear envelope?

A

Double membrane of 2 phospholipid bilayers

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29
Q

Where do the two layers of the nuclear envelope meet?

A

At nuclear pores

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30
Q

What is the outer bilayer continuous with?

A

The outer bilayer of the nuclear envelope is continuous with the cytoplasmic endoplasmic reticulum

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31
Q

What are the characteristics of nuclear pores?

A

The cytoplasmic face has 8 filaments

The nuclear face has a complex ring that forms a basket

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32
Q

What do nuclear pores allow?

A

The free diffusion of ions and small molecules while controlling the passage of proteins and RNA protein complexes made in the nucleoli

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33
Q

What is chromatin?

A

Linear chromosomes (DNA is divided into linear chromosomes) combined with proteins

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34
Q

What are the dark spots known as nucleoli composed of?

A

Genes encoding rRNA are clustered with rRNA and proteins

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35
Q

What are made in the nucleolus?

A

Large and small ribosomal subunits

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36
Q

What happens once large and small ribosomal subunits are made?

A

They move through the nuclear pores into the cytoplasm and assemble into ribosomes to make proteins

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37
Q

What is the largest internal membrane?

A

The endoplasmic reticulum

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38
Q

What is the inner region of the ER called?

A

Cisternal space or lumen

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39
Q

What is the outer region of the ER called?

A

The cytosol (the fluid component of the cytoplasm)

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40
Q

What is the function of the RER?

A

Crowded with ribosomes that make proteins for export

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41
Q

What happens to the proteins made from the RER?

A

They are tagged with carbohydrates to make glycoproteins and packaged into vesicles that are moved to the golgi for further modification

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42
Q

What does the SER contain?

A

No bound ribosomes but contains a network of tubules and flattened sacs with many embedded enzymes involved in the synthesis of a variety of carbs, steroid hormones, and other lipids

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43
Q

Where are the majority of membrane lipids assembled?

A

The smooth ER

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44
Q

What is stored in the SER?

A

Ca2+, a signaling ion that will therefore keep the cytoplasmic concentration low

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45
Q

What does the SER do?

A

Performs modification of foreign substances for detoxification

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46
Q

What is the golgi formed by and what do they do?

A

Stacks of membranes called cisternae that function in the collection, package, and distribution of molecules that are made in one portion of the cell then moved to another part for function

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47
Q

What its the function of the Golgi in plants?

A

They make the cell wall components

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48
Q

What are the sides of the Golgi known as?

A

The cis side and the trans side

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49
Q

How do proteins move through the Golgi?

A

They are received by the cis side of the Golgi, converted to glycoproteins and glycolipids by carbohydrate additions and discharged as vesicles that punch off the trans face

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50
Q

What happens to the vesicles the bud off the trans side of the golgi?

A

They diffuse to other parts of the cell to distribute their contents

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51
Q

What are lysosomes?

A

Organelles formed from vesicles budding off the golgi

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52
Q

What do lysosomes contain?

A

High levels of hydrolytic enzymes that are triggered by low pH and then degrade old organelles, proteins, nucleic acids, lipids, and carbs

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53
Q

How are lysosomes activated?

A

By fusing either with a food vesicle introduced by phagocytosis or a worn out organelle

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54
Q

How are hydrolytic enzymes activated?

A

By a low pH that results from the fusion of lysosomes that activates pumps in the lysosomal membrane that introduce protons which lowers the pH

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55
Q

What are peroxisomes?

A

Small organelles classified as micro bodies that bud off the ER and contain a large protein crystal structure and digestive and detoxifying enzymes

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56
Q

What are the detoxifying enzymes found in peroxisomes used for?

A

Oxidation of ferry acids

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57
Q

What is the by product that gives peroxisomes their name?

A

H2O2 (results from activity of the oxidative enzymes)

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58
Q

How is excess peroxide destroyed?

A

By excess catalase that turns it into water and oxygen

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59
Q

What are macromolecules?

A

Proteins, carbs, nucleic acids, and triglycerides that are produced thru a dehydration reaction

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60
Q

What do lipids comprise?

A

Comprise a large number of structures from FAs, TAGs, to steroids and water soluble vitamins (ADEK)

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61
Q

What are fatty acids?

A

Acids with long aliphatic chains of 12 or more carbons

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62
Q

Why do saturated and unsaturated FAs have different physical properties?

A

Differences in packing

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63
Q

What are the most common FAs in biological systems?

A

Cis-unsaturated fatty acids

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64
Q

Where are trans-FAs present?

A

In dairy products

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65
Q

Lauric acid

A

12:0

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66
Q

Myristic acid

A

14:0

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67
Q

Palmitic acid

A

16:0

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68
Q

Stearic acid

A

18:0

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69
Q

Arachidic acid

A

20:0

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70
Q

Lignoceric acid

A

24:0

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71
Q

Palmitoleic acid

A

16:1(𝚫9)

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72
Q

Oleic acid

A

18:1(𝚫9,12)

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73
Q

Linoleic acid

A

18:2(𝚫9,12)

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74
Q

alpha linolenic acid

A

18:3(𝚫9,12,15)

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75
Q

Arachidonic acid

A

20:4(𝚫5,8,11,14)

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76
Q

How are esters of fatty acids made?

A

Reaction of a fatty acid with an alcohol

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77
Q

What is a wax?

A

When a large alcohol (fatty alcohol) reacts with a fatty acid

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78
Q

What is the major component of beeswax?

A

Ester of palmitic acid and a long fatty alcohol

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79
Q

What are storage lipids or Tri-Acyl Glycerols (TAGs)

A

Esters of glycerol with 3 fatty acids

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80
Q

Where are store lipids (TAGs) normally stored?

A

In fat cells or adipocytes or used as a source of energy

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81
Q

What are phospholipids?

A

Molecules of glycerol esterified with 2 FAs and one substituted phosphate

82
Q

What are the most common membrane lipids present in all cells and organelles?

A

Phospholipids

83
Q

What are the types of storage lipids and how are they composed?

A

Triacylglycerols. Made with a glycerol backbone and 3 fatty acids

84
Q

What are the type of membrane lipids?

A

Phospholipids, glycolipids, archaebacterial ether lipids

85
Q

What are the types of phospholipids and what are they composed of?

A

Glycerophospholipids: A glycerol backbone with 2 fatty acids and a PO4 attached to an alcohol

Sphingolipids: A sphingosine backbone with a fatty acid and a PO4 attached to a choline

86
Q

What are the types of glycolipids and what are they composed of?

A

Glactolipids: A glycerol backbone with 2 fatty acids and a mono / disaccharide attached to SO4

Sphingolipids: A sphingosine backbone with a fatty acid and a mono / oligosaccharide

87
Q

What are plasmalogens?

A

Phospholipids that replace one ester by an ether linkage

88
Q

What does an ether substitution of an ester give the plasmalogens?

A

More resistance to hydrolysis by phospholipases

89
Q

Where are plasmalogens present?

A

In the heart and other critical tissues

90
Q

What are sphingolipids?

A

Have the amino alcohol sphingosine instead of glycerol

91
Q

What are the main lipid components of nervous tissue?

A

Sphingolipids

92
Q

What are sphingolipids used for?

A

Biological recognition such in blood type

93
Q

How many sphingolipids have been identified in cell membranes?

A

At least 60

94
Q

What are the antigens involved in blood typing?

A

Glycophospholipids in which sphingosine is attached to sugars of different types

95
Q

What is a peptide bond?

A

The amide bond formed when a macromolecule is made through dehydration

96
Q

What is the basic structure of alpha amino acids?

A

A central carbon surrounded by an amino, a carboxy, a hydrogen, and an R group

97
Q

What is the order of latin letters for the position of functional groups and where do they begin?

A

Begins on the carbon next to the carboxylic acid group. The order it: α, β, γ, δ, ε

98
Q

How do the aromatic amino acids look on a UV absorption spectrum?

A

Tryptophan is the largest
Tyrosine is the second largest
Phenylalanine is the smallest

99
Q

What happens for cysteine to turn into cystine?

A

2 cysteines undergo oxidation to form cystine. The oxidation creates a disulfide bond between the two sulfurs upon elimination of the two hydrogens

100
Q

What is a characteristic of aa at the pH of blood (7.4)?

A

They are zwitterions

101
Q

Do aa behave like acids or bases at the pH of blood (7.4)?

A

They can behave like acids or bases

102
Q

What are the definitions of acids and bases?

A

Acids: Proton donors
Bases: Proton acceptors

103
Q

How much of water is ionized?

A

1 molecule out of 10,000,000

104
Q

What can water act as?

A

A very weak acid and a very weak base

105
Q

At what pH do most biological reactions take place?

A

Between pH 6.5 and 8.0

106
Q

What is the physiological pH range?

A

6.5 to 8.0

107
Q

What is the equilibrium equation for the dissociation of a weak acid?

A

HA is in equilibrium with A- and H+

108
Q

Equation of Ka?

A

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

109
Q

Equations of pH and pKa?

A

pH = -log[H+]

pKa=-log[Ka]

110
Q

What is the Henderson-Hasselbach Equation?

A

pH=pKa + log[H+]/[HA]

111
Q

Compare how pH and pKa relate to A- and HA

A

pH > pKa means [HA] [A-]

112
Q

What is the buffering region?

A

The area one unit above and one unit below the pKa

113
Q

What are buffers?

A

Solutions composed of a weak acid (or base) and its conjugate salt

114
Q

How are buffers affected by pH?

A

Buffers resist pH changed following the addition of acid or base within about +/- 1 unit of pKa

115
Q

What can the Henderson-Hasselbach equation be used for?

A

Can be used to calculate average charge on an ionizable group at any pH

116
Q

What is the isoelectric point?

A

The pH at which the average charge on the molecule is zero

117
Q

How does one calculate isoelectric point?

A

You average two pKas, the pKas from which the charge is +1 and 0

118
Q

What is the primary structure of a polypeptide?

A

The sequence of amino acids

119
Q

How do you identify the number of pKas of a polypeptide?

A

By identifying the number of acidic or basic groups present

120
Q

How many isoelectric points (pI) does a polypeptide have?

A

1

121
Q

How do you identify a peptide bond?

A

It is made of a carbonyl in which the carbon is attached to an NH. The bond has something connected to the C of the carbonyl and the N of the NH

122
Q

What is the secondary structure of a protein?

A

An alpha helix

123
Q

What is the tertiary structure of a protein?

A

A polypeptide chain

124
Q

What is the quaternary structure of a protein?

A

Assembled subunits

125
Q

In what configuration do most peptide bonds occur?

A

Usually in the trans configuration

126
Q

What are the charges on the oxygen and nitrogen in a peptide bond?

A

The oxygen has a partial negative and nitrogen has a partial positive, which creates a small dipole

127
Q

What are the dihedral angles present in a peptide bond?

A

The bond of N to the C of an amino acid is a bond known as Φ and the bond of the carbonyl C to a C of the amino acid is φ

128
Q

How do you know what conformation of the dihedral angles is possible?

A

Ramachandran plots are used to show the allowed values

129
Q

When are Φ and φ nearly the same?

A

In a segment of a polypeptide known as a secondary structure

130
Q

What orientations are possible of an alpha helix?

A

Left handed and right handed; only right handed are observed in proteins

131
Q

Why do alpha helices have an electric dipole?

A

An electric dipole is transmitted through intrachain H-bonding

132
Q

What amino acid has the greatest tendency to form an alpha helix?

A

Ala (alanine)

133
Q

Which amino acids have the lowest tendency to form alpha helices?

A

Gly (glycine) and Pro (proline)

134
Q

What is the β conformation?

A

When a polypeptide chain extends in a zig zag fashion

135
Q

What arranges into β sheets?

A

Several segments from the same polypeptide chain can arrange into β sheets

136
Q

What are the two configurations of β sheets?

A

Antiparallel and parallel

137
Q

What conformation of β sheets are more stable and why?

A

Antiparallel β sheets are more common because the hydrogen bonds are vertical and not angled

138
Q

What is a β turn?

A

When globular proteins link α helices and β conformations

139
Q

Where are β turns common?

A

On antiparallel segments of β sheets

140
Q

What are the two types of β turns and which is more stable?

A

Type I and Type II. Type I is more stable because the hydrogen bonds are more vertical and not as slanted as type II

141
Q

What aa is common in β turns?

A

Glycine (it’s flexible)

Proline occurs in β turns too because ~6% ca adopt a cis configuration

142
Q

How often are most aa’s in the trans configuration?

A

99.95% of the time

143
Q

What are the two classifications of proteins?

A

Globular and fibrous

144
Q

What are fibrous proteins?

A

Fibrous proteins arrange in long strands or sheets

145
Q

What are proteins classified based on?

A

Folding patterns (repeated motifs)

146
Q

What is a motif?

A

A folding pattern involving 2+ elements of a secondary structure and their connection

147
Q

What occurs in a β barrel motif?

A

A large number of segments fold together

148
Q

What is a domain?

A

A segment that is independent in stability and movement within a protein

149
Q

What occurs in α/β?

A

The segments alternate regularly

150
Q

What occurs in α+β?

A

The segments alternate irregularly

151
Q

What occurs in the quaternary structure of proteins?

A

Several subunits are associated together and can function together or independently

152
Q

Why do some proteins have high densities of charged aa and which as are those?

A

In order to make them intrinsically disordered proteins to help in their function. The charged aa that are present are Lys(lysine), Arg (Arginine), and Glu (Glutamate)

153
Q

What is the active form of a protein known as?

A

A native

154
Q

What do misfolded proteins cause?

A

Prion diseases and other disorders

155
Q

When does denaturation of a protein occur?

A

By a change of conditions

156
Q

What causes steady denaturation?

A

Heat with a midpoint called melting

157
Q

When can renaturation occur?

A

When offending conditions are removed

158
Q

What determines the tertiary structure?

A

The primary structure

159
Q

What does folding to native conformation follow?

A

Follows a stepwise process dictated by the individual aa interactions

160
Q

What is an important function of proteins/

A

The reversible binding of a Ligand

161
Q

What is Myoglobin?

A

A single polypeptide with 8 helical segments

162
Q

What is Heme in Myoglobin?

A

A prosthetic group

163
Q

What is O2 in Myoglobin?

A

The ligand

164
Q

What is the Heme in Myoglobin composed of?

A

Flat four linked pyrrole rings with a coordinated Fe2+ in the center

165
Q

Where is the Fe2+ ion located in heme?

A

In the center of the pyrrole rings with two coordination bonds perpendicular to the plane

166
Q

What do the perpendicular coordination bonds in Myoglobin bond to?

A

One bonds to His (Histidine) residue and the other bonds to the ligand O2

167
Q

What is the bonding of protein P to ligand L?

A

A type of equilibrium

168
Q

What is the reverse of equilibrium that results from protein P and ligand L?

A

The dissociation constant, Kd

169
Q

What is θ?

A

The fraction of ligand-bonding sites occupied by the ligand

170
Q

What does lower Kd imply?

A

It means stronger binding

171
Q

What has one of the strongest bindings and what is it bound to?

A

Avidin has one of the strongest bindings to the vitamin biotin

172
Q

What happens when a radical OH mixes with a solution like alcohol?

A

It creates water and another radical on the O of the reactant you are mixing it with

173
Q

What are the oxidation numbers of an element bonded to another element of its kind?

A

The oxidation value for that bond is 0

174
Q

What is always the oxidation number of H?

A

+1

175
Q

What redox occurs when we breathe?

A

O2 -> H2O. A reduction

176
Q

How do cardiac muscles function?

A

From fats-ketones because they are always available and it needs to keep pumping

177
Q

How can you identify a dehydration reaction?

A

One in which water is in the products

178
Q

What do an acid and an alcohol make?

A

An ester

179
Q

What is more stable? An ester or a thiol ester?

A

A regular ester

180
Q

Why is a regular ester more stable than a thiol ester?

A

A regular ester has resonance structures while a thiol ester does not

181
Q

What is more stable, an amide or ester?

A

An amide is more stable (less reactive) than an ester. An amide has a resonance structure that makes the nitrogen highly unreactive

182
Q

What is lipase?

A

An enzyme that breaks down lipids

183
Q

What makes Glycine special?

A

Does not have an asymmetric center

184
Q

What is the largest protein in the body and what percentage of the protein in humans does it make up?

A

Collagen. Makes up 20-35% of protein in humans

185
Q

Where is collagen present?

A

Skin and Tendons

186
Q

What are the 3 amino acids that collagen is composed of?

A

Gly-X-Pro
Gly-HOPro-X

  • X is any aa
  • HOPro is a hydroxyproline
187
Q

What helps us produce hydroxyproline?

A

Vitamin C

188
Q

What is the most important function of glycine?

A

In collagen

189
Q

What is an important function of alanine?

A

To carry ammonia (NH4+)

190
Q

How is ammonia converted to alanine?

A

By a keto acid

191
Q

What is unique about proline?

A

It acts as a hydrogen acceptor only `

192
Q

How is ammonia produced from alanine?

A

It forms a keto acid and ammonia

193
Q

Where is proline usually present?

A

At the start of a protein

194
Q

Why is methionine important?

A

It is an important methylating agent and we need to consume it

195
Q

What breaks down the fragmented proteins that we ingest?

A

Serine proteases

196
Q

What are the essential aa?

A

Threonine, methionine, valine, leucine, isoleucine

197
Q

How do reactions occur in an enzyme?

A

They are anhydrous reactions

198
Q

What is the reaction that occurs in tissues (the reverse occurs in the lungs)?

A

CO2 + H2O -> HCO3- + H+

199
Q

What keeps Zn2+ grounded inside an enzyme?

A

His (Histidines)

200
Q

What is the enzyme that converts proteins to amino acids?

A

Aminotransferase

Bio 3100 (6 decks)

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