Phase 1 Flashcards
(200 cards)
1
Q
Nonpolar, aliphatic R groups
A
Glycine Alanine Proline Valine Leucine Isoleucine Methionine
2
Q
Polar, uncharged R groups
A
Serine Threonine Cysteine Asparagine Glutamine
3
Q
Negatively charged R groups
A
Aspartate
Glutamate
4
Q
Positively charged R groups
A
Lysine
Arginine
Histidine
5
Q
Aromatic R groups
A
Phenylalanine
Tyrosine
Tryptophan
6
Q
Glycine
A
Nonpolar, aliphatic R group
Functional group: hydrogen
7
Q
Alanine
A
Nonpolar, aliphatic R group
Functional group: methyl
8
Q
Proline
A
Nonpolar, aliphatic R group
Functional group: three carbon propyl group fused to the nitrogen
*makes it an imine
9
Q
Valine
A
Nonpolar, aliphatic R group
Functional group: isopropyl
10
Q
Leucine
A
Nonpolar, aliphatic R group
Functional group: isobutyl
11
Q
Isoleucine
A
Nonpolar, aliphatic R group
Functional group: sec-butyl
12
Q
Methionine
A
Nonpolar, aliphatic R group
Functional group: thiomethyl
13
Q
Serine
A
Polar, uncharged R group
Functional group: alcohol
14
Q
Threonine
A
Polar, uncharged R group
Functional group: alcohol
15
Q
Cysteine
A
Polar, uncharged R group
Functional group: thiol
16
Q
Asparagine
A
Polar, uncharged R group
Functional group: Amide
17
Q
Glutamine
A
Polar, uncharged R group
Functional group: amide
18
Q
Phenylalanine
A
Aromatic R group
Functional group: phenyl
19
Q
Tyrosine
A
Aromatic R group
Functional group: phenol
20
Q
Tryptophan
A
Aromatic R group
Functional group: ?
21
Q
Lysine
A
Positively charged R group
Functional group: primary amine
22
Q
Arginine
A
Positively charged R groups
Functional group: imine
23
Q
Histidine
A
Positively charged R group
Functional group: imidazole
24
Q
Aspartate
A
Negatively charged R group
Functional group: carboxylic acid
25
Glutamate
Negatively charged R group
| Functional group: Carboxylic acid
26
What is biochemistry?
The study of chemical processes in living organisms
27
What makes the cell and its organelles similar?
They are all surrounded by membranes that share the same basic composition: the phospholipid bilayer
28
What is the nuclear envelope?
Double membrane of 2 phospholipid bilayers
29
Where do the two layers of the nuclear envelope meet?
At nuclear pores
30
What is the outer bilayer continuous with?
The outer bilayer of the nuclear envelope is continuous with the cytoplasmic endoplasmic reticulum
31
What are the characteristics of nuclear pores?
The cytoplasmic face has 8 filaments
| The nuclear face has a complex ring that forms a basket
32
What do nuclear pores allow?
The free diffusion of ions and small molecules while controlling the passage of proteins and RNA protein complexes made in the nucleoli
33
What is chromatin?
Linear chromosomes (DNA is divided into linear chromosomes) combined with proteins
34
What are the dark spots known as nucleoli composed of?
Genes encoding rRNA are clustered with rRNA and proteins
35
What are made in the nucleolus?
Large and small ribosomal subunits
36
What happens once large and small ribosomal subunits are made?
They move through the nuclear pores into the cytoplasm and assemble into ribosomes to make proteins
37
What is the largest internal membrane?
The endoplasmic reticulum
38
What is the inner region of the ER called?
Cisternal space or lumen
39
What is the outer region of the ER called?
The cytosol (the fluid component of the cytoplasm)
40
What is the function of the RER?
Crowded with ribosomes that make proteins for export
41
What happens to the proteins made from the RER?
They are tagged with carbohydrates to make glycoproteins and packaged into vesicles that are moved to the golgi for further modification
42
What does the SER contain?
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
43
Where are the majority of membrane lipids assembled?
The smooth ER
44
What is stored in the SER?
Ca2+, a signaling ion that will therefore keep the cytoplasmic concentration low
45
What does the SER do?
Performs modification of foreign substances for detoxification
46
What is the golgi formed by and what do they do?
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
47
What its the function of the Golgi in plants?
They make the cell wall components
48
What are the sides of the Golgi known as?
The cis side and the trans side
49
How do proteins move through the Golgi?
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
50
What happens to the vesicles the bud off the trans side of the golgi?
They diffuse to other parts of the cell to distribute their contents
51
What are lysosomes?
Organelles formed from vesicles budding off the golgi
52
What do lysosomes contain?
High levels of hydrolytic enzymes that are triggered by low pH and then degrade old organelles, proteins, nucleic acids, lipids, and carbs
53
How are lysosomes activated?
By fusing either with a food vesicle introduced by phagocytosis or a worn out organelle
54
How are hydrolytic enzymes activated?
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
55
What are peroxisomes?
Small organelles classified as micro bodies that bud off the ER and contain a large protein crystal structure and digestive and detoxifying enzymes
56
What are the detoxifying enzymes found in peroxisomes used for?
Oxidation of ferry acids
57
What is the by product that gives peroxisomes their name?
H2O2 (results from activity of the oxidative enzymes)
58
How is excess peroxide destroyed?
By excess catalase that turns it into water and oxygen
59
What are macromolecules?
Proteins, carbs, nucleic acids, and triglycerides that are produced thru a dehydration reaction
60
What do lipids comprise?
Comprise a large number of structures from FAs, TAGs, to steroids and water soluble vitamins (ADEK)
61
What are fatty acids?
Acids with long aliphatic chains of 12 or more carbons
62
Why do saturated and unsaturated FAs have different physical properties?
Differences in packing
63
What are the most common FAs in biological systems?
Cis-unsaturated fatty acids
64
Where are trans-FAs present?
In dairy products
65
Lauric acid
12:0
66
Myristic acid
14:0
67
Palmitic acid
16:0
68
Stearic acid
18:0
69
Arachidic acid
20:0
70
Lignoceric acid
24:0
71
Palmitoleic acid
16:1(𝚫9)
72
Oleic acid
18:1(𝚫9,12)
73
Linoleic acid
18:2(𝚫9,12)
74
alpha linolenic acid
18:3(𝚫9,12,15)
75
Arachidonic acid
20:4(𝚫5,8,11,14)
76
How are esters of fatty acids made?
Reaction of a fatty acid with an alcohol
77
What is a wax?
When a large alcohol (fatty alcohol) reacts with a fatty acid
78
What is the major component of beeswax?
Ester of palmitic acid and a long fatty alcohol
79
What are storage lipids or Tri-Acyl Glycerols (TAGs)
Esters of glycerol with 3 fatty acids
80
Where are store lipids (TAGs) normally stored?
In fat cells or adipocytes or used as a source of energy
81
What are phospholipids?
Molecules of glycerol esterified with 2 FAs and one substituted phosphate
82
What are the most common membrane lipids present in all cells and organelles?
Phospholipids
83
What are the types of storage lipids and how are they composed?
Triacylglycerols. Made with a glycerol backbone and 3 fatty acids
84
What are the type of membrane lipids?
Phospholipids, glycolipids, archaebacterial ether lipids
85
What are the types of phospholipids and what are they composed of?
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
What are the types of glycolipids and what are they composed of?
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
What are plasmalogens?
Phospholipids that replace one ester by an ether linkage
88
What does an ether substitution of an ester give the plasmalogens?
More resistance to hydrolysis by phospholipases
89
Where are plasmalogens present?
In the heart and other critical tissues
90
What are sphingolipids?
Have the amino alcohol sphingosine instead of glycerol
91
What are the main lipid components of nervous tissue?
Sphingolipids
92
What are sphingolipids used for?
Biological recognition such in blood type
93
How many sphingolipids have been identified in cell membranes?
At least 60
94
What are the antigens involved in blood typing?
Glycophospholipids in which sphingosine is attached to sugars of different types
95
What is a peptide bond?
The amide bond formed when a macromolecule is made through dehydration
96
What is the basic structure of alpha amino acids?
A central carbon surrounded by an amino, a carboxy, a hydrogen, and an R group
97
What is the order of latin letters for the position of functional groups and where do they begin?
Begins on the carbon next to the carboxylic acid group. The order it: α, β, γ, δ, ε
98
How do the aromatic amino acids look on a UV absorption spectrum?
Tryptophan is the largest
Tyrosine is the second largest
Phenylalanine is the smallest
99
What happens for cysteine to turn into cystine?
2 cysteines undergo oxidation to form cystine. The oxidation creates a disulfide bond between the two sulfurs upon elimination of the two hydrogens
100
What is a characteristic of aa at the pH of blood (7.4)?
They are zwitterions
101
Do aa behave like acids or bases at the pH of blood (7.4)?
They can behave like acids or bases
102
What are the definitions of acids and bases?
Acids: Proton donors
Bases: Proton acceptors
103
How much of water is ionized?
1 molecule out of 10,000,000
104
What can water act as?
A very weak acid and a very weak base
105
At what pH do most biological reactions take place?
Between pH 6.5 and 8.0
106
What is the physiological pH range?
6.5 to 8.0
107
What is the equilibrium equation for the dissociation of a weak acid?
HA is in equilibrium with A- and H+
108
Equation of Ka?
Ka = [H+][A-]/[HA]
109
Equations of pH and pKa?
pH = -log[H+]
| pKa=-log[Ka]
110
What is the Henderson-Hasselbach Equation?
pH=pKa + log[H+]/[HA]
111
Compare how pH and pKa relate to A- and HA
pH > pKa means [HA] [A-]
112
What is the buffering region?
The area one unit above and one unit below the pKa
113
What are buffers?
Solutions composed of a weak acid (or base) and its conjugate salt
114
How are buffers affected by pH?
Buffers resist pH changed following the addition of acid or base within about +/- 1 unit of pKa
115
What can the Henderson-Hasselbach equation be used for?
Can be used to calculate average charge on an ionizable group at any pH
116
What is the isoelectric point?
The pH at which the average charge on the molecule is zero
117
How does one calculate isoelectric point?
You average two pKas, the pKas from which the charge is +1 and 0
118
What is the primary structure of a polypeptide?
The sequence of amino acids
119
How do you identify the number of pKas of a polypeptide?
By identifying the number of acidic or basic groups present
120
How many isoelectric points (pI) does a polypeptide have?
1
121
How do you identify a peptide bond?
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
What is the secondary structure of a protein?
An alpha helix
123
What is the tertiary structure of a protein?
A polypeptide chain
124
What is the quaternary structure of a protein?
Assembled subunits
125
In what configuration do most peptide bonds occur?
Usually in the trans configuration
126
What are the charges on the oxygen and nitrogen in a peptide bond?
The oxygen has a partial negative and nitrogen has a partial positive, which creates a small dipole
127
What are the dihedral angles present in a peptide bond?
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
How do you know what conformation of the dihedral angles is possible?
Ramachandran plots are used to show the allowed values
129
When are Φ and φ nearly the same?
In a segment of a polypeptide known as a secondary structure
130
What orientations are possible of an alpha helix?
Left handed and right handed; only right handed are observed in proteins
131
Why do alpha helices have an electric dipole?
An electric dipole is transmitted through intrachain H-bonding
132
What amino acid has the greatest tendency to form an alpha helix?
Ala (alanine)
133
Which amino acids have the lowest tendency to form alpha helices?
Gly (glycine) and Pro (proline)
134
What is the β conformation?
When a polypeptide chain extends in a zig zag fashion
135
What arranges into β sheets?
Several segments from the same polypeptide chain can arrange into β sheets
136
What are the two configurations of β sheets?
Antiparallel and parallel
137
What conformation of β sheets are more stable and why?
Antiparallel β sheets are more common because the hydrogen bonds are vertical and not angled
138
What is a β turn?
When globular proteins link α helices and β conformations
139
Where are β turns common?
On antiparallel segments of β sheets
140
What are the two types of β turns and which is more stable?
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
What aa is common in β turns?
Glycine (it's flexible)
| Proline occurs in β turns too because ~6% ca adopt a cis configuration
142
How often are most aa's in the trans configuration?
99.95% of the time
143
What are the two classifications of proteins?
Globular and fibrous
144
What are fibrous proteins?
Fibrous proteins arrange in long strands or sheets
145
What are proteins classified based on?
Folding patterns (repeated motifs)
146
What is a motif?
A folding pattern involving 2+ elements of a secondary structure and their connection
147
What occurs in a β barrel motif?
A large number of segments fold together
148
What is a domain?
A segment that is independent in stability and movement within a protein
149
What occurs in α/β?
The segments alternate regularly
150
What occurs in α+β?
The segments alternate irregularly
151
What occurs in the quaternary structure of proteins?
Several subunits are associated together and can function together or independently
152
Why do some proteins have high densities of charged aa and which as are those?
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
What is the active form of a protein known as?
A native
154
What do misfolded proteins cause?
Prion diseases and other disorders
155
When does denaturation of a protein occur?
By a change of conditions
156
What causes steady denaturation?
Heat with a midpoint called melting
157
When can renaturation occur?
When offending conditions are removed
158
What determines the tertiary structure?
The primary structure
159
What does folding to native conformation follow?
Follows a stepwise process dictated by the individual aa interactions
160
What is an important function of proteins/
The reversible binding of a Ligand
161
What is Myoglobin?
A single polypeptide with 8 helical segments
162
What is Heme in Myoglobin?
A prosthetic group
163
What is O2 in Myoglobin?
The ligand
164
What is the Heme in Myoglobin composed of?
Flat four linked pyrrole rings with a coordinated Fe2+ in the center
165
Where is the Fe2+ ion located in heme?
In the center of the pyrrole rings with two coordination bonds perpendicular to the plane
166
What do the perpendicular coordination bonds in Myoglobin bond to?
One bonds to His (Histidine) residue and the other bonds to the ligand O2
167
What is the bonding of protein P to ligand L?
A type of equilibrium
168
What is the reverse of equilibrium that results from protein P and ligand L?
The dissociation constant, Kd
169
What is θ?
The fraction of ligand-bonding sites occupied by the ligand
170
What does lower Kd imply?
It means stronger binding
171
What has one of the strongest bindings and what is it bound to?
Avidin has one of the strongest bindings to the vitamin biotin
172
What happens when a radical OH mixes with a solution like alcohol?
It creates water and another radical on the O of the reactant you are mixing it with
173
What are the oxidation numbers of an element bonded to another element of its kind?
The oxidation value for that bond is 0
174
What is always the oxidation number of H?
+1
175
What redox occurs when we breathe?
O2 -> H2O. A reduction
176
How do cardiac muscles function?
From fats-ketones because they are always available and it needs to keep pumping
177
How can you identify a dehydration reaction?
One in which water is in the products
178
What do an acid and an alcohol make?
An ester
179
What is more stable? An ester or a thiol ester?
A regular ester
180
Why is a regular ester more stable than a thiol ester?
A regular ester has resonance structures while a thiol ester does not
181
What is more stable, an amide or ester?
An amide is more stable (less reactive) than an ester. An amide has a resonance structure that makes the nitrogen highly unreactive
182
What is lipase?
An enzyme that breaks down lipids
183
What makes Glycine special?
Does not have an asymmetric center
184
What is the largest protein in the body and what percentage of the protein in humans does it make up?
Collagen. Makes up 20-35% of protein in humans
185
Where is collagen present?
Skin and Tendons
186
What are the 3 amino acids that collagen is composed of?
Gly-X-Pro
Gly-HOPro-X
* X is any aa
* HOPro is a hydroxyproline
187
What helps us produce hydroxyproline?
Vitamin C
188
What is the most important function of glycine?
In collagen
189
What is an important function of alanine?
To carry ammonia (NH4+)
190
How is ammonia converted to alanine?
By a keto acid
191
What is unique about proline?
It acts as a hydrogen acceptor only `
192
How is ammonia produced from alanine?
It forms a keto acid and ammonia
193
Where is proline usually present?
At the start of a protein
194
Why is methionine important?
It is an important methylating agent and we need to consume it
195
What breaks down the fragmented proteins that we ingest?
Serine proteases
196
What are the essential aa?
Threonine, methionine, valine, leucine, isoleucine
197
How do reactions occur in an enzyme?
They are anhydrous reactions
198
What is the reaction that occurs in tissues (the reverse occurs in the lungs)?
CO2 + H2O -> HCO3- + H+
199
What keeps Zn2+ grounded inside an enzyme?
His (Histidines)
200
What is the enzyme that converts proteins to amino acids?
Aminotransferase
