Unit 1 Flashcards
(171 cards)
1
Q
What are the 4 basic biomolecule compounds?
A
Lipids
Proteins
Carbohydrate
Nucleic Acid
2
Q
What are the monomeric units of proteins and nucleic acids?
A
Proteins: amino acids
Nucleic acids: nucleotides
3
Q
What is the parent sugar of most carbohydrates?
A
Glucose
4
Q
What functional group links the membrane mimics and nucleotides?
A
Glycerol
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
6
Q
What are the organic elements?
A
C, H, O, N, P, S
7
Q
Life is ______ based
A
Carbon
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
9
Q
What is a trace element?
A
Essential but do not require them in large amounts. Essential because our body cannot make them.
10
Q
Define nucleoside and nucleotide
A
Phosphate, sugar and base = nucleotide
Sugar and a base = nucleoside
11
Q
Describe purines and give examples
A
Dicyclic, ex: Adenosine, Guanine
12
Q
Describe Pyrimidines and give examples
A
Monocyclic
Ex: Uracil, thymine, cytosine
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.
14
Q
________ predominate at pH values between the pka values of the amino and carboxyl groups
A
Zwitterions
15
Q
When net charge is _______ when Zwitterions are present
A
Zero
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)
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
18
Q
________ binds to another _______ through their R groups to form disulfide bonds
A
Cysteine
Cysteine
19
Q
What amino acids have negatively charged R groups?
A
Aspartate and Glutamate
20
Q
A negative charge indicates the amino acid has donated a _______ at physiologic pH making it _______
A
Proton
Acidic
21
Q
What are the amino acids that contain positively charged (basic) R groups?
A
Lysine (K)
Arginine (R)
Histidine (H)
22
Q
Positive charge indicates the amino acids have _______ a proton at physiologic pH making it _______
A
Accepted
Basic
23
Q
Polar in charged R groups side chains can form _______ bonds
A
Hydrogen bonds
24
Q
What are the amino acids that have polar uncharged R groups
A
Serine
Threonine
Cysteine
Asparagine
Glutamine
25
What amino acids contain sites for phosphorylation?
Serine
Threonine
Tyrosine
26
What amino acids have aromatic R groups?
Phenylalanine
Tyrosine
Tryptophan
27
________ R groups absorb UV light at 270-280nm
Aromatic
28
What amino acids have nonpolar, aliphatic R groups?
```
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine
```
29
Polar uncharged, positively charged and negatively charged and 1 aromatic (tyrosine) are all ________ amino acids
Hydrophilic
30
Phenylalanine and tryptophan (aromatic R groups) and the non polar aliphatic amino acids are all ________ amino acids
Nonpolar, amino acids
31
Amino acids can act as buffers in two pH regimes pointed out via _______ and ______ on the graphs
Pk1 and pK2
32
When have an acidic amino acids, how do you find the isoelectric point?
Take pKr and pK1 and add them together then divide them by 2
33
If have a basic amino acid, how do you calculate the isoelectric point (pI)?
Take the pKR and the pK2 and add them together then divide them by 2.
34
Net charge is ______ when pI=pH
Zero
35
In any other case in finding the pI of an uncharged amino acid, what is the math?
take the pK1 and pKR and divide it by 2
36
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 _________
Hydrophobic
Hydrophilic
37
Cysteine is generally classified as having a ________ R group despite having a positive hydropathy index
Polar
38
What does a small positive or negative index indicate?
That the R is neither very hydrophobic nor very hydrophilic
39
What is the most hydrophobic amino acid, most hydrophilic amino acid?
Most hydrophobic: Isoleucine
Most hydrophilic: Arginine
40
What are the hydrophobic amino acids and their ranking on the hydropathy index
1) isoleucine
2) Valine
3) Leucine
4) Phenylalanine
5) methionine
6) Alanine
41
What is the rank of the most hydrophilic R groups based on the hydropathy index
1) Arginine
2) Lysine
3) asparagine
4) glutamine
5) aspartate
6) Glutamate
7) Histidine
42
How is cysteine classified as having a polar R group despite having a positive hydropathy index?
Because of the ability of the sulhydryl group to act as a weak acid to form a H bond with oxygen or nitrogen
43
What is the smallest amino acid?
Glycine
44
What is the amino acid that is classified as an imino acid?
Proline
45
What are the branched chain amino acids?
Isoleucine
Leucine
Valine
46
What is an example of a branched chain ketogenic amino acid?
Leucine
47
What amino acids contain sulfur?
Cysteine
Methionine
48
What is the largest amino acid?
Tryptophan
49
What amino acid can serve as a biological buffer?
Histidine
50
What amino acid has the lowest pI?
Aspartate
51
Life is ______ based
Carbon
52
What is the definition of a trace element?
Essential elements but are not required in large amounts.
53
```
What are the names of the following funcitonal groups?
R-CH3
R-CHO
R-SH
R1-CO-R2
R-OH
```
```
Methyl
Aldehyde
Sulfhydryl
Ketone
Hydroxyl
```
54
```
What are the names of the following functional groups?
R-COOH
R1-S-S-R1
R1-COO-R2
R1-O-R2
R-O-PO3H
```
```
Carboxylic acid
Disulfide
Ester
Ether
Phosphoryl
```
55
What qualifies as potential energy sources?
Nutrients in environment (complex molecules such as sugar, fats)
Sunlight
56
What qualifies as potential energy sources?
Nutrients in environment (complex molecules such as sugars and fats)
Sunlight
57
How can energy be wasted to surroundings in terms of enthalpy?
Heat is given off during reactions which is known as enthalpy
ATP can break down and heat can be a byproduct
58
Which form of potential energy is commonly generates by cells?
ATP
59
______ is the change in heat or enthalpy where the reaction either gives off heat or absorb heat (endothermic or exothermic)
Heat (enthalpy)
60
______ is equivalent to disorder or randomness. More entropic then the ________ the disorder. Less entropic then _________ disorder of the system
Entropy
Increases
Decreases
61
What is used to make predictions about direction and reaction feasibility?
The change in free energy
62
Why are standard conditions helpful when considering series of reactions?
Used to predict the direction and how far the reaction is from equillibrium
63
If Keq is positive then delta G is ________ and the reaction proceed ___________
Negative
Forward
64
If Keq is negative then the delta G is _______ and the reaction proceeds __________
In reverse
65
What is the delta G of the of a reaction when it reaches equilibrium?
Free energy is zero at equilibrium
66
What is the equation to find standard free energy?
-RT LnKeq
67
Endergonic vs exergonic reactions
Endergonic reactions require external energy
Exergonic reactions do not require external energy
68
What two ways do living organisms use to speed up a reaction and what are the barriers of the other two?
```
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
69
How do enzymes act as catalysts?
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
Metabolic pathways ____________
Signal transduction ______________
Produces energy or useful byproducts
Transmits information
71
What allows the DNA molecule to be more reliable in terms of making copies of code?
The semiconservative method of replication
| The antiparallel strands and replication can occur in both strands. Have coding and noncoding DNA
72
What is the central dogma?
Flow of genetic information from DNA transcribed to RNA translated to protein that perform specific cellular activity
73
Chiral molecules have __________
A chiral center example is _____
Different substituent groups
Carbon as the center with all the substituents being different
74
What are enantiomers?
Mirror images
75
_________ have identical physical properties (except with regard to polarized light) and react identically with achiral molecules
Enantiomers
76
________ is the process of converting genetic information from DNA to RNA
Transcription
77
_______ the process of converting mRNA to proteins
Translation
78
What are the 4 major functions of proteins?
Catalysis
Transport
Structure
Motion
79
What are some of the attributes of amino acids which allow them to perform a variety of biological functions?
Capacity to polymerize
Useful acid base properties
Varied physical properties
Varied chemical functionality
80
What is an alpha amino acid?
Carbon that is bound to the carboxylate group
81
Naming of amino acid begins from the ______ carbon
Alpha
82
Most of the amino acids exist in ______ form
L
83
Amino acids are classified based on their __________
R substituent
84
_________ is a nonpolar hydrophobic sulfur containing amino acid
Methionine
85
________ is an imino acid which adds kinks to the protein structure
Proline
86
______ is an aromatic amino acid which has a hydroxyl group
Tyrosine
87
_________ is a sulfhydryl group containing amino acid
Cysteine
88
______ is the biggest amino acid
Tryptophan
89
______ is the smallest amino acid
Glycine
90
In eukaryotes, this amino acid ___________ initiates protein synthesis
N-formyl-methionine
91
Name the amino acids that can undergo phosphorylation
Tyrosine, threonine and serine
92
Name the most hydrophobic and hydrophilic amino acid based on the hydropathy index
Most hydrophobic- Isoleucine
Most hydrophilic - Arginine
93
What are essential amino acids and what are their names?
Essential amino acids are those required though diet
H, I,L,K,M,F,T,W,V
94
Taurine is a _________ _______ amino acid and is a principle component of ______
Conditionally essential
Bile
95
Name the branched chain amino acids
Isoleucine, leucine and valine
96
Why are branched chain amino acids sold as supplements to boost muscle health?
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
Name the amino acid in beans, grains vegetables and corn
Methionine
98
What are complementary foods?
Complementary foods are sources of the essential amino acids that are not created in the body
99
________ are condensation products of amino acids linked by _____ bond.
Polypeptide
Peptide
100
Long weak bonds that result in unique properties, are important in structure and function of proteins, DNA, etc.
Hydrogen bond
101
H bonds are formed between H and __________ atom that have unshared electrons
Electronegative
102
________ molecules are molecules that contain a hydrophobic and a hydrophilic region
Amphipathic
103
______, oriented in a way to where hydrophobic regions are together and away from water while hydrophilic heads are oriented towards the water
Micelles
104
___________ ______ play an important role in folding of proteins and hormone receptors and ligand binding
Hydrophobic interactions
105
Van der Waals interactions:
- ________ individually
- ________ (occur btwn Andy two atoms that are near each other)
- determines _______ complementarity
- stabilizes _________ ________
- faciliates binding of ______ _______
```
Weak
Universal
Steric
Biological macromolecules
Polarizable ligands
```
106
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
Hypertonic solution
107
In _________ the solute concentration is high externally. Since there is less water outside the water rushes out and the cell shrinks
Hypertonic
108
In a ______ solution, water moves in creating outward pressure resulting in cell _______
Hypotonic solution
Lysis
109
When salt concentraiton is too low outside compared to the inside where does the water go?
The water rushes in and the cells lyse due to the excess water pressure inside the cell
110
_______ is the negative log of the hydrogen ion concentration
The pH
111
In neutral solution, the concentration of H+ and OH- are equal and the pH is ____
7
112
______ is a condition in which too much acid accumulates in the body causing the pH to fall below 7.35
Acidosis
113
______ occurs when too many bases accumulate in the body, this causes the pH to rise above 7.45
Alkalosis
114
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
Proton hopping
115
______ resist changes in pH
Buffers
116
When pH=pKa, the mixture of acid and conjugate base is ______
50:50
117
Buffering capacity of an acid/anion system is greatest at __________
pH=pKa
118
Buffering capacity is lost when ________
The pH differed from pKa by more than 1 pH unit
119
What amino acid can act as a buffer at neutral pH?
Histidine
120
Water is a ______ molecule in which oxygen atom carries a _____ charge and hydrogen atoms have a ______ charge
Dipolar
Negative
Positive
121
Water can serve as both a _________ ______ and _______ _______ due to ______ bonds
Hydrogen acceptor
Hydrogen donor
Hydrogen bonds
122
Hydrogen bonds are shown as three lines that are _______ and ________ than covalent bonds
Longer and weaker
123
The attraction between the partial electric charges are _________ when O-H-O atoms are aligned in a _________ (geometry)
Greatest
Straight
124
Water is a good solvent for ________ and _____ molecules such as ______
Charged and polar
Amino acids and peptides, small alcohols and carbohydrates
125
Water is a poor solvent for _______ molecules such as ______
Nonpolar molecules
Aromatic moieties, aliphatic chains and nonpolar gases
126
What is an example of an amphipathic molecule?
Phosphatidylcholine
127
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
Dielectric constant
Solvated
Increases
128
Van der Waals such interactions have two components __________ and _______
attractive (London Dispersion) and repulsive force (steric repulsion)
129
Why are non polar molecules poorly soluble in water?
Because they are unable to form H-bonds due to their low entropy
130
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
Micelles
Increased
131
The concentration of [H+] in acidic solutions is _____ than neutral and basic solutions
Higher
132
In neutral solutions [H+] is _______ to [OH-]
Equal
133
In basic solutions [H+] is _____ than [OH-]
Lower
134
What is the relationship between strength of an acid or base to its pKa?
The stronger the acid, the smaller its pKa value
The stronger the base, the larger its pKa value
135
When is the buffering capacity of a buffer at its maximum?
Buffering capacity of can acid/anion system is greatest at pH=pka
136
Why can some biomolecules act as buffers?
Because they carry charge and reactive R groups that can act as a proton donor or acceptor and have ionizable groups.
137
Amino acids with ________, __________ R groups can form Hydrogen bonds
Polar uncharged
138
_________ R groups can absorb UV light at 270-280nm
Aromatic
139
A positive charge indicates that the amino acid have ________ a proton at physiology pH. AKA _______
Accepted
Basic
140
Negative charge indicates the amino acid has _______ a proton at physiologic pH. AKA _______
Donated
Acidic
141
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
Secondary amine
Imino
142
_________ bonds are important in stabilizing proteins in nature
Disulfide bonds
143
____________ predominate at pH values between the pKa values of the amino and carboxyl groups
Zwitterions
144
What are the hydrophobic amino acids?
```
Glycine
Alanine
Proline
Valine
Isoleucine
Leucine
Methionine
Phenylalanine
Tryptophan
```
145
What are the hydrophilic amino acids?
```
Cysteine
Arginine
Glutamine
Asparagine
Serine
Threonine
Tyrosine
Glutamate
Aspartate
```
146
What are the basic and acidic amino acids?
Basic: Histidine, Lysine, Arginine
Acidic: Aspartate and glutamate
147
What amino acids contain sulfur?
Methionine
| Cysteine
148
What are the aliphatic amino acids
```
Glycine
Alanine
Proline
Valine
Isoleucine
Leucine
Methionine
```
149
What are the branched chain amino acids?
Valine, leucine and Isoleucine
150
What are the essential amino acids
```
Valine
Histidine
Methionine
Isoleucine
Leucine
Lysine
Phenylalanine
Theronine
Tryptophan
```
151
Conditionally essential
```
Cysteine
Glutamine
Arginine
Glycine
Proline
Tyrosine
```
152
Explain the difference between essential, nonessential and conditionally essential amino acids
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
With an uncharged R group the net charge of the amino acid at pH 1 is _______
+1
154
What is the net charge of an uncharged R group at pH 7?
0
155
What is the net charge of an uncharged R group at pH13
-1
156
What is the net charge of a positively charged R group at pH 1
+2
157
What is the net charge of a positively charged R group at pH 7
+1
158
What is the net charge of a positively charged R group at pH 13
-1
159
What is the net charge of a negatively charged R group at pH 1?
+1
160
What is the net charge of a negatively charged R group at pH 7?
-1
161
What is the net charge of a negatively charged R group at pH 13?
-2
162
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 _______
Inverse
Negative
Positive
163
How do you determine Keq?
(Products)/(reactants) = Keq
164
________ is the difference between free energy content of the products and reactants under standard conditions
Delta G’o
165
Explain isotonic
No net water movement
| Ideal environment for cell function.
166
In ______ environments, the concentration of molecules are equal inside and outside the cell
Isotonic
167
What is the ionic product of water?
1x10^-14
168
In pure water [H+] = [OH-]= _______
10^-7
169
pH=pKa + log [A-]/ [HA] is what equation
The henderson Hasselbach equation
170
Aggregation of non-polar groups in aquoues soltuion is called the _________________
Hydrophobic effect
171
What is the driving force of protein folding, protein protein interactions, formaiton of micelles and hormone receptors and hormone receptor interactions
Hydrophobic effect
