BioChem Exam #1 Flashcards
(149 cards)
1
Q
Carbon Review
A
Forms strong, stable covalent bonds;
Bonds up to 4 other atoms (tetrahedral arrangement);
Single, double, and triple bonds
2
Q
Oxygen Review
A
Very electronegative (pulls electrons); Final electron acceptor during energy production
3
Q
Hydrogen Review
A
H-bonding (very weak but large numbers make them stable);
Electron transport couple with energy production
4
Q
Nitrogen Review
A
Makes up proteins and nucleic acids
5
Q
Phosphorous Review
A
as (PO4)3-;
High energy compounds, nucleic acids, lipids;
Major buffer in systems
6
Q
Sulfur Review
A
Proteins (helps maintain structure and function)
7
Q
Non-Polar Covalent Bonds
A
Equal sharing of electrons (No separation of charge)
8
Q
Polar Covalent Bonds
A
Unequal charing of electrons (Partial charge separation)
9
Q
What causes the separation of charge in Polar Covalent bonds?
A
Differences in electronegativity
10
Q
Ionic Bonds
A
Transfer electrons;
Weak bonds in aqueous solution;
Bond formed in attraction of opposite electrical charges of ions;
Total separation of charges
11
Q
What property allows water to be a major solvent?
A
The fact that is polar;
H’s are partially positive;
O is partially negative
12
Q
Hydrogen bonding
A
Weak dipole-dipole interaction occurring between an electronegative atom and a hydrogen covalently bound to another electronegative atom
13
Q
What are the major physical properties of water?
A
High boiling point (liquid at room temp); High heat of vaporization (required for evaporation and why we sweat); High viscosity (responsible for water going up roots); Low density of ice (reason ice expands and floats)
14
Q
What is meant by “solvent shell”?
A
Area of partial charges that surround an ionic species that allow the attraction to the partial charges in water causing it to dissolve
15
Q
What type of compounds are Hydrophillic (water loving)?
A
Polar and Ionic;
Have separation of charges allowing water to attach to them
16
Q
What type of compounds are Hydrophobic?
A
Non-polar;
Lipids;
No partial charges doesn’t allow them to bind to water, but it becomes oriented around them
17
Q
What are Amphiphilic compounds
A
They are both hydrophobic and hydrophilic;
Hydrophilic (polar) head and hydrophobic (non polar) tail;
Micelles in the body that allow for digestion = a combo of lipids surrounded by H2O with heads towards water and tails toward lipids;
Cell bilayer
18
Q
How do proteins react in aqueous solution?
A
The amino acid side chains will interact;
Water will be on the protein surface interacting with polar and ionic molecules holding them in solution (blood, cells, etc)
19
Q
What is Osmosis?
A
Movement of water across a membrane;
A colligative property of solutions;
Based solely on the number of solutes that are in solution;
20
Q
What is Diffusion?
A
If a substance is able to pass through a semipermeable membrane, its movement will occur spontaneously DOWN its own concentration gradient;
Water is more concentrated on side with fewer solutes;
(HIGH TO LOW)
21
Q
What is the main factor in Osmosis?
A
Movement of H2O molecules depends ONLY on the number of particles dissolved in water – NOT size, charge, etc.
22
Q
Water’s moment…
A
Start with more solute on one side of the lipid bilayer than the other using molecules that cannot cross the membrane;
Water will then move to balance out the concentration
23
Q
What is a HYPOtonic solution?
A
Has fewer things dissolved in it (lower concentration)
24
Q
What is a HYPERtonic solution?
A
Has more things dissolved in it (higher concentration)
25
What is an ISOtonic solution?
Having the same concentration by comparison between two solutions
26
How does water dissociate per acid/base?
H+ and OH-
27
Smaller the pH...
Larger the concentration of [H3O+]
28
What is an acid?
Proton donor;
| MORE H+
29
What is a based?
Proton acceptor;
| Less H+, MORE OH-
30
What makes a Strong Acid?
Strong tendency to donate protons
31
What makes a Weak Acid?
(More naturally occurring in biological systems);
Less tendency to donate protons;
Do not totally dissociate in H2O, so do not have as many H+ to give up
32
What is the relationship between pKa and acidity?
LOWER the pKa;
| STRONGER the acid
33
Stronger acids...
have a HIGHER tendency to ionize which yields MORE products and a HIGHER Ka
34
A larger Ka means....
a LOWER pKa (stronger acid)
35
A smaller Ka means...
a HIGHER pKa (weaker acid)
36
Will a polar or ionic compound pass more readily through a membrane?
Polar;
b/c being Polar is closer to being Non-polar (like dissolves like);
The membrane is Hydrophobic (on polar) so is more accepting of the Polar molecule;
Only a slight separation of charge
37
As pH is lowered... (add protons)
H+ increases
38
As pH is increased... (remove protons)
H+ decreases
39
How does equilibrium shift when the pH is lowered? (add protons)
Shift to the left forming more HA;
| Too many H+ so trying to make more reactants that are not dissociated
40
How does equilibrium shift when the pH is raised? (remove protons)
Shift to the right to break HA apart and gain protons;
| Too few H+ so dissociating the reactant into more products
41
An equilibrium shift of LOWERING pH results in...
HA predominating
42
At a LOWER pH (more HA)
pK is GREATER than pH
43
An equilibrium shift of INCREASING pH results in...
A- predominating
44
At a HIGHER pH (more A-)
pH is GREATER than pK
45
What are Buffers?
A chemical system that tends to resist changes in pH when a moderate amount of acid or base is added;
Maintains the hydronium ion concentration relatively constant;
Adds or removes H+ when needed
46
What are the criteria for a good buffer system?
Concentration sufficiently large to compensate for amount of acid/base added (need enough buffer);
pKa near the desired pH (with +/- 1 pH unit, being in the middle allows maintenance of ~ the same pH)
47
When is a species totally protonated?
100% HA;
| When no equivalents of OH- have been titrated
48
When does the pH=pKa?
When the [HA]=[A-];
| Half an equivalence point
49
When is a species totally deprotonated?
100% A-
50
What is the Henderson-Hasselbalch equation?
Ka={H+][A-]/[HA]
51
pH equation
pKa + log[A-]/[HA]
52
pKa equation
-log_10(Ka)
53
What is the pKa?
Strength of the acid (lower pKa, stronger acid)
54
When pH=pKa?
the acid is 50% ionized;
| Weak acid is the best at buffering (buffer needs to be +/- 1 unit)
55
Why is the buffering capacity of the blood important?
Normal blood pH=7.4;
Lower (6.8) = acidosis = death;
Higher (7.8) = alkalosis = death
56
What are the 4 main buffer systems of the body?
**H2CO3/HCO3-;
H2PO4-/HPO42-;
Plasma protein system;
Hemoglobin (RBCs) = lots of amino acids can be weak acids/bases
57
Main buffer = H2CO3/HCO3-. Where do the components come from?
CO2 gas in the lungs;
Becomes to CO2 dissolved in the blood plasma;
CO2 (RBC's) combines with H2O yielding H2CO3 (carbonic anhydrase);
H2CO3 becomes dissolved in the blood plasma;
Then dissociates into H+ and HCO3-
58
Why is this our main buffer?
Because we have access to so much of it (we can make it), that the high concentration makes up for the pH and pKa difference;
Blood pH = 7.4;
H2CO3 pKa = 6.4
59
Overall equilibrium for carbonic anhydrase buffer
H20 + CO2 H2CO3 H+ + HCO3-
60
What is required for protonation of a molecule?
pK must be larger than the pH
61
What physiological problems cause changes in [HCO3-] that affect blood buffering?
Metabolic effects from metabolic processes
62
What happens when [HCO3-] is DECREASED?
pH DROPS;
Directly by diarrhea (fluid loss);
Indirectly by raising the H+ conc. with diabetes, lactic acid, and aspirin
63
What happens when [HCO3-] is INCREASED?
pH INCREASES;
| Indirectly by lowering [H+] by vomiting, excess alkali administration
64
What physiological problems cause changes in [H2CO3] that affect blood buffering?
Respiratory effects
65
What happens when [H2CO3] is INCREASED?
pH DROPS:
H2O + CO2 H2CO3;
Decreased removal of CO2;
Emphysema and pneumonia
66
What happens when [H2CO3] is DECREASED?
pH INCREASES;
Increased removal of CO2;
Hyperventilation, high altitudes
67
What are Amino acids?
Basic structural unit of proteins
68
What is an amino acid composed of?
```
Alpha Carbon with:
Carboxyl gorup;
Amino group;
Hydrogen atom;
R-side chain
```
69
The alpha carbon of amino acids is...
Chiral;
4 different things attached;
EXCEPT Glycine (H-side chian)
70
What are Enantiomers?
Nonsuperimposible mirror images (like our hands)
71
What makes amino acids different from one another and gives them their properties?
The variability of the R-groups
72
What is the pK range for -COOH?
1.5-3
73
What is the pK range for -NH3+?
9-11
74
Why can pK have a range if it is technically a constant?
Because it also depends on the whole structure, including the various side chains
75
For every pK value of an amino acid...
a dissociation will take place when titrated
76
What is the pI( Isoelectric point)?
the pH where there is NO net charge on the amino acid
77
How do you determine the pI value?
Average of the 2 pK values on both sides of the structure with NO net charge (at 1 equivalence point)
78
What are the Roles of Amino Acids?
Chemical messengers (Neurotransmitters, and hormones);
N-containing precursors;
Metabolic breakdown;
Specialized protein functions (Ser, Thr);
Protein synthesis
79
What proteins act as neurotransmitters?
```
Gly - inhibitory;
Glu - excitatory;
His - histamine;
Trp - serotonin;
Phe - Tyr - L-Dopa - dopamine - norepinephrine - epinephrine
```
80
What protein can be a hormone?
Tyr - Thyroxine
81
What are the N-containing precursors?
Heme, nucleotides, chlorophyll
82
An example of metabolic breakdown?
Arg - Urea
83
How are Amino Acids linked?
With a condensation reaction;
Covalent bond between the alpha-carboxyl and alpha-amino of neighboring amino acids;
Water is eliminated and peptide bond is formed
84
Stereochemistry of a peptide bond
Partial double bond character due to resonance causes the bond to be planar and stronger than normal;
Free rotation around the alpha-carbon, but no rotation at the peptide bond
85
Number of Amino Acids Linked Together in a Polypeptide
```
Dipeptide = 2
Tripeptide = 3;
Quatrapeptide = 4
Pentapeptide = 5;
Oligopeptide = < 10;
Polypeptide = < 50;
Protein = > 50
```
86
What are some biological roles of oligopeptides?
Enkephalins (endorphins);
Hormones;
Antibiotics (D-amino acids, circular amino acids);
Immunosuppressants (Cyclosporin; Fighting autoimmune diseases);
Amanatin (mushrooms)
87
Why is Amino Acid structure so important?
Structure determines all function!!
88
What is a Conservative change of an amino acid?
The amino acids that are changed are similar in nature and properties meaning that subsequent variation isn't that great
89
What is a Non-Conservatinve change of an amino acid
There is a big difference in the properties of the varying amino acids resulting in major alterations to the amino acid sequence and subsequent function
90
Why is the Order of the Amino acids so important?
The order of the amino acids (primary structure) is determines all other structure and function as the amino acids link to form polypeptides and as they link to from proteins;
Changing the order changes the structure which changes the function;
Ex: Changing the order of the AA's that make Aspartame changes the taste from sweet to bitter
91
What happens when Glutamine and Valine are switched in Hemoglobin at Beta 6?
A non-conservative change takes place;
Glu - neg. and hydrophilic;
Val - nonpolar, hydrophobic;
Causes Sickle Cell Anemia
92
What is Primary Protein structure?
Sequence of amino acids (type and order);
| Peptide bonds between the amino acids
93
Characteristics of the Peptide bonds
Shorter and stronger than normal;
Planar;
Extent of rotation is limited by the planar nature and the size of the R-groups with respect to one another
94
What is Secondary Protein structure?
Spatial relationships of the neighboring AA's;
Involves interactions between atoms of the backbone (NO R-groups);
Alpha-helix held together with H-bonding (Bends at every 4 amino acids);
Beta pleated sheet
95
How does Proline affect the secondary structure when found within a chain?
No H-bonding can occur because of the missing H on the alpha-amino group (only NH2+);
The helix will be broken at proline, but may resume afterwards
96
What is SuperSecondary Protein Structure?
Varied types of Secondary that occur in patters or Motifs;
| Can be repeating combos or protein specific orientation
97
What are the SuperSecondary Repeating Combos?
```
Beta-alpha-Beta;
Beta barrels;
Greek key;
Antiparallel alpha-helix;
These tell nothing about function of a protein because they are found in varying types of proteins
```
98
When is SuperSecondary Structure Protein Specific?
Does depict function;
Collagen triple helix;
3 chains wrapped around each other;
Mostly Proline, Hydroxyproline and Glycine;
The small nature of Glycine allows it to be wound very tight and make it strong
99
What is Tropocollagen?
3 collagen chains (full helices) twisted together to for a stiff rod;
Held together by H-bonding;
Like a Twizzler
100
What is Random Secondary Protein Structure?
No pattern at all;
| Non-repeating but consistent from one copy to another
101
What are Fibrous Proteins?
Generally all one type of secondary structure;
Appear as long, uniform rods with very organized structure;
All alpha-helix (alpha-keratin);
All beta-pleated sheet (fibroin);
Triple helix (collagen)
102
What are Globular Proteins?
Mixture of secondary structures;
Typically water-soluble and not uniform or spherical, but a compact mass;
Hydrophilic AA's on the outside (polar/positive/negative);
Hydrophobic AA's on the inside (non-polar aliphatic/aromatic)
103
What is Tertiary Protein structure?
3-D folding of the protein in solution, stabilized by the R-GROUPS!;
Only found in globular proteins;
Confirmation of side-chains and position of any prosthetic groups, and arrangement of the helix/sheet sections
104
What types of bonding interactions involving R-groups create tertiary structure?
```
H-bonding between R-groups;
Electrostatic interactions;
Hydrophobic interactions;
Interaction with polar aqueous environment;
Coordination with metal ions;
Disulfide bonds between Cys-Cys
```
105
H-bonding between R-groups
Between one partially charged H and an electronegative atom on another R-group
106
Electrostatic Interactions of Charged Groups
Between oppositely charged groups;
| Typically on the surface of the molecule
107
Hydrophobic Interactions
Nonpolar residues cluster together away from water in the interior of the protein
108
Interactions with the Polar Aqueous Environment
Polar groups become soluble in water allowing the protein to be dispersed within the fluid
109
Coordination of R-groups with Metal Ions
Help maintain function like Fe/Mg;
Metals are prosthetic groups;
Several side chains can be complexed in to a single metal ion
110
Disulfide Bonds Between Cys-Cys (only covalent bond)
Forms bridges between the 2 Sulfur molecules;
| "Complex Covalent Structure" = primary structure and location of the disulfide bonds
111
What is Quaternary Protein Structure?
Association of 2 or more individual polypeptide chains;
Interact electrostatically, H-bonding, and hydrophically;
Subunits may be the same (like Hb) or different (catalytic/regulatory proteins);
Stabilized by the same types of bonding interactions as tertiary structure
112
What happens when a protein is Allosteric?
A change in one subunit (polypeptide chain) causes subsequent change in another subunit;
Hemoglobin
113
What is Native Confirmation?
The sum of all levels of protein structure;
The bioactive form of a protein that is needed for it to work (Structure = Function);
Some degree of flexibility;
Misfolding causes loss of function
114
What is Denaturation?
Loss of native structure;
Loss of structure and function;
*Non-covalent interactions are very weak and easily broken
115
Can refolding of a protein occur?
Sometimes;
| All depends upon the conditions, the primary structure, and the extent to which it was unfolded
116
What causes Denaturing of a Protein?
```
Heat;
Strong Acids/Bases (changing pH);
Organic Solvents;
Concentrated Salt Solutions;
Detergents;
Reducing agents;
Urea;
Mechanical stress
```
117
How does Heat denature?
Messes up H-bonding;
| Increase in temp causes vibrations throughout the protein and energy can break tertiary binding of R-groups
118
How do Strong Acids/Bases denature?
Change the charge on the protein R-groups which can mess up interactions;
Electrostatic (charged groups);
At very high/low pH's some of the stabilizing charges are missing which limits the interactions and breaking bonds
119
How do Organic Solvents denature?
They disrupt hydrophobic interactions;
| Hydrophobic AA's are soluble in organic solvents therefore binding to that environment and not each other
120
How do Concentrated Salt Solutions denature?
They compete with water than may be bound to the protein or holding the protein in solution
121
How do Detergents denature?
Bind or break hydrophobic interactions;
If charged they can also break electrostatic interactions between charged R-groups;
Have a Hydrophilic (polar) head and a hydrophobic (non-polar) tails
122
How do Reducing Agents denature?
Reverse (add H+) and break disulfide bonds;
Urea can be used to make the bonds unfold and more accessible to the RA;
Native confirmation can typically be restore if urea and RA removed
123
How does Urea denature?
Polar groups on Urea break/interrupt H-bonds and attach to the proteins;
Forms stronger H-bonds than those already in the protein R-groups;
Can also disrupt hydrophilic
124
How does Mechanical Stress denature?
Enough disturbance in solution just breaks the weak covalent bonds down;
Typically only in the lab
125
What is the function of Hemoglobin?
Transport of O2 from the lungs to tissues
126
What is Hb composed of?
Tetramer = 4 subunits (2 alpha and 2 beta);
1 heme per subunit;
Iron
127
What is the Heme structure?
Non-polar (has some bonds throughout tho);
| Planar (coordinated double bonds)
128
What effect does O2 have on the binding of Hb?
Without O2 bound, iron cannot totally bind to the heme;
WIth O2 the atomic radius of the iron shrinks allowing it to totally bind to the Heme;
This binding pulls the His chain and changes the entire structure of Hb
129
What is the Oxygen binding curve for Myoglobin?
Hyperbolic (rises quickly then levels off)
130
What is the Oxygen binding curve for Hemoglobin?
Sigmoidal (S-shaped);
Shows cooperative interaction (positive cooperatively);
Binding of the first O2 facilitates the binding of the next and so on
131
How do the binding curves of Mb and Hb compare?
Hb's binding curve is still LOWER than Mb at any pressure of oxygen;
At any pressure of oxygen, Mb will have a higher percentage of saturation than Hb
132
Saturation of Mb and Hb
Mb - 50% saturated at 1 torr pp.;
| Hb - 50% saturated at 26 torr pp. (Muscles are ~20 torr)
133
What binds to Hb and affect the ability of O2 to bind by altering the 3-D structure?
Both H+ and CO2
134
What is the Bohr Effect?
The relative effect of H+ on O2 binding to Hb;
INCREASE in H+ (lower pH) reduces the affinity for O2;
DECREASE in H+ (higher pH) increases the affinity for O2
135
Why does INCREASING pH reduce the affinity for O2 to bind Hb?
Causes the protonation of key amino acids, including the N-terminals and the alpha-chains and His146 of beta-chains;
Protonated His is attracted to and stabilized by salt bridges with Asp94;
*Favors DEOXYGENATED Hb at tissues
136
What happens in the muscles?
Release of O2 from Hb and binds H+ and CO2;
Low pressure, Low pH, high conc. of H+ = Lose O2;
<50% saturation
137
What happens in the Lungs?
Binding O2 to Hb, release of H+ and CO2;
| High pressure, High pH, low conc. of H+ = Lose H+ and CO2
138
What is required for Cooperativity?
Ligans;
| Subunits (Quaternary structure)
139
Why doesn't Mb exhibit coopertativity?
Because it is a single subunit and does NOT have quaternary structure;
Therefore it has no R-groups to allow for interactions cooperative binding
140
What happens in a RIGHTWARD shift of O2 binding to Hb?
Less O2 is bound;
More O2 is released to tissues;
Less affinity for Hb to bind the O2 and therefore releases more than normal
141
What causes a RIGHTWARD shift of O2 binding (higher release)?
Deceased tissue pH;
Increased temp;
Increased CO2 conc.;
Increased BPG
142
When is the INCREASED RELEASE of O2 needed (Rightward shift)?
```
Exercise;
Increased Lactic Acid;
INcreased heat released from the body;
Increased CO2 build up;
Increased BPG
```
143
Why does Hb maintain ~50% saturation in the tissues?
That way it is a supply when the tissues need a sudden supply of O2 such as during immediate hyperactivity and increased respiration
144
What does CO2 bind to when O2 is released from Hb (less binding affinity of O2 to Hb)?
The terminal NH3+ group
145
What does H+ bind to when O2 is released from Hb (less binding affinity from O2 to Hb)?
Binds to His
146
How does BPG affect the binding of O2 to Hb?
More BPG causes the release of O2 in the tissues
147
What happens in a LEFTWARD shift of O2 binding to Hb?
O2 is bound more readily and not released
148
What makes Fetal Hb bind O2 more readily than maternal Hb?
The presence of the Gamma subunit (instead of Beta);
| Fetal has a higher affinity to bind the O2
149
Why does the Fetus need to bind O2 more readily?
To cause the passage of the O2 from the mother to the fetus;
| If fetal Hb and maternal Hb were the same, then none would be passed from the mother to the baby
