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Fall 2013 > BioChem Exam #1 > Flashcards

BioChem Exam #1 Flashcards

1
Q

Carbon Review

A

Forms strong, stable covalent bonds;
Bonds up to 4 other atoms (tetrahedral arrangement);
Single, double, and triple bonds

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2
Q

Oxygen Review

A 
Very electronegative (pulls electrons);
Final electron acceptor during energy production
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3
Q

Hydrogen Review

A

H-bonding (very weak but large numbers make them stable);

Electron transport couple with energy production

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4
Q

Nitrogen Review

A

Makes up proteins and nucleic acids

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5
Q

Phosphorous Review

A

as (PO4)3-;
High energy compounds, nucleic acids, lipids;
Major buffer in systems

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6
Q

Sulfur Review

A

Proteins (helps maintain structure and function)

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7
Q

Non-Polar Covalent Bonds

A

Equal sharing of electrons (No separation of charge)

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8
Q

Polar Covalent Bonds

A

Unequal charing of electrons (Partial charge separation)

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9
Q

What causes the separation of charge in Polar Covalent bonds?

A

Differences in electronegativity

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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

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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

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12
Q

Hydrogen bonding

A

Weak dipole-dipole interaction occurring between an electronegative atom and a hydrogen covalently bound to another electronegative atom

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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)
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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

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15
Q

What type of compounds are Hydrophillic (water loving)?

A

Polar and Ionic;

Have separation of charges allowing water to attach to them

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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

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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

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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)

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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;

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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)

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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.

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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

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23
Q

What is a HYPOtonic solution?

A

Has fewer things dissolved in it (lower concentration)

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24
Q

What is a HYPERtonic solution?

A

Has more things dissolved in it (higher concentration)

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25
Q

What is an ISOtonic solution?

A

Having the same concentration by comparison between two solutions

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26
Q

How does water dissociate per acid/base?

A

H+ and OH-

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27
Q

Smaller the pH…

A

Larger the concentration of [H3O+]

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28
Q

What is an acid?

A

Proton donor;

MORE H+

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29
Q

What is a based?

A

Proton acceptor;

Less H+, MORE OH-

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30
Q

What makes a Strong Acid?

A

Strong tendency to donate protons

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31
Q

What makes a Weak Acid?

A

(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

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32
Q

What is the relationship between pKa and acidity?

A

LOWER the pKa;

STRONGER the acid

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33
Q

Stronger acids…

A

have a HIGHER tendency to ionize which yields MORE products and a HIGHER Ka

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34
Q

A larger Ka means….

A

a LOWER pKa (stronger acid)

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35
Q

A smaller Ka means…

A

a HIGHER pKa (weaker acid)

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36
Q

Will a polar or ionic compound pass more readily through a membrane?

A

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

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37
Q

As pH is lowered… (add protons)

A

H+ increases

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38
Q

As pH is increased… (remove protons)

A

H+ decreases

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39
Q

How does equilibrium shift when the pH is lowered? (add protons)

A

Shift to the left forming more HA;

Too many H+ so trying to make more reactants that are not dissociated

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40
Q

How does equilibrium shift when the pH is raised? (remove protons)

A

Shift to the right to break HA apart and gain protons;

Too few H+ so dissociating the reactant into more products

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41
Q

An equilibrium shift of LOWERING pH results in…

A

HA predominating

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42
Q

At a LOWER pH (more HA)

A

pK is GREATER than pH

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43
Q

An equilibrium shift of INCREASING pH results in…

A

A- predominating

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44
Q

At a HIGHER pH (more A-)

A

pH is GREATER than pK

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45
Q

What are Buffers?

A

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

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46
Q

What are the criteria for a good buffer system?

A

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)

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47
Q

When is a species totally protonated?

A

100% HA;

When no equivalents of OH- have been titrated

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48
Q

When does the pH=pKa?

A

When the [HA]=[A-];

Half an equivalence point

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49
Q

When is a species totally deprotonated?

A

100% A-

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50
Q

What is the Henderson-Hasselbalch equation?

A

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

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51
Q

pH equation

A

pKa + log[A-]/[HA]

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52
Q

pKa equation

A

-log_10(Ka)

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53
Q

What is the pKa?

A

Strength of the acid (lower pKa, stronger acid)

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54
Q

When pH=pKa?

A

the acid is 50% ionized;

Weak acid is the best at buffering (buffer needs to be +/- 1 unit)

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55
Q

Why is the buffering capacity of the blood important?

A

Normal blood pH=7.4;
Lower (6.8) = acidosis = death;
Higher (7.8) = alkalosis = death

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56
Q

What are the 4 main buffer systems of the body?

A

**H2CO3/HCO3-;
H2PO4-/HPO42-;
Plasma protein system;
Hemoglobin (RBCs) = lots of amino acids can be weak acids/bases

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57
Q

Main buffer = H2CO3/HCO3-. Where do the components come from?

A

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-

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58
Q

Why is this our main buffer?

A

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

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59
Q

Overall equilibrium for carbonic anhydrase buffer

A

H20 + CO2 H2CO3 H+ + HCO3-

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60
Q

What is required for protonation of a molecule?

A

pK must be larger than the pH

61
Q

What physiological problems cause changes in [HCO3-] that affect blood buffering?

A

Metabolic effects from metabolic processes

62
Q

What happens when [HCO3-] is DECREASED?

A

pH DROPS;
Directly by diarrhea (fluid loss);
Indirectly by raising the H+ conc. with diabetes, lactic acid, and aspirin

63
Q

What happens when [HCO3-] is INCREASED?

A

pH INCREASES;

Indirectly by lowering [H+] by vomiting, excess alkali administration

64
Q

What physiological problems cause changes in [H2CO3] that affect blood buffering?

A

Respiratory effects

65
Q

What happens when [H2CO3] is INCREASED?

A

pH DROPS:
H2O + CO2 H2CO3;
Decreased removal of CO2;
Emphysema and pneumonia

66
Q

What happens when [H2CO3] is DECREASED?

A

pH INCREASES;
Increased removal of CO2;
Hyperventilation, high altitudes

67
Q

What are Amino acids?

A

Basic structural unit of proteins

68
Q

What is an amino acid composed of?

A 
Alpha Carbon with:
Carboxyl gorup;
Amino group;
Hydrogen atom;
R-side chain
69
Q

The alpha carbon of amino acids is…

A

Chiral;
4 different things attached;
EXCEPT Glycine (H-side chian)

70
Q

What are Enantiomers?

A

Nonsuperimposible mirror images (like our hands)

71
Q

What makes amino acids different from one another and gives them their properties?

A

The variability of the R-groups

72
Q

What is the pK range for -COOH?

A

1.5-3

73
Q

What is the pK range for -NH3+?

A

9-11

74
Q

Why can pK have a range if it is technically a constant?

A

Because it also depends on the whole structure, including the various side chains

75
Q

For every pK value of an amino acid…

A

a dissociation will take place when titrated

76
Q

What is the pI( Isoelectric point)?

A

the pH where there is NO net charge on the amino acid

77
Q

How do you determine the pI value?

A

Average of the 2 pK values on both sides of the structure with NO net charge (at 1 equivalence point)

78
Q

What are the Roles of Amino Acids?

A

Chemical messengers (Neurotransmitters, and hormones);
N-containing precursors;
Metabolic breakdown;
Specialized protein functions (Ser, Thr);
Protein synthesis

79
Q

What proteins act as neurotransmitters?

A 
Gly - inhibitory;
Glu - excitatory;
His - histamine;
Trp - serotonin;
Phe - Tyr - L-Dopa - dopamine - norepinephrine - epinephrine
80
Q

What protein can be a hormone?

A

Tyr - Thyroxine

81
Q

What are the N-containing precursors?

A

Heme, nucleotides, chlorophyll

82
Q

An example of metabolic breakdown?

A

Arg - Urea

83
Q

How are Amino Acids linked?

A

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
Q

Stereochemistry of a peptide bond

A

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
Q

Number of Amino Acids Linked Together in a Polypeptide

A 
Dipeptide = 2
Tripeptide = 3;
Quatrapeptide = 4
Pentapeptide = 5;
Oligopeptide = < 10;
Polypeptide = < 50;
Protein = > 50
86
Q

What are some biological roles of oligopeptides?

A

Enkephalins (endorphins);
Hormones;
Antibiotics (D-amino acids, circular amino acids);
Immunosuppressants (Cyclosporin; Fighting autoimmune diseases);
Amanatin (mushrooms)

87
Q

Why is Amino Acid structure so important?

A

Structure determines all function!!

88
Q

What is a Conservative change of an amino acid?

A

The amino acids that are changed are similar in nature and properties meaning that subsequent variation isn’t that great

89
Q

What is a Non-Conservatinve change of an amino acid

A

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
Q

Why is the Order of the Amino acids so important?

A

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
Q

What happens when Glutamine and Valine are switched in Hemoglobin at Beta 6?

A

A non-conservative change takes place;
Glu - neg. and hydrophilic;
Val - nonpolar, hydrophobic;
Causes Sickle Cell Anemia

92
Q

What is Primary Protein structure?

A

Sequence of amino acids (type and order);

Peptide bonds between the amino acids

93
Q

Characteristics of the Peptide bonds

A

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
Q

What is Secondary Protein structure?

A

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
Q

How does Proline affect the secondary structure when found within a chain?

A

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
Q

What is SuperSecondary Protein Structure?

A

Varied types of Secondary that occur in patters or Motifs;

Can be repeating combos or protein specific orientation

97
Q

What are the SuperSecondary Repeating Combos?

A 
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
Q

When is SuperSecondary Structure Protein Specific?

A

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
Q

What is Tropocollagen?

A

3 collagen chains (full helices) twisted together to for a stiff rod;
Held together by H-bonding;
Like a Twizzler

100
Q

What is Random Secondary Protein Structure?

A

No pattern at all;

Non-repeating but consistent from one copy to another

101
Q

What are Fibrous Proteins?

A

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
Q

What are Globular Proteins?

A

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
Q

What is Tertiary Protein structure?

A

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
Q

What types of bonding interactions involving R-groups create tertiary structure?

A 
H-bonding between R-groups;
Electrostatic interactions;
Hydrophobic interactions;
Interaction with polar aqueous environment;
Coordination with metal ions;
Disulfide bonds between Cys-Cys
105
Q

H-bonding between R-groups

A

Between one partially charged H and an electronegative atom on another R-group

106
Q

Electrostatic Interactions of Charged Groups

A

Between oppositely charged groups;

Typically on the surface of the molecule

107
Q

Hydrophobic Interactions

A

Nonpolar residues cluster together away from water in the interior of the protein

108
Q

Interactions with the Polar Aqueous Environment

A

Polar groups become soluble in water allowing the protein to be dispersed within the fluid

109
Q

Coordination of R-groups with Metal Ions

A

Help maintain function like Fe/Mg;
Metals are prosthetic groups;
Several side chains can be complexed in to a single metal ion

110
Q

Disulfide Bonds Between Cys-Cys (only covalent bond)

A

Forms bridges between the 2 Sulfur molecules;

“Complex Covalent Structure” = primary structure and location of the disulfide bonds

111
Q

What is Quaternary Protein Structure?

A

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
Q

What happens when a protein is Allosteric?

A

A change in one subunit (polypeptide chain) causes subsequent change in another subunit;
Hemoglobin

113
Q

What is Native Confirmation?

A

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
Q

What is Denaturation?

A

Loss of native structure;
Loss of structure and function;
*Non-covalent interactions are very weak and easily broken

115
Q

Can refolding of a protein occur?

A

Sometimes;

All depends upon the conditions, the primary structure, and the extent to which it was unfolded

116
Q

What causes Denaturing of a Protein?

A 
Heat;
Strong Acids/Bases (changing pH);
Organic Solvents;
Concentrated Salt Solutions;
Detergents;
Reducing agents;
Urea;
Mechanical stress
117
Q

How does Heat denature?

A

Messes up H-bonding;

Increase in temp causes vibrations throughout the protein and energy can break tertiary binding of R-groups

118
Q

How do Strong Acids/Bases denature?

A

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
Q

How do Organic Solvents denature?

A

They disrupt hydrophobic interactions;

Hydrophobic AA’s are soluble in organic solvents therefore binding to that environment and not each other

120
Q

How do Concentrated Salt Solutions denature?

A

They compete with water than may be bound to the protein or holding the protein in solution

121
Q

How do Detergents denature?

A

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
Q

How do Reducing Agents denature?

A

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
Q

How does Urea denature?

A

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
Q

How does Mechanical Stress denature?

A

Enough disturbance in solution just breaks the weak covalent bonds down;
Typically only in the lab

125
Q

What is the function of Hemoglobin?

A

Transport of O2 from the lungs to tissues

126
Q

What is Hb composed of?

A

Tetramer = 4 subunits (2 alpha and 2 beta);
1 heme per subunit;
Iron

127
Q

What is the Heme structure?

A

Non-polar (has some bonds throughout tho);

Planar (coordinated double bonds)

128
Q

What effect does O2 have on the binding of Hb?

A

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
Q

What is the Oxygen binding curve for Myoglobin?

A

Hyperbolic (rises quickly then levels off)

130
Q

What is the Oxygen binding curve for Hemoglobin?

A

Sigmoidal (S-shaped);
Shows cooperative interaction (positive cooperatively);
Binding of the first O2 facilitates the binding of the next and so on

131
Q

How do the binding curves of Mb and Hb compare?

A

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
Q

Saturation of Mb and Hb

A

Mb - 50% saturated at 1 torr pp.;

Hb - 50% saturated at 26 torr pp. (Muscles are ~20 torr)

133
Q

What binds to Hb and affect the ability of O2 to bind by altering the 3-D structure?

A

Both H+ and CO2

134
Q

What is the Bohr Effect?

A

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
Q

Why does INCREASING pH reduce the affinity for O2 to bind Hb?

A

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
Q

What happens in the muscles?

A

Release of O2 from Hb and binds H+ and CO2;
Low pressure, Low pH, high conc. of H+ = Lose O2;
<50% saturation

137
Q

What happens in the Lungs?

A

Binding O2 to Hb, release of H+ and CO2;

High pressure, High pH, low conc. of H+ = Lose H+ and CO2

138
Q

What is required for Cooperativity?

A

Ligans;

Subunits (Quaternary structure)

139
Q

Why doesn’t Mb exhibit coopertativity?

A

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
Q

What happens in a RIGHTWARD shift of O2 binding to Hb?

A

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
Q

What causes a RIGHTWARD shift of O2 binding (higher release)?

A

Deceased tissue pH;
Increased temp;
Increased CO2 conc.;
Increased BPG

142
Q

When is the INCREASED RELEASE of O2 needed (Rightward shift)?

A 
Exercise;
Increased Lactic Acid;
INcreased heat released from the body;
Increased CO2 build up;
Increased BPG
143
Q

Why does Hb maintain ~50% saturation in the tissues?

A

That way it is a supply when the tissues need a sudden supply of O2 such as during immediate hyperactivity and increased respiration

144
Q

What does CO2 bind to when O2 is released from Hb (less binding affinity of O2 to Hb)?

A

The terminal NH3+ group

145
Q

What does H+ bind to when O2 is released from Hb (less binding affinity from O2 to Hb)?

A

Binds to His

146
Q

How does BPG affect the binding of O2 to Hb?

A

More BPG causes the release of O2 in the tissues

147
Q

What happens in a LEFTWARD shift of O2 binding to Hb?

A

O2 is bound more readily and not released

148
Q

What makes Fetal Hb bind O2 more readily than maternal Hb?

A

The presence of the Gamma subunit (instead of Beta);

Fetal has a higher affinity to bind the O2

149
Q

Why does the Fetus need to bind O2 more readily?

A

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

Fall 2013 (6 decks)

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