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BMSC 200 > Midterm Ch. 1-5 > Flashcards

Midterm Ch. 1-5 Flashcards

1
Q

what is biochemistry?

A

the study of life at a molecular level; the application of the principles of chemistry to explain biology

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2
Q

what building blocks do all organisms use to create common categories of biomolecules?

A

nucleic acids, proteins, polysaccharides, and lipids

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3
Q

what 4 elements are most organisms made up of?

A

carbon, oxygen, hydrogen, and nitrogen

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4
Q

where do we get carbon?

A

from air through plants

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5
Q

where do we get oxygen?

A

from air

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6
Q

where do we get hydrogen?

A

from water

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7
Q

where do we get nitrogen?

A

from either the air (N2), or soil and and plant roots

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8
Q

what does the availability of nitrogen in soil cause?

A

causes limiting of plant growth, limiting the amount of food we can produce

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9
Q

why is silicon the next best candidate as a chemical foundation for life?

A

it can also form 4 covalent bonds, and is highly abundant in the earths crust

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10
Q

why are we based in carbon rather than silicon?

A
  • C to C bonds are stronger and more stable
  • there is more energy from carbon based nutrients
  • combustion products of carbon (CO2) are soluble (recyclable) and silicone dioxide is insoluble
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11
Q

what is conformation?

A

flexible spatial arrangement of atoms within a molecule (can be changed without breaking covalent bonds)

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12
Q

what is configuration?

A

fixed spatial arrangement of atoms within a molecule (cannot be changed without breaking covalent bonds)

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13
Q

how is configuration conferred?

A

either double bonds or chiral centres

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14
Q

how do you link 2 amino acids?

A

through a peptide bond (cis-trans) double bond
(single double double single double double)

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15
Q

what are stereoisomers?

A

mirror images

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16
Q

what are traits of chiral carbons?

A

asymmetric, no double bonds, must have 4 different groups attached

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17
Q

what is stereospecificity?

A

the synthesis of chemical compounds (drugs) which have asymmetric carbons resulting in a mix of all the chiral forms, each form has different biological activities

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18
Q

how many different proteins do we have in our bodies?

A

~20,000

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19
Q

what are the advantages of constructing biologicals as polymers?

A
  • simplicity (for synthesis and degradation)
  • recycling (biomolecules can be digested back to component building blocks which are reusable, can recycle amino acids
  • diversity (incredibly complex molecules can be generated)
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20
Q

what does every amino acid have?

A

a carboxyl group and an amino group

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21
Q

what are polysaccharides and what is their purpose?

A
  • they are monosaccharides linked together to form linear or branched polymers
  • their roles include greater structural complexity, energy storage, and cell recognition
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22
Q

what are nucleic acids and what is their purpose?

A
  • they are linear polymer of nucleotide building blocks (DNA and RNA)
  • they are involved in all aspects of storage and utilization of genetic info
  • 2 strands that are complimentary to each other help with disease fighting etc.
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23
Q

what are lipids and what are they used for?

A
  • they are aggregates (rather than defined polymers) of building blocks
  • they are aggregated together through non-covalent linkage
  • they serve in energy storage, formation of membranes, and signaling
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24
Q

what are prokaryotes?

A

small, simple, single cell organisms with a single compartment (the nucleoid) that contains nucleic acid and other biomolecules in a complex organized mix
one cell must do every function to keep alive

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25
Q

what are eukaryotes?

A

large complex cells, make up multicellular organisms (plants, fungi, vertebrates), contain organelles to support specialized functions, more organized but ability to respond is much slower than prokaryotes

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26
Q

how do prokaryotes (bacteria) help our gut?

A

they help digest food and maintain a functional immune system

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27
Q

why is our gut (microbiota) called our second brain?

A

it may impact mental health (depression, anxiety etc.), obesity, and intelligence

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28
Q

what are possible ways to influence the microbiota?

A

diet, pro and prebiotics, and fecal transplants

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29
Q

what is in vitro?

A

(in glass) studies the behaviour of molecules outside the context of the cell and organism ex. growing cancer cells in a dish

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30
Q

what is in vivo?

A

(in the living) studies occur within the complexity of the cell or organism

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31
Q

what is the first law of thermodynamics?

A
  • energy cannot be created or destroyed but transformed
  • the total amount of energy in the universe remains constant, but forms of energy may change
  • cells are highly effective transducers of energy, converting the energy of metabolized nutrients into work, heat, or generation of complex biomolecules
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32
Q

what is the second law of thermodynamics?

A
  • natural tendency towards increasing entropy (disorder)
  • the tendency in nature is towards even greater disorder
  • living systems and their biomolecules require a high degree of organization
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33
Q

what does Gibbs free energy state?

A

that free energy (G) of any closed system can be defined by:
- enthalpy (H) reflects the number and kinds of bonds
- entropy (S) the degree of randomness (temp (Kelvin) dependent)

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34
Q

what is the Gibbs free energy equation and the free energy change equation?

A

G = H - TS
deltaG = deltaH - TdeltaS

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35
Q

what does it mean if deltaG > 0?

A

non spontaneous process, needs input of free energy to proceed
ENDERGONIC

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36
Q

what does it mean if deltaG < 0?

A

spontaneous process, releases free energy which can be used to do work, proceeds until equilibrium is reached
EXERGONIC

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37
Q

what does it mean if deltaG = 0?

A

system is at equilibrium, there is no change in free energy in the system

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38
Q

what are energy coupling link reactions?

A

cells can drive thermodynamically unfavourable reactions by coupling endergonic and exergonic reactions

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39
Q

what is catabolic in metabolism?

A

breaking stuff down, proteins and fats in the diet are broken down (energy producing) to generate ATP

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40
Q

what is anabolic in metabolism?

A

building things up, creating proteins within the body (energy requiring)

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41
Q

what is ATP?

A
  • common energy currency
  • serves as the link between catabolic and anabolic reactions
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42
Q

genetic info must be …?

A
  • stored in a stable form over time
  • expressed accurately in the form of gene products
  • reproduced with minimal errors
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43
Q

what does DNA provide?

A
  • the instructions for forming all other cellular components
  • a template for production to identical DNA molecules to be distributed when a cell divides
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44
Q

how is DNA replicated?

A

DNA > transcription > RNA > translation > proteins

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45
Q

what is the structure of DNA?

A
  • 2 complimentary strands (double helix)
  • each strand is a linear polymer of 4 different building blocks (A and T, C and G)
  • the linear sequence in strands encodes info
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46
Q

what is the hexokinase gene and what does it do?

A

an enzyme involved in glycolysis (takes glucose and produces energy) than produces messenger RNA, than goes through translation and forms a polypeptide chain , which allows the enzyme to take glucose and phosphorylate it and generate energy from sugar

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47
Q

what does the nucleotide sequence of genes dictate?

A

the sequence of amino acids incorporated into the corresponding protein

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48
Q

what does the amino acid sequence dictate?

A

it’s structure

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49
Q

what does the structure of the protein dictate?

A

it’s biological activity

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50
Q

gene sequences are … ?

A

phenotypes

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51
Q

why are random changes in genotype a good thing?

A

can result in a changed phenotype which offers a survival advantage that will be selected over time

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52
Q

what is water’s passive role?

A

the structure/function of biomolecules forms in response to interaction with water ex. protein folding is driven in an effort to bury hydrophobic residues away from water

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53
Q

what is water’s active role?

A

water participates in many biochemical reactions ex. peptide bond formation releases a water molecule

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54
Q

what is H2Os structure?

A
  • O is more electronegative than H
  • permanent dipole
  • O has a partial negative charge
  • each H has a partial positive charge
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55
Q

what is the dipole of water?

A
  • forms electrostatic interactions
  • forms H bonds
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56
Q

Hydrogen bond rule?

A

if it can form a H bond it must

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57
Q

what are electrostatic interactions?

A

electronegative atom with a H linked (donor) to another electronegative atom with a free electron pair (acceptor)

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58
Q

why are O and N common hydrogen binders?

A

they can both serve as H bond donors and acceptors

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59
Q

how strong/big are H bonds and what does it depend on?

A

H bonds are double the length of a covalent bond
pretty weak (5% the strength of a covalent bond)
strength of an H bond depends on its geometry

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60
Q

which is more stable anti-parallel or parallel beta sheets and why?

A

anti-parallel beta sheets are more stable due to better geometry

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61
Q

how many H bonds can water form?

A

4 H bonds (2 donors, 2 acceptors)

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62
Q

why are most living organisms isothermic?

A

they need to regulate and maintain their temps

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63
Q

what helps our bodies to stay cool?

A

the high composition of water within our bodies, coupled with the high specific heat capacity of water

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64
Q

why does ice float on water?

A

ice takes up more volume, it has a lower density than water therefore ice floats on water

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65
Q

what is heat of vaporization?

A

the amount of heat required to vaporize a liquid at its boiling temp

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66
Q

what is specific heat capacity?

A

amount of heat required to raise the temp of a substance one degree (energy absorbed by a solution)

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67
Q

what is polywater?

A

a form of water with a higher boiling point, lower freezing point, and much higher viscosity than ordinary water

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68
Q

what type of group can interact favourably with water?

A

any type of group that has a charge (hydrophilic)

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69
Q

in water molecules as H bonding partners which group is the acceptor/donor?

A

carbon group is the acceptor
amide group is the donor

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70
Q

what is hydrophilic?

A

water loving - molecules are polar (have a + or -), can accept or donate, dissolvable

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71
Q

what is hydrophobic?

A

water fearing - molecules are non polar

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72
Q

what are amphipathic molecules?

A

both polar and non polar, have both hydrophobic and hydrophilic portions
ex. fatty acids

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73
Q

CO 2 and O2 are non polar and have limited solubility in water and blood why does this present a challenge?

A

presents a challenge for their transport, specialized transposed proteins are required for transport of CO2 and O2 (hemoglobin, myoglobin, etc.)

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74
Q

hydrophobic drive is a primary driving force for what?

A

for formation and stabilization of biomolecules structure

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75
Q

what are hydrophobic interactions?

A

the forces that hold the non polar regions of the molecule together

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76
Q

what are micelles?

A

mixed fatty acids as a result of interaction of water molecules (hydrocarbon tails join together, polar heads are on the surface interacting with water)

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77
Q

what are examples of non-covalent interactions?

A
  • hydrogen bonds
  • electrostatic interactions
  • hydrophobic interactions
  • van der waals interactions
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78
Q

what do non-covalent interactions enable?

A

transient, dynamic interactions and flexibility of structure and function

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79
Q

what do non-covalent forces influence?

A

formation and stability of biomolecules structures, recognition/interactions between biomolecules, binding of reactants to enzymes

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80
Q

what are hydrogen bonds?

A

functional groups have H born capacity and can form H bonds with:
- water molecules, groups in the same molecule, groups in other molecules
they are critical for biomolecular interactions but not for the formation of structures

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81
Q

what are the roles of adenine, thymine, guanine, and cytosine in H bonding?

A

A and T: one is a donor, one is an acceptor
G and C: on is a donor, one is an acceptor
- A and G aren’t complimentary with H bonds

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82
Q

what are electrostatic reactions?

A
  • between charged groups can either be attractive (opp. charge) or repulsive (same charge)
  • unpackages DNA by modifying amino acids that carry a positive charge
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83
Q

how does water affect the strength of electrostatic interactions?

A

the hydration dampens the strength, the water shields the charged groups which diminishes the strength

84
Q

what does the strength of electrostatic interactions depend on?

A

the distance separating the charged groups and the nature of the intervening medium

85
Q

what is the Van der Waals force?

A

interaction between permanent and induced dipoles, short range, low magnitude interactions, abundant in the core of folded proteins

86
Q

when is the Van der Waals attraction maximal?

A

when 2 atoms are separated by the sum of the van der waals radii

87
Q

how does the folding of protein contradict the 2nd law of thermodynamics?

A

the folding of protein involves creation of a more ordered state

88
Q

what does the introduction of non polar molecules to water molecules cause?

A

a decrease in entropy

89
Q

how does water increase entropy?

A

when non polar molecules release some of the ordered water

90
Q

how does the folding of a polypeptide effect the entropy?

A

decrease the entropy of the polypeptide; increase the entropy of the associated water

91
Q

what is homeopathy?

A

dilution of something 30 times; claims the water “remembers” the medicine in the solution
expensive water pre much

92
Q

what is the ionization of water?

A

when a water molecule deprotonates to become a hydroxide ion (OH-)

93
Q

how do strong acid and bases react in water?

A

they dissociate completely

94
Q

how do weak acids and bases react in water?

A

do not dissociate completely and the extent of the dissociation can be quantified

95
Q

what is the goal of a weak acid?

A

to donate its protons (depends how many protons are already present

96
Q

what is the buffering region of a titration curve?

A

when the weak acid is strong enough to donate its proton, the flat portion of the titration curve

97
Q

what is the pKa point of the titration curve?

A

the midpoint in buffering region, hasn’t been able to donate it’s proton, equal amount of base and acid forms

98
Q

if pKa = 4.7, what is the buffering region?

A

3.7-5.7

99
Q

if Ph = pKa what does this mean for the solution?

A

the solution is best able to resist changes in pH

100
Q

if pH is above pKa what does this mean?

A

there will be more unprotonated form
(below is protonated)

101
Q

what happens to an acid after it donates its proton?

A

it turns into a base

102
Q

what do disulfide bonds do and where are they found?

A
  • stabilize proteins by maintaining overall structure inter or intramolecular covalently between 2 cysteine residues
  • seen in extremophiles (higher temp, extreme pH), seen in proteins that are extracellular
103
Q

what is keratin made of and what does it do?

A
  • made up up disulfide bonds
  • seen in proteins that make up your hair and seen in rhino horns (obvi more disulfide bonds for stronger structure)
104
Q

what is zwitterion?

A

the dipolar (both positively and negatively charged) ion of an amino acid
ex. glycine

105
Q

what are peptide bonds?

A

covalent linkages between the carboxyl group of one amino acid and amino group of another amino acid

106
Q

how do peptide bonds form?

A

by condensation reaction involving the generation of a water molecule
(lose O from carboxyl group, lose 2 Hs from amino group = H2O)
- formation of peptide bonds are the same, independent of the residues being joined

107
Q

what does the formation of peptide bonds eliminate and why?

A

the charges on the alpha-carboxyl and alpha-amino charged groups, which is important for folding

108
Q

what is an example of post-translational modification?

A

Phosphorylation

109
Q

what are polypeptide main chains?

A
  • the constant portion of the polypeptide (side cabins are the variable portion)
  • results in a repeating pattern within the main chain (NCCNCC)
110
Q

what is the partial double bond characteristic and what is the consequence of it?

A
  • rotation around C-N peptide bond is restricted
  • as a consequence the 6 atoms of the peptide group are rigid and planar (limits structural flexibility)
111
Q

what is the partial double bond configuration?

A
  • creates cis-trans isomers
  • can anticipate peptide bonds in the trans position because in cis configuration there is likely steric interference
  • the O of the carbonyl group and the H of the amide nitrogen are usually trans to each other
112
Q

what is the primary protein structure?

A
  • linear arrangement of amino acids in a polypeptide
  • presented from the N amino (start) terminus to the C carboxyl terminus
  • has info specifying correct folding
  • can’t predict 3D structure
113
Q

what is the secondary structure?

A
  • represents localized patterns of folding in a polypeptide
  • maintained by H bond between main chain amide and carbonyl groups
  • elements of 2nd structure found in different proteins
  • they retain the same characteristics
114
Q

secondary structure examples?

A
  • alpha-helicies
  • beta-sheets
115
Q

what are the 2 key rules of secondary structure?

A
  • optimize the H bonding potential of the main chain carbonyl and snide groups
  • represent a favoured combination of the polypeptide chain
116
Q

what is the structure of the bonds Phi Ca-N and Psi Ca-C?

A

each alpha carbon is held within the main chain through single bonds about which there is complete freedom of rotation (can spin all the way around)

117
Q

what is the range for Phi and Psi?

A

-180 — 180

118
Q

what are partial double bonds in secondary structure?

A

a consequence of resonance; present between the amino acids in proteins

119
Q

why is there not many confirmations of secondary structure polypeptides?

A

steric interference

120
Q

what are the traits of an alpha helix?

A
  • right handed helix with 3.6 residue/turn
  • stabilized by H bonds which run parallel to the axis of the helix
  • carbonyl groups point towards C terminus; amide groups point towards N terminus
121
Q

in an alpha helix each carbonyl of residue n H bonds with amide group of residue…?

A

residue n+4

122
Q

why is proline not found in alpha-helicies?

A

because of its rigidity

123
Q

why is glycine uncommon in alpha-helicies?

A

because of its flexibility

124
Q

what groups of amino acids are not found in alpha helicies and why?

A
  • amino acids with side chain branches (Val, Thr, Ile) because of steric interference
  • amino acids with H bonding groups near the main chain (Ser, Asp, Asn)
125
Q

if the helix is super long has does this affect the dipole?

A

the longer the helix = the greater the dipole

126
Q

each helix dipole by H bonding has a net dipole what are they?

A
  • N terminus has a partial positive dipole charge
  • C terminus has partial negative charge
127
Q

what are the negatively charged residues at the N - terminus and the positively charged residues at the C - terminus?

A
  • negatively charged at N: Asp, Glu
  • positively charged at C: Lys, Arg, His
128
Q

what do amphipathic helicies residues look like?

A
  • residues separated by 3 or 4 positions in the primary sequence will be on the same side of an alpha helix
  • residues separated by 2 residues in the primary structure will be on opposite sides of the helix
129
Q

what are beta-sheets?

A
  • involve multiple (4 or 5) B strands arranged side by side
  • fully extended polypeptide chains
  • stabilized by H bonds between C=O and -NH
  • either parallel (more flexible) or anti parallel (more stable)
130
Q

what are amphipathic beta sheets?

A
  • side chains tend to alternate above and below the polypeptide chain
  • alternating polar and non polar residues within the primary structure of a beta-sheet = amphipathic
131
Q

what is the tertiary structure of a protein?

A
  • the final folding pattern of a single polypeptide chain
  • the long range of aspects of sequence interactions within a polypeptide
132
Q

how might residues in primary structure and tertiary structure relate?

A

residues separated by great distance in primary structure may be close in proximity in tertiary structure
(primary structure determines tertiary structure)

133
Q

the stability of a protein in tertiary structure reflects what?

A

the difference in free energies if the folded and unfolded states

134
Q

in tertiary protein structure the protein conformation with the lowest free energy is what?

A
  • the most stable
  • the one with the max. number of weak interactions
135
Q

in tertiary protein structure how is stability defined?

A

stability is the tendency to maintain a native conformation

136
Q

if proteins can’t spontaneously fold to their native conformation what do they need the help of?

A

chaperones or heat shock proteins (proteins with larger and more complex structures)

137
Q

in a protein in the unfolded state there is the greatest amount of what?

A

entropy/disorder

138
Q

what is denaturation?

A

unfold a protein
- disruption of native conformation with loss of biological activity
- cooperative and usually reversible process

139
Q

how much energy does denaturation need?

A
  • very small energy, only a few H bonds
140
Q

what is quaternary structure?

A
  • consists of multiple polypeptide chains
  • may involve multiple copies of the same or different polypeptides
  • reserved for proteins of more complex biological function
  • subunits formed usually associate through non-covalent interactions
141
Q

what are the biological advantages of quaternary structure?

A
  • help stabilize subunits and prolong life of proteins
  • unique active sites produced at the interfaces between sub unuts
  • help facilitate unique/dynamic combinations of structure/function
  • more efficient
142
Q

what are the biological roles of protein structure/function?

A

enzymes, storage and transport, physical cell support/shape, mechanical movement, decoding cell info, hormones/hormone receptors etc.

143
Q

how many proteins do bacteria have?

A

5000

144
Q

how many proteins do fruit flies have?

A

16,000

145
Q

how many proteins do humans have?

A

25,000 (minimum; could be up to 1 mil)

146
Q

how big are typical proteins? (biggest and smallest)

A

100 — 1000 amino acids in length typically
- smallest is 51 (insulin)
- largest is 34,350 (titin)

147
Q

what are examples of fibrous proteins?

A

keratin, collagen, silk

148
Q

what are examples of globular proteins?

A

myoglobin, hemoglobin

149
Q

what is keratin?

A

the main component of hair, wool, horns, and nails

150
Q

what structure does keratin at the primary level?

A

pseudo-seven repeat where positions A and D are hydrophobic (non polar)
- non complex

151
Q

what structure does keratin form at a secondary level?

A

an alpha helix
- residues from positions A and D end up on the same face of the helix which results in a hydrophobic strip along the length of the helix
- every 4th residue will be non polar

152
Q

2 amphipathic helicies of keratin interact how and what is the result?

A

interact by burying hydrophobic face together which results in a formation of a coiled coil

153
Q

what does a coiled coil of keratin involve?

A

2 right hand helicies wrapped around each other in a left hand fashion

154
Q

what does the strength of keratin arise from?

A

covalent linkages of individual units (linked by disulfide bonds) into higher order structures
- the extent of the disulfide bonds determines the strength

155
Q

what is collagen?

A

the major structural protein within your body holding you together, major protein of vertebrates (25% of total protein)

156
Q

what is the structure of collagen at a primary level?

A

repeats of Gly-X-Y
- X is often proline

157
Q

what is the structure of collagen at a secondary level?

A

forms a left handed helix of 3 residues per turn (different shape than an alpha helix) 3 left handed helicies wrap around each other in a right handed fashion to get a stronger more stable structure

158
Q

where are proline and glycine residues in collagen secondary structure?

A
  • the bulky side chains of proline are on the outside of the coiled-coil
  • the small side chains of glycine residues are in the tightly packed core of the coiled-coil
159
Q

where does the strength of collagen arise from?

A

same as keratin but instead of disulfides the linkages occur from residues that undergo post translational modification (adding hydroxyl groups to proline and lysine)
- increasing brittle character of aging connective tissue and tougher meat

160
Q

what do enzymes in collagen need to perform post translation modifications (stable cross links)?

A

vitamin C

161
Q

how does scurvy affect collagen?

A

vitamin C deficiency leads to weakened structure of collagen which manifests in skin lesions, fragile blood, bleeding gums etc.

162
Q

what do collagen genetic diseases all have in common?

A

can be associated with brittle and abnormal bone structure, weakened cardiovascular capabilities, loose skin and joints, hyper flexibility

163
Q

what is silk?

A
  • produced by insects and spiders for formation of webs and cocoons (both need to be strong and flexible)
164
Q

what is the structure of silk at a primary level?

A

has a 6 residue repeat (GSGAGA)

165
Q

what is silk made for at the secondary structure level?

A

primarily for beta-sheets (the fully extended polypeptide of beta offer considerable strength)
- one of the strongest know materials

166
Q

what makes silk strong?

A

fully extended polypeptides

167
Q

what makes silk flexible?

A
  • association of strands by H bonding
  • association of sheets by van der waals and hydrophobic interactions
168
Q

what are the side chains of silk and how do they come together?

A

one side chain alanine, one side chain glycine and they zipper together (both have non polar side chains)

169
Q

what are prions diseases?

A
  • infectious disease based in the misfiling of a self protein into a pathological, infectious conformation
  • they are fatal, untreatable neurodegenerative diseases
170
Q

misfolding dependent epitopes are termed what?

A

disease specific epitopes (ideal vaccine targets

171
Q

what do antibodies induced against DSEs do?

A

only bind the unhealthy form of protein (PrPsc) and spare the function of the healthy form (PrPc)

172
Q

what is a ligand?

A

a molecule that is reversibly bound by the protein

173
Q

what is a binding site?

A

a specific site (or multiple) on the protein where a ligand binds
(complimentary for shape, charge, hydrophobicity, and H bonding potential)

174
Q

what is induced fit?

A

the binding of a ligand causes a conformational change of a protein, which can change the properties of the protein

175
Q

what are the challenges for oxygen deliver and storage in multicellular organisms?

A

for multicellular organisms the solubility of oxygen to too low to meet oxygen requirements through passive diffusion, amino side chains not well suited for reversible binding of oxygen

176
Q

what is the solution for oxygen delivery and storage?

A

specialized proteins for O2 storage and delivery

177
Q

what is myoglobins structure?

A

tertiary structure that binds a single oxygen molecule in the muscles, has a single heme

178
Q

what is hemoglobin’s structure?

A

quaternary structure, 4 structures each with an oxygen molecule, 4 heme groups, can bind 4 oxygen molecules

179
Q

what is myoglobin and what does it do?

A

monomeric protein that facilitates oxygen storage and peripheral tissue

180
Q

what is hemoglobin and what does it do?

A

tetrameric protein found in red blood cells that transport oxygen from lungs to the periphery (hemoglobin has lower affinity for O2 than myoglobin)

181
Q

what does cellular iron do?

A

bound in forms that make it less reactive

182
Q

what does heme consist of?

A

protoporphyrin ring rusted bound to a single Fe2+ iron atom

183
Q

can Fe2 and Fe3 bind oxygen?

A

Fe2 binds reversibly, Fe3 does not bind O2

184
Q

what does the electron donating characteristic of nitrogen prevent?

A

the conversion of Fe2 to Fe3

185
Q

Fe2 seeks 6 coordinating interactions where do they come from?

A

4 come from interactions with heme, a 5th comes from interaction with an imidazole group of a proximal histidine residue, and the 6th is for O2 binding

186
Q

how does carbon monoxide exert its deadly effects?

A

by competing with oxygen for bond to heme (CO binds heme 200 times greater affinity than O2)

187
Q

what is myoglobin made of?

A

small globular protein consisting of a single polypeptide of 153 residues arranged in 8 alpha-helicies

188
Q

what are allosteric protein forms?

A

T (inactive) and R (active)
T and R are rapid in equilibrium

189
Q

a protein that binds O2 with high and constant affinity would do what?

A

would saturate effectively with O2 in the lungs but not release it to the tissues

190
Q

a protein with lower O2 affinity does what?

A

would be able to release O2 to tissues but would not have sufficient affinity to saturate in the lungs

191
Q

what do allosteric activators do?

A

stabilize the R state

192
Q

what do allosteric inhibitors do?

A

stabilize the T state

193
Q

how does T transition to R?

A

with the T state hemoglobin the iron atom is just outside the plane of the heme ring; with transition to R state the iron moves into plane of the ring

194
Q

what is the p50 of hemoglobin?

A

the partial pressure of O2 found in periphery

195
Q

what is 2,3 bisphospho-D-glycerate?

A

a heterotrophic allosteric inhibitor of hemoglobin; it decreased hemoglobin’s affinity for oxygen
(carries 5 units of negative charge)

196
Q

what is fetal hemoglobin like compared to adult hemoglobin?

A

fetal Hb has a higher oxygen affinity
adult Hb has 6+ residues at the binding site, fetal Hb has 4

197
Q

adaptation to high altitude can rapidly occur through what?

A

increased production of 2,3 BPG (this decreases Hbs O2 affinity to ensure sufficient O2 delivery to periphery)

198
Q

what is the bohr effect?

A

describes the pH dependence of hemoglobin’s affinity of O2

199
Q

why do active tissues have lower pH?

A

increased muscle activity increases production of CO2 which then decreases pH (in extreme exercise muscles produce lactic acid to further decrease pH)

200
Q

what are the 2 primary challenges to cellular respiration and metabolism?

A
  • delivering sufficient O2 to tissues
  • removing CO2 (the exhaust of metabolism) from the periphery
201
Q

what is mechanism 1 for O2 delivery and CO2 removal?

A

CO2 is taken up in red blood cells and converted to bicarbonate and a proton by the enzyme carbonic anhydrase, CO2 is converted into a soluble form for transport to the lungs and the decreases pH decreases Hbs O2 affinity to promote O2 release

202
Q

what is mechanism 2 for O2 delivery and CO2 removal?

A

CO2 can form a covalent carbamate linkage to the N terminus of each chain of Hb to form carbaminohemoglobin
- converts CO2 to more soluble form to assist its transport to the lungs, CHG has a lower O2 affinity to promote O2 release, the released proton promoted O2 release through the bohr effect

203
Q

what does sickle cell anemia result from?

A

a molecular disease of hemoglobin:
- results from a single amino acid change
- formation of fibers from the deoxy form of Hbs
- fibers tend to form capillaries (where O2 is the lowest) which blocks blood flow to the body

204
Q

who has resistance to malaria?

A

individuals heterozygous for sickle cell anemia

205
Q

what is malaria?

A

infects red blood cells, infection decreases pH in rbcs which causes release of oxygen from Hb

206
Q

why can’t people with sickle cell anemia get malaria?

A

deoxy hemoglobin form fibres that deform the red blood cells, the deformed red blood cells containing malaria are selectively destroyed by the sperm

207
Q

how is hemocyanin different from hemoglobin?

A

hemocyanin uses copper rather than iron (blue blood), 2 copper atoms bind a single oxygen molecule, no gene ring group, the copper atom is coordinated through histidine residues, hemocyanin is not localized within specialized O2 transport cells

BMSC 200 (2 decks)

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