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Biochemistry 1 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

What is the Plasma Membrane?

A

Lipid bilayer in which proteins are embedded in

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2
Q

What is the Cytoplasm?

A

semifluid matrix that contains the nucleus and other organelles

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3
Q

What is the Mitochondrion?

A

Organelle in which energy is extracted from during oxidative metabolism

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4
Q

What is a Secretory Vesicle?

A

Vesicle fusing with the plasma membrane releasing materials to be secreted from the cell

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5
Q

What is the Cytoskeleton?

A

supports organelles and cell shape it plays a role in cell motion

  • microtubules
  • intermediate filament
  • Actin Filaments
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6
Q

What are microtubules?

A

a type of cytoskeleton; tube of protein molecules present in cytoplasm, centriole, cilia and flagella

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7
Q

What are Intermediate Filaments?

A

a type of cytoskeleton; intertwined protein fibres that provide support and strength

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8
Q

What are Actin Filaments?

A

a type of cytoskeleton; twisted protein fibres that are responsible for cell movement

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9
Q

What is the nucleus?

A

command centre of the cell

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10
Q

what is the nucleolus?

A

inside the nucleus; site where ribosomes are produced

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11
Q

What is the nuclear envelope?

A

double membrane between the nucleus and cytoplasm

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12
Q

What are nuclear pores?

A

an opening embedded with proteins that regulate passage into and out of the nucleus

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13
Q

What are ribosomes?

A

small complexes of RNA and protein that are the site of protein synthesis

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14
Q

What is peroxisome?

A

vesicles that contain enzymes that carry out particular reactions, such as detoxifying potentially harmful molecules

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15
Q

What are lysosomes?

A

vesicles that break down macromolecules and digests worn out cell components

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16
Q

What is the Smooth Endoplasmic Reticulum?

A

system of internal membranes that aids in the manufactures of carbohydrates and lipids

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17
Q

What is the Rough Endoplasmic Reticulum?

A

Internal membranes studded with ribosomes that carry out synthesis

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18
Q

What is the Golgi Apparatus?

A

It collects, packages and distributes molecules manufactured in the cell

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19
Q

What are the types of molecules that are the main components of living tissue?

A
  1. Proteins
  2. Carbohydrates
  3. Lipids
  4. Nucleic Acids
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20
Q

What is the monomer unit for proteins?

A

Amino Acids

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21
Q

What is the monomer unit for carbohydrates?

A

Glucose

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22
Q

What is the monomer unit for lipids

A

Glycerol and fatty acids

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23
Q

What is the monomer unit for nucleic acids?

A

Nucleotide

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24
Q

What is the most abundant molecule in living organisms (70%)?

A

Water is the most abundant molecule in living organisms

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25
Q

What are some characteristics of water?

A
  • Acts as a solvent; is Polar
  • Is a reactant in many processes
  • Gives cells structure support (like a filled water balloon)
  • Source of H3O+ protons and OH- ions
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26
Q

What is Proton Hoping?

A

proton hoping is called the ionization of water, this ionization creates H3O+ and OH- molecule

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27
Q

Do protons exist in a free solution?

A

Protons do not exist in a free solution

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28
Q

In water Ionization and water molecules the covalent and hydrogen bonds are what?

A

the covalent and hydrogen bonds are interchangeable. This allows for an extremely fast mobility of protons in water, via proton hoping

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29
Q

O-H Bonds are what?

A

are polar and can dissociate heterolytically

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30
Q

What does heterolytically mean?

A

bond breaking in which bonding electron pair is split unevenly between the products. Heterolytic cleavage produces at least one ion

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31
Q

What are the Physiochemical properties of water?

A

High Heat of Vaporization: good evaporation
- coolant (helps maintain temperature)
High Specific Heat Capacity: good heat buffer
- prevents dramatic temperature changes

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32
Q

What is electronegativity?

A

is the ability of an atom to attract bonding electrons to itself
-Therefore water is slightly positive and slightly negative because of electronegativity

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33
Q

Hydrogen and Covalent Bonds account for what?

A

accounts for all the characteristics of water without this water would be a gas at room temperature

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34
Q

What is the lifetime of each hydrogen bond?

A

the lifetime of each hydrogen bond is 1-20 picoseconds; breaking and forming “flickering clusters”

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35
Q

What are Amphipathic Compounds in aqueous solutions?

A

long-chain of fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered water molecules

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36
Q

Hydrogen bonds are…?

A

hydrogen bonds are longer and weaker than covalent bonds

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37
Q

What happens to water when it freezes?

A

In ice, each water molecule forms four hydrogen bonds, the maximum, water can form, creating a regular crystal lattice. This crystal lattice structure makes ice less dense than liquid water, thus why it floats on liquid water

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38
Q

What occurs spontaneously?

A

the phase change of liquid water to solid, gas, or liquid water

ΔG(free energy) = ΔH(enthalpy change) - T(temp)ΔS(entropy)

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39
Q

For a reaction to be spontaneous what has to happen?

A

For a reaction to be spontaneous ΔG must be negative

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40
Q

What is entropy?

A

Randomness change; increased entropy means less order

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41
Q

What is water as a solvent?

A

water dissolves many crystalline salts by hydrating their ion components. High dielectric constants reduce attraction between oppositely charged ions in a lattice. Entropy increases as ordered crystal lattice is dissolved

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42
Q

Water is a poor solvent for which substances?

A

water is poor solvent for non-polar (hydrophobic) substances

  • non-polar gases (N2, O2, CO2)
  • Fatty Acids
  • Oils and Waxes
  • Hydrophobic Amino Acids
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43
Q

What do hydrophobic compounds do in water?

A

Hydrophobic compounds disrupt the H-bond network of bulk water because a highly organized cage structure forms around hydrophobic compound

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44
Q

What are amphipathic molecules?

A

Ex. Water: polar regions react with water but non-polar avoids it

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45
Q

What happens in dispersion of Lipids in H2O

A

each lipid molecule forces surrounding H2O molecules to become highly ordered

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46
Q

What are clusters of lipid molecules?

A

only lipid portions at the edge of the cluster force the ordering of water molecules are ordered, and entropy is increased

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47
Q

What are micelles?

A

all hydrophobic groups are sequestered from water; ordered shell of H2O molecules is minimized, and entropy is further increased

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48
Q

what does clustering in micelles achieve?

A

clustering together in micelles exposes the smallest possible hydrophobic surface are of water, and fewer water molecules are required in the shell of ordered water

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49
Q

What is the hydrophobic effect?

A

refers to the association or folding of non-polar molecules in an aqueous solution
- does NOT arise because of some attractive forces between two non-polar molecules

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50
Q

Hydrophobic effect is one of the main factors behind?

A
  • Protein folding
  • Protein-Protein Association
  • Formation of Lipid Micelles
  • Binding of steroid hormones to their receptors
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51
Q

What is the “Partition” Coefficient?

A

ratio of the concentration of a compound in two phases such as water (hydrophilic) and octanol (Hydrophobic). Gives idea of lipophicility

P = [compound]octanol / [compound]water

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52
Q

what does lipophilicity mean?

A

refers to the ability of a chemical compound to dissolve in fats, oils, lipids and non-polar solvents; which is important in pharmacology/toxicology

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53
Q

What are some types of important non-covalent bonds between molecules?

A
  1. Hydrogen Bonds
  2. Ionic Bonds
  3. Hydrophobic Bonds
  4. Van der Waals Interactions
    - All these interactions are weak, the relative amount will vary with each interaction, collectively they are strong
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54
Q

What are Hydrogen Bonds?

A

hydrogen bonds form when a hydrogen atom is sandwiched between two electron-attracting atoms, usually oxygen or nitrogen
H - hydrogen donor
F,O,N - Hydrogen Acceptor

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55
Q

What are some of the importances of hydrogen bonds?

A
  • structure of DNA, polysaccharides, and proteins
  • Binding of substrates to enzymes
  • Binding of hormones to receptors
  • Matching of mRNA and tRNA
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56
Q

What are Ionic Bonds?

A

Ionic bonds occur between charged groups (positive and negative)
- in aqueous solutions the charged groups or molecules are shielded by H2O molecules and other ions in the solution and so are quite weak

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57
Q

What are Hydrophobic Bonds?

A

when hydrophobic molecules or chemical groups are placed in an aqueous environment, they are forced together to minimize their distributive effects on the complex network of hydrogen bonding water molecules. These groups are said to be held together by Hydrophobic Bonds
- the basis of their attraction is due to the common repulsion of water molecules

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58
Q

What are Van Der Waals Interactions?

A

Weak interactions between all atoms, regardless of polarity

- Attractive (dispersion) and repulsive (steric) component

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59
Q

What is pH and its biological relevance?

A

essential to all sciences to have a scale that measures acidity or the basicity of “aqueous” solutions of organelles, cells , tissues, environment, etc.

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60
Q

What is the pH of pure?

A

Pure water has a pH 7.0 at 25°C

  • An acid lowers pH
  • A base increases pH
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61
Q

What is an Equilibrium Constant?

A

The degree of ionization of water at equilibrium is described by the equilibrium constant

Keq = [H+][OH-]/[H2O]
- At 25°C the [H2O] is 55.5M

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62
Q

What is Kw?

A

Ionic Product of water is designated by Kw:

Kw = Keq[H2O] = [H+][OH-]
= 1.810^-16M x 55.5M
= 1.0*10^-14 M^2

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63
Q

In pure water what is the concentration for OH- and H+?

A

in pure water [H+] and [OH-] both equal 1.0*10^-7M

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64
Q

What is pH?

A

pH is defined as the negative logarithm of the hydrogen ion concentration
- The pH + pOH always equals 14
pH = -log[H+]
-log[H+] - log[OH] = +14

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65
Q

What is the Dissociation of Weak Electrolytes Principle?

A

weak electrolytes dissociate only partially in water, extent of dissociation is determined by the acid dissociation Constant (Ka)
- we can calculate the pH if the Ka is known

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66
Q

Acids and Bases occur in what?

A

Acids and Bases occur in conjugate acid and base pairs

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67
Q

what is a conjugate base?

A

The conjugate base of an acid is the base that is formed when the acid has donated a hydrogen atom

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68
Q

What is a conjugate acid?

A

The conjugate acid of a base is the acid that forms when base accepts a hydrogen ion

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69
Q

What is the Henderson - Hasselbalch Equation?

A

it shows why the pKa of a weak acid is equal to the pH of the solution at mid-point of its titration. At that point, [HA] = [A-]

pH = pKa + log1 = pKa + 0 = pKa

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70
Q

The Henderson - Hasselbalch Equation?

A

pH = pKa - log([HA]/[A-])
or
pH = pKa + log([A-]/[HA])

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71
Q

How can a buffering capacity be overcome?

A

buffering capacity can be overcome by the addition of excessive acid or base

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72
Q

What is Methylmalonic Aciduria?

A

an instance of too much acid affecting the pH of blood occurs in this disease. A metabolic disorder in which methylmalonic acid builds up in the blood and overcomes the buffering capacity

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73
Q

What is methylmalonyl-CoA mutase (MUT)?

A

requires vitamin B12 binding for activity, catalyzes the conversion of methylmalonyl-CoA to succinyl-CoA. in the absence of vitamin B12, methylmalonyl-CoA is converted is instead converted into methylmalonic acid, build up of this acid can cause blood pH to lower.

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74
Q

Hos is Methylmalonic Aciduria caused?

A

can be caused by insufficient B12 intake but most times it is caused by a genetic mutation, in the gene encoding MUT. A single amino-acid substitution from a glycine to a arginine(much larger) can destroy all MUT acitivity

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75
Q

What is Osmosis?

A

net movement of water molecules through a semipermeable membrane, from an area of higher water to an area of lower water potential

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76
Q

In Plant cells excessive osmosis is prevented due to what?

A

In a plant cell, excessive osmosis is prevented due to the osmotic pressure exerted by the cell wall thereby, stabilizing the cell

77
Q

The cell membrane is more permeable to…?

A

The cell membrane is more permeable to hydrophobic compounds than to hydrophilic compounds
-membrane protein may “transport” specific molecules across membrane

78
Q

What are proteins?

A

proteins carry out most of the work within the cell

79
Q

What are some functions of proteins?

A
  1. Catalysis
  2. Transport
  3. Structure
  4. Motion
80
Q

How are Amino Acids Important for proteins and life?

A

Amino acid sequence of proteins encoded in DNA, each cell makes a different repertoire of proteins

81
Q

What is a genome?

A

refers to all the genes encoded in a cell’s DNA

82
Q

what is transcriptome?

A

refers to complete RNA profile

83
Q

What is Proteome?

A

refers to the complete protein complement expressed by a cell

84
Q

What is the Human Genome Project?

A

The human genome project has revealed that the human genome encodes 30,000 genes

85
Q

The Human Proteome is estimated to be…?

A

The Human Preteome is estimated to be 50,000-100,000 proteins
- the difference between the number of genes and proteins is due to post-translation modifications

86
Q

What is Post-Translation Modifications (PTM)?

A

Is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis for many proteins.

87
Q

What is a peptide?

A

A small protein contains 2-50 amino acids; M.W < 5000 Daltons(g/mol)

88
Q

What is a polypeptide (protein)?

A

term for molecules that contain more than 50 amino acids

89
Q

What is Protein Diversity?

A

simple but complex; using the 20 natural occurring amino acids, it is possible to generate an enormous array of proteins
20^10 = 1x10^13 different combinations

90
Q

What are soluble proteins (Globular)?

A

polypeptide chains folded into spherical or globular shape. Often contain several types of secondary structure, most enzymes and regulatory proteins are globular proteins

91
Q

What are membrane proteins?

A

hydrophobic proteins (need detergents to solubilize)

  • transporters (ie. sodium pumps, H+ pumps)
  • receptors
92
Q

What are Firbous/Structural Proteins?

A

polypeptide chains in long strands or sheets. Fibrous proteins usually consist largely of a single type of secondary structure and their tertiary structure is relatively simple. Fibrous proteins provide support, shape and external protection.

93
Q

Proteins are what to alpha-amino acids?

A

proteins are heteropolymers to alpha-acids

94
Q

In alpha amino acids, the amino group is where?

A

the amino group by convention the leftmost residue is called the amino terminus or N-terminus

95
Q

Where is the residue with carboxyl group placed?

A

the residue with the carboxyl group is always at the right is called the carboxyl terminus or C-terminus

96
Q

What is the R group of an amino acid?

A

The R group or side chain attached to the alpha carbon is different in each amino acid

97
Q

What is an alpha carbon?

A
  • most alpha carbons are chiral
  • the alpha carbon always has 4 substituents, its a tetrahedral
  • have an acidic carboxyl group, basic amino group, and an alpha hydrogen and a unique R group attached to it
98
Q

What is glycine?

A

it is the smallest amino acid and in glycine, the fourth substituent is also hydrogen

99
Q

What are enantiomers?

A

enantiomers are one of two stereoisomers that are non-superimposed, complete mirror images of each other

100
Q

What are some essential amino acids?

A
  1. Isoleucine
  2. Leucine
  3. Lysine
  4. Methionine
  5. Phenylalanine
  6. Threonine
  7. Tryptophan
  8. Valine
101
Q

What are some Inessential amino acids?

A
  1. Alanine 2.Asparagine
  2. Aspartic Acid 4. Cysteine
  3. Glutamic Acid 6. Glycine
  4. Proline 8.Histidine
  5. Serine 10. Tyrosine
  6. Arginine
102
Q

Amino acids can be placed in 5 different groups related to their R groups, what are they?

A
  1. Nonpolar Aliphatic (Hydrophobic)
  2. Aromatic (Hydrophobic)
  3. Polar Uncharged (Hydrophilic)
  4. Positively Charged (Hydrophilic)
  5. Negatively Charged (Hydrophilic)
103
Q

Proline is a special amino acid because?

A

it is special because it lacks the NH2 group because of the cyclization of the side chain and is known as imino acid

104
Q

Cysteine can be involved with what?

A

Cysteine can be involved with covalent disulfide bonds; which are very important in stabilizing the structure of proteins

105
Q

What happens during the ionization of Amino Acids at an acidic pH?

A

At an acidic pH, the carboxyl group is pronated and the amino group is in cationic form

106
Q

What happens during the Ionization of Amino Acids in a basic pH?

A

At alkaline pH, the amino group is neutral -NH2 and the amino acid is in the anionic form

107
Q

What happens during the Ionization of Amino Acids in a neutral pH?

A

At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions

108
Q

What is the pKa for the ionization of carboxylic acid group?

A

about 1.8 - 2.4

109
Q

What is the pKa for the ionization of the amino group?

A

about 9.0 - 9.7

110
Q

Amino acids with uncharged side chains have two pKa values, what are they?

A

The pKa for the alpha carboxyl group is 2.34
The pKa for the alpha amino group is 9.6
- it can act as a buffer in two pH regions

111
Q

Where are Zwitterions most predominant?

A

Zwitterions predominate at pH values between the pKa values of amino and carboxyl groups

112
Q

What is the Isoelectric Point?

A

is the equivalence point for amino acids that have ionizable side chains (at this point, the net charge is zero, amino acid does not migrate in electric field)

pI = pK1 + pK2/2

113
Q

In a neutral solution the carboxyl group is most likely?

A

negatively charged

114
Q

In a neutral solution the amino group is most likely?

A

positively charged

115
Q

In a neutral solution the R group for aspartate and glutamate are most likely?

A

negatively charged

116
Q

In a neutral solution the R group for lysine and arginine is most likely?

A

positively charged

117
Q

In a neutral solution the R group tyrosine is most likely?

A

neutral

118
Q

In a neutral solution the R group of histidine has a 10% chance of being what and a 50% chance of increasing to what?

A

have a pH of 7 and increase to a pH of 6. Histidine is very sensitive to pH change in the physiological range

119
Q

How are peptides formed?

A

Peptides are formed by condensation (lost water) reactions between amino acids
- small peptides are used commercially

120
Q

How many different levels of protein structure are there?

A

There are 4 different levels of structure in proteins, each level depending on the previous

  1. Primary
  2. Secondary
  3. Tertiary
  4. Quaternary
121
Q

What is the Primary structure of proteins?

A

Primary structure is the linear sequence of a protein, we begin at the free amino end of N-terminal and end at the carboxyl end or C-terminal
-contains the chemical information that allows secondary and tertiary structure

122
Q

What does the double bond character of a peptide bond do?

A

The double bond character of the peptide bond restricts rotation about the peptide bond
- double bond character arises from resonance

123
Q

Rotation around what bonds are permitted?

A

Rotation around bonds connected to the alpha carbon is permitted

124
Q

What is the Secondary structure of proteins?

A

secondary structure refers to highly regular local sub-structures defined by patterns of hydrogen bonds between the main-chain peptide groups.

  • interactions lead to patterns such as
    1. α-helix
    2. β-sheets
    3. β-turns
125
Q

What is an α-helix?

A

it is one of the most important elements of the secondary structure. It is a helix shape in which every N-H group donates a Hydrogen bond to the C=O group of amino acid located 3 or 4 residues along the protein sequence

126
Q

What is the function of the α-helix?

A

hydrophobic and ion bonds can help stabilize helix structure

127
Q

What is the dipole moment of an α-helix?

A

The dipoles of peptide units are aligned along the α-helix axis, which creates an overall dipole moment, positive at the amino end and negative at the carboxyl end

128
Q

What are parallel(same direction) and antiparallel(opposite directions) β-sheets?

A

more extended than helix and forms a zig-zag structure, H-bonds form between adjacent segments of the polypeptide. Segments can be nearby or at a distance, fibrous proteins such as silk
- Have Hydrophilic and Hydrophobic sides w

129
Q

What are β-turns ?

A

Nearly 1/3 of residues are in turns. β-turns link segment of α-helix and β-sheets. They make the protein change directions

  • 180degree turn is accomplished over 4 amino acids
  • turn stabilized by hydrogen bond from carboxyl oxygen to amide proton 3 residues down the sequence
130
Q

What is the Tertiary structure for Proteins?

A

Tertiary structure refers to the overall spatial arrangements of atoms in a polypeptide chain or in a protein.
- describes how the secondary structure folds onto itself, in a way that hydrophobic residues are hidden from water

131
Q

What is the Quaternary structure for proteins?

A

A super structure formed by association of two or more polypeptide chains
-These units may be homomeric complex or heteromeric complex

132
Q

What does homomeric complex mean?

A

Subunits being the same

133
Q

What does Heteromeric complex mean?

A

consists of different subunits

134
Q

What are membrane proteins?

A

There are two types of membrane proteins

  1. Peripheral membrane proteins
  2. Integral membrane proteins
135
Q

What are peripheral membrane proteins?

A

these are generally globular proteins that associate with the membrane via

  • electrostatic interactions with phospholipids head group
  • proteins modified with a lipid tail
  • proteins are anchored to the membrane via protein-protein interactions
136
Q

What are Integral membrane proteins?

A

These proteins have one or more segments that transverse the lipid bilayer, these segments are referred to as transmembrane domains (TMD’s)
- because of TMD’s hydrophobivity integral membrane proteins require detergents or organic solvents for solubility in aqueous solutions

137
Q

What are TMD’s?

A

TMD’s are composed of almost exclusively hydrophobic amino acids.

138
Q

What is α-Keratin?

A

It is a fibrous protein, found only in mammals; related to intermediate filament that perform structural functions in all animal cells

  • interacting surfaces are hydrophobic
  • strength increased by covalent disulfide bonds
139
Q

α-Keratin is rich in what amino acids?

A

Phe, Met, Ala, Val, Ile, Leu

- α-Keratin is a right handed α-helix

140
Q

What is the Structure of Collagen?

A

collagen is an important constituent in connective tissue (tendons cartilage, bones, etc.)
- 3 collagen chains intertwine into a right handed superhelical triple helix

141
Q

Collagen is rich in what amino acids?

A

each collagen chain is a long Gly- and Pro-rich left handed helix

142
Q

What is 4-Hydroxyproline in Collagen?

A

offer more hydrogen bonds between the three strands of collagen
- The post-translational processing is catalyzed by propyl hydroxylase and requires α-ketoglutarate, molecular oxygen and ascorbate (Vitamin C)

143
Q

What are Collagen Fibrils?

A

Collagen fibrils are made up of collagen molecules aligned in a staggered fashion and cross-linked for strength

144
Q

What are Cofactors?

A

a substance (other than the substrate) whose presence is essential for the activity of an enzyme

145
Q

What are the 2 types of cofactors?

A
  1. Prosthetic Groups: Heme in myoglobin hemoglobin cytochrome C
  2. Metals: Mg2+ DNA Polymerase, Zn2+ Carbonic Anhydrases
146
Q

A proteins function depends on what?

A

depends on its 3Dimensional structure

147
Q

What is protein denaturation?

A

Loss of structural integrity with accompanying loss of activity is called denaturation

148
Q

What are some ways can be denatured by?

A
  • heat or cold
  • pH extremes
  • organic solvents
  • detergents
149
Q

What is a Chaotropic agent or Chaotrope?

A

is a substance which disrupts the 3D structure in a macromolecule such as proteins, DNA, RNA and denatures them
- interferes with stabilizing intra-molecular interactions

150
Q

What is Protein Purification?

A

To study protein function and structure it is essentially to purify proteins to homogeneity (one type of protein)

151
Q

What are the 5 different ways proteins can be fractionated?

A
  1. Solubility
  2. Size
  3. Charge
  4. Affinity Chromatography
  5. Charge and Size
152
Q

What is a critical requirement for the purification of proteins?

A

Is an assay or method to determine the desired protein is being enriched

  1. Enzymatic activity
  2. Bioassay (Biological Assay)
  3. Immunological-ELISA and immunobolt
153
Q

What is Specific Activity?

A

The purification of a protein from a complex is monitored by measuring the specific activity

Spec act. = total activity/total protein

154
Q

What is Chromatography?

A

The process of differentiating/separating particles on the basis of their interaction with a solid support. Two components required for chromatography

  1. Stationary Phase
  2. Mobile Phase
155
Q

What is the Stationary Phase of Chromatography?

A

a support matrix, with which components to be separated interact

156
Q

What is the Mobile Phase of Chromatography?

A

a solvent that promotes differential partitioning of a molecule from the stationary phase

157
Q

What is an example of chromatography based on size?

A

Gel filtration chromatography

158
Q

What is an example of chromatography based on charge?

A

ion exchange chromatography

159
Q

What is an example of chromatography based on affinity?

A

ligand or antibodies chromatography

160
Q

What is Ion exchange chromatography?

A

separation of proteins on the basis of charge, proteins remain native
- depending on the pH the protein will either carry a net negative or positive charge

161
Q

What is affinity chromatography?

A

A very powerful technique, which can be used to isolate a single protein from a complex mixture with a single step
- Technique uses a stationary phase containing either a substrate or a ligand that is bound by the protein with high affinity

162
Q

What does affinity mean?

A

affinity is the tendency of a molecule to associate with another molecule

163
Q

What is Imidazole Metal Affinity Chromatography?

A

this form of affinity is widely used to rapidly purify recombinant proteins over-expressed in E.coli
- Recombinant proteins are engineered to contain a hexahistidine sequence either at the amino or carboxyl terminus

164
Q

What is Electrophoresis for Protein Analysis?

A

separation in analytical scale is commonly done by electrophoresis

  • electric field pulls proteins according to their charge
  • gel matrix (Polyacrylamide) hinder the mobility of proteins according to their size and shape
165
Q

What is SDS Page?

A

Sodium Dodecyl Sulfate - a detergent

- separates proteins in 2D according to size

166
Q

What is the Function of SDS?

A
  • It binds to and unfolds proteins
  • gives all proteins a uniformly negative charge
  • native shape of proteins doesn’t matter
  • Rate of movement will only depend on the size: small proteins will move faster
167
Q

What is 2D polyacrylamide gel electrophoresis?

A

combines Isoelectric fusing, and SDS Page, using these two electrophoresis techniques, complex protein mixtures containing thousands different can be resolved into individual spots

168
Q

What is Isoelectric Fusing?

A

separates proteins according to their isoelectric point (pI), separation on the basis of charge

169
Q

Like Proteins, Amino acids also have what?

A

Also have an isoelectric point

- at its pI, a protein will not migrate in an electric field

170
Q

What are enzymes?

A

enzymes are proteins that function to increase the rate of a reaction
- most enzymes are globular proteins

171
Q

How are enzymes characterized?

A

Enzymes are characterized according to the reactions they catalyze
- with a few exceptions (Trypsin and lysozyme) enzymes are identified by the suffix “ase”

172
Q

What is the function of the enzyme Oxidoreductase?

A

catalyze a variety of oxidation-reduction reactions

- common names include (dehydrogenase, oxidase, reductase, and catalase)

173
Q

What is the function of the enzyme Transferase?

A

catalyze transfers of groups (acetyl, methyl,etc.)

- common names include (acetyltrasnferase, methylase, protein kinase and polymerase

174
Q

What is acetylation?

A

The addition of acetyl group to lysines R group

175
Q

What is methylaction?

A

The addition of a methyl group to cytosine

176
Q

What is phosphorylation?

A

The addition of a phosphate group to R group tyrosine, serine, or threonine

177
Q

What is the function of the enzyme Histone Acetyltransferase (HAT)?

A

enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to for e-N-acetyl lysine

178
Q

What is the function of the enzyme Hydrolase?

A

catalyze hydrolysis reactions where molecules are split into two or more molecules by the addition of water

179
Q

What is the function of the enzyme Lyase?

A
  1. catalyze the addition of groups across a double bond

2. or eliminate the groups to generate double bonds

180
Q

What is the function of the enzyme Isomerase?

A

catalyze atomic rearrangements within a molecule

Ex) from trans to cis stereoisomers

181
Q

What is the function of the enzyme Ligase?

A

catalyze the reaction that joins two molecules and uses energy derived from ATP
Ex) peptide synthase, DNA ligase, RNA ligase

182
Q

Many proteins require what to complete the active site of an enzyme?

A

Non-protein substances called Cofactor

183
Q

What are Cofactors?

A
  • May bind to the apoenzyme via non-covalent bond. These can dissociate from apoenzyme
  • May Interact via a covalent bond and do not dissociate from enzyme even after denaturation
184
Q

What are the 2 classes of Cofactors?

A
  1. Inorganic: consists of metal ions (Zn2+, Na+)

2. Organic (coenzymes and prosthetic groups): also referred to as vitamins

185
Q

What is Ascorbic Acid (Vitamin C)

A
  • vital for collagen syntheisis

- cofactor for propyl hydroxylase and lysyl hydroxylase

186
Q

What is Folic Acid?

A
  • essential for cell growth and multiplication
  • required for nucleic acid synthesis
  • deficiency results in anemia
    Ex) leafy greens, vegetables, liver, yeast, wheat germ
187
Q

What is Vitamin K?

A
  • required for prothrombin formation clotting protein

- deficiency leads to increased clotting time for minor cuts and bruises (deficiency rare)

188
Q

What is Thiamine (B1) ?

A
  • deficiency causes beriberi (nervous system ailment)
  • nerve degeneration, muscle disease (heart)
  • vitamin B1 is temperature sensitive, prolonged cooking destroys B1

Biochemistry 1 (1 decks)

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