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BME 501 > Section 2 - Proteins and Nucleic Acids > Flashcards

Section 2 - Proteins and Nucleic Acids Flashcards

1
Q

What are the most structurally complex and functionally sophisticated molecules known?

A

Proteins

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2
Q

What gives proteins their unique shapes?

A

A unique amino acid sequence, which defines shape and function

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3
Q

How many different types of amino acids are there?

A

20

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4
Q

How come DNA is not as functionally sophisticated or functionally complex as proteins?

A

DNA has a relatively simple structure (regular) and function (storage)

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5
Q

Why is a protein structurally complex and functionally sophisticated?

A

Proteins do every function in the cell, and have structures that cannot be generalized

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6
Q

What bonds hold amino acids together?

A

Covalent peptide bonds

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7
Q

What reactions form peptide bonds?

A

Condensation reactions

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8
Q

How do secondary (noncovalent) bonds arise in proteins?

A

Different side chains of amino acids

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9
Q

What is the general amino acid structure?

A

A central carbon, which connects an amino group, a carboxylic acid group, a hydrogen, and an R group

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10
Q

What enantiomers do proteins consist of?

A

L amino acids

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11
Q

How is a peptide bond formed?

A

An OH is lost from the carboxylic acid group, and an H is lost from the amino group to create a peptide bond and water

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12
Q

What is the n-terminus of a protein?

A

Where the free amino group is (start)

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13
Q

What is the c-terminus of a protein?

A

Where the free carboxylic acid group is (end)

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14
Q

What groups of side chains are there for an amino acid?

A

Basic, acidic, uncharged polar, and disulfide

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15
Q

What is the side chain for glycine?

A

H

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16
Q

True or false: amino acids in the same group have very similar structures

A

False: there can be very different structures in the same group (such as nonphobic)

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17
Q

What are the special amino acids?

A

Serine, threonine, and tyrosine

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18
Q

What group do the special amino acids belong to?

A

Uncharged polar

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19
Q

What is the common structural motif of the special amino acids?

A

OH group

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20
Q

What is special about the special amino acids?

A

Kinases add phosphate groups to those three amino acids (serine, threonine, and tyrosine)

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21
Q

Which bonds dictate protein folding?

A

Weaker (noncovalent) bonds

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22
Q

What principle does protein folding operate under?

A

Fold to minimize energy

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23
Q

What considerations are needed for protein folding to minimize energy?

A

Weak bonding events, sterics, etc.

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24
Q

What is the 3D structure of a protein determined by?

A

Amino acid sequence, and how they interact

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25
Q

What is the conformation of a protein?

A

Final 3D shape

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26
Q

What is sterics?

A

Two molecules can’t be in the same place at the same time (dictates folding)

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27
Q

What is the advantage of using weaker bonds for protein folding (as opposed to covalent bonds)?

A

Allows for flexibility in the shape of the proteins

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28
Q

Why do proteins need some flexibility in their shapes?

A

Allows for catalysis events and other functions

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29
Q

In an aqueous environment, where are the hydrophilic side chains found?

A

On the outside of the protein (near water)

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30
Q

In an aqueous environment, where are the hydrophobic side chains found?

A

On the inside of the protein (away from water)

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31
Q

How can active zones of a protein be shielded by water?

A

By having them in the hydrophobic core of the protein

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32
Q

True or false: there are rotations around peptide bonds

A

True: all single bonds (such as peptide bonds) allow for rotation

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33
Q

What are molecular chaperones?

A

Proteins that bind to partially folded proteins

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34
Q

What do molecular chaperones do?

A

Help proteins fold, and mark that the protein is not folded

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35
Q

What are the common folding motifs in proteins?

A

Alpha helices, and beta sheets

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36
Q

What drives secondary structure in proteins?

A

H-bonding between N-H and C=O (in peptide backbone)

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37
Q

What are the advantages of alpha helices?

A

Increase packing density, can make large hydrophilic or large hydrophobic regions

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38
Q

Why would you want large hydrophilic or hydrophobic regions in a protein?

A

Transmembrane proteins (needs to be hydrophobic or hydrophilic along the membrane)

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39
Q

What structure allows for large hydrophilic or hydrophobic regions in a protein?

A

Alpha helices

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40
Q

What are the advantages of beta sheets?

A

Packing density

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41
Q

What are the two organizations of beta sheets?

A

Parallel and antiparallel

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42
Q

What is the structure of parallel beta pleated sheets?

A

/\ /\ /\

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43
Q

What is the structure of antiparallel beta pleasted sheets?

A

/\ \/ /\

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44
Q

Which beta pleated sheets are more common?

A

Antiparallel

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45
Q

Why are antiparallel beta pleated sheets more common?

A

Smaller loop (less amino acids/ secondary structures) and stronger H bonds (close together)

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46
Q

For parallel beta pleasted sheets, how are the loops generated?

A

Usually through alpha helices

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47
Q

How many levels of protein organization are there?

A

4

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48
Q

What is the primary structure of a protein?

A

Amino acid sequence

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49
Q

What is the secondary structure of a protein?

A

Alpha helices and beta pleated sheets

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50
Q

What is the tertiary structure of a protein?

A

Full 3D structure

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51
Q

What is the quaternary structure of a protein?

A

Different polypeptides interacting with each other

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52
Q

What are the four ways to represent a protein?

A

Scribble, secondary structures, space filling, and side chains

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53
Q

What is a protein domain?

A

A functional sub-section of a protein

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54
Q

True or false: domains are not conserved between proteins or species

A

False: a domain can be conserved between different proteins or species

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55
Q

What is an example of a conserved protein domain?

A

Src domain (SH2) (helps with docking)

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56
Q

What are protein families?

A

Groups of proteins with a similar function

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57
Q

True or false: protein families have similar structures and amino acid sequences

A

True: since their function is similar, their structure and amino acid sequence are also similar

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58
Q

What do serine proteases do?

A

Use an active serine to digest proteins

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59
Q

What is an example of a protein family?

A

Serine proteases

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60
Q

True or false: humans have significantly more genes than other organisms

A

False: we only have at most 2x the amount of genes in other organisms, and 7% of our genes are vertebrate specific

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61
Q

How does human complexity arise?

A

Protein domains and modules can interact with many different proteins, thus creating many functions between proteins

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62
Q

What are protein modules?

A

Small protein domains

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63
Q

How can larger protein structures form?

A

Disulfide bonds, self-assembly (aided by other molecules)

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64
Q

What forms can assembled protein monomers take?

A

Dimers, helices, rings, etc.

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65
Q

What does “assembly on a core” refer to?

A

One protein can act as a core, while other proteins can attached to that

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66
Q

What does “accumulated strain” refer to?

A

Proteins aligning into different arrays for increased stress bearing

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67
Q

What does “vernier mechanism” refer to?

A

Multiple proteins can hook together (based on protrusions) to create larger structures

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68
Q

True or false: the mechanical motions of the protein are directly coupled to chemical events

A

True: this provides an extraordinary set of dynamic events for the cell

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69
Q

What is an example of mechanical motion being coupled to chemical events?

A

An enzyme can physically move two substrates together, perform a chemical reaction, then move to release them

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70
Q

True or false: a protein can only function if it interacts with other molecules

A

True: there needs to be some binding for a reaction or function to occur

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71
Q

True or false: the binding strength for a particular protein is very specific

A

True: this allows for the specified reaction to occur

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72
Q

What is a ligand?

A

The molecule that binds to the protein

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73
Q

True or false: ligand binding to a protein is very weak

A

False: the binding can be strong or weak depending on the protein and ligand

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74
Q

What two checks will proteins use to make sure the ligand is correct?

A

A shape check (does it fit correctly), and a binding check (are the noncovalent bonds right)?

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75
Q

How does a protein aid in ligand binding?

A

Through its folding and amino acid side chains

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76
Q

What would happen if a binding site is on the exterior of a protein?

A

There would be competition between the ligand and water molecules

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77
Q

What is the risk of having water molecules bind to a binding site on a protein?

A

This could affect noncovalent bonds, and thus the protein check for the proper ligand

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78
Q

What are the most common interactions between a ligand and an enzyme?

A

Hydrogen binding, or electrostatic interactions

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79
Q

How do electrostatic interactions aid in ligand binding?

A

Enhance reactivity of enzymes (activate side chains on amino acids)

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80
Q

What is the equilibrium constant (K)?

A

A measure of binding strength

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81
Q

How is K calcualted?

A

Association rate / dissociation rate

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82
Q

If a reaction has a high K, what does that mean?

A

There is a high association rate

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83
Q

If a reaction has a low K, what does that mean?

A

There is a high dissociation rate

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84
Q

What do “on” kinetics refer to?

A

Association

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85
Q

What do “off” kinetics refer to?

A

Dissociation

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86
Q

What do hydrolases do?

A

Catalyze hydrolytic cleavage reaction (such as proteases, nucleases, etc.)

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87
Q

What do nucleases do?

A

Break down nucleic acids

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88
Q

What do proteases do?

A

Break down proteins

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89
Q

What do synthases do?

A

Synthesize molecules (anabolic reactions)

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90
Q

What do ligases do?

A

Join together two molecules

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91
Q

What do isomerases do?

A

Catalyze the rearrangement of bonds

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92
Q

What do polymerases do?

A

Catalyze polymerization reactions (DNA, RNA, etc.)

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93
Q

What do kinases do?

A

Add phosphate groups to molecules

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94
Q

What do phosphatases do?

A

Remove phosphate groups from molecules

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95
Q

What do oxido-reductases do?

A

Catalyzed oxidation-reduction reactions

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96
Q

What do ATPases do?

A

Hydrolyze ATP (harvest energy)

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97
Q

What do GTPases do?

A

Hydrolyze GTP (G-protein signaling)

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98
Q

True or false: all enzymes end with “-ase”

A

False: most enzymes do, but some (ex: pepsin) do not

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99
Q

What is the general process for enzyme functions?

A

E + S -> ES -> EP -> E + P

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100
Q

If substrate concentration increases, what happens to the rate of product formation?

A

It increases (up to a point)

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101
Q

What is Vmax?

A

The maximal reaction rate

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102
Q

What is Km?

A

The subtrate concentration to work at half of the maximal rate (Vmax)

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103
Q

What can you say about an enzyme that has a low Km?

A

Enzyme binds tightly, and thus need less substrate to get a maximal response

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104
Q

What can you say about an enzyme that has a high Km?

A

Enzyme binds weakly, and thus needs lots of substrate to get a maximal response

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105
Q

What are the constraints of how fast an enzyme reacts?

A

Inherent movements of protein (molecularly)

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106
Q

What would be an “optimal” enzyme (in terms of Vmax and Km)?

A

A high Vmax (high rate), and a low Km (low substrate to achieve rate)

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107
Q

How do enzymes work?

A

They stabilize any intermediary products

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108
Q

How does stabilizing the intermediary help reduce activation energy?

A

The free energy is reduced, thus making it easier to reach the transition state

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109
Q

Assuming that S has more energy than P, rate the following in terms of increasing energy: S, P, St

A

P, S, St

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110
Q

Assuming that S has more energy than P, rate the following in terms of increasing energy, S, P, ES, EP, ESt

A

EP, P, ES, S, ESt

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111
Q

Which is more stable: S or ES?

A

ES (lower energy)

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112
Q

Which is more stable: P or EP?

A

EP (lower energy)

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113
Q

In terms of stabilization and energy, how does an enzyme catalyze a reaction?

A

The activation energy from S to St is less than the activation energy from ES to ESt

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114
Q

Why does ES and EP have lower energies than S and P, respectively?

A

Bonding events stabilizes the molecules in the enzyme

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115
Q

Which is more stable: St or ESt?

A

ESt (lower energy)

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116
Q

How does EP go to P?

A

Enzyme is not stable as EP, so it can use an activate carrier or a conformational change to remove P

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117
Q

Which is more stable: E or EP?

A

E (more stable by itself, so it can remove P)

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118
Q

How do cells control the quantity of enzymes present?

A

Via gene expression

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119
Q

How is ligand/enzyme binding restricted?

A

Through localization

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120
Q

What does proteolysis control?

A

Quantity of formed enzymes present

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121
Q

How is regulation present in protein pathways?

A

Through feedback mechanisms

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122
Q

What questions (from a control perspective) are important for enzyme reactions?

A

Which enzymes are turned on/off, and when

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123
Q

What are the typical sites on an enzyme?

A

Ligand binding sites and regulatory binding sites

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124
Q

How is the rate of enzyme activity controlled?

A

Regulatory molecule binding (negative or positive)

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125
Q

Are most biological mechanisms negative or positive feedback?

A

Negative feedback

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126
Q

What is negative feedback?

A

(Usually) a downstream product inhibits an upstream protein

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127
Q

What is positive feedback?

A

(Usually) an upstream product activates a downstream protein

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128
Q

Why can ADP be considered more biologically active than ATP?

A

ADP can start many reactions through cell signaling (make more ATP)

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129
Q

True or false: regulatory binding sites can be positive or negative

A

True: there are different effects based on the specific protein

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130
Q

True or false: a pathway can only have either positive or negative feedback

A

False: there can be a smaller loop of positive feedback inside a larger loop of negative feedback

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131
Q

What are the three examples of positive feedback in biology?

A

Inflammation, coagulation, and child birthing

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132
Q

What happens when a molecule binds to a regulatory site?

A

Change in conformation, which changes activity

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133
Q

In an engineering perspective, how does a molecule binding to a regulatory site alter the the enzyme?

A

Changes the kinetics (need to know conditions)

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134
Q

How come enzymes can be described as a “dial”?

A

Range of control, from both positive and negative inputs

135
Q

True or false: enzymes cannot function without its regulatory molecule (positive)

A

False: they just function very slowly

136
Q

Do most enzymes catalyze one reaction, or many?

A

One (easier from a biological perspective)

137
Q

What is the charge of a phosphate group?

A

2 negative charges

138
Q

Why can phosphates alter the activity of proteins?

A

Can drastically alter the conformation of the protein (due to highly negative charge)

139
Q

True or false: phosphorylation always leads to activation

A

False: it can also lead to inhibition

140
Q

True or false: phosphorylation is a repeatable process

A

True: unlike mechanical processes, it can be repeated very often without significant wear

141
Q

What can phosphorylation do (other than activate a protein by changing conformation)?

A

Can act as docking sites to attract other regulatory proteins to drive assembly

142
Q

Where is phosphorylation most commonly seen?

A

Signal transduction pathways

143
Q

What causes mechanical motion in biology?

A

Motor proteins

144
Q

What do motor proteins do?

A

Undergo conformation changes to induce motion

145
Q

What functions are motor proteins seen in?

A

Muscle contraction, organelle movement, chromosome movement)

146
Q

What are some examples of motor proteins?

A

Myosin, kinesin, and DNA helicases

147
Q

What is the speed of DNA helicase?

A

1000 nt/s

148
Q

How to motor proteins keep moving forward (and not randomly)?

A

Have an irreversible step that requires a large amount of energy (ATP hydrolysis)

149
Q

What is the challenge of motor proteins?

A

Overcome thermodynamics and cause unidirectional motion

150
Q

What is meant by an “irreversible” reaction?

A

Large energy to go in the backwards direction, so it rarely happens

151
Q

What is the irreversible step in motor protein movement?

A

ATP hydrolysis

152
Q

What does myosin do?

A

Aids in muscle contraction

153
Q

What does kinesin do?

A

Aids in organelle movement

154
Q

What does DNA helicase do?

A

Used during DNA replication (unzip DNA)

155
Q

What was the controversy in the 1940s?

A

Most people did not accept a simple structure for complicated DNA molecule

156
Q

What led to an understanding of the function of DNA?

A

Discovery of double helix DNA structure

157
Q

What is the structure of DNA?

A

Two complementary strands help together by H-bonds

158
Q

What holds the two strands of DNA together?

A

H-bonds

159
Q

What is DNA composed of?

A

A sugar (deoxyribose), a base (A, C, T, G), and a phosphate group

160
Q

What composes the backbone of DNA?

A

Sugar and phosphate group

161
Q

What holds the backbone of DNA together?

A

Covalent bonds

162
Q

How many H-bonds are between C and G?

A

3

163
Q

How many H-bonds are between A and T?

A

2

164
Q

What is the structure of the purines?

A

2 rings

165
Q

What is the structure of the pyrimidines?

A

1 ring

166
Q

What bases are purines?

A

A, G

167
Q

What bases are pyrimidines?

A

C, U, T

168
Q

True or false: the DNA helix is symmetrical

A

False: there is a major and a minor groove

169
Q

How is the major groove seen in DNA?

A

The large gap in the twists

170
Q

How is the minor groove seen in DNA?

A

The small gap in the twists

171
Q

Why is DNA always the same size across?

A

A purine always binds with a pyrimidine

172
Q

What determines the exact base binding?

A

Size (a purine must bind to a pyrimidine) and H-bonds (2 vs 3)

173
Q

How far apart are the sugar molecules in DNA?

A

0.34 nm

174
Q

How long is one full turn of DNA?

A

10 base pairs (3.4 nm)

175
Q

How are the bases arranged in DNA (in terms of space)?

A

Similar to steps on a staircase

176
Q

Why are DNA bases arranged similar to steps on a staircase?

A

Stop extra H-bond interactions between different base pairs

177
Q

What is the 5’ end of DNA?

A

Phosphate group (5’ carbon)

178
Q

What is the 3’ end of DNA?

A

Hydroxyl group (3’ carbon)

179
Q

What is the importance of the major / minor groove?

A

Gene regulation

180
Q

How did the structure of DNA show a link to its function in genetics?

A

Structure suggests that strands could be replicated if pulled apart

181
Q

How much DNA is found in cells?

A

2m

182
Q

What percentage of volume does the nucleus make up?

A

~10%

183
Q

What does the nuclear envelope do?

A

Concentrates all important molecules near DNA

184
Q

Which is more selective: nuclear envelope or plasma membrane?

A

Nuclear envelope

185
Q

What do nuclear pores do?

A

Allow for passage between nucleus and cytosol

186
Q

How is control seen in the nuclear envelope?

A

Lots of control regarding the passage of molecules into and out of the nucleus

187
Q

Why is accurate duplication of DNA needed?

A

Needed to ensure template / product is accurate

188
Q

True or false: there is backup DNA if the old copy gets “corrupted”

A

False: there is no backup DNA present

189
Q

What happens if DNA maintenance does not occur?

A

Passage of genetic material is not stable

190
Q

True or false: not having DNA maintenance is always bad

A

False: while it is usually bad, it can also lead to mutations that increases survivability

191
Q

What is a mutation?

A

A change in the DNA sequence

192
Q

When does a mutation have no effect?

A

If it occurs in the non-coding region, or if it doesn’t change the conformation

193
Q

What is a silent mutation?

A

A mutation that have no effect on the subsequent protein structure

194
Q

What is the mutation rate in E. Coli?

A

~1 nt/ 10^9 nt (per cell generation)

195
Q

What is the mutation rate in humans?

A

~ 1 random, non-silent mutation / 200000 years (in a typical protein)

196
Q

What plot can be used to show which proteins are critical for life (unchanged)?

A

Plot (survivable) changes per time

197
Q

In a plot of survivable changes per time, what slope corresponds to a protein that is critical for life (unchanged)?

A

Shallow slope (few changes)

198
Q

In a plot of survivable changes per time, what slope corresponds to a protein that is not critical for life (unchanged)?

A

Steep slope (many changes)

199
Q

What is an example of a protein that is critical for life (unchanged)?

A

Histones

200
Q

What do histones do that makes then critical for life (unchanged)?

A

Need to wrap around DNA to condense it

201
Q

What is an example of a protein that is not critical for life (unchanged)?

A

Fibrinopeptides

202
Q

What do fibrinopeptides do that makes then not critical for life (unchanged)?

A

Just needs to be soluble

203
Q

What is DNA replication based on?

A

Being able to recognize the partner base pair based on the template strand

204
Q

What is meant by “semiconservative”?

A

One template strand is used to synthesize the complementary strand

205
Q

What are the incoming nucleotides for DNA replication?

A

Triphosphates

206
Q

What drives the energy of DNA replication?

A

Removal of a pyrophosphate (P-P) from a nucleotide triphosphate

207
Q

How is the information in DNA “read” for DNA replication?

A

H-bonds in the center are separated, and H-bonds on bases can be read

208
Q

What determines what the next base will be in DNA replication?

A

Based on the new H-binding events (donors / acceptors)

209
Q

What is the DNA replication fork?

A

The Y-shaped region of DNA where DNA replication is happening (lots of enzymes / nucleotides)

210
Q

True or false: the DNA replication fork is symmetrical

A

False: one side goes from 5’ -> 3’, and the other side goes from 3’ -> 5’

211
Q

What does DNA polymerase do?

A

Creates new DNA

212
Q

Which enzyme is responsible for creating new DNA?

A

DNA polymerase

213
Q

What direction does DNA polymerase work in?

A

5’ to 3’ direction

214
Q

What is the leading strand?

A

The strand that is formed continuously (3’ to 5’) (towards fork)

215
Q

What is the lagging strand?

A

The strand that is formed discontinuously (5’ to 3’) (away from fork)

216
Q

What are Okazaki fragments?

A

Small DNA fragments on the lagging strand of DNA

217
Q

What is the structure of DNA polymerase?

A

Similar to a neck pillow

218
Q

What is found in the “channel” of DNA polymerase?

A

Pool of nucleotide triphosphates

219
Q

True or false: DNA polymerase can read the DNA strand to find the matching nucleotide

A

False: the right nucleotide comes in based on H-bonding and fusion length of the bases

220
Q

What happens to DNA polymerase if the nucleotide is correct?

A

The DNA shifts down

221
Q

What happens to DNA polyermase if the nucleotide is incorrect?

A

The DNA stalls in the polymerase

222
Q

True or false: single stranded DNA is stable

A

False: it has weird kinks and folds (trying to stabilize itself with a double strand), showing that it is unstable

223
Q

When does DNA polymerase stop?

A

When it sees double stranded DNA

224
Q

What is the shape of bacterial DNA?

A

Circular

225
Q

How many origins of replication are found in mammalian DNA?

A

Many different sites (bubbles) throughout the chromosome

226
Q

What are some possible mutations (based on base binding)?

A

G can bind to T with some small changes in helix geometry, and C isoforms can bind to both A and G

227
Q

How many checks does DNA polymerase do for proofreading?

A

2

228
Q

What is the first proofreading check of DNA polymerase?

A

Check H-bonds

229
Q

Why do mismatched bases fall off easily?

A

High dissociation constant

230
Q

What is the second proofreading check of DNA polymerase?

A

Check backbone (gets stalled if not aligned)

231
Q

How does DNA polymerase fix backbone issues?

A

Has exonucleolytic site to remove a mismatched base pair

232
Q

What is the P site on DNA polymerase?

A

Polymerizing site (make more DNA)

233
Q

What is the E site on DNA polymerase?

A

Exonucleolytic site (remove mismatched bases)

234
Q

What does DNA polymerase need to start replication?

A

Primer

235
Q

Why does DNA polymerase need a primer to start replication?

A

Prevent it from starting anywhere in the DNA

236
Q

What enzyme produces primers?

A

DNA primase

237
Q

What does DNA primase do?

A

Produces RNA primers

238
Q

What types of primers are made by DNA primase?

A

RNA primers

239
Q

True or false: DNA primase has a high accuracy

A

False: it has a fairly low accuracy

240
Q

What are the problems with DNA primase?

A

The primers are made of RNA, and how does DNA primase know where to start

241
Q

Why is it ok for DNA primase to be fast but inaccurate?

A

The primers do not stay on the DNA

242
Q

What does DNA ligase do?

A

Seals gaps between Okazaki fragments

243
Q

What enzyme seals gaps between Okazaki fragments?

A

DNA ligase

244
Q

How is DNA polymerase like a snowplow?

A

The primers are bound so weakly that DNA polymerase can push them away and continue polymerization

245
Q

Why is DNA hard to denature?

A

It is a very stable molecule

246
Q

What does helicase do?

A

Opens DNA strands via hydrolysis of ATP

247
Q

What enzyme opens DNA strands?

A

Helicase

248
Q

What is the structure of helicase?

A

Circular (donut)

249
Q

True or false: helicase can help stabilize single stranded DNA

A

True: although this only occurs for a little bit

250
Q

True or false: helicase can open up double stranded DNA

A

False: it can only work on single stranded DNA (needs to be opened a little bit first)

251
Q

True or false: helicase contains nucleic acids in its structure

A

True: this is a combined protein / nucleic acid

252
Q

True or false: DNA helicase is very fast

A

True: once it starts working, it is very fast

253
Q

What is another name for single-strand DNA-binding proteins?

A

Helix-destabilizing proteins

254
Q

What do single-strand DNA-binding proteins do?

A

Bind to single stranded DNA to stabilize and straighten it

255
Q

What enzymes bind to single stranded DNA to stabilize and straighten it?

A

Single-strand DNA-binding proteins

256
Q

What is the structure of single-strand DNA-binding proteins?

A

Gloves or hands

257
Q

Why does DNA polymerase need to be stabilized?

A

It favors dissociation kinetics, so it could come off

258
Q

Why are the association kinetics for DNA polymerase binding to DNA low?

A

Don’t want DNA polymerase binding so tightly to DNA

259
Q

What helps hold DNA polymerase in place?

A

A sliding clamp

260
Q

When does the sliding clamp release?

A

When DNA polymerase hits double stranded DNA

261
Q

What does the sliding clamp do?

A

Hold DNA polymerase in place

262
Q

What does a clamp loader do?

A

Puts the sliding clamp onto the DNA

263
Q

What protein puts the sliding clamp on the DNA?

A

A clamp loader

264
Q

True or false: lots of control is needed for DNA replication

A

True: there is a lot of protein machinery that needs to be controlled

265
Q

How does the sliding clamp prevent DNA polymerase from falling off?

A

Noncovalent binding interactions between sliding clamp and DNA polymerase

266
Q

Why can DNA replication errors be found?

A

Errors will not form the proper 3D structure

267
Q

How does the cell know which strand of the DNA is the template strand (for mismatch repair)?

A

Template strand has no nick, and has some methylated A’s

268
Q

When do A’s get methylated?

A

A long time after DNA polymerase (separate mechanism)

269
Q

Why does DNA go under tension in DNA replication (if there were no enzymes)?

A

Similar to braided rope being pulled apart - fold in on itself

270
Q

What does topoisomerase do?

A

Relieve tension in DNA

271
Q

What enzymes relieve tension in the DNA?

A

Topoisomerases

272
Q

What is the difference between topoisomerase 1 and topoisomerase 2?

A

Different mechanisms for the same effect (tension relief)

273
Q

How does topoisomerase 1 work?

A

It breaks one phosphodiester bond, allowing for free rotation and relief of tension

274
Q

True or false: topoisomerase 1 covalently binds to DNA

A

True: this is one of the rare cases of proteins being covalently linked to DNA

275
Q

When is DNA attached to a “fixed end”?

A

In the lab (adhere DNA), or having two replication forks coming together

276
Q

How does topoisomerase 2 work?

A

It breaks one DNA strand to allow another strand to go through

277
Q

What is the pictorial representation of the topoisomerase 2 mechanism?

A

/ ____ / ___ _______

________ /

278
Q

Where does topoisomerase 2 mainly act (what regions of DNA)?

A

Loops (where the DNA crosses itself)

279
Q

What is the replication origin?

A

Where DNA replication occurs

280
Q

How does DNA replication occur?

A

Through special initiator proteins

281
Q

What is the structure of a replication origin region in DNA?

A

A/T rich

282
Q

Why is the replication origin region of DNA A and T rich?

A

Less H-bonds, so easier to break apart

283
Q

True or false: a TATA box refers to the replication origin

A

False: while replication origins have many A’s and T’s, the TATA box is not involved in DNA replication

284
Q

If there was only one fork, how long would it take to replicate an entire chromosome?

A

~800 hours

285
Q

What is meant by “replication units”?

A

Groups of ~50 origins are arranged into different units

286
Q

Are replication units all activated at the same time?

A

No: different units are activated at different times

287
Q

How far apart are replication units?

A

~30K to 250K nucleotides apart

288
Q

What phase of the cell cycle does DNA replication occur in?

A

S phase

289
Q

How long does S phase take?

A

~8 hours

290
Q

True or false: chromosome replication happens randomly

A

False: they are replicated in a controlled manner

291
Q

What is heterochromatin?

A

DNA in a very condensed state

292
Q

What is euchromatin?

A

DNA in a less condensed state

293
Q

Which DNA (heterochromatin or euchromatin) is replicated earlier?

A

Euchromatin

294
Q

What determines whether a gene will be in euchromatin or heterochromatin?

A

How often that gene needs to be transcribed in that particular cell

295
Q

Where does replication start?

A

In the middle of the chromosome (not the ends), which spread out

296
Q

What are the three things needed for a sequence to be an origin of replication?

A
  1. Binding site for initiator protein (ORC)
  2. Rich A/T region
  3. At least one binding site for proteins that attract ORC
297
Q

What does ORC stand for?

A

Origin recognition complex

298
Q

Why is a binding site for proteins that attract the ORC necessary for an origin of replication?

A

Without this enhancer protein, the ORC will not bind and start replication

299
Q

What is the ORC regulated by?

A

Two loading proteins (Cdc6 and Cdt1)

300
Q

What does the prereplicative complex do?

A

Aids in helicase binding and opening DNA

301
Q

When does loading of the ORC occur?

A

During G1 phase of cell cycle

302
Q

What happens to the ORC at the beginning of S phase?

A

Cdk’s phosphorylate ORC, activate helicase, and degrade loading proteins

303
Q

What do the loading proteins do (in ORC)?

A

Keep ORC in place until the S phase

304
Q

Where does the ORC split DNA?

A

At the A/T regions

305
Q

When is the ORC activated?

A

At the G1/S boundary (move into S phase)

306
Q

What happens to the ORC in G2?

A

It stays phosphorylated and on the DNA

307
Q

Why does phosphorylated ORC remain on the DNA in G2?

A

Signal that this strand has already been replicated, and that this origin was used already (control)

308
Q

What are histones?

A

Proteins that DNA wrap around

309
Q

What happens to histones during DNA replication?

A

They also need to be replicated

310
Q

True or false: DNA replication is the only event that happens during S phase

A

False: histone mRNA also increases (50x)

311
Q

What happens to histone mRNA in S phase?

A

It increases (50x), then degraded after S phase

312
Q

What happens to the “old” histones after they pass the replication fork?

A

They are split randomly between the two strands

313
Q

True or false: an entire “old” histones stays with one DNA strand randomly during replication

A

False: the histone splits into a tetramer and 2 dimers

314
Q

How does the histone split when it is with DNA (during replication)?

A

Tetramer stays with DNA, and 2 dimers are released

315
Q

What is a histone made out of?

A

A tetramer and 2 dimers (3 parts)

316
Q

What happens to the 2 histone dimers after being released?

A

Can be used for any other histones on the DNA

317
Q

What are histone chaperones?

A

Chromatin assembly factors

318
Q

What do histone chaperones do?

A

Assemble dimers and tetramers of histones

319
Q

What proteins assemble histone dimers and tetramers?

A

Histone chaperones

320
Q

Where are histone chaperones localized?

A

Replication fork

321
Q

True or false: in histone replication, all the dimers need to be redone

A

True: half are already there, and half need to be made

322
Q

True or false: in histone replication, all the tetramers need to be redone

A

False: only half need to be redone, since the other half stays bound to DNA

323
Q

What is a telomere?

A

Repeating sequence of nucleotides at the ends of chromosomes

324
Q

What is the telomere sequence in humans?

A

GGGTTA

325
Q

What is the purpose of telomeres?

A

Act as a buffer zone for the genes, since the ends of DNA don’t get replicated

326
Q

Why do we need telomeres?

A

The ends of DNA don’t get replicated properly (due to lagging strand primer on end), so we need a buffer zone

327
Q

What does telomerase do?

A

Recognizes and replenishes telomeres

328
Q

What enzyme recognizes and replenishes telomeres?

A

Telomerase

329
Q

Why are the ends of DNA hard to replicate?

A

Lagging strand can’t put a primer on the last portion of DNA, so it cannot be replicated

330
Q

What is the thought concerning telomerase and telomeres?

A

They are related to aging (longer telomeres means shorter age)

331
Q

What type of enzyme is telomerase?

A

A reverse transcriptase

332
Q

How does telomerase works?

A

Creates an RNA template, which can be used to replicate the DNA (by polyermase)

333
Q

True or false: telomerase is more than just protein

A

True: it also has RNA to recognize DNA strand

334
Q

How much do telomeres shrink by?

A

~100 nucleotides per division

BME 501 (5 decks)

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