Section 2 - Proteins and Nucleic Acids Flashcards
1
Q
What are the most structurally complex and functionally sophisticated molecules known?
A
Proteins
2
Q
What gives proteins their unique shapes?
A
A unique amino acid sequence, which defines shape and function
3
Q
How many different types of amino acids are there?
A
20
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)
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
6
Q
What bonds hold amino acids together?
A
Covalent peptide bonds
7
Q
What reactions form peptide bonds?
A
Condensation reactions
8
Q
How do secondary (noncovalent) bonds arise in proteins?
A
Different side chains of amino acids
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
10
Q
What enantiomers do proteins consist of?
A
L amino acids
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
12
Q
What is the n-terminus of a protein?
A
Where the free amino group is (start)
13
Q
What is the c-terminus of a protein?
A
Where the free carboxylic acid group is (end)
14
Q
What groups of side chains are there for an amino acid?
A
Basic, acidic, uncharged polar, and disulfide
15
Q
What is the side chain for glycine?
A
H
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)
17
Q
What are the special amino acids?
A
Serine, threonine, and tyrosine
18
Q
What group do the special amino acids belong to?
A
Uncharged polar
19
Q
What is the common structural motif of the special amino acids?
A
OH group
20
Q
What is special about the special amino acids?
A
Kinases add phosphate groups to those three amino acids (serine, threonine, and tyrosine)
21
Q
Which bonds dictate protein folding?
A
Weaker (noncovalent) bonds
22
Q
What principle does protein folding operate under?
A
Fold to minimize energy
23
Q
What considerations are needed for protein folding to minimize energy?
A
Weak bonding events, sterics, etc.
24
Q
What is the 3D structure of a protein determined by?
A
Amino acid sequence, and how they interact
25
What is the conformation of a protein?
Final 3D shape
26
What is sterics?
Two molecules can't be in the same place at the same time (dictates folding)
27
What is the advantage of using weaker bonds for protein folding (as opposed to covalent bonds)?
Allows for flexibility in the shape of the proteins
28
Why do proteins need some flexibility in their shapes?
Allows for catalysis events and other functions
29
In an aqueous environment, where are the hydrophilic side chains found?
On the outside of the protein (near water)
30
In an aqueous environment, where are the hydrophobic side chains found?
On the inside of the protein (away from water)
31
How can active zones of a protein be shielded by water?
By having them in the hydrophobic core of the protein
32
True or false: there are rotations around peptide bonds
True: all single bonds (such as peptide bonds) allow for rotation
33
What are molecular chaperones?
Proteins that bind to partially folded proteins
34
What do molecular chaperones do?
Help proteins fold, and mark that the protein is not folded
35
What are the common folding motifs in proteins?
Alpha helices, and beta sheets
36
What drives secondary structure in proteins?
H-bonding between N-H and C=O (in peptide backbone)
37
What are the advantages of alpha helices?
Increase packing density, can make large hydrophilic or large hydrophobic regions
38
Why would you want large hydrophilic or hydrophobic regions in a protein?
Transmembrane proteins (needs to be hydrophobic or hydrophilic along the membrane)
39
What structure allows for large hydrophilic or hydrophobic regions in a protein?
Alpha helices
40
What are the advantages of beta sheets?
Packing density
41
What are the two organizations of beta sheets?
Parallel and antiparallel
42
What is the structure of parallel beta pleated sheets?
/\ /\ /\
43
What is the structure of antiparallel beta pleasted sheets?
/\ \/ /\
44
Which beta pleated sheets are more common?
Antiparallel
45
Why are antiparallel beta pleated sheets more common?
Smaller loop (less amino acids/ secondary structures) and stronger H bonds (close together)
46
For parallel beta pleasted sheets, how are the loops generated?
Usually through alpha helices
47
How many levels of protein organization are there?
4
48
What is the primary structure of a protein?
Amino acid sequence
49
What is the secondary structure of a protein?
Alpha helices and beta pleated sheets
50
What is the tertiary structure of a protein?
Full 3D structure
51
What is the quaternary structure of a protein?
Different polypeptides interacting with each other
52
What are the four ways to represent a protein?
Scribble, secondary structures, space filling, and side chains
53
What is a protein domain?
A functional sub-section of a protein
54
True or false: domains are not conserved between proteins or species
False: a domain can be conserved between different proteins or species
55
What is an example of a conserved protein domain?
Src domain (SH2) (helps with docking)
56
What are protein families?
Groups of proteins with a similar function
57
True or false: protein families have similar structures and amino acid sequences
True: since their function is similar, their structure and amino acid sequence are also similar
58
What do serine proteases do?
Use an active serine to digest proteins
59
What is an example of a protein family?
Serine proteases
60
True or false: humans have significantly more genes than other organisms
False: we only have at most 2x the amount of genes in other organisms, and 7% of our genes are vertebrate specific
61
How does human complexity arise?
Protein domains and modules can interact with many different proteins, thus creating many functions between proteins
62
What are protein modules?
Small protein domains
63
How can larger protein structures form?
Disulfide bonds, self-assembly (aided by other molecules)
64
What forms can assembled protein monomers take?
Dimers, helices, rings, etc.
65
What does "assembly on a core" refer to?
One protein can act as a core, while other proteins can attached to that
66
What does "accumulated strain" refer to?
Proteins aligning into different arrays for increased stress bearing
67
What does "vernier mechanism" refer to?
Multiple proteins can hook together (based on protrusions) to create larger structures
68
True or false: the mechanical motions of the protein are directly coupled to chemical events
True: this provides an extraordinary set of dynamic events for the cell
69
What is an example of mechanical motion being coupled to chemical events?
An enzyme can physically move two substrates together, perform a chemical reaction, then move to release them
70
True or false: a protein can only function if it interacts with other molecules
True: there needs to be some binding for a reaction or function to occur
71
True or false: the binding strength for a particular protein is very specific
True: this allows for the specified reaction to occur
72
What is a ligand?
The molecule that binds to the protein
73
True or false: ligand binding to a protein is very weak
False: the binding can be strong or weak depending on the protein and ligand
74
What two checks will proteins use to make sure the ligand is correct?
A shape check (does it fit correctly), and a binding check (are the noncovalent bonds right)?
75
How does a protein aid in ligand binding?
Through its folding and amino acid side chains
76
What would happen if a binding site is on the exterior of a protein?
There would be competition between the ligand and water molecules
77
What is the risk of having water molecules bind to a binding site on a protein?
This could affect noncovalent bonds, and thus the protein check for the proper ligand
78
What are the most common interactions between a ligand and an enzyme?
Hydrogen binding, or electrostatic interactions
79
How do electrostatic interactions aid in ligand binding?
Enhance reactivity of enzymes (activate side chains on amino acids)
80
What is the equilibrium constant (K)?
A measure of binding strength
81
How is K calcualted?
Association rate / dissociation rate
82
If a reaction has a high K, what does that mean?
There is a high association rate
83
If a reaction has a low K, what does that mean?
There is a high dissociation rate
84
What do "on" kinetics refer to?
Association
85
What do "off" kinetics refer to?
Dissociation
86
What do hydrolases do?
Catalyze hydrolytic cleavage reaction (such as proteases, nucleases, etc.)
87
What do nucleases do?
Break down nucleic acids
88
What do proteases do?
Break down proteins
89
What do synthases do?
Synthesize molecules (anabolic reactions)
90
What do ligases do?
Join together two molecules
91
What do isomerases do?
Catalyze the rearrangement of bonds
92
What do polymerases do?
Catalyze polymerization reactions (DNA, RNA, etc.)
93
What do kinases do?
Add phosphate groups to molecules
94
What do phosphatases do?
Remove phosphate groups from molecules
95
What do oxido-reductases do?
Catalyzed oxidation-reduction reactions
96
What do ATPases do?
Hydrolyze ATP (harvest energy)
97
What do GTPases do?
Hydrolyze GTP (G-protein signaling)
98
True or false: all enzymes end with "-ase"
False: most enzymes do, but some (ex: pepsin) do not
99
What is the general process for enzyme functions?
E + S -> ES -> EP -> E + P
100
If substrate concentration increases, what happens to the rate of product formation?
It increases (up to a point)
101
What is Vmax?
The maximal reaction rate
102
What is Km?
The subtrate concentration to work at half of the maximal rate (Vmax)
103
What can you say about an enzyme that has a low Km?
Enzyme binds tightly, and thus need less substrate to get a maximal response
104
What can you say about an enzyme that has a high Km?
Enzyme binds weakly, and thus needs lots of substrate to get a maximal response
105
What are the constraints of how fast an enzyme reacts?
Inherent movements of protein (molecularly)
106
What would be an "optimal" enzyme (in terms of Vmax and Km)?
A high Vmax (high rate), and a low Km (low substrate to achieve rate)
107
How do enzymes work?
They stabilize any intermediary products
108
How does stabilizing the intermediary help reduce activation energy?
The free energy is reduced, thus making it easier to reach the transition state
109
Assuming that S has more energy than P, rate the following in terms of increasing energy: S, P, St
P, S, St
110
Assuming that S has more energy than P, rate the following in terms of increasing energy, S, P, ES, EP, ESt
EP, P, ES, S, ESt
111
Which is more stable: S or ES?
ES (lower energy)
112
Which is more stable: P or EP?
EP (lower energy)
113
In terms of stabilization and energy, how does an enzyme catalyze a reaction?
The activation energy from S to St is less than the activation energy from ES to ESt
114
Why does ES and EP have lower energies than S and P, respectively?
Bonding events stabilizes the molecules in the enzyme
115
Which is more stable: St or ESt?
ESt (lower energy)
116
How does EP go to P?
Enzyme is not stable as EP, so it can use an activate carrier or a conformational change to remove P
117
Which is more stable: E or EP?
E (more stable by itself, so it can remove P)
118
How do cells control the quantity of enzymes present?
Via gene expression
119
How is ligand/enzyme binding restricted?
Through localization
120
What does proteolysis control?
Quantity of formed enzymes present
121
How is regulation present in protein pathways?
Through feedback mechanisms
122
What questions (from a control perspective) are important for enzyme reactions?
Which enzymes are turned on/off, and when
123
What are the typical sites on an enzyme?
Ligand binding sites and regulatory binding sites
124
How is the rate of enzyme activity controlled?
Regulatory molecule binding (negative or positive)
125
Are most biological mechanisms negative or positive feedback?
Negative feedback
126
What is negative feedback?
(Usually) a downstream product inhibits an upstream protein
127
What is positive feedback?
(Usually) an upstream product activates a downstream protein
128
Why can ADP be considered more biologically active than ATP?
ADP can start many reactions through cell signaling (make more ATP)
129
True or false: regulatory binding sites can be positive or negative
True: there are different effects based on the specific protein
130
True or false: a pathway can only have either positive or negative feedback
False: there can be a smaller loop of positive feedback inside a larger loop of negative feedback
131
What are the three examples of positive feedback in biology?
Inflammation, coagulation, and child birthing
132
What happens when a molecule binds to a regulatory site?
Change in conformation, which changes activity
133
In an engineering perspective, how does a molecule binding to a regulatory site alter the the enzyme?
Changes the kinetics (need to know conditions)
134
How come enzymes can be described as a "dial"?
Range of control, from both positive and negative inputs
135
True or false: enzymes cannot function without its regulatory molecule (positive)
False: they just function very slowly
136
Do most enzymes catalyze one reaction, or many?
One (easier from a biological perspective)
137
What is the charge of a phosphate group?
2 negative charges
138
Why can phosphates alter the activity of proteins?
Can drastically alter the conformation of the protein (due to highly negative charge)
139
True or false: phosphorylation always leads to activation
False: it can also lead to inhibition
140
True or false: phosphorylation is a repeatable process
True: unlike mechanical processes, it can be repeated very often without significant wear
141
What can phosphorylation do (other than activate a protein by changing conformation)?
Can act as docking sites to attract other regulatory proteins to drive assembly
142
Where is phosphorylation most commonly seen?
Signal transduction pathways
143
What causes mechanical motion in biology?
Motor proteins
144
What do motor proteins do?
Undergo conformation changes to induce motion
145
What functions are motor proteins seen in?
Muscle contraction, organelle movement, chromosome movement)
146
What are some examples of motor proteins?
Myosin, kinesin, and DNA helicases
147
What is the speed of DNA helicase?
1000 nt/s
148
How to motor proteins keep moving forward (and not randomly)?
Have an irreversible step that requires a large amount of energy (ATP hydrolysis)
149
What is the challenge of motor proteins?
Overcome thermodynamics and cause unidirectional motion
150
What is meant by an "irreversible" reaction?
Large energy to go in the backwards direction, so it rarely happens
151
What is the irreversible step in motor protein movement?
ATP hydrolysis
152
What does myosin do?
Aids in muscle contraction
153
What does kinesin do?
Aids in organelle movement
154
What does DNA helicase do?
Used during DNA replication (unzip DNA)
155
What was the controversy in the 1940s?
Most people did not accept a simple structure for complicated DNA molecule
156
What led to an understanding of the function of DNA?
Discovery of double helix DNA structure
157
What is the structure of DNA?
Two complementary strands help together by H-bonds
158
What holds the two strands of DNA together?
H-bonds
159
What is DNA composed of?
A sugar (deoxyribose), a base (A, C, T, G), and a phosphate group
160
What composes the backbone of DNA?
Sugar and phosphate group
161
What holds the backbone of DNA together?
Covalent bonds
162
How many H-bonds are between C and G?
3
163
How many H-bonds are between A and T?
2
164
What is the structure of the purines?
2 rings
165
What is the structure of the pyrimidines?
1 ring
166
What bases are purines?
A, G
167
What bases are pyrimidines?
C, U, T
168
True or false: the DNA helix is symmetrical
False: there is a major and a minor groove
169
How is the major groove seen in DNA?
The large gap in the twists
170
How is the minor groove seen in DNA?
The small gap in the twists
171
Why is DNA always the same size across?
A purine always binds with a pyrimidine
172
What determines the exact base binding?
Size (a purine must bind to a pyrimidine) and H-bonds (2 vs 3)
173
How far apart are the sugar molecules in DNA?
0.34 nm
174
How long is one full turn of DNA?
10 base pairs (3.4 nm)
175
How are the bases arranged in DNA (in terms of space)?
Similar to steps on a staircase
176
Why are DNA bases arranged similar to steps on a staircase?
Stop extra H-bond interactions between different base pairs
177
What is the 5' end of DNA?
Phosphate group (5' carbon)
178
What is the 3' end of DNA?
Hydroxyl group (3' carbon)
179
What is the importance of the major / minor groove?
Gene regulation
180
How did the structure of DNA show a link to its function in genetics?
Structure suggests that strands could be replicated if pulled apart
181
How much DNA is found in cells?
2m
182
What percentage of volume does the nucleus make up?
~10%
183
What does the nuclear envelope do?
Concentrates all important molecules near DNA
184
Which is more selective: nuclear envelope or plasma membrane?
Nuclear envelope
185
What do nuclear pores do?
Allow for passage between nucleus and cytosol
186
How is control seen in the nuclear envelope?
Lots of control regarding the passage of molecules into and out of the nucleus
187
Why is accurate duplication of DNA needed?
Needed to ensure template / product is accurate
188
True or false: there is backup DNA if the old copy gets "corrupted"
False: there is no backup DNA present
189
What happens if DNA maintenance does not occur?
Passage of genetic material is not stable
190
True or false: not having DNA maintenance is always bad
False: while it is usually bad, it can also lead to mutations that increases survivability
191
What is a mutation?
A change in the DNA sequence
192
When does a mutation have no effect?
If it occurs in the non-coding region, or if it doesn't change the conformation
193
What is a silent mutation?
A mutation that have no effect on the subsequent protein structure
194
What is the mutation rate in E. Coli?
~1 nt/ 10^9 nt (per cell generation)
195
What is the mutation rate in humans?
~ 1 random, non-silent mutation / 200000 years (in a typical protein)
196
What plot can be used to show which proteins are critical for life (unchanged)?
Plot (survivable) changes per time
197
In a plot of survivable changes per time, what slope corresponds to a protein that is critical for life (unchanged)?
Shallow slope (few changes)
198
In a plot of survivable changes per time, what slope corresponds to a protein that is not critical for life (unchanged)?
Steep slope (many changes)
199
What is an example of a protein that is critical for life (unchanged)?
Histones
200
What do histones do that makes then critical for life (unchanged)?
Need to wrap around DNA to condense it
201
What is an example of a protein that is not critical for life (unchanged)?
Fibrinopeptides
202
What do fibrinopeptides do that makes then not critical for life (unchanged)?
Just needs to be soluble
203
What is DNA replication based on?
Being able to recognize the partner base pair based on the template strand
204
What is meant by "semiconservative"?
One template strand is used to synthesize the complementary strand
205
What are the incoming nucleotides for DNA replication?
Triphosphates
206
What drives the energy of DNA replication?
Removal of a pyrophosphate (P-P) from a nucleotide triphosphate
207
How is the information in DNA "read" for DNA replication?
H-bonds in the center are separated, and H-bonds on bases can be read
208
What determines what the next base will be in DNA replication?
Based on the new H-binding events (donors / acceptors)
209
What is the DNA replication fork?
The Y-shaped region of DNA where DNA replication is happening (lots of enzymes / nucleotides)
210
True or false: the DNA replication fork is symmetrical
False: one side goes from 5' -> 3', and the other side goes from 3' -> 5'
211
What does DNA polymerase do?
Creates new DNA
212
Which enzyme is responsible for creating new DNA?
DNA polymerase
213
What direction does DNA polymerase work in?
5' to 3' direction
214
What is the leading strand?
The strand that is formed continuously (3' to 5') (towards fork)
215
What is the lagging strand?
The strand that is formed discontinuously (5' to 3') (away from fork)
216
What are Okazaki fragments?
Small DNA fragments on the lagging strand of DNA
217
What is the structure of DNA polymerase?
Similar to a neck pillow
218
What is found in the "channel" of DNA polymerase?
Pool of nucleotide triphosphates
219
True or false: DNA polymerase can read the DNA strand to find the matching nucleotide
False: the right nucleotide comes in based on H-bonding and fusion length of the bases
220
What happens to DNA polymerase if the nucleotide is correct?
The DNA shifts down
221
What happens to DNA polyermase if the nucleotide is incorrect?
The DNA stalls in the polymerase
222
True or false: single stranded DNA is stable
False: it has weird kinks and folds (trying to stabilize itself with a double strand), showing that it is unstable
223
When does DNA polymerase stop?
When it sees double stranded DNA
224
What is the shape of bacterial DNA?
Circular
225
How many origins of replication are found in mammalian DNA?
Many different sites (bubbles) throughout the chromosome
226
What are some possible mutations (based on base binding)?
G can bind to T with some small changes in helix geometry, and C isoforms can bind to both A and G
227
How many checks does DNA polymerase do for proofreading?
2
228
What is the first proofreading check of DNA polymerase?
Check H-bonds
229
Why do mismatched bases fall off easily?
High dissociation constant
230
What is the second proofreading check of DNA polymerase?
Check backbone (gets stalled if not aligned)
231
How does DNA polymerase fix backbone issues?
Has exonucleolytic site to remove a mismatched base pair
232
What is the P site on DNA polymerase?
Polymerizing site (make more DNA)
233
What is the E site on DNA polymerase?
Exonucleolytic site (remove mismatched bases)
234
What does DNA polymerase need to start replication?
Primer
235
Why does DNA polymerase need a primer to start replication?
Prevent it from starting anywhere in the DNA
236
What enzyme produces primers?
DNA primase
237
What does DNA primase do?
Produces RNA primers
238
What types of primers are made by DNA primase?
RNA primers
239
True or false: DNA primase has a high accuracy
False: it has a fairly low accuracy
240
What are the problems with DNA primase?
The primers are made of RNA, and how does DNA primase know where to start
241
Why is it ok for DNA primase to be fast but inaccurate?
The primers do not stay on the DNA
242
What does DNA ligase do?
Seals gaps between Okazaki fragments
243
What enzyme seals gaps between Okazaki fragments?
DNA ligase
244
How is DNA polymerase like a snowplow?
The primers are bound so weakly that DNA polymerase can push them away and continue polymerization
245
Why is DNA hard to denature?
It is a very stable molecule
246
What does helicase do?
Opens DNA strands via hydrolysis of ATP
247
What enzyme opens DNA strands?
Helicase
248
What is the structure of helicase?
Circular (donut)
249
True or false: helicase can help stabilize single stranded DNA
True: although this only occurs for a little bit
250
True or false: helicase can open up double stranded DNA
False: it can only work on single stranded DNA (needs to be opened a little bit first)
251
True or false: helicase contains nucleic acids in its structure
True: this is a combined protein / nucleic acid
252
True or false: DNA helicase is very fast
True: once it starts working, it is very fast
253
What is another name for single-strand DNA-binding proteins?
Helix-destabilizing proteins
254
What do single-strand DNA-binding proteins do?
Bind to single stranded DNA to stabilize and straighten it
255
What enzymes bind to single stranded DNA to stabilize and straighten it?
Single-strand DNA-binding proteins
256
What is the structure of single-strand DNA-binding proteins?
Gloves or hands
257
Why does DNA polymerase need to be stabilized?
It favors dissociation kinetics, so it could come off
258
Why are the association kinetics for DNA polymerase binding to DNA low?
Don't want DNA polymerase binding so tightly to DNA
259
What helps hold DNA polymerase in place?
A sliding clamp
260
When does the sliding clamp release?
When DNA polymerase hits double stranded DNA
261
What does the sliding clamp do?
Hold DNA polymerase in place
262
What does a clamp loader do?
Puts the sliding clamp onto the DNA
263
What protein puts the sliding clamp on the DNA?
A clamp loader
264
True or false: lots of control is needed for DNA replication
True: there is a lot of protein machinery that needs to be controlled
265
How does the sliding clamp prevent DNA polymerase from falling off?
Noncovalent binding interactions between sliding clamp and DNA polymerase
266
Why can DNA replication errors be found?
Errors will not form the proper 3D structure
267
How does the cell know which strand of the DNA is the template strand (for mismatch repair)?
Template strand has no nick, and has some methylated A's
268
When do A's get methylated?
A long time after DNA polymerase (separate mechanism)
269
Why does DNA go under tension in DNA replication (if there were no enzymes)?
Similar to braided rope being pulled apart - fold in on itself
270
What does topoisomerase do?
Relieve tension in DNA
271
What enzymes relieve tension in the DNA?
Topoisomerases
272
What is the difference between topoisomerase 1 and topoisomerase 2?
Different mechanisms for the same effect (tension relief)
273
How does topoisomerase 1 work?
It breaks one phosphodiester bond, allowing for free rotation and relief of tension
274
True or false: topoisomerase 1 covalently binds to DNA
True: this is one of the rare cases of proteins being covalently linked to DNA
275
When is DNA attached to a "fixed end"?
In the lab (adhere DNA), or having two replication forks coming together
276
How does topoisomerase 2 work?
It breaks one DNA strand to allow another strand to go through
277
What is the pictorial representation of the topoisomerase 2 mechanism?
/ ____ / ___ _______
| ________ /
278
Where does topoisomerase 2 mainly act (what regions of DNA)?
Loops (where the DNA crosses itself)
279
What is the replication origin?
Where DNA replication occurs
280
How does DNA replication occur?
Through special initiator proteins
281
What is the structure of a replication origin region in DNA?
A/T rich
282
Why is the replication origin region of DNA A and T rich?
Less H-bonds, so easier to break apart
283
True or false: a TATA box refers to the replication origin
False: while replication origins have many A's and T's, the TATA box is not involved in DNA replication
284
If there was only one fork, how long would it take to replicate an entire chromosome?
~800 hours
285
What is meant by "replication units"?
Groups of ~50 origins are arranged into different units
286
Are replication units all activated at the same time?
No: different units are activated at different times
287
How far apart are replication units?
~30K to 250K nucleotides apart
288
What phase of the cell cycle does DNA replication occur in?
S phase
289
How long does S phase take?
~8 hours
290
True or false: chromosome replication happens randomly
False: they are replicated in a controlled manner
291
What is heterochromatin?
DNA in a very condensed state
292
What is euchromatin?
DNA in a less condensed state
293
Which DNA (heterochromatin or euchromatin) is replicated earlier?
Euchromatin
294
What determines whether a gene will be in euchromatin or heterochromatin?
How often that gene needs to be transcribed in that particular cell
295
Where does replication start?
In the middle of the chromosome (not the ends), which spread out
296
What are the three things needed for a sequence to be an origin of replication?
1. Binding site for initiator protein (ORC)
2. Rich A/T region
3. At least one binding site for proteins that attract ORC
297
What does ORC stand for?
Origin recognition complex
298
Why is a binding site for proteins that attract the ORC necessary for an origin of replication?
Without this enhancer protein, the ORC will not bind and start replication
299
What is the ORC regulated by?
Two loading proteins (Cdc6 and Cdt1)
300
What does the prereplicative complex do?
Aids in helicase binding and opening DNA
301
When does loading of the ORC occur?
During G1 phase of cell cycle
302
What happens to the ORC at the beginning of S phase?
Cdk's phosphorylate ORC, activate helicase, and degrade loading proteins
303
What do the loading proteins do (in ORC)?
Keep ORC in place until the S phase
304
Where does the ORC split DNA?
At the A/T regions
305
When is the ORC activated?
At the G1/S boundary (move into S phase)
306
What happens to the ORC in G2?
It stays phosphorylated and on the DNA
307
Why does phosphorylated ORC remain on the DNA in G2?
Signal that this strand has already been replicated, and that this origin was used already (control)
308
What are histones?
Proteins that DNA wrap around
309
What happens to histones during DNA replication?
They also need to be replicated
310
True or false: DNA replication is the only event that happens during S phase
False: histone mRNA also increases (50x)
311
What happens to histone mRNA in S phase?
It increases (50x), then degraded after S phase
312
What happens to the "old" histones after they pass the replication fork?
They are split randomly between the two strands
313
True or false: an entire "old" histones stays with one DNA strand randomly during replication
False: the histone splits into a tetramer and 2 dimers
314
How does the histone split when it is with DNA (during replication)?
Tetramer stays with DNA, and 2 dimers are released
315
What is a histone made out of?
A tetramer and 2 dimers (3 parts)
316
What happens to the 2 histone dimers after being released?
Can be used for any other histones on the DNA
317
What are histone chaperones?
Chromatin assembly factors
318
What do histone chaperones do?
Assemble dimers and tetramers of histones
319
What proteins assemble histone dimers and tetramers?
Histone chaperones
320
Where are histone chaperones localized?
Replication fork
321
True or false: in histone replication, all the dimers need to be redone
True: half are already there, and half need to be made
322
True or false: in histone replication, all the tetramers need to be redone
False: only half need to be redone, since the other half stays bound to DNA
323
What is a telomere?
Repeating sequence of nucleotides at the ends of chromosomes
324
What is the telomere sequence in humans?
GGGTTA
325
What is the purpose of telomeres?
Act as a buffer zone for the genes, since the ends of DNA don't get replicated
326
Why do we need telomeres?
The ends of DNA don't get replicated properly (due to lagging strand primer on end), so we need a buffer zone
327
What does telomerase do?
Recognizes and replenishes telomeres
328
What enzyme recognizes and replenishes telomeres?
Telomerase
329
Why are the ends of DNA hard to replicate?
Lagging strand can't put a primer on the last portion of DNA, so it cannot be replicated
330
What is the thought concerning telomerase and telomeres?
They are related to aging (longer telomeres means shorter age)
331
What type of enzyme is telomerase?
A reverse transcriptase
332
How does telomerase works?
Creates an RNA template, which can be used to replicate the DNA (by polyermase)
333
True or false: telomerase is more than just protein
True: it also has RNA to recognize DNA strand
334
How much do telomeres shrink by?
~100 nucleotides per division
