Section 2 - Proteins and Nucleic Acids Flashcards
What are the most structurally complex and functionally sophisticated molecules known?
Proteins
What gives proteins their unique shapes?
A unique amino acid sequence, which defines shape and function
How many different types of amino acids are there?
20
How come DNA is not as functionally sophisticated or functionally complex as proteins?
DNA has a relatively simple structure (regular) and function (storage)
Why is a protein structurally complex and functionally sophisticated?
Proteins do every function in the cell, and have structures that cannot be generalized
What bonds hold amino acids together?
Covalent peptide bonds
What reactions form peptide bonds?
Condensation reactions
How do secondary (noncovalent) bonds arise in proteins?
Different side chains of amino acids
What is the general amino acid structure?
A central carbon, which connects an amino group, a carboxylic acid group, a hydrogen, and an R group
What enantiomers do proteins consist of?
L amino acids
How is a peptide bond formed?
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
What is the n-terminus of a protein?
Where the free amino group is (start)
What is the c-terminus of a protein?
Where the free carboxylic acid group is (end)
What groups of side chains are there for an amino acid?
Basic, acidic, uncharged polar, and disulfide
What is the side chain for glycine?
H
True or false: amino acids in the same group have very similar structures
False: there can be very different structures in the same group (such as nonphobic)
What are the special amino acids?
Serine, threonine, and tyrosine
What group do the special amino acids belong to?
Uncharged polar
What is the common structural motif of the special amino acids?
OH group
What is special about the special amino acids?
Kinases add phosphate groups to those three amino acids (serine, threonine, and tyrosine)
Which bonds dictate protein folding?
Weaker (noncovalent) bonds
What principle does protein folding operate under?
Fold to minimize energy
What considerations are needed for protein folding to minimize energy?
Weak bonding events, sterics, etc.
What is the 3D structure of a protein determined by?
Amino acid sequence, and how they interact
What is the conformation of a protein?
Final 3D shape
What is sterics?
Two molecules can’t be in the same place at the same time (dictates folding)
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
Why do proteins need some flexibility in their shapes?
Allows for catalysis events and other functions
In an aqueous environment, where are the hydrophilic side chains found?
On the outside of the protein (near water)
In an aqueous environment, where are the hydrophobic side chains found?
On the inside of the protein (away from water)
How can active zones of a protein be shielded by water?
By having them in the hydrophobic core of the protein
True or false: there are rotations around peptide bonds
True: all single bonds (such as peptide bonds) allow for rotation
What are molecular chaperones?
Proteins that bind to partially folded proteins
What do molecular chaperones do?
Help proteins fold, and mark that the protein is not folded
What are the common folding motifs in proteins?
Alpha helices, and beta sheets
What drives secondary structure in proteins?
H-bonding between N-H and C=O (in peptide backbone)
What are the advantages of alpha helices?
Increase packing density, can make large hydrophilic or large hydrophobic regions
Why would you want large hydrophilic or hydrophobic regions in a protein?
Transmembrane proteins (needs to be hydrophobic or hydrophilic along the membrane)
What structure allows for large hydrophilic or hydrophobic regions in a protein?
Alpha helices
What are the advantages of beta sheets?
Packing density
What are the two organizations of beta sheets?
Parallel and antiparallel
What is the structure of parallel beta pleated sheets?
/\ /\ /\
What is the structure of antiparallel beta pleasted sheets?
/\ \/ /\
Which beta pleated sheets are more common?
Antiparallel
Why are antiparallel beta pleated sheets more common?
Smaller loop (less amino acids/ secondary structures) and stronger H bonds (close together)
For parallel beta pleasted sheets, how are the loops generated?
Usually through alpha helices
How many levels of protein organization are there?
4
What is the primary structure of a protein?
Amino acid sequence
What is the secondary structure of a protein?
Alpha helices and beta pleated sheets
What is the tertiary structure of a protein?
Full 3D structure
What is the quaternary structure of a protein?
Different polypeptides interacting with each other
What are the four ways to represent a protein?
Scribble, secondary structures, space filling, and side chains
What is a protein domain?
A functional sub-section of a protein
True or false: domains are not conserved between proteins or species
False: a domain can be conserved between different proteins or species
What is an example of a conserved protein domain?
Src domain (SH2) (helps with docking)
What are protein families?
Groups of proteins with a similar function
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
What do serine proteases do?
Use an active serine to digest proteins
What is an example of a protein family?
Serine proteases
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
How does human complexity arise?
Protein domains and modules can interact with many different proteins, thus creating many functions between proteins
What are protein modules?
Small protein domains
How can larger protein structures form?
Disulfide bonds, self-assembly (aided by other molecules)
What forms can assembled protein monomers take?
Dimers, helices, rings, etc.
What does “assembly on a core” refer to?
One protein can act as a core, while other proteins can attached to that
What does “accumulated strain” refer to?
Proteins aligning into different arrays for increased stress bearing
What does “vernier mechanism” refer to?
Multiple proteins can hook together (based on protrusions) to create larger structures
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
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
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
True or false: the binding strength for a particular protein is very specific
True: this allows for the specified reaction to occur
What is a ligand?
The molecule that binds to the protein
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
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)?
How does a protein aid in ligand binding?
Through its folding and amino acid side chains
What would happen if a binding site is on the exterior of a protein?
There would be competition between the ligand and water molecules
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
What are the most common interactions between a ligand and an enzyme?
Hydrogen binding, or electrostatic interactions
How do electrostatic interactions aid in ligand binding?
Enhance reactivity of enzymes (activate side chains on amino acids)
What is the equilibrium constant (K)?
A measure of binding strength
How is K calcualted?
Association rate / dissociation rate
If a reaction has a high K, what does that mean?
There is a high association rate
If a reaction has a low K, what does that mean?
There is a high dissociation rate
What do “on” kinetics refer to?
Association
What do “off” kinetics refer to?
Dissociation
What do hydrolases do?
Catalyze hydrolytic cleavage reaction (such as proteases, nucleases, etc.)
What do nucleases do?
Break down nucleic acids
What do proteases do?
Break down proteins
What do synthases do?
Synthesize molecules (anabolic reactions)
What do ligases do?
Join together two molecules
What do isomerases do?
Catalyze the rearrangement of bonds
What do polymerases do?
Catalyze polymerization reactions (DNA, RNA, etc.)
What do kinases do?
Add phosphate groups to molecules
What do phosphatases do?
Remove phosphate groups from molecules
What do oxido-reductases do?
Catalyzed oxidation-reduction reactions
What do ATPases do?
Hydrolyze ATP (harvest energy)
What do GTPases do?
Hydrolyze GTP (G-protein signaling)
True or false: all enzymes end with “-ase”
False: most enzymes do, but some (ex: pepsin) do not
What is the general process for enzyme functions?
E + S -> ES -> EP -> E + P
If substrate concentration increases, what happens to the rate of product formation?
It increases (up to a point)
What is Vmax?
The maximal reaction rate
What is Km?
The subtrate concentration to work at half of the maximal rate (Vmax)
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
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
What are the constraints of how fast an enzyme reacts?
Inherent movements of protein (molecularly)
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)
How do enzymes work?
They stabilize any intermediary products
How does stabilizing the intermediary help reduce activation energy?
The free energy is reduced, thus making it easier to reach the transition state
Assuming that S has more energy than P, rate the following in terms of increasing energy: S, P, St
P, S, St
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
Which is more stable: S or ES?
ES (lower energy)
Which is more stable: P or EP?
EP (lower energy)
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
Why does ES and EP have lower energies than S and P, respectively?
Bonding events stabilizes the molecules in the enzyme
Which is more stable: St or ESt?
ESt (lower energy)
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
Which is more stable: E or EP?
E (more stable by itself, so it can remove P)
How do cells control the quantity of enzymes present?
Via gene expression
How is ligand/enzyme binding restricted?
Through localization
What does proteolysis control?
Quantity of formed enzymes present
How is regulation present in protein pathways?
Through feedback mechanisms
What questions (from a control perspective) are important for enzyme reactions?
Which enzymes are turned on/off, and when
What are the typical sites on an enzyme?
Ligand binding sites and regulatory binding sites
How is the rate of enzyme activity controlled?
Regulatory molecule binding (negative or positive)
Are most biological mechanisms negative or positive feedback?
Negative feedback
What is negative feedback?
(Usually) a downstream product inhibits an upstream protein
What is positive feedback?
(Usually) an upstream product activates a downstream protein
Why can ADP be considered more biologically active than ATP?
ADP can start many reactions through cell signaling (make more ATP)
True or false: regulatory binding sites can be positive or negative
True: there are different effects based on the specific protein
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
What are the three examples of positive feedback in biology?
Inflammation, coagulation, and child birthing
What happens when a molecule binds to a regulatory site?
Change in conformation, which changes activity
In an engineering perspective, how does a molecule binding to a regulatory site alter the the enzyme?
Changes the kinetics (need to know conditions)
How come enzymes can be described as a “dial”?
Range of control, from both positive and negative inputs
True or false: enzymes cannot function without its regulatory molecule (positive)
False: they just function very slowly
Do most enzymes catalyze one reaction, or many?
One (easier from a biological perspective)
What is the charge of a phosphate group?
2 negative charges
Why can phosphates alter the activity of proteins?
Can drastically alter the conformation of the protein (due to highly negative charge)
True or false: phosphorylation always leads to activation
False: it can also lead to inhibition
True or false: phosphorylation is a repeatable process
True: unlike mechanical processes, it can be repeated very often without significant wear
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
Where is phosphorylation most commonly seen?
Signal transduction pathways
What causes mechanical motion in biology?
Motor proteins
What do motor proteins do?
Undergo conformation changes to induce motion
What functions are motor proteins seen in?
Muscle contraction, organelle movement, chromosome movement)
What are some examples of motor proteins?
Myosin, kinesin, and DNA helicases
What is the speed of DNA helicase?
1000 nt/s
How to motor proteins keep moving forward (and not randomly)?
Have an irreversible step that requires a large amount of energy (ATP hydrolysis)
What is the challenge of motor proteins?
Overcome thermodynamics and cause unidirectional motion
What is meant by an “irreversible” reaction?
Large energy to go in the backwards direction, so it rarely happens
What is the irreversible step in motor protein movement?
ATP hydrolysis
What does myosin do?
Aids in muscle contraction
What does kinesin do?
Aids in organelle movement
What does DNA helicase do?
Used during DNA replication (unzip DNA)
What was the controversy in the 1940s?
Most people did not accept a simple structure for complicated DNA molecule
What led to an understanding of the function of DNA?
Discovery of double helix DNA structure
What is the structure of DNA?
Two complementary strands help together by H-bonds
What holds the two strands of DNA together?
H-bonds
What is DNA composed of?
A sugar (deoxyribose), a base (A, C, T, G), and a phosphate group
What composes the backbone of DNA?
Sugar and phosphate group
What holds the backbone of DNA together?
Covalent bonds
How many H-bonds are between C and G?
3
How many H-bonds are between A and T?
2
What is the structure of the purines?
2 rings
What is the structure of the pyrimidines?
1 ring
What bases are purines?
A, G
What bases are pyrimidines?
C, U, T
True or false: the DNA helix is symmetrical
False: there is a major and a minor groove
How is the major groove seen in DNA?
The large gap in the twists
How is the minor groove seen in DNA?
The small gap in the twists
Why is DNA always the same size across?
A purine always binds with a pyrimidine
What determines the exact base binding?
Size (a purine must bind to a pyrimidine) and H-bonds (2 vs 3)
How far apart are the sugar molecules in DNA?
0.34 nm
How long is one full turn of DNA?
10 base pairs (3.4 nm)
How are the bases arranged in DNA (in terms of space)?
Similar to steps on a staircase
Why are DNA bases arranged similar to steps on a staircase?
Stop extra H-bond interactions between different base pairs
What is the 5’ end of DNA?
Phosphate group (5’ carbon)
What is the 3’ end of DNA?
Hydroxyl group (3’ carbon)
What is the importance of the major / minor groove?
Gene regulation
How did the structure of DNA show a link to its function in genetics?
Structure suggests that strands could be replicated if pulled apart
How much DNA is found in cells?
2m
What percentage of volume does the nucleus make up?
~10%
What does the nuclear envelope do?
Concentrates all important molecules near DNA
Which is more selective: nuclear envelope or plasma membrane?
Nuclear envelope
What do nuclear pores do?
Allow for passage between nucleus and cytosol
How is control seen in the nuclear envelope?
Lots of control regarding the passage of molecules into and out of the nucleus
Why is accurate duplication of DNA needed?
Needed to ensure template / product is accurate
True or false: there is backup DNA if the old copy gets “corrupted”
False: there is no backup DNA present
What happens if DNA maintenance does not occur?
Passage of genetic material is not stable
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
What is a mutation?
A change in the DNA sequence
When does a mutation have no effect?
If it occurs in the non-coding region, or if it doesn’t change the conformation
What is a silent mutation?
A mutation that have no effect on the subsequent protein structure
What is the mutation rate in E. Coli?
~1 nt/ 10^9 nt (per cell generation)
What is the mutation rate in humans?
~ 1 random, non-silent mutation / 200000 years (in a typical protein)
What plot can be used to show which proteins are critical for life (unchanged)?
Plot (survivable) changes per time
In a plot of survivable changes per time, what slope corresponds to a protein that is critical for life (unchanged)?
Shallow slope (few changes)
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)
What is an example of a protein that is critical for life (unchanged)?
Histones
What do histones do that makes then critical for life (unchanged)?
Need to wrap around DNA to condense it
What is an example of a protein that is not critical for life (unchanged)?
Fibrinopeptides
What do fibrinopeptides do that makes then not critical for life (unchanged)?
Just needs to be soluble
What is DNA replication based on?
Being able to recognize the partner base pair based on the template strand
What is meant by “semiconservative”?
One template strand is used to synthesize the complementary strand
What are the incoming nucleotides for DNA replication?
Triphosphates
What drives the energy of DNA replication?
Removal of a pyrophosphate (P-P) from a nucleotide triphosphate
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
What determines what the next base will be in DNA replication?
Based on the new H-binding events (donors / acceptors)
What is the DNA replication fork?
The Y-shaped region of DNA where DNA replication is happening (lots of enzymes / nucleotides)
True or false: the DNA replication fork is symmetrical
False: one side goes from 5’ -> 3’, and the other side goes from 3’ -> 5’
What does DNA polymerase do?
Creates new DNA
Which enzyme is responsible for creating new DNA?
DNA polymerase
What direction does DNA polymerase work in?
5’ to 3’ direction
What is the leading strand?
The strand that is formed continuously (3’ to 5’) (towards fork)
What is the lagging strand?
The strand that is formed discontinuously (5’ to 3’) (away from fork)
What are Okazaki fragments?
Small DNA fragments on the lagging strand of DNA
What is the structure of DNA polymerase?
Similar to a neck pillow
What is found in the “channel” of DNA polymerase?
Pool of nucleotide triphosphates
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
What happens to DNA polymerase if the nucleotide is correct?
The DNA shifts down
What happens to DNA polyermase if the nucleotide is incorrect?
The DNA stalls in the polymerase
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
When does DNA polymerase stop?
When it sees double stranded DNA
What is the shape of bacterial DNA?
Circular
How many origins of replication are found in mammalian DNA?
Many different sites (bubbles) throughout the chromosome
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
How many checks does DNA polymerase do for proofreading?
2
What is the first proofreading check of DNA polymerase?
Check H-bonds
Why do mismatched bases fall off easily?
High dissociation constant
What is the second proofreading check of DNA polymerase?
Check backbone (gets stalled if not aligned)
How does DNA polymerase fix backbone issues?
Has exonucleolytic site to remove a mismatched base pair
What is the P site on DNA polymerase?
Polymerizing site (make more DNA)
What is the E site on DNA polymerase?
Exonucleolytic site (remove mismatched bases)
What does DNA polymerase need to start replication?
Primer
Why does DNA polymerase need a primer to start replication?
Prevent it from starting anywhere in the DNA
What enzyme produces primers?
DNA primase
What does DNA primase do?
Produces RNA primers
What types of primers are made by DNA primase?
RNA primers
True or false: DNA primase has a high accuracy
False: it has a fairly low accuracy
What are the problems with DNA primase?
The primers are made of RNA, and how does DNA primase know where to start
Why is it ok for DNA primase to be fast but inaccurate?
The primers do not stay on the DNA
What does DNA ligase do?
Seals gaps between Okazaki fragments
What enzyme seals gaps between Okazaki fragments?
DNA ligase
How is DNA polymerase like a snowplow?
The primers are bound so weakly that DNA polymerase can push them away and continue polymerization
Why is DNA hard to denature?
It is a very stable molecule
What does helicase do?
Opens DNA strands via hydrolysis of ATP
What enzyme opens DNA strands?
Helicase
What is the structure of helicase?
Circular (donut)
True or false: helicase can help stabilize single stranded DNA
True: although this only occurs for a little bit
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)
True or false: helicase contains nucleic acids in its structure
True: this is a combined protein / nucleic acid
True or false: DNA helicase is very fast
True: once it starts working, it is very fast
What is another name for single-strand DNA-binding proteins?
Helix-destabilizing proteins
What do single-strand DNA-binding proteins do?
Bind to single stranded DNA to stabilize and straighten it
What enzymes bind to single stranded DNA to stabilize and straighten it?
Single-strand DNA-binding proteins
What is the structure of single-strand DNA-binding proteins?
Gloves or hands
Why does DNA polymerase need to be stabilized?
It favors dissociation kinetics, so it could come off
Why are the association kinetics for DNA polymerase binding to DNA low?
Don’t want DNA polymerase binding so tightly to DNA
What helps hold DNA polymerase in place?
A sliding clamp
When does the sliding clamp release?
When DNA polymerase hits double stranded DNA
What does the sliding clamp do?
Hold DNA polymerase in place
What does a clamp loader do?
Puts the sliding clamp onto the DNA
What protein puts the sliding clamp on the DNA?
A clamp loader
True or false: lots of control is needed for DNA replication
True: there is a lot of protein machinery that needs to be controlled
How does the sliding clamp prevent DNA polymerase from falling off?
Noncovalent binding interactions between sliding clamp and DNA polymerase
Why can DNA replication errors be found?
Errors will not form the proper 3D structure
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
When do A’s get methylated?
A long time after DNA polymerase (separate mechanism)
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
What does topoisomerase do?
Relieve tension in DNA
What enzymes relieve tension in the DNA?
Topoisomerases
What is the difference between topoisomerase 1 and topoisomerase 2?
Different mechanisms for the same effect (tension relief)
How does topoisomerase 1 work?
It breaks one phosphodiester bond, allowing for free rotation and relief of tension
True or false: topoisomerase 1 covalently binds to DNA
True: this is one of the rare cases of proteins being covalently linked to DNA
When is DNA attached to a “fixed end”?
In the lab (adhere DNA), or having two replication forks coming together
How does topoisomerase 2 work?
It breaks one DNA strand to allow another strand to go through
What is the pictorial representation of the topoisomerase 2 mechanism?
/ ____ / ___ _______
________ /
Where does topoisomerase 2 mainly act (what regions of DNA)?
Loops (where the DNA crosses itself)
What is the replication origin?
Where DNA replication occurs
How does DNA replication occur?
Through special initiator proteins
What is the structure of a replication origin region in DNA?
A/T rich
Why is the replication origin region of DNA A and T rich?
Less H-bonds, so easier to break apart
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
If there was only one fork, how long would it take to replicate an entire chromosome?
~800 hours
What is meant by “replication units”?
Groups of ~50 origins are arranged into different units
Are replication units all activated at the same time?
No: different units are activated at different times
How far apart are replication units?
~30K to 250K nucleotides apart
What phase of the cell cycle does DNA replication occur in?
S phase
How long does S phase take?
~8 hours
True or false: chromosome replication happens randomly
False: they are replicated in a controlled manner
What is heterochromatin?
DNA in a very condensed state
What is euchromatin?
DNA in a less condensed state
Which DNA (heterochromatin or euchromatin) is replicated earlier?
Euchromatin
What determines whether a gene will be in euchromatin or heterochromatin?
How often that gene needs to be transcribed in that particular cell
Where does replication start?
In the middle of the chromosome (not the ends), which spread out
What are the three things needed for a sequence to be an origin of replication?
- Binding site for initiator protein (ORC)
- Rich A/T region
- At least one binding site for proteins that attract ORC
What does ORC stand for?
Origin recognition complex
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
What is the ORC regulated by?
Two loading proteins (Cdc6 and Cdt1)
What does the prereplicative complex do?
Aids in helicase binding and opening DNA
When does loading of the ORC occur?
During G1 phase of cell cycle
What happens to the ORC at the beginning of S phase?
Cdk’s phosphorylate ORC, activate helicase, and degrade loading proteins
What do the loading proteins do (in ORC)?
Keep ORC in place until the S phase
Where does the ORC split DNA?
At the A/T regions
When is the ORC activated?
At the G1/S boundary (move into S phase)
What happens to the ORC in G2?
It stays phosphorylated and on the DNA
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)
What are histones?
Proteins that DNA wrap around
What happens to histones during DNA replication?
They also need to be replicated
True or false: DNA replication is the only event that happens during S phase
False: histone mRNA also increases (50x)
What happens to histone mRNA in S phase?
It increases (50x), then degraded after S phase
What happens to the “old” histones after they pass the replication fork?
They are split randomly between the two strands
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
How does the histone split when it is with DNA (during replication)?
Tetramer stays with DNA, and 2 dimers are released
What is a histone made out of?
A tetramer and 2 dimers (3 parts)
What happens to the 2 histone dimers after being released?
Can be used for any other histones on the DNA
What are histone chaperones?
Chromatin assembly factors
What do histone chaperones do?
Assemble dimers and tetramers of histones
What proteins assemble histone dimers and tetramers?
Histone chaperones
Where are histone chaperones localized?
Replication fork
True or false: in histone replication, all the dimers need to be redone
True: half are already there, and half need to be made
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
What is a telomere?
Repeating sequence of nucleotides at the ends of chromosomes
What is the telomere sequence in humans?
GGGTTA
What is the purpose of telomeres?
Act as a buffer zone for the genes, since the ends of DNA don’t get replicated
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
What does telomerase do?
Recognizes and replenishes telomeres
What enzyme recognizes and replenishes telomeres?
Telomerase
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
What is the thought concerning telomerase and telomeres?
They are related to aging (longer telomeres means shorter age)
What type of enzyme is telomerase?
A reverse transcriptase
How does telomerase works?
Creates an RNA template, which can be used to replicate the DNA (by polyermase)
True or false: telomerase is more than just protein
True: it also has RNA to recognize DNA strand
How much do telomeres shrink by?
~100 nucleotides per division
