Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Biochemistry III > Shirley's Notes Molecular Biochem I (Ben) > Flashcards

Shirley's Notes Molecular Biochem I (Ben) Flashcards

1
Q

What are the primary DNA polymerases involved in processive elongation of new DNA in prokaryotes?

And eukaryotes?

A

DNA polymerase III for prokaryotes

DNA polymerase ε for the leading strand and DNA pol δ for the lagging strand in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the proteins responsible for strand separation in the formation of replication bubbles…

in prokaryotes?

in eukaryotes?

A

prokaryotes - SSBs (single stranded DNA binding proteins)

eukaryotes - replication protein A (RPA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the protein complexes responsible for unwinding of DNA in the formation of replication bubbles…

in prokaryotes?

in eukaryotes?

A

pro - a hexameric DNA β protein complex

euk - MCM complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What do cyclins activate?

Which specific cyclins are associated with which of these cyclin-activated molecules?

What are the functions of these cyclin-activated thing complexes?

A

Cyclins activate cyclin dependent kinases (CDKs) which phosphorylate cell cycle-related molecules.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How are double-strand breaks in DNA repaired?

(What two methods? And what determines which method is used?)

A

Non-homologous End Joining is used during G0 or G1 phases.

Homologous recombination is used during S, G2, or M phases.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What important gene plays a role in “checkpoint control” DNA damage monitoring in G1/G2 phases of the cell cycle?

How?

A

Tumor Suppressor p53

  • normally very unstable, somehow stabilizes in presence of DNA damage
  • increased p53 activates transcription of cell-cycle delaying genes (including p21, a CDK-cyclin complex inhibitor that halts cell cycle progression)
  • if DNA damage is too extensive, cells undergo a p53-dependent apoptosis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What does DNA ligase bind to before performing strand ligation in prokaryotes?

In eukaryotes?

(Via what part of the enzyme and with the release of what?)

A

prokaryotes - binds NAD+ to make ligase-NMN

eukaryotes - binds ATP to make ligase-AMP

(P binds to enzyme via a lysine residue, releasing PPi)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Where does replication start in prokaryotes?

What characterizes this region?

A

Ori C

rich in A and T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the seven important components of the replicaton bubble?

A
  1. DNA A Protein - binds dsDNA to initiate unwinding
  2. SSB Proteins - bind ssDNA to prevent re-annealing
  3. Helicase (DNA B) - unwinds/separates strands w/ ATP
  4. DNA C Protein - w/ DNA B helps primase make primer
  5. Primase - makes 4-10 bp RNA primer
  6. Topoisomerase II - makes (-) supercoils w/ ATP
  7. DNA Polymerase III - main synthesis enzyme
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How do topoisomerase I and II differ?

A

Type I cuts only a single strand of the DNA and reconfigures it to relax the double helix and is ATP independent

Type II cuts both strands to form negative supercoils in the dsDNA just ahead of the replication fork (which prevents its entanglement with the replicating ssDNA). It is ATP-dependent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What makes up the “primosome”?

A

DNA B (helicase) protein

DNA C protein

Primase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Describe the structure and function of polymerase alpha

A
  • Gap-filling
  • Lagging strand synthesis
  • has primase subunit (for RNA primers)
    • 4 subunits total
  • delta and epsilon take over elongation after alpha does a few 100 nucleotides

(analogous to polymerase I in prokaryotes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Describe the functions of polymerases beta and gamma.

A

Beta - DNA repair (may have 3–>5 exonuclease)

Gamma - mitochondrial DNA synth + repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Describe the functions of DNA polymerases delta and epsilon.

A

Delta - Lagginig strand (proofreads + repairs)

Epsilon - main leading strand synthesizer, can fill gaps and proofread, requires PCNA as its “sliding clamp”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Describe the function of telomerase.

What “template” sequence does it use to do its thing?

What sequence does it add (in vertebrates)?

A
  • adds a 5’-TTAGGG sequence to the 3’ free end of chromosomes after the removal of the RNA primer from the last Okazaki fragment (to prevent loss of coding DNA from the strand’s end)
  • contains a 3’-CAAUCCCAAUC-5’ RNA template
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

In what phase of the cell cycle does replication occur?

And how long does it take?

A

in S phase

about 8 hours

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

During replication, where do the histones of the original dsDNA molecule go?

Where are new histones added?

A

the “old” histones stay with the leading strand

the new ones are assembled into the lagging strand

(b/c histones only bind to dsDNA and the leading strand is more immediately dsDNA at the beginning of replication)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is a nucleosome?

What connects nucleosomes?

What is a chromatosome?

A
  • Nucleosome = histone octamer (2 each of H2A + H2B + H3 + H4) plus ~140 nucleotides
    • 1.75 turns of DNA
  • linker DNA of ~60 nucleotides wrapped around H1 histone connects nucleosomes
  • Chromatosome = linker DNA + H1 + nucleosome
    • = 200 nucleotides + 9 histones
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How many DNA molecules are there in a G2 phase cell?

A

92 molecules

  • double the usual 46 because DNA is fully replicated and mitosis is about to occur to split the nucleus in two
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the six main types of DNA lesions?

And the general mechanism/factor causing each?

A
  1. Depurination - purine rings removed by heat/acid
  2. Deamination - amine removed from bases by radiation/alkylation (as in chemotherapy)
  3. Dimerization - same-strand adjacent Ts dimerize via UV radiation
  4. Deletion/Insertion - AKA frameshift, intercalating agents (histo dyes)
  5. Strand Breaks/Crosslinks - polymerase errors
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What results from deamination of cytosine?

Of adenine?

A

Cytosine - becomes uracil + is complemented by adenine

Adenine - becomes hypoxanthine + comp’d by cytosine

22
Q

Why is thymine in DNA instead of uracil?

A

Because it’s easier for DNA repair mechanisms to distinguish between thymine and a de-aminated cytosine (which = uracil) when proofreading.

If uracil was supposed to be there, the proofreading would think de-aminated Cs were just normal Us.

23
Q

How is depurination repaired?

3 steps, 3 enzymes

A
  1. Endonucleases - cleave P-diester bonds @ missing purine
  2. Polymerase I / Beta - replaces missing purine base, but “nick” remains where P-diester is cleaved
  3. DNA Ligase - re-seals nick with new P-diester bond
24
Q

How is deamination repaired?

A
  1. DNA Gylcosylase - removes “odd” bases by breaking N-glycosyl bond btwn base and ribose
  2. Same 3 steps from depurination repair
    • endonuclease
    • polymerase I/B
    • ligase
25
How is **thymine dimerization** repaired?
**UV-specific endonucleases** - activated by UV light, remove dimerized T-T - polymerase + ligase complete repair
26
What is a **mismatch** and how is it repaired?
* Polymerase mistakes can result in **base mismatch** and the resulting base pair _can not form an H bond_ * In _prokaryotes_: * Parent strand recognized via its **methylation** * Repair enzyme **MutS** binds the mismatch and **MutL** finds the nearest methylation (**MutH** also helps somehow) * **Helicase II + exonuclease** unwind + digest daughter strand from methylation site to mismatch * **DNA Polymerase III** + **Ligase** complete repair * In _eukaryotes_: * Daughter strand recognized by **nicks** (parents strand not methylated)
27
What are the two main types of _point mutations_? And their sub-types?
1. **_Substitutions_** * **Transitions** - base is subbed by same time of base * _spontaneous_, _chemical_ or _radiation_ causes * **Transversions** - pyrim subbed by purine or v.v. * _polymerase error_ causes 2. **_Frame Shift_** * **​****Insertion**or**Deletion** of base pair
28
What are the _three_ possibilities for results of a **substitution mutation**?
1. **Silent Mutation** - mutated codon codes for same AA 2. **Missense Mutation** - mutated codon codes for different AA 3. **Nonsense Mutation** - mutated codon is stop codon
29
What is the mechanism for spontaneous mutation? Tell how this results in eventual substitution.
* Normally **oxo-form** bases can spontaneously change to **enol form** which _changes their complementary base_ * Example: * oxo-thymine changes to enol-thymine and its new complementary base is _guanine_ * _T-G_ base pair yields one normal T-A pair and one _substitution mutation G-C pair_ upon second replication
30
How is RNA transcription different in prokaryotes than eukaryotes? 7 items
​In **prokaryotes**... 1. RNA transcript = mRNA _without any modification_ 2. mRNA is _polycistronic_ 3. TATA box promoter is _closer to coding region_ 4. mRNA has _shorter life span_ 5. transcription/translation happen _in same place_ 6. RNA polymerase can _work alone_ (no transcr. factors) 7. _only one_ RNA polymerase exists (3 in euk.)
31
What is the subunit make-up of E. coli **RNA polymerase**?
5 _core_ subunits, 1 extra factor * 2 **alpha subunits** - recognize regulatory factors * **beta subunit** - has _polymerase activity_ * **beta prime** - _binds DNA_ * (omega subunit - unknown function) * **sigma factor** - non-core subunit, _binds promoter region_ to allow _transcription initiation_
32
Describe the initiation of transcription by E. coli RNA polymerase.
1. polymerase _binds DNA_ to _seek promoter_ 2. **sigma factor** binds promoter = **close promoter complex** 3. **polymerase** unwinds DNA = **open promoter complex** 4. first **P-diester** bond forms 5. **sigma factor** dissociates + core subunits **elongate** RNA
33
What are the two main **consensus sequences** in prokaryotic promoter regions?
1. **Pribnow Box (TATAAT)** - 10 bases upstream 2. **TTGACA** - 35 bases upstream
34
Describe some structural features of **polycistronic mRNA**
* **pppA/pppG** sequences before structural genes (5' end) * **AUG** start codon (= formyl-Met) * start + stop codons btwn cistrons * 3' end has **non-coding region + terminator sequence**
35
What are the common **eukaryotic consensus sequences** for transcription promoter regions?
1. **_TATA Box_** - (TATAAA @ -25 bp) binds _obligatory_ transcription factors via **TATA-binding protein** 2. **_CAAT Box_** - at -100 bp 3. **_Gc Box_** - common on _constitutive_ genes on _template_ strand, at -45 bp, binds to **SP1** transcr. factor
36
Describe the _eukaryotic_ RNA polymerases. (location, products, inhibition)
* **RNA polymerase I** - in the _nucleolus_**​** * makes _rRNA_ (18s, 5.8s, 28s) * _not_ inhibited by alpha-amantin * **RNA polymerase II** - in the _nucleus_ * makes _mRNA_ precursors + _snRNA_ (for splicing) * _strongly_ inhibited by alpha-amantin * **RNA polymerase III** - in the _nucleus_ * makes _rRNA_ (5s) and _tRNA_ * _weakly_ inhibited by alpha-amantin
37
What are the 3 main _primary transcript modifications_ in eukaryotic mRNA?
1. **_5' Methylguanylate Cap_** - pppA/pppG loses a P + remaining PPi binds GMP which is methylated 2. **_3' polyA tail_** - _polyA addition signal_ shows _endonuclease_ where to cut + then _polyA polymerase_ adds ~250 As there _using ATP_ (prolongs mRNA life) 3. **_Splicing/Ligation_** - introns are spliced out + exons are connected
38
Describe the 3 splicing sites for the removal of introns. And which snRNA splices each one? Briefly, how do snRNAs splice?
* **5' site** - AG/GUAAGU (exon/intron) * U1-RNA splices * **3' site** - UUUUUUUUUXCAG/G * U5-RNA splices * **Branch site** - in middle of intron, varying sequence * U2-RNA splices - snRNAs _transesterify_ by breaking one P-diester and forming another
39
Describe the structure of **tRNA** and the function of its different parts.
**Single stranded** + **partially double helixed** with a secondary **cloverleaf** and tertiary **L-shaped** structure. * **_Acceptor arm_** - 5' P + 3' ACC to **_acc_**ept AAs * **_D loop/arm_ -** binds aminoacyl-tRNA synthetase * has **dihydrouridine** * **_T loop/arm_ -** binds ribosome * has **TᴪC** sequence (ᴪ = pseudouridine) * **_Anticodon loop/arm_** - binds codon
40
How many codons are their for AAs? And how many tRNAs? How does this work?
**61 codons** **31 tRNAs** Because the tRNA anti-codon sequence often contains one non-binding modified base, so only two bases participate in codon-tRNA binding. Most AAs have multiple codons with the same first two bases, so multiple codons can bind the same two-base tRNA anti-codon sequence.
41
Describe the steps of "charging/activating" a tRNA with an amino acid.
**Aminoacyl-tRNA synthetase** has binding sites for AA, ATP and tRNA. 1. AA and ATP bind synthetase. 2. AA + ATP ---\> AA-AMP + PPi 3. tRNA binds synthetase 4. AA is transfered to 3' end of tRNA, forming **_ester bond_** btwn AA -COOH and tRNA -OH groups * (either on C2 or C3 of tRNA's 3' ribose) 5. AMP is released
42
What are 2 important bacterial **rRNAs** and their general functions?
1. **_16s rRNA_** - part of the 30s small ribosome subunit, _selects the protein synthesis start site_ (translation stops w/out it) 2. **_23s rRNA_** - part of 50s large subunit, interacts w/ tRNA to allow _peptidyl transferase_ activity
43
Describe the initiation of translation / ribosome assembly in _prokaryotes_.
1. **_16s rRNA_** binds a **_3' purine rich region_** before codons on mRNA 2. Small **_30s ribosome unit_** complexes w/ **_IF-1_ + _IF-3_** 3. **_IF-2_** binds _GTP_ and complexes with **_fMET-tRNA_** 4. All this complexes w/ 30s + IF-1/3 at its **_P-site_** 5. IF-3 is _released_ and **_50s ribosome unit_** joins 30s 6. GTP on IF-2 is _hydrolyzed_ 7. Remaining IFs are _released_ and 50s + 30s assemble into **_70s ribosome_**.
44
What is the initiation codon for the first AA of _every_ prokaryotic protein? What is that AA?
**AUG** codes for **formyl-Met**
45
What is the **Shine-Dalgarno sequence**?
the _purine-rich_ (AGGAGG) sequence at the beginning of prokaryotic mRNA that attracts 30s binding for translation initiation
46
Describe the initiation of translation in _eukaryotes_.
1. **eIF-2** binds _GTP_ and **tRNAf** 2. This complex binds **40s** **ribosomal unit** 3. 40s then binds **5' methyl-guanylate** **cap** on mRNA (with the help of **eIF-3** and slides down to **AUG** start codon ( = Met ) 4. (Sometimes more 40s units line up btwn cap + codon) 5. **eIF-4** helps to unwind the mRNA at its 5' end (_using ATP_)
47
Briefly, what do the following initiation factors do... ## Footnote **IF-2** **IF-3** **eIF-2 through 4**
* **IF-2** binds GTP and **fMet-tRNA** (prokaryotes) * **IF-3** release from 30s allows 50s binding (prok.) * **eIF-2** binds GTP and **tRNAf** (euk.) * **eIF-3** helps 40s bind 5' cap (euk.) * **eIF-4** unwinds mRNA 5' end _using ATP_
48
What are the functions of the 3 prokaryotic _and_ eukaryotic **elongation factors**?
1. **_EF-Tu / EF-1α_** - brings aminoacyl-tRNA into A site _using GTP_ 2. **_EF-Ts / EF-1βγ_** - helps EF-Tu / EF-1α release GDP 3. **_EF-G / EF-2_** - is a _translocase_ which uses GTP to move peptidyl-tRNA from A site back to P site
49
What are the release factors in _prokaryotes_ and their functions? And in _eukaryotes_?
* **RF1** recognizes UAA/**UAG** stop codons * **RF2** recognizes UAA/**UGA** stop codons * both 1 + 2 act at A site * **RF3** stimulates binding of RF1/2 _using GTP_ * RF binding alters _peptidyl transferase_ such that it cuts peptide-tRNA bond to release PP chain, leading to 50s/30s dissociation * _only_ **eRF** acts as RF in eukaryotes
50
There are 6 basic possibilities for where a protein needs to go after translation, based on their **signal peptides**. What are those 6 possibilities and what are the 2 possible intermediate destinations in which the protein will be placed before moving on?
* Signal peptides sending proteins to **nucleus, mitochondria** or **peroxisomes** will cause proteins to first remain in the **cytosol** * Those sending proteins to the **membrane**, **lysosomes** or **secretory vesicles** will first send the protein to the **RER** * **​**PTMs will occur in RER/Golgi before protein moves on

Biochemistry III (35 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions