DNA-Protein Interactions and Recognition

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Questions and Answers

Which amino acids commonly form hydrogen bonds with guanine?

Glutamine (correct)

Cysteine

Threonine (correct)

Aspartic Acid

What feature makes the alpha helix suitable for DNA sequence recognition?

The dimensions match the width and depth of the major groove (correct)

It can bind to the minor groove exclusively

Its ability to form multiple hydrogen bonds simultaneously

It does not require a specific orientation to bind

What is true about the major groove of DNA?

It provides less information than the minor groove.

It is exclusively recognized by beta sheets.

It is less accessible than the minor groove.

It is more accessible and contains more information. (correct)

How do proteins recognize long DNA sequences?

By acting as dimers with separate DNA binding domains. Signup and view all the answers

What factors affect the strength of hydrogen bonds in DNA?

Distance and orientation of the atoms involved. Signup and view all the answers

What does the absence of a universal code for DNA-protein interactions imply?

Different proteins require unique binding strategies. Signup and view all the answers

What characteristics do single amino acids have in regards to base-pair recognition?

They can simultaneously recognize both bases in a pair. Signup and view all the answers

In the context of dimerization, how long is the sequence that CAP recognizes?

22 base pairs long. Signup and view all the answers

What type of interaction do small blue dots represent in the context of DNA binding?

Ionic interactions with the DNA backbone Signup and view all the answers

Which structures are involved in the specific hydrogen bonding to bases in the major groove of DNA?

Recognition helices Signup and view all the answers

What is the consequence of removing one interaction from CAP’s binding site?

CAP is still likely to bind with high affinity Signup and view all the answers

What is the significance of the positions 4-8 in the context of CAP binding?

They are the most critical bases for binding affinity Signup and view all the answers

In the context of proteins that bind to DNA, what does the helix-turn-helix motif specifically interact with?

The major groove of DNA Signup and view all the answers

In the helix-turn-helix motif, how do proteins typically interact with the DNA?

By making specific and non-specific interactions Signup and view all the answers

What characterizes the spacing between two recognition helices in dimeric proteins?

It matches the helical pitch of DNA Signup and view all the answers

Which characteristic is true about most proteins that utilize a helix-turn-helix motif?

They are generally dimeric proteins Signup and view all the answers

What role does the sigma subunit play in RNA polymerase function?

It helps the core polymerase recognize and bind to the promoter. Signup and view all the answers

What happens to the sigma subunit once the RNA strand reaches 15 nucleotides in length?

It is pushed off and can bind to another core RNA polymerase. Signup and view all the answers

How do mechanisms like anti-termination and attenuation affect RNA synthesis levels?

They allow RNA polymerase to transcribe through controlled terminators, increasing full-length RNA levels. Signup and view all the answers

What is the function of the core RNA polymerase in bacteria?

It is efficient for translation but cannot recognize promoters alone. Signup and view all the answers

What distinguishes strong promoters from weaker ones?

Strong promoters lead to higher levels of mRNA synthesis. Signup and view all the answers

What is the biggest environmental mutagen mentioned?

UV light-induced damage Signup and view all the answers

What type of DNA damage repair involves using energy from visible light?

Photoreactivation Signup and view all the answers

Which of the following is true regarding DNA photolyases?

They utilize a redox-activating cofactor. Signup and view all the answers

What is the role of DNA-alkyltransferases in DNA repair?

Repair of some alkylated bases Signup and view all the answers

What distinguishes the different repair methods in excision repair?

The size of the gap made Signup and view all the answers

What happens to the Ada protein during the alkylation repair process?

It becomes alkylated and does not turnover. Signup and view all the answers

What is the primary specificity of mismatch repair in excision repair?

Specificity for damaged bases Signup and view all the answers

In the context of excision repair, what is meant by cutting on both sides of the damage?

It facilitates the removal of the damaged portion. Signup and view all the answers

What does gene conversion involve?

The non-reciprocal transfer of genetic material from one homologous chromosome to another Signup and view all the answers

Which mechanism primarily repairs double-strand breaks (DSBs) in unicellular organisms?

Homologous recombination Signup and view all the answers

What is the role of the 3' end in the context of DSB repair?

It is involved in the homology search corresponding to the Spo11 cut site Signup and view all the answers

In gene arrangement, which segments bring together to form a variable domain?

Diversity, joining, and variable segments Signup and view all the answers

What is essential for chromosome pairing during meiosis?

Gene conversion and crossover Signup and view all the answers

What characteristic is common across kingdoms regarding DSB repair?

Shared mechanistic features of repair pathways Signup and view all the answers

What type of antibodies do immune cells generate through VDJ recombination?

A vast array of antibodies capable of recognizing diverse antigens Signup and view all the answers

Which part of the mRNA encodes the constant region of a protein?

The 3' end of the mRNA Signup and view all the answers

What role does rho play in rho-dependent termination?

It pulls RNA out of paused RNA polymerase. Signup and view all the answers

What is the significance of the Rut region in rho-dependent genes?

It is a sequence where rho binds. Signup and view all the answers

How does antitermination typically occur in terms of RNA polymerase activity?

By allowing the polymerase to bypass termination signals. Signup and view all the answers

What happens when a riboswitch binds a metabolite?

It changes the riboswitch's structure to regulate transcription. Signup and view all the answers

What is the relationship between the presence of amino acids and riboswitch function?

Riboswitches only function in the absence of amino acids. Signup and view all the answers

What is a key feature of an intrinsic terminator?

It relies on a hairpin followed by a run of uracils. Signup and view all the answers

How do riboswitches control transcription?

By controlling formation of terminator sequences. Signup and view all the answers

Which of the following is NOT a mechanism of transcription regulation mentioned?

Formation of transcription factors. Signup and view all the answers

Study Notes

DNA Replication

DNA polymerases are accurate machines for copying DNA.
E. coli K12 has a circular genome of 4,639,221 bp and 4485 genes (4288 protein-coding).
DNA polymerases have eight distinct families (A, B, C, D, X, Y, PrimPol, reverse transcriptases).
Core catalytic domains of these families are unrelated, resulting in different protein folds.
DNA Polymerase III is the main replicating enzyme and is comprised of three polypeptides.
ε subunit = 3'→5' exonuclease activity
θ subunit stimulates ε subunit
E. coli DNA Pol I (A-family) = Klenow fragment; role in completing Okazaki fragments; one polypeptide.
DNA polymerases are accurate machines but errors can happen.
Reducing errors in replication, 5′→3′ polymerization, 3'→5' exonucleolytic proofreading, strand-directed mismatch repair.
Error rate is 1 in 10^5
Consensus shape for active site to accommodate AT, TA, GC and CG
Incorrect base pairing excluded by steric clashes.
Hydrogen bonding not required for catalytic selectivity.
Different types of DNA Pol enzymes: based on how many Polypeptides, how they operate.

DNA Replication 3

Eukaryotic chromosomes are replicated exactly once per cell cycle.
Telomeres protecting chromosomes (repeated 6 base sequences)
Telomere repeats allow DNA ends to extend.
Telomerase enzyme helps synthesize repeats

Prokaryotic Gene Expression

Transcription = DNA to RNA
Translation = from codons to AAs = ribosomes
mRNA is produced by RNAP 2, it is exported from the nucleus for translation.
In prokaryotes, transcripts are translated whilst they are being produced. > lag between notation of transcription and appearance of active protein is short > bacteria rely heavily n transcriptional responses to stresses and environmental changes.
Strong promoter > makes lots of mRNA
Core has 5 subunits > beta and beta prime are largest subunits
Complex is efficient for translation
Can't recognise promoter or start transcription
Core needs to associate with sigma subunit > forms holoenzyme > recognises and binds to promoter.
Both prokaryotes and eukaryotes have to recognise promoters.
In eukaryotes, the sigma subunit associates with the RNA pol before the whole complex binds to DNA.

Prokaryotic Gene Regulation

Strong promoters make lots of mRNA
Transcriptional regulation > repression/negative regulation(protein acts by turning a promoter off), activation/positive regulation (turning a promoter on)
E.coli contains at least 132 transcription factors
Approx 70% of sigma 70 dependent promoters are regulated by at least one repressor
50% by at least one activator >
Many transcription factors are global regulators = act at multiple promoters > single transcription factor portion can act at multiple promoters.
Prokaryotic activators usually bind within 100 bp of +1
Repression of transcription > blocks transcription of weak promoters
DNA-binding proteins recognize site that overlaps blue site that RNA pol wants to bind to.
Binds and blocks binding by RNA pol
Strong or activated promoter >bind repressor in RNA pol site then doesn't matter than activators are stabilizing RNA pol since it can't get on to DNA
Strong promoter repression allows low level background translation.
Lac repressor works by blocking binding of RNA polymerase.

Mechanism of Eukaryotic Transcription

Activator > activates transcription
Binds to specific place on genome > can recruit proteins to the genome > coactivators cause transcription eg by recruiting the pre initiation complex
Co-activators = SWI/SNF, mediators, SAGA complex, NuA4 complex
Mediator coactivator
Transcription factors are often at promoter proximal locations in euk and can also be enhancer regions distal from promoter.
Mediator stimulates transcription stronger in the presence of a TF
In vitro transcription experiment > 1 tube two templates, 1] a transcription factor binding site for Gcn4, a core promoter and a 400bp reporter gene 2] a transcription factor binding site for Gal4, a core promoter and a 300bp reporter gene
Mediator is a huge and modular protein complex
TBP-associated factors (TAFs).
TBP is a very important subunit for TFIID

Eukaryotic mRNA Processing

Transcription termination and mRNA processing
mRNA processing is essential for translation into portions > processing = 5' capping, splicing and 3/ polyandenylation
Only RNAP2 transcripts are processed this way
The CTD undergoes dynamic cycles of phosphorylation > ser2-P and Ser5-P are the most abundant and studied
2 major functions = to coordinate the trancprtion cycle, enabling RNAP2 to transition through each face > for maturation of the mRNA eg 5 capping, splicing and polyadenylation
Ser2 kinase brl comes to polymerase and starts phosphorylation at the serine > =
phosphorylated more repeats >

Alternative Splicing

Tissue-specific alternative splicing variants
Order of exons can't change, only whether they're included
Detection of mRNA splice variants (mRNA isolation > RNA-seq)
Alternative splicing > shapes cellular and organismal diversity
Types of alternative splicing (e.g., retained introns).
Splice sites > strength and consensus sequences >
Trans-acting RNA binding proteins regulate splice site selection > Enhancer or repressor motifs (ESE, ISE, ESS, ISS)

MicroRNAs

RNA interference > microRNA biogenesis > miRNAs post-transcriptionally regulate > 60% of human genes > miRNA dyrsgulation dsrupts human development and disease
Genomics of miRNAs > coded within genome > clusters of miRNAs or single miRNAs can be encoded in introns, exons or intervening regions
Several enzymes > Drosha and dicer

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Description

This quiz explores the intricate relationships between DNA and proteins, focusing on how specific amino acids interact with guanine and the structural features that facilitate DNA sequence recognition. Additionally, it addresses the mechanisms of hydrogen bonding and the effects of various factors on DNA-protein interactions.