Exam 4 Flashcards BIO262

DNA → transcription → RNA → translation → Protein

Determine the order of steps in the Central Dogma of biology, including transcription and translation

The left is bacterial rna polymerase and the right is eukaryotic rna polymerase

Which enzyme is bacterial RNA polymerase? which one is eukaryotic?

RNAP I - rRNA

RNAP II - mRNA, miRNA (micro rna), ncRNA (non-coding RNA)

RNAP III - tRNA

How many RNA Polymerase are there? What do each of them encode for?

RNP stands for Ribonuclearprotein

what does RNP stand for?

Transcription factors are enzymes that assist in promoting transcription. There are 3 transcription factors, TFI, TFII, TFIII.

What is the function of Transcription Factors? How many are important in transcription?

The TATA box is a sequence high in A & T bases. The TATA box is a unique promotor sequence that which signals where transcription starts.

What is the TATA Box and what’s its role in transcription.

TATA box binding proteins

What are TBPs?

Once eukaryotic transcription begins it cannot stop

Why is it essential for the protein complex used in transcription to be present at the same time?

Phosphates bind to RNAP to “energize” the molecule, once RNAP gets energized this way transcription starts.

Why do phosphate molecules bind to RNA Polymerase?

The C-terminus domain of the Quaternary protein complex. Is also called “CTD Phosphorylation”

Where do the phosphate groups used in RNA phosphorylation bind to?

Transcription does not occur under these conditions

If any of the proteins needed for transcription are absent? What happens to transcription?

The Mediator stabilizes RNAPs connection to the DNA it is transcribing

What is the role of the Mediator?

TBP, TFIID, TFIIB, TFIIH, TFIIA, TFIIF, TFIIJ, TFIIH

Which proteins are present on the transcription complex

Transcription Factor II H (TFIIH)

Which Transcription Factor remains once transcription begins?

Cytoplasm for prokaryotes, Nucleus for eukaryotes

Where does transcription take place in prokaryotes? and Eukaryotes?

Rough Endoplasmic Reticulum (Rough ER)

Which organelle does translation take place in in eukaryotes?

Chemical tags and protective molecules are added to RNA before exiting the nucleus.

What gets added to RNA before it can leave the nucleus?

Head - 5’ methyl G-cap (methyl added to guanine)

Tail - Poly(A) Tail (AAAAA)

What gets added to the “Head” and “Tail” of RNA

The Middle - the portion of RNA where all the spliced exons get ligated back together.

In between the “Head” and “Tail” of processed RNA

polycistronic = many genes from one single strand of mRNA during one translation

alternative splicing = many potential genes from one single strand of mRNA, but to get the other potential forms you'd need to translate another strand of the same mRNA and splice it differently. It's pre-translational processing

Why isn’t Exon Splicing the same as Polycistronic mRNA?

Poly (A) Polymerase - adds the Poly (A) tail to the tail of RNA.

What is the PAP enzyme’s function?

5’ Methyl G Cap attaches to guanine and changes the shape of the molecule, allowing it to be recognized as important and avoid being degraded in cytoplasm.

What is the purpose of the 5’ MeG Cap?

Alternative Splicing is the process of splicing specific genes in order to create multiple unique proteins

Explain Alternative Splicing.

Alternative Splicing is an optimization of our body’s processes. it allows for one gene to code for different proteins used in multiple parts of the body

What makes Alternative Splicing useful?

Large RNA and protein complex that catalyzes the removal of introns from mRNA.

What is the Spliceosome?

The Lariat

What is the name of the “Loop” structure created during intron splicing?

Adenine residue

The residue of which base is present during intron splicing?

snRNP - small nuclear Ribonucleic Proteins

These proteins act as enzymes that hold introns and exons together for reactions

Define snRNP and describe their function.

Ran has a GTP and GDP form.

Ran (GTP) binds to exportin to allow mRNA to pass through nuclear pores of the nucleus

Ran (GDP) binds to importin and brings RNA back into nucleus

The protein, Ran, has two forms. Identify which two forms this protein takes and their functions?

Exosome

Which complex is responsible for the degradation of mRNA?

1) Multiple regulatory and coding sequences

2) Much larger in size

3) More complex

Name 3 Differences between Mammalian genes and Yeast genes.

Euchromatin allows for transcription to occur since the histones are less tightly wound around the DNA.

Which chromatin structure allows for transcription to occur?

No, in heterochromatin the histones are too tightly wound around the DNA for RNAP to bind.

Does transcription occur with Heterochromatin?

Hox genes are a 180bp (60 amino acid) sequence that is conserved in most organisms.

What is a Hox gene?

Hox genes code for different phenotypes in animals.

What do Hox genes code for?

Giant and Kruppel

Which developmental proteins are Repressors?

Bicoid and Hunchback

Which developmental proteins are Activators?

Using latitude and longitude, areas where proteins are expressed are mapped along an embryo by looking at where “on” and “off” sections overlap.

How is protein expression graphed on an embryo?

When Hox genes get mutated, this causes proteins to get translated differently and can lead to the development of new body parts in organisms.

What happens to an organism if Hox genes get mutated?

Gene Knockout, Transgenic, Gene Knock-in

What are the three main gene editing techniques involved with CRISPR

Removal of a specific sequence of DNA

Explain the Gene Knockout Technique

Animals that have had new genes added into them.

What are Transgenic animals?

Changing specific bases in a known sequence

What is a gene knock-in?

ssODN, ZFN, and TALEN

What gene editing techniques came before CRISPR?

DNA gets targeted with cRNA → gRNA guides cas nuclease to cut site → cas nuclease cuts DNA → new base gets added → DNA gets ligated

How does CRISPR Cas9 work?

Cas was discovered in bacteria defense enzyme and CRISPR was an adaptive bacterial immune response.

Where was CRISPR Cas originally discovered?

The immunization stage is when bacteria reads viral DNA and adds spacers of bacteriophage DNA and holds on to this to be transcribed later.

What is the “Immunization Stage” of bacterial infection?

guide RNA and Cas9 Nuclease

What pieces make up the RNP Complex of CRISPR Cas9?

The PAM Sequence (Protospacer Adjacent Motif) site is a three nucleotide sequence that cas9 can recognize. Must be present for the enzyme to cut.

What is the PAM Sequence?

NHEJ - Non-Homologous End Joining

HDR - Homology Directed Repair

What are the two repair paths for DNA with a double stranded break?