central dogma: transcription- lecture 2

Question 1

c value paradox

Answer 1

the “constant” value of DNA content in a cell

the total haploid content of a genome doesnt correlate strongly with level of complexity (onion has more dna but isnt smarter than human, despite having 5* as much dna)

Question 2

what is a gene

Answer 2

a gene is the dna sequence required for the production of an rna that either has its own particular biological activity or that can in turn be translated into a functional protein

Question 3

main function of dna

Answer 3

to encode the instructions needed to produced rna, which in turn are read by the cell to produce proteins

Question 4

how many genes in human

Answer 4

20000

Question 5

what does natural selection do with genes

Answer 5

eliminates mutations that disrupt function (mutations that land in regions of genomes that are functionally important)

Question 6

The main enzyme involved in transcription

Answer 6

RNA polymerase

Question 7

RNA polymerase builds an RNA strand in what direction

Answer 7

5’ to 3’ direction, adding each new nucleotide to the 3’ end of the strand

Question 8

stages of transcription: Initiation

Answer 8

RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene (or group of co-transcribed genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription

Question 9

stages of transcription: Elongation

Answer 9

One strand of DNA, the template strand, acts as a template for RNA polymerase. As it “reads” this template one base at a time, the polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5’ to 3’. The RNA transcript carries the same information as the non-template (coding) strand of DNA, but it contains the base uracil (U) instead of thymine (T)

Question 9

stages of transcription: Termination

Answer 9

Sequences called terminators signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase. An example of a termination mechanism involving formation of a hairpin in the RNA is shown below

Question 10

In bacteria, RNA transcripts can act as messenger RNAs (mRNAs) right away. In eukaryotes, the transcript of a protein-coding gene is called a

Answer 10

pre-mRNA and must go through extra processing before it can direct translation

Question 11

how are pre-mrna’s modified

Answer 11

Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5’ cap (at the beginning) and 3’ poly-A tail (at the end).

Many eukaryotic pre-mRNAs undergo splicing. In this process, parts of the pre-mRNA (called introns) are chopped out, and the remaining pieces (called exons) are stuck back together

End modifications increase the stability of the mRNA, while splicing gives the mRNA its correct sequence. (If the introns are not removed, they’ll be translated along with the exons, producing a “gibberish” polypeptide.)

Question 11

are all genes transcribed at the same time

Answer 11

Not all genes are transcribed all the time. Instead, transcription is controlled individually for each gene (or, in bacteria, for small groups of genes that are transcribed together). Cells carefully regulate transcription, transcribing just the genes whose products are needed at a particular moment

Question 12

the stretch of dna transcribed into an rna molecule and the bits of nearby dna that control it is called

Answer 12

a transcriptional unit

Question 13

promoter

Answer 13

sequence at which proteins that use the dna as a template to make rna bind and initiate synthesis (like rna polymerase)

Question 14

rna coding region

Answer 14

dna sequence that codes for the rna that is transcribed

Question 15

transcription start site

Answer 15

location in the dna corresponding to the first rna nucleotide incorporated into the transcribed rna

Question 16

terminator

Answer 16

a dna sequence that disrupts the activity of the rna polymerase and induces it to stop transcription

Question 17

transcriptional termination site

Answer 17

dna site of the last nucleotide incorporated into the transcribed rna

Question 18

upstream

Answer 18

sequences before the transcription start site such as promoter and other regulatory elements

Question 19

downstream

Answer 19

sequences after the transcription start site including the coding sequence of the gene and transcriptional termination site

Question 20

non template strand

Answer 20

after it is transcribed the rna will have a sequence similar to this strand of dna

Question 21

template strand

Answer 21

the rna polymerases uses base-pairing with this strand to create a complementary rna transcript

Question 22

why can you have transcription in either direction

Answer 22

because dna is double stranded

Question 23

explain transcription

Answer 23

Question 24

which mushroom is a potent inhibitor of rna polymerase

Answer 24

amanita

Question 25

lac operon

Answer 25

typically needs glucose, but in absence of glucose begins to break down lactose for energy

Question 26

transcriptional activator

Answer 26

According to the conventional wisdom, transcription factors are typically classified as “activators” or “repressors”. Activators recruit coactivators, resulting in gene activation, while repressors recruit corepressors, leading to transcriptional repression.

A transcriptional activator is a protein (transcription factor) that increases transcription of a gene or set of genes. Activators are considered to have positive control over gene expression, as they function to promote gene transcription and, in some cases, are required for the transcription of genes to occur

An activator facilitates the up regulation of the transcription process by binding to enhancers, while promoter is the site at which RNA polymerase binds, and transcription initiation takes place, and repressor down regulates transcription by binding to silencers
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Question 27

what is the difference between exons and introns

Answer 27

exons are amino acid coding
dna is transcribed into rna, and introns are removed by rna splicing

Question 28

post-transcriptional processing

Answer 28

capping and poly-a tail addition make the message stable enough to leave nucleus to go to ribosome

Question 29

alternative splicing

Answer 29

different exon are used in a different situation, meaning that a single gene can produce a large number of different proteins

Question 30

how to shut down genes using rna (rna interference or RNAi)

Answer 30

inject complementary strand of the messenger rna, so double stranded rna which cant be translated so gene essentially shuts down

Question 31

Dicer protein

Answer 31

The Dicer protein aids in the production of a molecule called microRNA (miRNA). MicroRNAs are short lengths of RNA, a chemical cousin of DNA. Dicer cuts (cleaves) precursor RNA molecules to produce miRNA. MicroRNAs control gene expression by blocking the process of protein production

Question 32

Small interfering RNA (siRNA)

Answer 32

siRNA is a synthetic RNA duplex designed to specifically target a particular mRNA for degradation

Small interfering RNA (siRNA) are double-stranded RNA molecules that offer new opportunities for therapeutic intervention because they act inside the cell to reduce protein expression. They do this by targeting RNA to prevent the production of disease-associated proteins

Question 33

micro rna

Answer 33

MicroRNA are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression

dont need the exact complement, more tolerating than sirna

Question 34

siRna vs miRna

Answer 34

sirna: specifically target a particular mRNA for degradation

miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3’-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing.

Question 35

what is upstream of the rna coding region

Answer 35

promoter

Question 36

what is a promoter

Answer 36

dna sequence at which proteins such as rna polymerase bind to initiate transcription

Question 37

what do activator and repressor transcription factors do

Answer 37

enhance or inhibit rna polymerase binding to the promoter

Question 38

what does the core/minimal promoter contain

Answer 38

minimal sequences required for transcription

Question 39

tata box

Answer 39

dna sequence bound by the tata binding protein and other core transcriptional machinery (deletion/disruption of tata box prevent transcriptions entirely, because without it, the general transcription
factors and RNA polymerase will be unable to bind and initiate RNA synthesis)

Question 40

which forms of small rna molecules involved in gene regulation start out as double stranded rna molecules

Answer 40

small interfering rnas and micro rnas

Question 41

what enzyme complex picks up double stranded rna molecules and dices them into short sequences

Answer 41

dicer

Question 42

these 21 base pair RNAs then form a complex with more proteins to produce the

Answer 42

RNA-induced Silencing Complex (RISC). The “silencing” component of the name comes from its activity: it acts to silence the target gene by interfering with
its translation into protein. One of the two strands of the RNA (either siRNA or miRNA) is eliminated.

Question 43

The active RISC has a single stranded
21 nucleotide RNA that is called the

Answer 43

guide RNA. This is complementary to
a target sequence on the mRNA of the gene that is being regulated. For siRNAs, that complementarity applies to the entire 21 nucleotide sequence. Therefore, siRNA binding is highly specific (it will only bind to a single specific sequence). For miRNAs, that complementarity only applies to a short segment of the guide RNA, meaning that an miRNA will bind to
many more mRNA sites than an siRNA (i.e. an miRNA’s mRNA binding is much less specific than an siRNA’s).

Question 44

Both siRNAs and miRNAs mess up translation of the protein, effectively silencing the gene. how?

Answer 44

siRNAs typically result in the mRNA being cleaved at the site of siRNA attachment; a snapped mRNA cannot be used for translation and is degraded by the cell. miRNAs, in contrast, do not typically break the mRNA, but, rather, inhibit translation by simply getting in the way of the translation machinery

Question 45

core promoter

Answer 45

The core promoter region is located most proximal to the start codon and contains the RNA polymerase binding site, TATA box, and transcription start site

Question 46

regulatory

Answer 46

The regulatory sequences include the promoter region together with enhancer elements. Every gene has a promoter, which is the binding site for the basal transcriptional apparatus - RNA polymerase and its co-factors. This provides the minimum machinery necessary to allow transcription of the gene