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Biochemistry > Transcription > Flashcards

Transcription Flashcards

1
Q

Single-stranded DNA binding protein

A

Bind to the single-stranded DNA that has been separated and keep it stable

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2
Q

Helicase

A

Opens up the double stranded DNA (like you break apart the teeth on your zipper)

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3
Q

DNA polymerase

A

ase=enzyme

Helps put together the small parts (nucleotides) of the DNA molecule. Busses in all the correct nucleotides

Uses help of RNA primase

Also corrects mistakes

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4
Q

RNA primer

A

Makes a primer for synthesis to start. Follows in helicase and lays down primer. Primer is made of RNA

RNA primase: makes RNA primer

*Doesn’t use Thymine (b/c it’s RNA). Uses uricil instead

DNA pol α lays down 25 DNA nucleotides

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5
Q

DNA synthesis direction

A

Synthesized 5’–>3’

Goes towards the 5’ far end

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6
Q

DNA does not control biological properties of the cell

A

True

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7
Q

What determine cell functions?

A

Proteins

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8
Q

DNA uses RNA as intermediary in protein synthesis

A

True

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9
Q

Piece of DNA

A

Gene

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10
Q

Copying a gene into RNA

A

Transcription

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11
Q

RNA is used as template to make protein. Process called________

A

Translation

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12
Q

RNA and DNA similarities

A

Both are linear polymers

Made of nucleotides and connected by phosphodiester bonds

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13
Q

RNA and DNA differences

A

RNA is single stranded

RNA has ribonucleotides instead of deoxyribonucleotides

RNA can fold into complex 3D structures allowing to have catalystic function

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14
Q

Telomerase

A

There is no free 3’ OH to prime DNA synthesis at the end of the lagging strand

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15
Q

How many major types of RNA are there?

A

3

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16
Q

rRNA

A

Function: structural and functional (catalytic) components of ribosomes. Form the core of the ribosome and catalyze protein synthesis

Features: stable, long-lived, GC rich, folded w/ extensive internal base pairing

80%

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17
Q

What are the types of rRNA?

A

28s (longest)
18s
5.8s
5s (shortest)

eukaryotic ribosome has 83 different proteins

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18
Q

tRNA

A

Function: carry AA’s to ribosomes to make polypeptide chains

Features: stable, small, has modified bases

15%

Cloverleaf: has CCA at 3’ end (carries AA), anticodon (base-pairs w/ codon in mRNA)

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19
Q

How many different tRNA’s are there?

A

56 different tRNA’s

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20
Q

mRNA

A

Function: carrier of genetic info from genes to ribosomes for protein synthesis. Direct protein synthesis. Non-coding RNA serve as enzymatic and structural components for many biological processes

Features: short-lived (like mission impossible..”self destruct”)

1-5%

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21
Q

snRNA

A

These are packaged with proteins to form small nuclear ribonucleoproteins (snRNP’s or “snurps”) that are part of “spliceosomes.” They are involved in the splicing of precursor mRNA and export of mature mRNA

i.e. U1 snRNA

22
Q

siRNA

A

Small interfering RNA: regulate eukaryotic gene expression by degrading select mRNA

These are short (21-24 nucleotides) antisense transcript derived from transposons and complementary to certain mRNAs. siRNAs inhibit the translation of target mRNAs and enhance their degradation in RNA-induced silencing complexes (RISCs)

23
Q

miRNA

A

Micro RNA: regulate gene expression by blocking translation of selective mRNA

24
Q

Transcription begins with….

A

Begins with binding of RNA polymerase to promoter on DNA

25
Q

Nucleotides are covalently linked by _______

A

Phosphodiester bonds on the backbone

3’OH—-5’ phosphate

26
Q

Transcription: Reaction catalyzed by ________

A

RNA polymerase

27
Q

RNA transcribed in which direction?

A

5’–>3’

Released as a single strand

28
Q

New RNA sequence is same as (except it has U for T)

A

RNA sequence is same as coding/non-template/sense strand (5’–>3’)

29
Q

General transcription factors for polymerase II:

A

TFIIA, TFIIB, TFIIC, TFIID etc

Assemble at the promoter before transcription

30
Q

What is function of TFII’s? (transcription factors for polymerase II)

A
  1. Help position RNA polymerase correctly at promoter
  2. Help pull apart the two strands of DNA to allow for transcription
  3. Release RNA polymerase from promoter into elongation mode once transcription has begun
31
Q

Eukaryotic Transcription-Initation

A
  1. TFIID binds to TATA box (causes distortion in DNA)
  2. TFIIB recruited, followed by TFIIF, RNA Pol II, TFIIE and TFIIH
  3. All these factors join to make transcription initiation complex
  4. TFIIH unwinds the DNA double helix and exposes template strand
  5. RNA Pol II makes short lengths of RNA
  6. Phosphorylation of CTD(carboxy terminal domain) by TFIIH (causes polymerase to leave promoter and begin elongation/transcription
32
Q

General steps of Transcription

A

Initiation, Elongation and Termination

33
Q

Key features of Initiation

A
  1. Histone acetylation/deacetylation reaction (acetylation/deacetylation of lysines on histone tails by Histone Acetyl Transferase (HAT) and histone deacytelases (HDAC)
  2. Formation of an RNA dinucleotide
  3. Formation of 7-methylguanosine cap at 5’ end
34
Q

Promoters

A

Where polymerase binds. Helps polymerase find start site for transcription.

35
Q

Homeodomain proteins (regulation of transcription)

A

Contain a conserved 60 residue DNA binding motif or homeodomain

36
Q

Zinc finger proteins (regulation of transcription)

A

Have short regions containing Cys and His residues that interact w/ Zn ions that produce multiple loops or Zn fingers that insert into major grooves of DNA

37
Q

Leucine zipper proteins (regulation of transcription)

A

Contain DNA binding sequence where every 7th residue is leucine which promotes dimerization and coiling of these sequences

38
Q

Basic Helix Loop Helix proteins (regulation of transcription)

A

Similar to bZIP except α helical regions separated by non-helical loop sequence

39
Q

Transcription Factors and cancer

A

Inappropriate inactivation/activation of genes that control cell growth by deregulation of transcription factors may lead to cancer.

Mutated genes for TF’s represent a significant fraction of oncogenes

Mis-regulation may occur by aberrant increase in expression or by mutations in the coding sequence that alters activity of the TF

40
Q

Fragile X Mental Retardation (FMR1)

A

FMR1 gene encodes for a protein with neurological function

DNA sequence has 30 repeats of CGG in most people

In patients w/ FMR1 the CGG repeat expanded to >200 copies

Expansion makes it susceptible to methylation of cytosine

The FMR1 gene becomes silent even though the triplet expansion is upstream of proton coding sequence

As methylation repeat region extends into the promoter region, transcription is turned off

41
Q

B form of DNA

A

Right handed, has 10 base pairs per turn, each base pair separated by 3.4A

A form is more compact
Z form=left handed

42
Q

X-shaped chromosomes

A

Metaphase chromosomes are the most compact form of chromatin

43
Q

4 histones

A

H2A, H2B, H3, H4 (w/ DNA makes nucleosomes–>chromatin)

Chromatin condenses during M phase of cell cycle into chromosomes

44
Q

Transcription-General Features

A

Begins w/ binding of RNA polymerase to promoter on DNA

Unwind DNA double helix to get template for making RNA

Reaction catalyzed by RNA polymerase

New RNA strand is released from DNA as a single strand

45
Q

Histones have a high content of what?

A

Argenine and lysine

46
Q

RNA molecules have extensive base pairing

A

True

Can produce secondary and tertiary structures that are important for RNA function

47
Q

Coding strand, sense strand etc

A

5’——3’
coding/sense/non-template

3’——5’
non-coding/antisense/template

mRNA 5’—-3’
Read in 5’–>3’ direction
NH2 terminus–>COOH terminus

48
Q

Ribozymes

A

Usually precursors of rRNA, remove internal segments of themselves, splicing the ends together

49
Q

Histone acetylation and deacetylation

A

Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.

Histone acetylation and deacetylation are essential parts of gene regulation. These reactions are typically catalysed by enzymes with “histone acetyltransferase” (HAT) or “histone deacetylase” (HDAC) activity. Acetylation is the process where an acetyl functional group is transferred from one molecule (in this case, Acetyl-Coenzyme A) to another. Deacetylation is simply the reverse reaction where an acetyl group is removed from a molecule.

Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.

50
Q

Chromatin remodeling and bromodomains

A

An ATP-driven chromatin remodeling complex will bind to the regions of DNA that contain acetylated histones. Bromodomains on proteins within the complex recognize the acetylated histones. Once bound, using ATP as an energy source, the complex will move and displace histones to free up an area of DNA for transcription.

51
Q

mRNA’s can be degraded

A

mRNA can be degraded by nucleases after their synthesis in the nucleus and before their translation in the cytoplasm.

Interferon stimulates the synthesis of 2’,5’-oligo(A) which activates a nuclease that degrades mRNA

Biochemistry (41 decks)

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