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Biology 101 flashcards
1
Q

Who proposed the central dogma of biology and when?

A

1956 Francis Crick proposed a fundamental concept in genetics

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2
Q

Central Dogma

A 
flow of heredity information	
 DNA provides the code that eventually leads to proteins- DNA does not directly code for proteins 
DNA ---> RNA ---> protein 
DNA- RNA= transcription 
RNA- protein= translation
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3
Q

Transcription

A

DNA is converted to RNA

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4
Q

What are the 3 stages of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
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5
Q

Describe the basic process of transcription?

A

DNA is converted to mRNA

Uses one strand of DNA (called the template strand) to make single-stranded RNA

The new RNA molecule is synthesised via RNA polymerase

Direction of transcription is 5’-to-3’
 Antiparallel to the template strand

The complementary DNA strand to the template strand is the coding strand (older term no longer used: non-template strand)

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6
Q

What is the direction of transcription?

A

Direction of transcription is 5’-to-3’

Antiparallel to the template strand

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7
Q

RNA polymerase

A

Pairs template-strand nucleotides with RNA- specific complementary nucleotides

catalyses the formation of phosphodiester bond to join the RNA nucleotide (NTP)
adds the nucleotides to the 3’ end of the growing RNA strand

synthesizes the new RNA strand from the template DNA strand

Complementary and antiparallel nucleotide base-pairing to the template strand

Attaches to a promoter- that is upstream of the gene to be transcribed
Ends transcription at the termination sequence,- which is downstream of the gene to be transcribed (3’ to the end of the coding region)

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8
Q

coding strand

A

The complementary DNA strand to the template strand
(older term no longer used: non-template strand)

Same direction (5’-to-3’) and sequence as mRNA, only has T’s instead of U’s

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9
Q

Promoters

A

are regions on the DNA template strand that RNA polymerase recognises and initiates transcription (“this is the start of the gene this is where we need to begin”)

are not transcribed but rather direct the RNA polymerase to the correct starting place, the start of transcription

upstream of the gene to be transcribed

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10
Q

Where is DNA transcribed?

A

The DNA is transcribed between the start of transcription region and the termination sequence

nucleus

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11
Q

start of transcription

A

the DNA location where transcription of a sequence begins

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12
Q

termination sequences

A

Transcription ends
tells RNA polymerase to stop

is downstream of the gene to be transcribed (3’ to the end of the coding region)

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13
Q

Introns

A

are regions that are transcribed but do not code for specific proteins (ie non-coding) and so will get removed before the mRNA is translated

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14
Q

Exons

A

are the regions of mRNA that do code for proteins and will remain in the mRNA for translation

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15
Q

What are the 4 mains kinds of RNA?

A

Messenger RNA (mRNA): transcription, carries genetic code

Ribosomal RNA (rRNA): translation, part of ribosomes

Transfer RNA (tRNA): translation, carries amino acids

Small nuclear RNA (snRNA): mRNA processing and intron removal

Micro RNA (miRNA) and small interfering RNA (siRNA): regulatory RNA

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16
Q

What are some Features of RNA ?

A

Contains 4 ribonucleotides: (made of ribose sugar instead of deoxy)
 Uracil (U) instead of Thymine (T)
 Adenine, cytosine, guanine same as DNA

Hydroxyl (OH) group on 2’ carbon in ribose

Usually single stranded

  • Can form short double-stranded hairpin structures
  • Helps in tertiary protein folding
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17
Q

RNA polymerase core

A

(Bacteria)
Protein complex composed of 5 subunits
2 alpha subunits, 2 beta subunits, 1 omega subunit
Binds to a 6th polypeptide called sigma subunit

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18
Q

sigma subunit

A

sixth polypeptide that when rna polymerase core attaches to it switches polymerase to the active form- holoenzymee

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19
Q

Describe bacterial promoters

A

are double stranded regulatory DNA sequences that bind transcription proteins (RNA polymerase)

In bacteria, 2 promoter regions

although they are double stranded they are written in a single shot hand form that gives the 5’- 3’ sequence of the coding strand

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20
Q

What are the 2 promoter regionsin bacteria?

A

Pribnow box sequence (aka -10 consensus sequence) (minus means upstream from gene)

5’-TATAAT-3’

-35 consensus sequence

5’-TTGACA-3’

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21
Q

closed promoter complex

A

initial stage of transcription when the RNA polymerase core enzyme and sigma subunit (together form holoenzyme) bind to the promoter consensus sequences,

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22
Q

open promoter complex

A

forms when DNA unwinds near the transcription start site to

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23
Q

Outline bacterial Transcription Initiation

A
  1. The RNA polymerase core enzyme and sigma subunit bind to the promoter consensus sequences, forming a closed promoter complex
  2. DNA unwinds near the transcription start site to form the open promoter complex
  3. The holoenzyme (RNA polymerase + sigma subunit) progresses downstream to initiate RNA synthesis at the +1 nucleotide on the template strand
    sigma subunit dissociates shortly after transcription initiation and the core enzyme continues transcription
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24
Q

Outline bacterial Transcription Elongation

A

The core enzyme of the RNA polymerase synthesises RNA until it reaches the termination sequence

As the RNA polymerase progresses, DNA unwinds to allow the template strand to direct RNA assembly
- Progresses at ~40bp/s in the 5’-to-3’ direction

The DNA immediately returns to a helix after RNA polymerase passes by

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25
Q

Outline bacterial Transcription Termination

A

Once the polymerase reaches the termination sequence, it is released from the template strand and dissociates from the mRNA transcript

mRNA transcript is 5’-to-3’ (same as coding strand of DNA except has U’s instead of T’s)

mRNA transcript is complementary and antiparallel to the template DNA strand

26
Q

intrinsic terminators

A

rho(rho is a type of protein) independent)

Dependent on specialized DNA sequences that induce the formation of hairpins (loops) in the RNA

Rich in GC nucleotides

Stretches of T’s in the coding strand (A’s in the template strand) mean lots of U’s in the RNA (ie polyU tail) which cause the RNA polymerase to slow down and destabilize

27
Q

Rho-dependent termination

A

Rho protein binds to RNA at the rut site once the rho utilisation site is transcribed

Protein causes RNA polymerase to dissociate at the terminator region due to the formation of a stem-loop structure

28
Q

State a difference between bacterial and eukaryotic transcription?

A

Unlike bacteria which have a single core polymerase, eukaryotes have 3 different RNA polymerases

29
Q

general transcription factors

A

6 proteins
eukaryotic transcription proteins that bind the promoter region to form part of the apparatus that initiates transcription

30
Q

List the different RNA polymerases present in Eukaryotes and function?

A

RNA polymerase I (RNA pol I): transcribes ribosomal genes

RNA polymerase II (RNA pol II): transcribes mRNA

RNA polymerase III (RNA pol III): transcribes tRNAs

31
Q

RNA polymerase II

A

binds to several promoter regions in eukaryotic DNA

32
Q

What are the promoter regions in eukaryotic DNA?

A

TATA box -> located -25 bases upstream of the transcriptional start site

CAAT box -> located -80 bases upstream of the transcriptional start site

GC-Rich box -> located -90 or more upstream of the start site

Not all genes have all 3 promoter regions….

33
Q

Describe the process of Eukaryotic transcription initiation

A

TFIID (TATA-binding protein + TBP- associated factor) binds to the TATA box

Forms the initial committed complex

Other TFs (TFIIA, TFIIB, TFIIF) and RNA polymerase join the initial committed complex

TFIIE and TFIIH then join the complex, forming preinitiation complex (PIC)

All of these TFs are commonly called general transcription factors (GTFs)

Once the PIC is formed, transcription starts at the +1 nucleotide on the template strand

34
Q

silencer sequences

A

repress transcription

Bind to proteins that bend the DNA such that genes get hidden behind the bended segment, thus blocked from RNA polymerase activity

35
Q

Enhancer sequences

A

Often promoters alone cannot initiate transcription in RNA pol ii

are DNA regulatory sequences that increase (“enhance”) gene transcription

Bind to specific proteins that interact with proteins bound at promoter regions, forming “bridges” that bend the DNA and links the transcription complex

36
Q

Transcription factors

A

help bind the RNA polymerase to the DNA promoter regions

37
Q

Chromatin

A

mixture of DNA + associate proteins (the “spaghetti” state)

38
Q

TFIID

A

TFIID (TATA-binding protein + TBP- associated factor) binds to the TATA box

Forms the initial committed complex

39
Q

Euchromatin

A

not densely compacted genetic material, actively transcribed

40
Q

What affects/ regulates transcription in eukaryotes

A

Chromosome state also affects/regulates transcription

enhancer/ silencer sequences

41
Q

Heterochromatin

A

highly compacted genetic material, not transcribed

42
Q

Outline Eukaryotic elongation

A

RNA polymerase synthesises RNA until it reaches the termination sequence

As the RNA polymerase progresses, DNA unwinds to allow the template strand to direct RNA assembly

The DNA immediately returns to a helix after RNA polymerase passes by

elongation follows very similar to prokaryotic transcription

43
Q

What are 2 types of transcription termination mechanisms in bacteria?

A

intrinsic (more common) and rho dependent

44
Q

Outline Eukaryotic Termination

A

occurs once the RNA polymerase transcribes the polyA tail, dissociating the RNA polymerase from the template DNA strand and RNase cuts the pre-MRNA strand off.

45
Q

consensus sequence

A

short regions of DNA sequences that are highly similar though not necessarily identical to one another and are located in the same position relative to the start of transcription of different genes

46
Q

rut site

A

a strech of approx 50 nucleotides that are rich in cysteine and poor in g

47
Q

preinitiation complex (PIC)

A

in eukaryotic transcription a large multiprotein complex containing several general transcription factors and RNA polymerase 2

48
Q

pre-mRNA

A

the initial transcript of a eukaryotic gene requiring mrna processing prior to translation

49
Q

mRNA

A

the fully processed mRNA that comes out of the nucleus to the cytoplasm for translation

50
Q

What are the steps to modify the pre mRNA to mature mRNA

A

1) 5’ capping
2) Polyadenylation of the 3’ pre-mRNA
3) intron splicing

51
Q

What must happen after termination

A

After transcription termination, the pre-mRNA must be modified before exportation from the nucleus

52
Q

Addition of the 5’-cap:

A

protects the mRNA from degradation as its transported across the nuclear envelope and introns are spliced out

Guanylyl transferase adds a guanine to the 5’ end of the pre-mRNA

Produces an unusual 5’-to-5’ bond forming a triphosphate linkage

Methylation of that guanine finalises the cap

53
Q

Polyadenylation of the 3’ pre-mRNA

A

Cleavage and polyadenylation specificity factor (CPSF) binds to a region of AAUAAA downstream of the stop codon (therefore is non-coding)
- Polyadenylation signal sequence

Cleavage stimulating factor (CStF) binds to a uracil rich sequence downstream of the polyadenylation signal sequence
- Other cleavage factors (CFI, CFII) and polyadenylate polymerase (PAP) also join the complex

The complex cleaves 15-30 nucleotides downstream of the AAUAAA

Once cut, the pre-mRNA has 20-200 adenine nucleotides added to its 3’ end to create a poly-A tail

54
Q

what does the poly A tail function in?

A

Facilitating the transport of mRNA across the nuclear membrane

Protecting the mRNA from degradation

Enhancing translation by enabling ribosomal recognition of the mRNA

55
Q

Splicing

A

removes introns and joins together the exons

56
Q

Introns:

A

“intervening regions”

57
Q

Exons:

A

“expressed regions”, gets translated into proteins

58
Q

spliceosome

A

(protein complex that removes introns)

59
Q

Alternative splicing

A

one region that is an intron in one gene may be an exon region in depending on the protein that is to be translated

60
Q

When does Posttranscriptional modification occurs?

A

Posttranscriptional modifications are coupled with transcription

The 5’ cap is added after ~ 20-30 nucleotides have been transcribed

61
Q

What are some key differences in transcription in eukrayotes and prokaryotes?

A 
Prokaryotes 
 No posttranscriptional modifications in prokaryotes
Happens in the cytoplasm
Has a terminator sequence
no intron

Eukaryotes
Yes posttranscriptional modifications in eukaryotes
Happens in the nucleus
No terminator sequence

Genetics (12 decks)

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