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Principles 2018 > Biochemistry Part 2 > Flashcards

Biochemistry Part 2 Flashcards

1
Q

What is the process converting DNA to RNA?

A

Transcription

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2
Q

What is the process converting RNA to protein?

A

Translation

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3
Q

Where does transcription occur?

A

Inside nucleus

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4
Q

Where does translation take place?

A

Ribosome

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5
Q

What is a nucleoside?

A

Base + sugar

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6
Q

What is a nucleotide

A

Nucleoside + phosphate groups

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7
Q

Which four bases occur in DNA?

A

A, C, G, T

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8
Q

Which four bases occur in RNA?

A

A, C, G, U

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9
Q

Describe polymerisation?

A

A phosphodiester bond is formed between a free 3 OH group and a 5’ triphosphate (consumes two high energy bonds)

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10
Q

What is the direction of nucleic acids?

A

New nucleic acids are only added to 3’ end

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11
Q

How to nucleotide analogues work as drugs?

A

Incorporate into the growing viral DNA, lacks 3’ OH group therefore chain elongation is terminated

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12
Q

What must happen to DNA before cell division?

A

It must be replicated

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13
Q

Describe the process of replication?

A

-Semi-conservative
-Catalsyed by DNA polymerase
>can only add to existing nucleic acids
>can not start DNA synthesis on their own
>require an RNA primer to start replication

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14
Q

What are the points of replication in eukaryotic genomes?

A

-Many origins
-simultaneously at several points in the genome
>bidirectional
>ensures that replication can be finished in a reasonable time

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15
Q

Why is replication discontinuous

A

Nucleotides can only be added to free 3’ ends

Other strand has to be replicated in short segments

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16
Q

What are the building blocks of DNA replication?

A

dATP, dTTP, dCTP, dGTP
>one phosphate group forms the phosphodiester bond
>two leave as PPi (energy)

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17
Q

What is needed to unwind the helix?

A

Helicase

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18
Q

What does DNA synthesis require?

A

RNA primer

- synthesised by primase

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19
Q

What kind of activity does DNA polymerase have?

A

Exonuclease activity

- removes incorrect nucleotide

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20
Q

What is the structure of RNA?

A

Single stranded
Can contain local stretched of intramolecular base pairing (Stem loops)
contains U instead of T

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21
Q

What are the 3 main classes of RNA?

A

ribosomal RNA (rRNA) – combines with proteins to form ribosomes where protein synthesis takes place

transfer RNA (tRNA) – carries the amino acids to be incorporated into the protein

messenger RNA (mRNA) – carries the genetic information for protein synthesis

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22
Q

Describe the structure of tRNA

A

Adapters between nucleic acid code and amino acid code
Anticodon consists of three nucleotides
Specific amino acids is attached to 3’ end

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23
Q

What determines the amino acid binding to tRNA 3’ end?

A

the anticodon sequence

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24
Q

What makes RNA?

A

ENA polymerases

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25
Q

How many types of polymerase to prokaryotic cells have?

A

1

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26
Q

How many types of polymerase to eukaryotic cells have?

A

Three

Pol I, Pol II, Pol III

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27
Q

What does pol II do?

A

Synthesised all mRNA

28
Q

How can RNA polymerases be differentiated?

A

Sensitivity to toxins like a amanitin

29
Q

What are the 5 steps of transcription?

A
  • RNA polymerase binding
  • DNA chain separation
  • Transcription initiation
  • Elongation
  • Termination
30
Q

What is TBP?

A

TATA box binding protein, recognises TATA box

31
Q

Where is the TATA box found?

A

about 25 nucleotides before the transcriptional start (-25)

32
Q

What is the role of TBP?

A

> Part of TFIID

  • TFIID is a general transcription factor
  • required for all Pol II transcribed genes

Introduces kink into DNA
-determines transcriptional start and direction

Provides a landing platform for further transcription factors and for RNA polymerase

33
Q

What does initiation of transcription require?

A

Additional general transcription factors

34
Q

How is transcription initiated?

A

TTFID binds to TATA box

  • Joined by transcription factors
  • RNA polymerase II binds only after several transcription factors are already bound to DNA
  • More transcription factors are added
  • RNA polymerase is really to transcribe
35
Q

What is transcription elongation?

A

A transcription bubble moves in one direction along the DNA

DNA unwound infront of polymerase and rewound behind it

36
Q

How is transcription termination achieved?

A

Newly synthesised RNA makes a stem-loop structure

A specific enzyme cleaves the now finished RNA

  • RNA is released
  • polymerase dissociates
37
Q

What does regulation of transcription require?

A

DNA-binding proteins

Bind to specific DNA sequences in the vicinity of a promoter

Can up regulate or down regulate

38
Q

What can gene expression be a response to?

A

Stimulu e.g. hormones, cellular stress

39
Q

What are steroid receptors?

A
  • Family of transcription factors, subset of much larger family of nuclear hormone receptors
  • structurally similar
40
Q

Where are steroid receptors located?

A 
Cell cytoplasm (inactive)
On binding ligand (steroid) move to nucleus and bind to DNA at steroid-response elements (SREs)
41
Q

How are steroids transported?

A

In the blood bound to albumin or specific transport proteins

42
Q

How do steroids enter the cell?

A

By diffusion

43
Q

What do steroids do?

A

Bind to inactive steroid receptor in the cytoplasm, activate the receptor and translocate to the nucleus. Bind to response elements (usually as a homodimer)

44
Q

What must be removed before translation into protein?

A

Introns (non-coding regions)

45
Q

How are the ends of mRNAa processed?

A

A 5’ cap is added- consists of modified GTP

A Poly-a-tail is added

46
Q

What happens to anticodons of tRNA in translation?

A

Base pairs with codons on mRNA

therefore genetic code is based on triplets

47
Q

Why is the genetic code degenerate?

A

Many amino acids have more than one codon

48
Q

Why is the genetic code unambiguous?

A

Each codon codes only for one amino acid

49
Q

What is a reading frame?

A

Each RNA molecule can be translated in three different reading dramas

50
Q

What is the function of aminoacyl-tRNA synthesases?

A

Bind amino acids to their corresponding tRNA molecules

- at least one for each amino acid

51
Q

What provides the energy for bonding with aminoacyl-trna transferases?

A

ATP

52
Q

How many rRNA molecules do ribosomes contain ?

A

four

three in bacteria

53
Q

How many binding sides do tRNA have?

A

E=exit
P=peptidyl
A=aminoacyl

54
Q

Describe the process of Initiation?

A

-Requires initiation factors (IFs)
-GTP is hydrolysed to provide energy for initiation
-Small ribosomal subunit binds to 5’ end of mRNA
-Moves along the mRNA until AUG (start codon) is found (ATP-dependent)
-Special ‘initiator’ tRNA with UAC anticodon base-pairs with the start codon
>carries methionine
-Large subunit joins assembly and initiator tRNA is located in P site

55
Q

Describe the process of elongation?

A

> An elongation factor (EF-1a), brings the next aminoacyl-tRNA to the A site
-anticodon (here: CGU) base-pairs with codon (here: GCA)
GTP is hydrolysed, EF is released from tRNA
A second elongation factor (EFbg) regenerates EF1a to pick up the next aminoacyl-tRNA

56
Q

Describe the bond formation and translocation

A

-Peptidyl transferase catalyses peptide bond formation between amino acids in the P and A sites
>peptide now located in A site
>Elongation factor EF-2 moves ribosome along the mRNA
-by one triplet
>‘Empty’ tRNA moves to E site
-can exit and become reloaded with an amino acid
-tRNA with the growing peptide moves from the A to the P site
-A site is free for the next aminoacyl-tRNA

57
Q

Describe the process of termination?

A

-Occurs when the A site of the ribosome encounters a stop codon
>UAA, UAG or UGA
-No aminoacyl-tRNA base-pairs with stop codons
-Release factor RF binds stop codon
>GTP hydrolysis
-Finished protein is cleaved off tRNA
-The components – rRNA, mRNA and tRNA – dissociate from one another
-Whole process starts all over again with small subunit being bound by IF ready for translation of a new protein

58
Q

Name 5 types of mutation?

A

-point
-missense
-nonsense
-silent
-frameshift
-chromosomal mutations
>deletions
>duplications
>inversions
>translocations

59
Q

What is targeting?

A

> moving a protein to its final cellular destination

> many possible locations within a cell

> depends on the presence of specific amino acid sequences within the translated protein

60
Q

What is modification?

A

Addition of further functional groups

61
Q

What is degradation?

A

unwanted or damaged proteins have to be removed

62
Q

What kind of proteins do free ribosomes in the cytosol produce?

A 
Proteins destined for
>cytosol
>nucleus
>mitochondria
>translocated post-translationally
63
Q

What kind of proteins do bound ribosomes on rough endoplasmic reticulum make?

A 
Proteins destined for
>plasma membrabe
>ER
>Golgi apparatus
>secretion
>translocated co-translationally
64
Q

What is glycosylation?

A

Addition and processing of carbohydrates in the ER and the golgi

65
Q

What other post-translational modifications occurs?

A

Formation of disulfide bonds in the ER
Folding and assembly of multisubunit proteins in the ER
Specific proteolytic cleavage in the ER, Golgi, and secretory vesicles
Hereditary form of emphysema results from misfolding of the protein a1-antitrypsin in the ER

Principles 2018 (34 decks)

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