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Principles Biochemistry > Lecture 5 DNA to Protein > Flashcards

Lecture 5 DNA to Protein Flashcards

1
Q

In the sugar molecule to which carbon does the base and phosphate attach

A

Base= Carbon 1’ Phosphate = Carbon 5’

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2
Q

What is a Nucleoside

A

Base + Sugar

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3
Q

What is a Nucleotide

A

Nucleoside + phosphate

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4
Q

What are the purines

A

Adenine and Guanine

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5
Q

What are the Pyrimidines

A

Thymine, Cytosine and Uracil

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6
Q

Name all the Nucleotides which include these bases

A

Adenine= Adenosine

Gaunine= Guanosine

Thymine= Thymidine

Cytosine= Cytidine

Uracil= Uridine

DNA= dATP, dGTP, dTTP, dCTP

RNA= ATP, GTP, CTP and UTP

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7
Q

What bonds are formed between the nucleotides

A

Phosphodiester bonds

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8
Q

Where are the phosphodiester bonds formed

A

between the 3’ OH and the 5’ Trophosphate group

When this bond formed the other 2 phosphated from the triphosphate group is released = 2 High energy bonds provide energy for polymerisation

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9
Q

What is the direction of nuleotides growth

A

from 5’ to 3’

New nuleotides are added are the 3’ end only

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10
Q

What are the actions of drugs AZT and ZDT

A

These are NRTI- Neucloside reverse transcriptase iinhibitors

  • Competes with nucleodies to present their incoporation into the Growing viral DNA
  • they lack 3’ OH - chain elongation is terminated
  • Viral transcriptase has a higher affinity for ZDV
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11
Q

How many hydrogen bonds betwee A-T and G-C

A

2 between AT

3 between CG

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12
Q

Can DNA Polymerase start DNA synthesis on their own

A
  • no - can only add to existing Nucleic acid
  • Requires an RNA primer
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13
Q

Origins of replication?

A
  • Seqeunces in a genome where DNA replication is initiated
  • Many in Eukaroyotic cells
  • Bidirectional
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14
Q

Leading Strand ?

A

The strand in DNA replication which is always has a free 3’ ends

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15
Q

Lagging strand

A

the strand from 3’ to 5’ has to be replicated in segments

  • DNA polymerase can only go 5’ to 3’
  • Short segments = Okazaki fragments

Therefore DNA replication is Discontinous

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16
Q

What is mechanism of DNA replication

A
  • Helicase unwinds DNA
  • Primase synthesie an RNA Primer
  • DNA Polymerase synthesises a complementory strand
  • The lagging strand is synthesised as okazaki fragments- primase lies down primers for DNA to wrok from 5’ to 3’
  • RNA primers are degraded
  • Spaces are filled by DNA polyerase
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17
Q

DNA major points

A

•dATP, dTTP, dCTP, dGTP as building blocks

–one phosphate group forms phosphodiester bond

–two leave as PPi (pyrophosphate) – energy supply

  • Helicase needed to unwind helix (and stop it rewinding)
  • Replication fork with leading (3’-5’) and lagging (5’-3’) template strands forms
  • Copying leading strand template in 5’-3’ direction leaves free 3’ end for next nucleotide
  • Copying lagging strand template is more complex

–Okazaki fragments

•DNA synthesis needs an RNA primer

–synthesized by primase

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18
Q

What is exonuclease activity

A

DNA polymerase has proof reading ability where it is can detect mutations and remove it from the growing DNa stand

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19
Q

What are Stem loops

A

Single stranded RNA molecule can pair with itself forming local streches

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20
Q

What are the 3 types of RNA’s

A
  1. rRNA- combines with proteins to from ribosomes
  2. tRNA- Carries the amino acid to be incorported
  3. mRNA- carries genetic information for protein synthesis

rRNA and tRNA = Stable

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21
Q

Discribe the Structure of tRNA and its function

A
  • Adapter between amino acid and mRNA
  • Carries the Amino acid on the 3’ end
  • Has a 3 nucleotide anticodon for each codon on the mRNA molecule
  • Cloverleaf shaped
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22
Q

What are RNA Polymerase

A
  • Enzyme synthesises RNA
  • Uses one DNA strand as a template to copy the neuleotide
  • Pol I, Pol II, Pol III
  • Distinguished by sensitivity to a-amanitin
  • Pol II synthesises all MRNA
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23
Q

What are the Steps in transcription

A
  • RNA Polymerase binding
  • DNA chain separation
  • Transcription initiation
  • Elongation
  • Termination
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24
Q

What is the RNA Pol II specific promoter

A
  • TATABOX
  • Transcrition starts at nucleotide +1
  • TATAbox is located 25 nucleotides before the transcription starts = -25 nucleotide
25
Q

What is the TBP

A
  • TATAbox binding protein
  • Is a part of TFIID required for all pol II transcribed genes
  • TBP binds to TATAbox and creates a landmark that starts transcription- tells RNA where to bind
  • Introduces a kink in the DNA 900 - landing platform for other transcription factors and RNA Polymerase
26
Q

Transcription Initiation

A
  • TFIID and TBP
  • More transcription factors come in - TFIIF
  • Poll II and TFIIF extend the transcript
  • TFIID remains at promoter site and new initiation complex is assembled
  • Allows transcription at low basal rates
27
Q

Transcription Elongation

A
  • Transcription factor moves in one bubble along DNA molecule
  • DNA unwinds infront and rewinds behind
  • from 5’ to 3’
  • Complementatory to Template strand and identicle to coding strand
28
Q

Transcription termination

A
  • Newly synthesised RNA Makes a stem-loop structure
  • Followed by a strech of UUU
  • Enzyme cleves the finishes
  • RNA released
  • RNA polymerase dissociates
29
Q

What is the specific regulation of transcription

A
  • Requires specific transcritpion factors which bind to DNA
  • They have 2 domains one binds to DNA molecule and one Acts to activate transcription
  • They binds to Enhancers - far from promoter region
  • Regulate transcription positively or negativity
  • Activator protiens bind to enhancers far away- DNA bends and protein in brought in contact with transcription factors
30
Q

What is co-ordinated gene expression

A
31
Q

What are steroid receptors

A

Transcription factors

32
Q

Whats the mechanism of steroid receptor activation

A
  • DNA and ligand binding domains
  • Located in the cytoplasm in an inactive form
  • Unpon binding a ligand is activated and transported to the nucleus
  • Binds to Stress responce element on DNA
33
Q

How are steriods transporte in blood

A

bound to albumin or specific transport proteins

34
Q

What is the mechanism of a gluccocorticoid receptor

A
  • Free steroids enter cell by diffusion
  • Bind to inactive steroid receptor in cytoplasm
  • Receptor is activated and translocates to nucleus
  • Binds to stress-responce element and
  • regulates a set of genes
35
Q

What are introns and exons

A

Introns = non-coding regions

Exons= Coding regions

There are both transcriped to together but then

Introns are spliced out and leaves a mature mRNA

36
Q

How are the ends of mRNA processed

A
  • Gcap is added to 5’ end
  • poly AAAA added to 3’ end
37
Q

How many naturally occuring amino acids

A
  • 4 nucleotides
  • 64 combinations
  • 20 amino acids
38
Q

what does it mean by the genetic code is degenerate

A

many amino acids have more than 1 codon

  • but each codon (3 base pairs) can only code for 1 amino acid
39
Q

How many Reading frames are in 1 Rna molecule

A

3 reading frames

40
Q

What components are needed for Translation

A
  • Amino acids
  • tRNA
  • Aminoacytle tRNA synthase
  • A set of protein factors for - initiation, elongation and termination
  • ATP and GTP
  • Ribosomes
  • mRNA
41
Q

What is the function of Aminoacyl tRNA synthase

A
  • They bind amino acids to their corresponding tRNA molecules - specific
  • There is 1 for each amino-acid
  • Uses ATP for covelent bond formation
42
Q

What are ribosomes made of

A
  • 4 rRNA molecules
  • Protien
43
Q

Are the 3 binding sites of ribosomes for tRNA molecules

A
  • E - exit
  • P - Peptidyl
  • A - Aminoacyl
44
Q

What is the initiation process

A
  • Required Initiation factors - IFs
  • GTP hyrolysis for energy
  • Small ribosomal sub-unit binds mRNA 5’ end
  • AUG - start codon binds tRNA
  • Large sub-unit joins and tRNA located at p-site
45
Q

What is the elongation process

A
  • Elonagation factor brings next aminoacyl tRNA synthase to A site
  • Anticodon pairs codon
  • GTP is hyrolysed and EF is released to pick up next At-synthase
46
Q

What is the process of peptide bond formation

A
  • Peptidyl transferase catalyses peptide bond formation between amino acids in the P and A sites
  • Elongation factor EF-2 moves ribosome along the mRNA- By one triplet
  • Empty tRNA moves to E-site
  • tRNA with the growing peptide moves from A to P site
  • A site free for next At-synthase
47
Q

What is the Terminatin process

A
  • Stop codon at A site - UAA, UAG, UGA
  • Release factor binds to stop codon on mRNA
  • GTP hydrolysis
  • Components dissociate
  • Process will repeat when next initiation factor binds small subunit of ribosome
48
Q

What is the polysome

A

Many ribosomes translating 1 mRNA

49
Q
A
50
Q

What is a Point mutation

A

Change in a single base in DNA

51
Q

Missense mutation

A
  • This is a point mutation - single nucleotide chage
  • Which results in change of amino acid sequence
  • Altered Haemoglobin - sickle cell anaemia
52
Q

Nonsense Mutation

A
  • Change to chain-temrination code
  • May result in ealy or late termination
53
Q

Silent mutation

A
  • Changes codon
  • But no change in amino acid due to
  • Degenracy of genetic code
  • No affect on protein function
54
Q

Frame Shift Mutation

A
  • Addition of base
  • Deletion of base
  • Changes reading frame of translation into protein
55
Q

What are the types of chromosomal mutations

A
  • Deletions
  • Duplication
  • Inversion
  • Translocation
56
Q

What are Free ribosomes

A
  • Located in cytosol- proteins desined for
  • Cytosol
  • Nucleous
  • Mitochondria
  • Translocated- Post translationally
57
Q

what are Bound ribosomes

A
  • Ribosomes bound to RER
  • Plasma membrane
  • ER
  • Golgi apparatus
  • Secretion
  • Translocated- Co-translationally
58
Q

What happens in post-tranlational modification

A
  • Glycosylation - add carbohydrates - ER and Golgi
  • Disulfide bond formation - ER
  • Folding and assembly - ER
  • Proteolysis- Cleaving polypeptides
  • Emphysema - misfolding proteins in ER
59
Q
A

Principles Biochemistry (7 decks)

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