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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
What is the **TBP**
* 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
Transcription Initiation
* 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
**Transcription Elongation**
* 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
Transcription termination
* Newly synthesised RNA Makes a stem-loop structure - Followed by a strech of UUU * Enzyme cleves the finishes * RNA released * RNA polymerase dissociates
29
What is the specific regulation of transcription
* 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
What is co-ordinated gene expression
31
What are steroid receptors
Transcription factors
32
Whats the mechanism of steroid receptor activation
* 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
How are steriods transporte in blood
bound to albumin or specific transport proteins
34
What is the mechanism of a gluccocorticoid receptor
* 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
What are introns and exons
**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
How are the ends of mRNA processed
* **Gcap** is added to **5' end** * **poly AAAA** added to **3' end**
37
How many naturally occuring amino acids
* 4 nucleotides * 64 combinations * 20 amino acids
38
what does it mean by the genetic code is **degenerate**
**many amino acids have more than 1 codon** * but each codon (3 base pairs) can only code for 1 amino acid
39
How many **Reading frames** are in 1 Rna molecule
**3 reading frames**
40
What components are needed for **T**ranslation
* Amino acids * tRNA * Aminoacytle tRNA synthase * A set of protein factors for - initiation, elongation and termination * ATP and GTP * Ribosomes * mRNA
41
What is the function of **Aminoacyl tRNA synthase**
* They bind amino acids to their corresponding tRNA molecules - specific * There is 1 for each amino-acid * Uses **ATP** for covelent bond formation
42
What are ribosomes made of
* **4 rRNA molecules** * **Protien**
43
Are the **3 binding** sites of ribosomes for tRNA molecules
* **E - exit** * **P - Peptidyl** * **A - Aminoacyl**
44
What is the **initiation process**
* 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
What is the **elongation process**
* 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
What is the process of peptide bond formation
* **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
What is the **Terminatin process**
* 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
What is the polysome
Many ribosomes translating 1 mRNA
49
50
What is a **Point mutation**
Change in a single base in DNA
51
**Missense mutation**
* This is a point mutation - single nucleotide chage * Which results in change of amino acid sequence * **Altered Haemoglobin** - sickle cell anaemia
52
**Nonsense Mutation**
* Change to chain-temrination code * May result in ealy or late termination
53
**Silent mutation**
* Changes codon * But no change in amino acid due to * **Degenracy of genetic code** * No affect on protein function
54
**Frame Shift Mutation**
* Addition of base * Deletion of base * Changes reading frame of translation into protein
55
What are the types of chromosomal mutations
* **Deletions** * **Duplication** * **Inversion** * **Translocation**
56
What are **Free ribosomes**
* Located in **cytosol**- proteins desined for * Cytosol * Nucleous * Mitochondria * Translocated- **Post translationally**
57
what are **Bound ribosomes**
* Ribosomes bound to **RER** * Plasma membrane * ER * Golgi apparatus * Secretion * Translocated- **Co-translationally**
58
What happens in **post-tranlational modification**
* **Glycosylation -** add carbohydrates - ER and Golgi * **Disulfide bond formation -** ER * **Folding and assembly -** ER * **Proteolysis-** Cleaving polypeptides * **Emphysema -** misfolding proteins in ER
59

Principles Biochemistry (7 decks)

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