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2020 Biotherapeutics molecular biology revision material

Some recent COVID-19 science articles

While a rapidly evolving area, here are a few recent articles on the science of COVID-19 that may be of interest to read up on.
Please ensure you obtain your information from trusted sources.  A lot of "opinions" out there, so always consider the quality of your sources.
​

In this video, UC Berkeley professor and IGI Investigator Britt Glaunsinger explains the evolution, genetics, and virulence of coronaviruses. Watch first 20 mins.
 Principle of probe based qPCR – approach being used in COVID testing.  Requires primers and a ‘probe’ (3 mins).

Some recent articles that may be of interest
​....click links below to read
  1. DNA Could Hold Clues to Varying Severity of COVID-19
  2. PCR versus antibody tests: What’s the difference?
  3. COVID and ACE2 interacting amino acids  See Fig 4 and Fig 5; view the interacting amino acids (one letter code; amino acid number e.g. K353 = Lysine at position 353).
  4. Will antibody tests for the coronavirus really change everything?
  5. NewScientist latest Covid-19 news page
  6. ​The race for coronavirus vaccines: a graphical guide
  7. ​The sprint to solve coronavirus protein structures — and disarm them with drugs

A podcast worth considering...

The Guardian's Science Weekly
​Short, snappy and up to date episodes…well worth a listen – you can even submit questions!
​



​Review of material covered in
​1st half of module

(2020)

00:17 Overview of 1st section (Therepeutics, biopharma, production, biosimilars etc.) 

03:59 General cytokines and cell signalling 

05:47 Interferons 

09:04 Haematopoietic growth factors / Erythropoietin 

13:32 Monoclonal antibodies & radio-immuno conjugates 

​19:42 Summary 
​


Biosimilars animation
Plan for week commencing 30th Mar 2020 (week 11) 
& week commencing 20th April 2020 (week 12 after Easter break)

  1. Submit your Bioinformatics lab report on Moodle.
  2. Watch the Translation Part 1 video below
  3. Perform exercise at end of video
  4. Watch NDSU's Virtual Cell Translation video  ==>
  5. Watch the Translation Part 2 video below.
  6. Research topic: 'Inosine in tRNA'
  7. Watch the Translation Part 3 video below​
  8. ​Self-assessment quiz will follow also.
  9. PCR/Gel Virtual lab 250-word summary due on Moodle Friday April 3rd.
NDSU Virtual Cell Translation Video

1.   Translation (Part 1)
00:28 Points we are going to cover 
01:56 Where is translation in the flow of information 
03:49 Some key points on Translation 
07:13 Definition of Translation 
09:16 Starting translation/AUG/reading frames 
09:56 Our key diagram 
19:10 An adaptor molecule that speaks two languages 
20:57 How a codon is linked to a specific amino acid 
22:09 Impact of changes to the code/degeneracy of the genetic code 
27.39 An amino acid can't recognise a codon 
28:19 The anticodon-codon relationship 
​29:18 Exercise for you 
2.   Translation (Part 2)
3.   Translation (Part 3)
00:00 What is covered in this video 
00:32 The adaptor molecule 
00:52 Considering the 5' to 3' directions 
02:14 Structure & features of tRNA 
08:14 More on the 5'-3' directions of the codon/anticodon 
09:57 Outcome of exercise 
11:48 The stages of translation & Ribosomes 
15:56 The A,P & E sites of the Ribosome 
20:57 The process of translation 
30:10 Home exercise 
​

​NDSU Virtual cell's video of the translation process: 
00:00 The 3 topics in this video 
00:18 The differences between Prokaryotic and Eukaryotic translation (5 topics) 
15:58 The Wobble position and Inosine 
34:47 Rough ER vs free ribosomes 
35:49 How antibiotics and toxins can inhibit Translation 
39:05 Summary 

Translation Review Quiz:
Click here to access Socrative and enter the room number:   TRANSLATE
(23 question quiz covering the 3 mini-lecture videos above; you can take it more than once).
Plan for week commencing 23rd March 2020
Recently, we were discussing standard PCR and also qPCR (quantitative, real time, PCR). 
You can download the specific slides/images in the two methods handouts linked above.
1.     The PCR topic:   Please watch my three mini-lecture videos below covering various aspects as indicated below.
2.     Complete the Quiz below in the yellow box below the PCR videos (feedback provided to assist your learning).
3.     Ensure you have performed the PCR pre-practical quiz (see 13th March e mail from me).  Important to do this.
4.     Regarding your last lab, complete this virtual lab on PCR and also this one on gel electrophoresis by Friday 3rd April. Note that with the agarose gel, we stain with SYBR safe during the process, while in this example they stain the DNA at the end with a different chemical.  As a 'virtual lab manual exercise', please submit one 250 word (max) summary of these virtual sessions to Moodle by April 3rd.
5.     Reminder: CA exam takes place at 1pm online on Friday 27th March (see recent e mail sent last Friday).
​
1.   PCR overview & controls
2.   Reverse Transcription PCR
3.   qPCR (real time PCR)
00:00 Introduction  

PCR pre-practical video to watch
​ 

01:21 The PCR process

07:18 Controls in PCR ; Exercise 

​
17:43 Summary & applications 
00:00 Introduction 

01:00 What is Reverse Transcription (RT)? 

01:47 Transcriptome / Presence of an mRNA = gene expressed 

04:19 The RT-PCR technique 
​

10:51 Short animation of RT-PCR process 
00:00 Introduction 
00:23 Comparison of standard PCR and qPCR 
01:22 What a qPCR machine measures (SYBR green in qPCR)
05:12 Comparison of qPCR approaches 
08:16 Points to become aware of 
09:11 How qPCR results are interpreted (Ct value determination) 
16:15 The melting curve analysis 
​20:09 Review questions 

PCR Review Quiz:
Click here to access Socrative and enter the room number:   PCRREVIEW
(23 question quiz covering the 3 mini-lecture videos above; you can take it more than once).

Revision video for molecular methods

Complementing our methods handout, the pre-practical video playlist on YouTube represents a nice revision too.

Just click the links in this box to go to the relevant video!  
Revision slides on calculations
File Size: 240 kb
File Type: pdf
Download File

  • Using autopipettes in the Laboratory
  • Making a buffer
  • DNA Extractions
  • UV Spectrophotometry and DNA
  • Agarose Gel Electrophoresis
  • Polymerase Chain Reaction (PCR)
  • Restriction Enzymes
Revision videos for Transcription

Video 1:  YouTube link here.
Timestamp hyperlinks:
00:17 Transcription 'Bubble' 
01:49 Flow of information from gene to protein; what is a gene?, a promoter? etc. 
06:58 The role of the template and coding strands 
08:39 3 stages; initiation, elongation and termination 
13:45 Summary 

Video 2: YouTube link here.
Timestamp hyperlinks:
00:13 Regulation of transcription 
05:31 mRNA Processing 
06:48 5' cap 
07:44 3' Poly A Tail
10:58 Splicing
16:09 Alternative Splicing 
20:35 Summary 


​Revision video for DNA replication

Best to open this in YouTube.
​
Please see timestamps both in YouTube video description and on the right of this box under the video (you can click to access relevant parts of the video)
​

Link here opens full video in YouTube

An overview of our DNA replication slides (revision). Timestamp hyperlinks below:
02:22 General replication info.
06:37 DNA polymerase. 
10:00 Helicase/topoisomerase. 
11:10 The Replication Fork. 
14:20 Problems encountered (exercise). 
17:17 Whiteboard drawing video of replication fork. 
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