> For the complete documentation index, see [llms.txt](https://zhonglab.gitbook.io/3dgenome/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://zhonglab.gitbook.io/3dgenome/appendix-homework/homework.md).

# Homework

## Review of Molecular Biology

### Question 1 (15 points)

a. Describe how polymerase chain reaction (PCR) work. (5 pts)

b. Describe how microarrays work. (5 pts) 

c. Why is the central dogma incorrect/incomplete nowadays? (5pt)

## DNA-seq

### Questions 2 (15 points)

a. Describe how Sanger sequencing work. (10 pts)

b. What does the role of ddNTP play in Sanger sequencing? (5 pts)

### Question 3 (10 points)

a. Describe how Illumina’s sequencing work. (10 pts)

## RNA-seq

### Question 4 (10 points)

a. Draw the typical structure of coding genes (5 pts)

b. Apart from coding genes, what are other annotated elements in genome? (5 pts)

### Question 5 (20 points)

a. Describe five ways in which gene expression can be altered from Transcription to post-translation step. (5pt)

b. What is alternative splicing? (5pts) 

c. If a gene has “x” number of exons, how many proteins could potentially be created? (5pts) 

d. If exactly “y” exons are to be retained in the final transcript, how many proteins can be created? (5pts)

### Question 6 (30 points)

a. Describe how experimental pipeline of RNA-seq works. (10 pts) 

b. What are the steps of RNA-seq data analysis after RNA-seq run is performed (5 pts)? 

c. What goals can RNA-seq analysis achieve (5 pts) ? 

d. What are four pros and four cons of RNA-seq compared to microarray? (10 pts)