Chapter 9 - Intro to Genomics

Question 1

What is a Polymerase Chain Reaction

Answer 1

A method of copying DNA (in test tube-> Vitro) by mimicking DNA synthesis

Question 2

In PCR instead of Helicase it uses….

Answer 2

separates DNA strands by heat and then uses DNA polymerase

Question 3

What is the process of copying DNA by PCR called

Answer 3

Amplification

Question 4

What is the copied chunk of DNA called in PCR

Answer 4

Amplicon

Question 5

What does PCR require

Answer 5

The same thing as DNA Synthesis requires

• dNTP: DNA nucleotides with three phosphates
• Denatured DNA (heat) template
• Primers; specific to DNA being amplified

Question 6

What is Exponential amplification

Answer 6

when the copies are made, they serve as a template for future replications

Question 7

Temperatures of denaturalization, amplification, and elongation

Answer 7

1. 94-96 degrees Celsius
   2.(Negative) -68 degrees Celsius
2. 72 degrees Celsius

Question 8

Elongation

Answer 8

Addition of nucleotides to a new DNA strand

Question 9

DNA Sequencing is a PCR reaction but ..

Answer 9

there’s a mix of dNTPs and ddNTPs

ddNTPs= dideoxynucleoside triphosphates

It has a fluorescent label

(Chain terminator bc there’s no OH group to bond to)

Question 10

Electrophoresis

Answer 10

Separating the fragments by size

Question 11

The color of the fluorescent colors signifies

Answer 11

the sequence of nucleotides of the DNA template

Question 12

Genomes contain __ or __ of base pairs

Answer 12

Millions or billions

Question 13

Sequencing reactions generate

Answer 13

500-800 bp of sequence per reaction

Question 14

In the future there hopes for

Answer 14

No chain termination step,
no separation step
Still PCR-based, but products are fully synthesized
Everything is done in-solution
Millions of reads in a single reaction

Question 14

In order to build an entire chromosome

Answer 14

Sequences must overlap

Question 15

Entire genomes can be sequences in

Answer 15

A couple of weeks

Question 16

Genome Annotation

Answer 16

Process of identifying and mapping genes and functional regions in a genome.

Question 16

cDNA Sequencing

Answer 16

cDNA is reverse-transcribed DNA from mRNA (only coding regions, no introns), used to identify protein-coding genes.

Question 17

Challenges of cDNA Sequencing

Answer 17

• Not all genes are expressed in all cell types.
• Lowly expressed genes may go undetected.
• Does not reveal RNA genes (non-protein-coding).

Question 18

Computational Tools

Answer 18

Used to detect genes and analyze natural selection signals in the genome.

Question 19

Natural Selection & Genome

Answer 19

Natural selection conserves important genomic regions, causing them to be more similar across species, while nonfunctional regions diverge faster.

Question 20

Protein-Coding Gene Identification (Finding Protein-Coding Genes)

Answer 20

Tools analyze DNA sequence patterns to identify regions that may encode proteins (Open Reading Frames, ORFs).

Question 21

Noncoding DNA Distribution (Finding Protein-Coding Genes)

Answer 21

Noncoding DNA behaves randomly in nucleotide distribution (e.g., ATG should appear every ~200bp, STOP codons every ~63bp).

Question 22

Characteristics of ORFs (Finding Protein-Coding Genes)

Answer 22

• Underrepresentation of ATG and STOP codons.
• ATG without a STOP codon for longer than 63bp.
• Codon usage bias (certain codons are used more frequently).

Question 23

Six Reading Frames (Finding Protein-Coding Genes)

Answer 23

Each stretch of DNA has six possible reading frames (three on each strand, + and -).

Question 24

Gene Orientation (Finding Protein-Coding Genes)

Answer 24

Genes can be on either strand of the DNA (+ or - strand).

Question 25

Splice Sites (Finding Protein-Coding Genes)

Answer 25

Splice donor and acceptor sites tend to be near each other more often than expected.

Question 26

Regulatory Elements (Finding Protein-Coding Genes)

Answer 26

• CAAT box and TATA box often appear near each other.
• Poly-A signal (AATAAA) is also near other regulatory elements.

Regulatory elements are binding sites for transcription factors, which are involved in gene regulation

Question 27

Computational Tools (Finding Protein-Coding Genes)

Answer 27

Used to detect patterns such as codon usage, splice sites, and regulatory sequences, and analyze their proximity to each other.

Question 28

Mutations in noncoding DNA is always

Answer 28

Neutral

Question 29

Within coding regions, the ratio of synonymous-to-nonsynonymous mutations

Answer 29

higher than expected

Question 30

Non-synonymous mutations

Answer 30

Harmful and eliminated

Question 31

Synonymous mutations

Answer 31

Silent and persist

Question 32

Computational tools

Answer 32

Detect the type of mutation

non0syn
syn