Lecture 1 - Introduction and Genetics

Question 1

What is the simplest eukaryote studied?

Answer 1

Yeast (S. cerevisiae) because it has all the same cellular organization as a human

Question 2

What model plant is studied?

Answer 2

Arabidopsis (mustard seed)

Question 3

What is the simplest multicellular eukaryotic model organism?

Answer 3

C. elegans, a tiny worm because it is so small with approximately 900 cells, is see-through which helps to observe the division and formation of cells, and they multiply quickly

Question 4

What common sophisticated multi-cellular organism is studied?

Answer 4

Drosophila melanogaster - study how brain and memory work and valuable for studying developmental environment

Question 5

What are the two accessible models for studying vertebrate development?

Answer 5

Zebrafish, because they are see-through and an alternative to using mice to study genetics, and frogs because they have giant eggs that represent a great source of protein for biochemical studies - Both fairly distant relatives of humans

Question 6

What is the predominant mammalian model organism?

Answer 6

Mouse because they are basically identical to humans at the cellular level

Question 7

What does DNA consist of?

Answer 7

Two complementary chains of nucleotides

Question 8

What is a nucleotide made up of?

Answer 8

Sugar, phosphate, and nitrogenous base

Question 9

How are the sugars in the DNA backbone attached?

Answer 9

Via phosphodiester bonds

Question 10

How are nitrogenous bases connected?

Answer 10

H-bonds

Question 11

What are the constraints for base pairing?

Answer 11

1) Two purines or two pyrimidines cannot form base pairs because purines are too large and pyrimidines are too small
2) A is only complementary to T and U and C is only complementary to G

Question 12

How is eukaryotic DNA packaged?

Answer 12

Into chromatin (DNA, histones, and proteins) which is then condensed into chromosomes

Question 13

How can you immediately see if chromosomes have abnormalities?

Answer 13

Taking a human cell in mitosis at its most condensed stage to create a human karyotype and add fluorescent dye

Question 14

What does each DNA molecule that forms a linear chromosome have to contain?

Answer 14

A centromere, two telomeres, and replication origins

Question 15

Why are centromeres important?

Answer 15

Important for cell division since mitotic cells recognize it and allow chromosomes to separate

Question 16

What are telmoeres?

Answer 16

The ends of chromosomes

Question 17

What is heterochromatin?

Answer 17

The parts of the chromosome where the DNA is extra compacted and tends to have a low number of genes and regions near the centromere

Question 18

What is euchromatin?

Answer 18

Part of the chromosome that is gene-rich and less compact but more accessible to transcription factors

Question 19

What is the central dogma of genetics?

Answer 19

1) DNA to DNA - replication
2) DNA to RNA - transcription
3) RNA to protein - translation

Question 20

What is the useful function of transcription?

Answer 20

Makes lots of RNA copies that can be translated to make the same protein

Question 21

Exons vs. Introns?

Answer 21

Exons are the only ones left after splicing because they form mRNA and introns are left out

Question 22

What does RNA polymerase need to bind and initiate transcription?

Answer 22

Promoter

Question 23

What is forward genetics?

Answer 23

Classical approach of studying genes by observing a phenotypic difference and working your way back to the gene that caused it by random mutagenesis - chemical mutagen or insertional mutagenesis

Question 24

What is reverse genetics?

Answer 24

Making deliberate mutations in a gene to study the phenotype by site-directed mutagenesis - homologous recombination and gene editing - or by RNAi which knockdown genes

Question 25

What is the general process of transfection/transformation and what can it be?

Answer 25

It is the introduction of genes into cells or animals and it can be transient (DNA will eventually be lost from the cell) or stable (DNA is integrated into the host genome)

Question 26

What happens if a transgene is passed on to germline cells

Answer 26

Transgenic animals can be obtained

Question 27

How can transgenes be used to study gene function?

Answer 27

Overexpression, gene reporters, epitope or GFP tag, structure/function studies

Question 28

How can genes be cloned using bacteria?

Answer 28

1) Circular double-stranded plasmid DNA is cleaved with restriction nuclease
2) DNA fragment to be cloned is covalently linked by DNA ligase
3) Double-stranded recombinant plasmid DNA is introduced into a bacterial cell
4) Cell culture produces hundreds of millions of new bacteria
5) Many copies of the purified plasmid are isolated from lysed bacteria

Question 29

How is an entire genome represented in a DNA library?

Answer 29

1) Double-stranded DNA is cleaved with restriction nuclease
2) Millions of genomic DNA fragments are inserted into plasmids
3) Recombinant DNA molecules in plasmids are now introduced into bacteria
* Good genomic library should have a plasmid for every sequence of DNA

Question 30

What is PCR?

Answer 30

The polymerase chain reaction is a powerful and versatile method for amplifying DNA and provides a straightforward approach to DNA cloning, particularly in organisms whose complete genome sequence is known

Question 31

What are the steps for PCR?

Answer 31

1) Denature dsDNA by heating at 95 degrees C for 30 seconds
2) Anneal primers by cooling to 58 degrees C for 1 minute
3) Incubate mixture with DNA polymerase and four deoxyribonucleoside triphosphates
4) Extend DNA using DNA polymerase (Taq) which starts at the primers when cooled to 62 degrees C for 2 minutes
5) Repeat

Question 32

What is the key to PCR?

Answer 32

Taq polymerase because it is immune to boiling