Chapter 8

Question 1

Where in an animal cell is genetic information found? Plant? Bacteria?

Answer 1

Animal: Cell Nucleus

Plant: Cell Nucleus

Bacteria: Nucleoid

Question 2

In what forms can viral genetic information be found?

Answer 2

CIRCULAR & LINEAR
(bacteriophages have circular DNA)

(ALSO: RNA Viruses, DNA Viruses, Reverse Transcribed DNA, Proviral DNA, mRNA)

Question 3

What does (+) Positive Sense refer to? (ex: (+)ssDNA)

Answer 3

Positive-sense means that the genetic sequence of the viral genome can be directly translated into proteins, similar to cellular messenger RNA (mRNA)

Question 4

How is (+)ssDNA turned into proteins?

Answer 4

DNA -> Transcription -> RNA -> Translation -> Protein

Question 5

How does +ssRNA become protein and why does it return back to +ssRNA?

Why is this important?

Answer 5

RNA -> Translation -> Protein

To return back to +ssRNA:
Viral RNA is replicated into complementary negative-sense RNA (-ssRNA) in order to create new copies of the +ssRNA

• THIS ENSURES THE CONTINUITY OF THE VIRAL LIFE CYCLE

Question 6

How do retroviruses create proteins and do viral replication?

Answer 6

Reverse Transcription!

The reverse transcriptase synthesizes a complementary DNA strand (cDNA) using the viral RNA as a template. This results in the formation of a double-stranded DNA molecule.

Question 7

Why is it that if you swallow a rhinovirus you will not get sick? Why doesn’t the rhinovirus infect dogs?

Answer 7

The primary site of infection for rhinoviruses is the upper respiratory tract, particularly the nasal passages and throat. Rhinoviruses primarily target and replicate in the cells lining the nose and throat.

Rhinoviruses don’t infect dogs because viruses often show a high degree of HOST SPECIFICITY (they have evolved to infect humans), as well as RECEPTOR SPECIFICITY and the fact that viruses can’t survive long if they can’t replicate in certain types of cells (SPECIES BARRIER)

Question 8

Characterize e. Coli’s genome.

Answer 8

Circular, double-stranded DNA genome

Relatively small (only 4.6 million base pairs)

Genes & Coding Regions

Operons

(Plasmids)

Question 9

What is a BAC library and how are bacterial plasmids used in sequencing?

Answer 9

A collection of cloned DNA fragments from a particular organism’s genome that have been inserted into Bacterial Artificial Chromosomes (BACs). BACs are large plasmid vectors that can accommodate large DNA fragments, typically ranging from 100 to 300 kilobase pairs (kb).

BAC libraries are used for genome mapping, allowing researchers to create physical maps of an organism’s genome.

Question 10

What are “Orthologs”?

Answer 10

Genes found in different organisms that have similar purpose and can be traced back to a gene present in their common ancestor.

Question 11

What is the difference between Genomics, Transcriptomics, and Proteomics?

Answer 11

Genomics: DNA genome comparisons

Transcriptomics: mRNA comparisons (studying SPLICING!)

Proteomics: Protein Comparisons

Question 12

What is splicing? Why is mRNA splicing necessary? Why might alternative splicing be beneficial?

Answer 12

Removing sections (introns) of mRNA transcript and ligating (fusing) together the remaining exons.

-> product is mRNA that is ready for translation

NECCESSARY for the formation of continuous coding sequences and the enhancement of mRNA stability and transport

Question 13

Roughly how much of the human genome is made up of protein-coding genes?

Answer 13

~1.5%

Question 14

What are SNPs? How are they useful?

Answer 14

Predictable locations for point mutations that allow us to only look at places where bases can vary between person to person. HELPS WITH DNA SEQUENCING. EVERY PERSON HAS THE SAME DNA EXCEPT FOR THE SNPs

(Single Nucleotide Polymorphisms)

Question 15

What are some large-scale chromosomal alterations that can occur?

Answer 15

Inversions
Duplications
Transpositions

Question 16

Can you define and explain inversions, duplications, and transpositions?

Answer 16

Inversions: flipped or inverted!! an inversion is a segment of DNA is reversed in orientation within a chromosome

Duplications: the presence of multiple copies of the same gene or genomic region within an organism’s genome.
- can be caused by unequal crossing-over and transposons

Transpositions: the movement of genetic elements, often specific DNA sequences called transposons or “jumping genes,” within a genome.

Question 17

What are linked genes?

Answer 17

Linked genes are genes that are located close to each other on the same chromosome. They tend to be inherited together.

Question 18

How do you connect genes with diseases/phenotypes?

Answer 18

Identify SNPs, Focus on specific potential genes in studies, Observe proteins formed

Question 19

How do you distinguish between healthy and diseased individuals on a pedigree? How about living vs. deceased?

Answer 19

Healthy = empty box
Diseased = red box
Living = no line through
Deceased = line through

Question 20

What is a dot plot in the context of genomics?

Answer 20

A graphical method for comparing two biological sequences and identifying regions of close similarity after sequence alignment

Question 21

What is a “Genome Map” and what can it tell us?

Answer 21

Species-specific map of the genome. It can offer firm evidence that a disease transmitted from parent to child is linked to one or more genes. Mapping also provides clues about which chromosome contains the gene and precisely where the gene lies on that chromosome.

Question 22

What is a sequencing “read”?

Answer 22

A shorter segment of DNA
- Used with A LOT of other reads to create contigs. Multiple reads create higher fold coverage.

Question 23

What is a “sequencing assembly”?

Answer 23

Aligning and merging reads from a longer DNA sequence in order to reconstruct the original sequence.

Question 24

What is a sequencing “contig”?

Answer 24

A set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region.

Question 25

What is a consensus sequence?

Answer 25

The most common nucleotide(s) or amino acid residue(s) at each position
(THE MOST LIKELY CONTIG)

Question 26

What is sequencing “fold coverage”?

Answer 26

A number representing the amount of read overlaps within a contig

Question 27

What is precision medicine?

Answer 27

Medical care designed to optimize efficiency or therapeutic benefit for particular groups of patients, especially by using genetic or molecular profiling

Question 28

What is a diploid genome?

Answer 28

Two complete sets of chromosomes in an organism’s cells, with each parent contributing a chromosome to each pair.

Question 29

What is a homolog?

Answer 29

A gene or protein that is similar between species due to SHARED ANCESTOR ^

• Homologous genes BECOME SEPARATED in evolution in two different ways: separation of two populations with the ancestral gene into two species or gene duplication of the ancestral gene within a lineage

Question 30

What are orthologs?

Answer 30

Type of Homologs: Two or more genes found in two or more different species that share a common ancestor. Result of SPECIATION.

Question 31

What are paralogs?

Answer 31

Type of Homologs: Two or more genes in the same genome that are a product of GENE DUPLICATION

Question 32

What is synteny?

Answer 32

Multiple Orthologs

Question 33

What is Linkage Analysis?

Answer 33

A powerful tool to detect the chromosomal location of disease genes. Used to determine whether traits are linked or not. It is also used to calculate the experimental distance between two linked genes. Linkage analysis can be applied to map the location of disease-causing genes.

Question 34

What are the differences between homologous chromosomes and sister chromatids?

Answer 34

Homologous Chromosomes: Pairs of genetically distinct chromosomes (one from mom and one from dad)
* BEFORE REPLICATION!

Sister Chromatids:
Identical halves joined together via the centromere
* AFTER REPLICATION!