Week 1: Introduction and Tree of Life

Question 1

What is genetics?

Answer 1

The study of genome sequence variation

Question 2

What is a genome?

Answer 2

the complete set of inherited instructions that contribute to the traits of an organism (DNA and RNA)

Question 3

What was the previous definition of a gene?

Answer 3

a unit of inheriting traits from one individual to the next (defined before we knew what DNA was)

HEREDITY

Question 4

What is a gene?

Answer 4

CURRENT:
specific locus of DNA that is transcribed into a single RNA molecule

OR

the entire sequence of DNA that is required to transcribe a single RNA molecule (all exons, introns, and sequences at beginning and end of RNA that are not translated, as well as rRNA, tRNA and non mRNA)

Question 5

What is the broader definition of gene (that may be incorrect)?

Answer 5

“gene” includes things that are required to transcribe and encode RNA molecule - regulatory sequences (promotor, terminating regions)

Question 6

Examples of genes?

Answer 6

• protein coding
• non coding RNA
• introns for protein coding genes
• tRNA, rRNAs

Question 7

Characteristics of gene is a physical molecule?

Answer 7

1. specific DNA sequence
2. associated with a specific genome location
3. encodes for 1+ RNAs/proteins
4. part of genetic network that influences traits

Question 8

What is an allele?

Answer 8

gene variant/version

Question 9

characteristic of DNA?

Answer 9

chemically inert (just instructions for transcript)

Question 10

where is the chemistry of life?

Answer 10

some RNA mainly protein

Question 11

How do we know the origin of a majority of NY COVID 19 infections were from Europe?

Answer 11

• COVID-19 is an RNA virus
  -single covid-19 genome infected a human and it replicated and infected other humans but during replication, new alleles arose
• these alleles match the sequence in Europe

Question 12

important property of genomes?

Answer 12

unstable (sequence information changes all the time due to replication errors)

Question 13

What is the result of replication mistakes?

Answer 13

generation of alleles: a sequence variant

Question 14

in a growing population of genomes with no selection pressure, the total number of alleles …

Answer 14

increases every generation

Question 15

What is the mechanism for human genome sequencing?

Answer 15

human genomes have migrated and diverged -> assign origins with similar sequences in different locations

Question 16

What happens if an allele is advantageous to the organism?

Answer 16

genomes containing advantageous alleles becomes dominant genome

Question 17

Consequences of genome instability?

Answer 17

• genome of zygote accumulates alleles as it divides during development
• fibroblast cells in skin will have alleles not present in zygote
• new alleles can lead to cancer
• also no living fossils

Question 18

What are the 3 things the study of genetics tells us?

Answer 18

1. history of life and its evolution
2. how inheritance works (Mendel and nuclear inheritance)
3. chemistry of life

Question 19

divergence in alleles leads to …

Answer 19

speciation

Question 20

what does the tree of life look like?

Answer 20

side view: trunk = oldest, branches = newest

top view: middle = oldest, outside = newest

Question 21

What are the 3 models for how life first arrived?

Answer 21

1. protein world
2. RNA world
3. DNA world

Question 22

What are the characteristics of the protein world?

Answer 22

• can catalyse chemical reactions
• can potentially alter other proteins conformation (ex. prions)
• “protocells” may have existed (concentrated proteins surrounded by lipid membranes)

Question 23

What are the explanations of why the protein world is not the origin of life?

Answer 23

1. generally unstable
2. function but no heredity (can’t store genetic info)

Question 24

What are the characteristics of the DNA World?

Answer 24

• stores genetic info
• very stable

Question 25

What are the explanations of why the DNA world is not the origin of life?

Answer 25

without other molecules, DNA can’t do anything

Question 26

What are the characteristics of the RNA world?

Answer 26

• can store genetic info (ex. covid)
• can catalyze reactions: ribosymes
• able to make proteins
• makes more stable template of self (DNA)

Question 27

Characteristics of LUCA?

Answer 27

last universal common ancestor
- ~3.5 bya
- in DNA world
- diverged to 3 domains of life (bacteria, eukarya, archaea)

Question 28

Characteristics of RNA world ancestor

Answer 28

• prior to DNA world
• ~4.1 bya

Question 29

common feature found in all living organisms?

Answer 29

similar genetic systems (genome as nucleic acid)

Question 30

What are the 2 eukaryotic genomes?

Answer 30

1. nuclear
2. mitochondrial

Question 31

What are the types of genome found in animal/protist genomes?

Answer 31

1. 1/3 alpha-proteobacteria
2. 1/3 archae
3. 1/6 other bacteria
4. 1/6 novel (not found in bacteria or archaea)

Question 32

What are the alpha-proteobacteria genomes involved in?

Answer 32

metabolism

Question 33

What are the archaea genes involved in?

Answer 33

information storage and processing

Question 34

What is the proposition for the origin of eukaryotes?

Answer 34

genetic merger (involving endosymbiosis) of alphaproteobacterium (bacteria) and loki (archaea)

Question 35

What are the steps for creating a euyaryote according to the endosymbiosis hypothesis?

Answer 35

1. host archaeal cell feeding on bacteria
2. endosymbiosis
3. sharing of metabolites
4. entrapment (one organisms requires the other)
5. transfer of control and genetic integration