Week 1 material

Question 1

Pyrimidines

Answer 1

C, T, U

Question 2

Purines

Answer 2

A, G

Question 3

How many H bonds in G - C?

Answer 3

3

Question 4

How many H bonds in A - T/U?

Answer 4

2

Question 5

Do all bp (e.g. A-T/U or G - C) have equivalent energy despite having the same # of bonds?

Answer 5

No

Question 6

Laws vs Rules

Answer 6

Laws: NO exceptions

Rules: exceptions but not always

Question 7

Rule 1a: for every rule, there is an exception
When can a law turn into a rule?
Is this rule valid?

Answer 7

When an exception to a law is found
No, given the rule must have an exception too

Question 8

What are rules 1a + b

Answer 8

1a: for every LAW of science, there is NO exception

1b: the more you understand, the less you need to memorize

Question 9

Variation in codon position attributed to G - C position?

aka the graph

Answer 9

Position 1: MEDIUM variation
Position 2: LEAST variation
Position 3: GREATEST variation

Most important 2 > 1 > 3

Question 10

Which position is most important? why?

Which position is least important? why

Answer 10

Position 2 given greatest variation

Position 3 given least variation

Question 11

What does P1 deals w/ in terms of aa?

Answer 11

IDENTITY of aa

AKA which of the 22 aa

Question 12

What does P2 deals w/ in terms of aa?

Answer 12

TYPE of aa

AKA hydrophobic, semipolar, hydrophilic

Question 13

What does P3 deals w/ in terms of aa?

Answer 13

Wobble except in initiation

p1 is wobble in initiation: rule 4

Question 14

Position 2 + 3 are ALWAYS…
a) purines
b) pyrimidines

Answer 14

Purines

Question 15

Position 2 is always purines. Which purine is MOST common?
a) A
b) G

Answer 15

A

Question 16

If codon P2 is T, then the type of aa will be…

Answer 16

Hydrophobic

Question 17

If codon P2 is C, then the type of aa will be…

Answer 17

Semipolar aa

Question 18

If codon P2 is A, then the type of aa will be…

Answer 18

Hydrophillic + ocher + amber

Question 19

If codon P2 is G, then the type of aa will be…

Answer 19

Semipolar + opal + Arg (exception)

Question 20

P2 determined importance of P3. If P2 is C, then P3 is…
a) irrelevant
b) relevant
c) somewhat relevant

Answer 20

a) irrelevant

Question 21

P2 determined importance of P3. If P2 is A, then P3 is…
a) irrelevant
b) relevant
c) somewhat relevant

Answer 21

b) relevant

Question 22

P2 determined importance of P3. If P2 is G/T, then P3 is…
a) irrelevant
b) relevant
c) somewhat relevant

Answer 22

c) somewhat relevant

Question 23

When is wobble position important?
a) when P1 is A or T
b) when P1 is C or G

Answer 23

a) when P1 is A or T

Question 24

When is wobble position NOT important?
a) when P1 is A or T
b) when P1 is C or G

Answer 24

b) when P1 is C or G

Question 25

Why is P1 being A or T important for P3?

Answer 25

Given H bond strength of the sum of P2 + P1

Question 26

Which stop codon is the MOST used?

Answer 26

Ocher (UAA) Weakest of ALL stop codons Only has 6 H bonds total

Question 27

Which stop codon is the 2nd most used?

Answer 27

Amber (UAG)

Question 28

What does it mean the MORE codons you have in terms of aa?

Answer 28

The MORE codons you have, the MORE of that aa

Question 29

Rule 5: if P1 is U, p2 + p3 MUST be a) purines b) pyrimidines

Answer 29

a) purines

Question 30

Rule 6: what does a COMMON codon correspond to? | in regards to tRNA

Answer 30

to tRNA present in LARGE amounts (rare codons = LOW tRNA present)

Question 31

What does it mean by ZIGZAG?

Answer 31

Gene horizontally transferred from another organism w/ a diff codon freq

Question 32

Rule 7: when position 3 is important, what are the exceptions to these rules?

Answer 32

ile/met/trp/opal

Question 33

Nucleotide is essential for...

Answer 33

binding strength

Question 34

does A - T equal T - A? what orientation is stonger? | in respect to which base is in the mRNA and which in the tRNA?

Answer 34

No. T will be in mRNA, A in tRNA

Question 35

does C-G equal G - C? what orientation is stonger?

Answer 35

NO. C in mRNA, G in tRNA

Question 36

1. Order needed for life to occur What happens in a CLOSED system? Does entropy increase over time? What enters? what leaves? What happens to internal disorder? external?

Answer 36

Entropy/disorder INCREASES within system Yes Nothing enters/leaves Disorder INCREASES internally only, external disorder remains untouched

Question 37

1. Order needed for life to occur What happens in an OPEN system? Does entropy increase over time? What enters? what leaves? What happens to internal disorder? external?

Answer 37

Entropy INCREASES in surroundings Yes Matter + energy Enters - matter in form of food + energy from food source Leaves - matter in form of waste + energy in form of heat Internal order INCREASES, external disorder INCREASES

Question 38

2. All of bio is cellular - all life is enclosed in membranes What proves this law?

Answer 38

The lipid mosaic model aka phospholipid bilayer

Question 39

2. All of bio is cellular - all life is enclosed in membranes Are viruses considered alive?

Answer 39

no given they lack a lipid mosaic model + require another life form + use RNA, not DNA

Question 40

2. All of bio is cellular - all life is enclosed in membranes Things considered alive if they have what? (2 things)

Answer 40

DNA + genes

Question 41

3. All living things arose from evolutionary processes - DARWIN Possibly way nano bacteria came to be?

Answer 41

they were once big bacteria but shrunk over time under possibly stressful conditions

Question 42

3. All living things arose from evolutionary processes - DARWIN 2nd Possibly way nano bacteria came to be?

Answer 42

Nano bacteria have always been little

Question 43

What is a symbiont?

Answer 43

organisms that live in close + prolonged association w/ each other Can be Harmful/Neutral/Beneficial to one OR both partners

Question 44

what is Episymbionts?

Answer 44

A type of symbionts - live on/in association w/ another symbiont Dani flow - 3 way relationship composed of symbiont pair + another organism

Question 45

what is DPANN? can they survive on their own given their composition?

Answer 45

grouping of archaea based on shared characteristics + potential evolutionary links

Question 46

What kind of chromosomes do bacteria have?

Answer 46

Linear + circular + both

Question 47

What does the Endosymbiont theory encompass?

Answer 47

How mitochondria + eukaryotes arose Bacteria invaded archaea for endosymbiosis Eukaryotes made from Asgard archaeon - eukaryotic like genes in ribosomes + cytoplasm found inside archaea

Question 48

Aerobic pathways are found in nanobacteria. What does this suggest? would the suggestion be correct?

Answer 48

Suggests they are aerobic but its NOT correct given they CAN'T tolerate oxygen

Question 49

MVA? MEP?

Answer 49

MVA - biochemical pathways found in Archaea MEP - biochemical pathways found in bacteria

Question 50

What is the fundamental diff in cell membrane composition between archaea + bacteria?

Answer 50

Lipid divide. Fatty acid linkage in bacteria = eSTer and in Archaea = eTHer

Question 51

What was Darwin correct to point out? what was he wrong to point out?

Answer 51

Correct: evolution given universal codon code which shows signs of evolution + change Incorrect: survival of the fittest > mutations - cooperation = competition