Week 1: Central Dogma + DNA and RNA Structure

Question 1

What are the “big 4” macromolecules

Answer 1

nucleic acids, proteins, lipids, carbohydrates

Question 2

DNA basic structure

Answer 2

nucleic acid
A,G,T,C nucleotides
has directionality (5’–3’)
antiparallel strands
stable polymer (RNA is less stable)

Question 3

lipid vs carbohydrate relationship to water

Answer 3

lipids = water-fearing
carbs = water-loving

Question 4

What 2 big steps are important in the DNA replication

Answer 4

Accurate replication and segregation (transmission) of the genome

Question 5

Briefly explain how our understanding of intergenic regions has evolved

Answer 5

Intergenic regions were once thought to be “junk.” Now we know otherwise

(e.g. transposable elements)

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Question 6

Correlation between gene number and organismal complexity

Answer 6

Gene number and organization vary among organisms, but there is no strong correlation between organism complexity and number of genes. Genomes can encode different numbers of functional products and gene density varies among organisms

Question 7

Describe briefly the role/position of plasmids

Answer 7

Plasmids are extra-chromosomal, but also carry genetic info

Question 8

The Central Dogma

(as a flowchart)

Answer 8

Question 9

In what dimensions is gene expression regulated?

Answer 9

Time & Space

By environment (and more)

Question 10

What is significant about the structure of eukaryotic cells?

Answer 10

Compartamentalization: eukaryotes have membrane-bound compartments
Nucleus, mitochondria, chloroplasts, ER, golgi apparatus

Question 11

In what way is higher ploidy advantageous?

Answer 11

Higher ploidy is generally advantageous with mutations

Question 12

Forward Genetics

Answer 12

A method in which you look at phenotypical changes based on genotypical changes

Question 13

Characteristics of mutations to think about

Answer 13

recessive vs dominant
null, silent, missense, nonsense

Question 14

Somatic vs germline cells in terms of mutations

Answer 14

In somatic cells, mutations affect individual,
In germline cells, mutations affect offspring

Question 15

The 3 domains of life

Answer 15

bacteria, archaea, eukaryotes

Question 16

Key distinctions of model organisms

Answer 16

model organisms have features of agricultural/medical importance yet are easy to manipulate in a lab

Question 17

Virus structure

Answer 17

nucleic acid-based genome surrounded by a protein coat

bacteriophages infect bacteria

Question 18

What is an important tool used to look at DNA structure?

Answer 18

X-Ray Crystallography

Question 19

Important Aspects of DNA structure

Answer 19

1. Made up of 4 different nucleotide bases - complementary base-paired
2. made up of 2 strands where nucleotides are attached in a chain with covalent bonds (phosphodiester bonds) - these two strands twist around each other in double helix: hydrogen bonds (non-covalent) between base pairs hold together (antiparallel structure)
3. the backbone is outside and negatively charged (hydrophilic)
4. bases are relatively hydrophobic but they are buried (have polar groups, but overall lots of carbon and hydrogen)

Question 20

What is important about the double helical structure of DNA?

Answer 20

The double helical structure leads to there being grooves of different widths on outside of helix as the bases in the helix are not completely flat, but rather tilted
* major and minor groove leads to diff parts of bases being accessible
* This is important because proteins often interact with specific DNA sequences
* How does this work? aa on proteins interact non-covalently with particular bases

Question 21

Non-covalent interactions used in DNA structure + function

Answer 21

1. Hydrogen bonds
2. Ionic Bonds (non-specific, but important for things binding to negatively-charged backbone)
3. van der waals
4. hydrophobic interactions

Question 22

Main aspects of purines and pyrimidines (basic structure, abbreviation, nucleotide bases) for DNA

Bonus: How many hydrogen bonds between each complementary base pair?

Answer 22

Purines: 2 rings, “R”, G,A bases
Pyrimidines: 1 ring, “Y”, A,T bases

G-C have triple hydrogen bonding, A-T have double hydrogen bonding

Question 23

What are the alternative DNA structures we can see in vitro? What are their basic characteristics?

Answer 23

A - RNA-DNA duplex, some DNA sequences, does not really have major/minor grooves (has a deeper major groove, and shallower minor groove, only type of double stranded helix RNA can form
B - most DNA, “normal structure”
Z - completely different, turns in a different way (left-handed), question is…is it just a “whacked” crystal, or is it relevant in vivo? - may be relevant for certain DNA sequeces: some proteins seem to be specific to Z-DNA
(there are others)

Question 24

What is supercoiling?

Answer 24

Supercoiling is when DNA double helix wraps around itself
Occurs in circular (bacterial) chromosomes or linear segments with fixed ends

Question 25

Effects of supercoiling

Answer 25

• affects base-pair strength
• DNA can wrap around things = negative supercoiling in one direction, positive in the other
• DNA strands can separate

Question 26

Supercoiling equation

Answer 26

L = T+W
L = linking (fixed if with fixed ends)
- describes the number of times one strand of duplex DNA wraps around the other
T = twist (double helix turns)
- represents the number of turns in the DNA double helix in a given fragment of DNA
- if 360degree twist in fragment, twist = +1
W = writhe (# of turns of double helix on itself)
- describes supercoiling
- relaxed plasmid: W = 0, positively supercoiled: W>0, negatively supercoiled W<0
Linking number, twist, and writhe can quantitatively describe the relation between supercoiling/winding/unwinding
Any change in twist must be balanced in opposite change in value of writhe

Topoisomerases introduce or remove supercoils

Question 27

Basics of RNA structure

Answer 27

• single stranded
• has Uracil instead of Thymine –> really doesnt have any consequence for RNA
• 2’OH on sugar –> very reactive therefore RNA is unstable

Question 28

Role of nucleic acids

Answer 28

store + transmit genetic info

Question 29

Nucleic acids as polymers

Answer 29

nucleotides as monomers
DNA, RNA: synthesized from nucleotides… RNA contains ribose, DNA contains deoxyribose

Question 30

Process of creating a nucleotide chain (DNA or RNA)

Bonus: explain naming of nucleosides

Answer 30

1. base + sugar form a glycosidic bond = nucleoside (named for base (e.g. uridine) – prefix indicates sugar used (e.g. deoxyadenosine would be in DNA)
2. 1 or more phosphate groups (acidic… negatively charged) added to nucleoside = nucleotide
3. nucleotides in DNA linked 3’ to 5’ to create directionality - phosphodiester linkages

Final product: sugar-phosphate backbone with different bases on the nucleotides

Question 31

Importance of 2’ Oxygen in Ribose

Answer 31

makes RNA more chemically reactive than DNA + has a greater number of 3D structures it can adopt –> greater functional versatility
- facilitates a rxn that can cleave phosphodiester bonds
- this hydroxyl group also makes it so RNA exists only in A-type helices
- it also allows RNA to be able to form hydrogen bonds more extensively than DNA

Question 32

What are tautomers?

Answer 32

where a proton in a base is in an alternate position, very rare, but genomes are very large so affects exactness of DNA replication and is one mechanism for generating genetic variation

Question 33

Alternate role of nucleotides

Answer 33

store energy in the high energy covalent bonds of ATP, and carry chemical groups to other molecules

Question 34

DNA can bend… what sequences bend more readily and what are the two types of ways the bending can occur

(supercoiling)

Answer 34

T-A steps bend more readily than helices with G-C steps
this can lead to supercouling in circular DNA
negative supercoils: clockwise undwinding equivalent to unwinding the strands
positive supercoils: twisting in a clockwise direction
can also occur in linear fragments of DNA when ends are immobilized

Question 35

How do topoisomerases introduce or remove supercoils?

Answer 35

1. introduce a transient break in one or both strands
2. enzyme that add supercoils must use energy from ATP hydrolysis

Question 36

Negative supercoiling favors what kind of unwinding of DNA

Answer 36

Local.
the unfavorable energy from strand separation is compensated for by the favorable energy from the relief in negative superhelical tension

Question 37

RNA is genetically modified after it is synthesized… describe

Answer 37

Post-transcriptional modifications
generally irreversible and dont play regulatory role
generally not in mRNA, but yes in tRNA and rRNA
position + nature of these modifications is conserved among different species which suggests they play important roles

Question 38

RNA folding can occur: What kind of structures does this lead to?

Answer 38

RNA can fold to form compact structures which are typically non-coding, but can carry out structural, catalytic, and regulatory roles in many cellular processes (conformation determined by nucleotide base sequence)

Question 39

Short RNA helices

Answer 39

~6-8 base pairs
if complementary sequences are close together, may form a hairpiin
far-away sequences can also pair to form double-helical stretches, but dont create a hairpin

Question 40

Non-canonical base pairs

Answer 40

*differ from watson-crick base pairing
* often have been chemically modified in some way - e.g. methylation
* causes distortions important for function
* also G-U nucleotide base pairs (wobble pairing)

Question 41

Coaxial Stacking

Answer 41

when base pairs stack upon one another in RNA

Question 42

Name + describe two types of intereactions between nucleotides in unpaird and base-paired regions of a single RNA molecule

Answer 42

1. base-triple interaction - 3 bases interact: 1 by watson crick, the 3rd by H-bond to the edge
2. A-minor motif: adenosine from a part of the molecule inserts itself into a minor groove

Question 43

How does RNA overcome barrier to folding created by negative charge of backbone?

Answer 43

by binding to lots of cations (e.g. magnesium)

Question 44

Importance of Phylogenetic analysis

Answer 44

RNA secondary structures can be identified by this analysis - functionally equivalent RNA molecules have similar secondary and tertiary structures, even if nucleotide sequence isnt conserved

Question 45

LUCA =

Answer 45

the common ancestor of all modern life

dependent on RNA, DNA, proteins, carbs, lipids to fulfill requirements for life

Question 46

What do we have as evidence for earlier existence of an RNA world?

Answer 46

1. nucleic acids are replicable - RNA can store info, catalyze chemical rxns, among other functions (can perform all tasks needed in a primitive life world)
2. many coenzymes are ribonucleotides that are built from a core structure of adenosine - suggested that dependence of all other organisms upon these cofactors became fixed early in evolution

Question 47

Primordial soup relevance

Answer 47

Scientists have tried to see how RNA developed by simulating the “primordial soup” but it has been difficult to identify the conditions that lead to synthesis of nucleic acids