Week 1: Central Dogma + DNA and RNA Structure Flashcards
What are the “big 4” macromolecules
nucleic acids, proteins, lipids, carbohydrates
DNA basic structure
nucleic acid
A,G,T,C nucleotides
has directionality (5’–3’)
antiparallel strands
stable polymer (RNA is less stable)
lipid vs carbohydrate relationship to water
lipids = water-fearing
carbs = water-loving
What 2 big steps are important in the DNA replication
Accurate replication and segregation (transmission) of the genome
Briefly explain how our understanding of intergenic regions has evolved
Intergenic regions were once thought to be “junk.” Now we know otherwise
(e.g. transposable elements)
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Correlation between gene number and organismal complexity
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
Describe briefly the role/position of plasmids
Plasmids are extra-chromosomal, but also carry genetic info
The Central Dogma
(as a flowchart)
In what dimensions is gene expression regulated?
Time & Space
By environment (and more)
What is significant about the structure of eukaryotic cells?
Compartamentalization: eukaryotes have membrane-bound compartments
Nucleus, mitochondria, chloroplasts, ER, golgi apparatus
In what way is higher ploidy advantageous?
Higher ploidy is generally advantageous with mutations
Forward Genetics
A method in which you look at phenotypical changes based on genotypical changes
Characteristics of mutations to think about
recessive vs dominant
null, silent, missense, nonsense
Somatic vs germline cells in terms of mutations
In somatic cells, mutations affect individual,
In germline cells, mutations affect offspring
The 3 domains of life
bacteria, archaea, eukaryotes
Key distinctions of model organisms
model organisms have features of agricultural/medical importance yet are easy to manipulate in a lab
Virus structure
nucleic acid-based genome surrounded by a protein coat
bacteriophages infect bacteria
What is an important tool used to look at DNA structure?
X-Ray Crystallography
Important Aspects of DNA structure
- Made up of 4 different nucleotide bases - complementary base-paired
- 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)
- the backbone is outside and negatively charged (hydrophilic)
- bases are relatively hydrophobic but they are buried (have polar groups, but overall lots of carbon and hydrogen)
What is important about the double helical structure of DNA?
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
Non-covalent interactions used in DNA structure + function
- Hydrogen bonds
- Ionic Bonds (non-specific, but important for things binding to negatively-charged backbone)
- van der waals
- hydrophobic interactions
Main aspects of purines and pyrimidines (basic structure, abbreviation, nucleotide bases) for DNA
Bonus: How many hydrogen bonds between each complementary base pair?
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
What are the alternative DNA structures we can see in vitro? What are their basic characteristics?
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)
What is supercoiling?
Supercoiling is when DNA double helix wraps around itself
Occurs in circular (bacterial) chromosomes or linear segments with fixed ends
Effects of supercoiling
- affects base-pair strength
- DNA can wrap around things = negative supercoiling in one direction, positive in the other
- DNA strands can separate
Supercoiling equation
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
Basics of RNA structure
- single stranded
- has Uracil instead of Thymine –> really doesnt have any consequence for RNA
- 2’OH on sugar –> very reactive therefore RNA is unstable
Role of nucleic acids
store + transmit genetic info
Nucleic acids as polymers
nucleotides as monomers
DNA, RNA: synthesized from nucleotides… RNA contains ribose, DNA contains deoxyribose
Process of creating a nucleotide chain (DNA or RNA)
Bonus: explain naming of nucleosides
- base + sugar form a glycosidic bond = nucleoside (named for base (e.g. uridine) – prefix indicates sugar used (e.g. deoxyadenosine would be in DNA)
- 1 or more phosphate groups (acidic… negatively charged) added to nucleoside = nucleotide
- nucleotides in DNA linked 3’ to 5’ to create directionality - phosphodiester linkages
Final product: sugar-phosphate backbone with different bases on the nucleotides
Importance of 2’ Oxygen in Ribose
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
What are tautomers?
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
Alternate role of nucleotides
store energy in the high energy covalent bonds of ATP, and carry chemical groups to other molecules
DNA can bend… what sequences bend more readily and what are the two types of ways the bending can occur
(supercoiling)
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
How do topoisomerases introduce or remove supercoils?
- introduce a transient break in one or both strands
- enzyme that add supercoils must use energy from ATP hydrolysis
Negative supercoiling favors what kind of unwinding of DNA
Local.
the unfavorable energy from strand separation is compensated for by the favorable energy from the relief in negative superhelical tension
RNA is genetically modified after it is synthesized… describe
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
RNA folding can occur: What kind of structures does this lead to?
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)
Short RNA helices
~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
Non-canonical base pairs
*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)
Coaxial Stacking
when base pairs stack upon one another in RNA
Name + describe two types of intereactions between nucleotides in unpaird and base-paired regions of a single RNA molecule
- base-triple interaction - 3 bases interact: 1 by watson crick, the 3rd by H-bond to the edge
- A-minor motif: adenosine from a part of the molecule inserts itself into a minor groove
How does RNA overcome barrier to folding created by negative charge of backbone?
by binding to lots of cations (e.g. magnesium)
Importance of Phylogenetic analysis
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
LUCA =
the common ancestor of all modern life
dependent on RNA, DNA, proteins, carbs, lipids to fulfill requirements for life
What do we have as evidence for earlier existence of an RNA world?
- nucleic acids are replicable - RNA can store info, catalyze chemical rxns, among other functions (can perform all tasks needed in a primitive life world)
- 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
Primordial soup relevance
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
