Nucleic Acids Flashcards
difference in DNA and RNA
- presence or absence of oxygen at 2’ position
- no O = DNA
- O = RNA
pyrimidines
- 6 membered heterocyclic rings of C and N
- heterocyclic
purines
- fused 6 membered + 5 membered heterocyclic rings of C & N
- heterocyclic
- A and G
bases
N-groups can accept protons giving basic properties to molecule
-C and T and U
theobromine and theophylline
- secondary metabolites of cocoa beans and tea leaves
- act as diuretic, cardiac stimulant, and vasodilator
caffeine
- stimulant, diuretic
- antagonist to adenosine
nucleotide components
- nitrogenous base
- pentose sugar
- phosphate
main components of nucleic acids
A,T,C,G, and U
Xanthine and hypoxanthine
- rarely occur due to spontaneous deamination of G and A
- removed during DNA repair
- intermediates in nucleotide catabolism
uracil
occurs in RNA where it replaces T
free bases
poorly soluble, rarely occur
nucleosides
- nitrogenous bases attached to sugars
- sugar is either ribose or deoxyribose
- rotation about glycosidic bond is possible
syn vs anti configurations of nucleosides
- rotation about glycosidic bond results in syn and anti configuration
- anti configuration favored
- pyrimidines don’t form syn configuration bc steric hindrance between C2 oxygen and ribose ring
common ribonucleosides
- cytidine
- uridine
- guanosine
- adenosine
adenosine
- physiologically active nucleoside
- inhibitory neurotransmitter synthesized in brain
- binds to adenosine receptors
- binding causes drowsiness and vasodilation (allows more oxygen in during sleep)
- accumulates during wakefulness
- clinically used as anti-arrhythmic to defibrillate abnormally fast heart beats
- caffeine competes with same receptor
cordycepin
- physiologically active nucleoside
- antibiotic produced by fungus
- inhibits final step of RNA biosynthesis by termination of ribonucleotide chain due to absence of 3’ hydroxyl group
- analog of adenosine
cytokinins
- plant hormones derived from adenine
- containe adenine ring system with an attached 5-carbon hydrophobic group at the free NH2
- promotes cell division in plants
nucleotides
- nucleosides with one or more phosphates
- base, sugar, and phosphate group
common ribonucleotides
- adenosine-5’-monophosphate (AMP)
- guanosine-5’-monophosphate (GMP)
- cytidine-5’-monophosphate (CMP)
- uridine-5’-monophosphate(UMP)
- inosine-5’-monophosphate (IMP)
common deoxy-ribonucleotides
- deoxyadenosine-5’-monophosphate (dAMP)
- thymidine-5’-monophosphate (dTMP)
- deoxyguanosine-5’-monophosphate (dGMP)
- deoxycyctidine-5’-monophosphate (dCMP)
metabolic functions of nucleotides
- building blocks of nucleic acids
- atp
- gtp
- ctp
- utp
atp
- phosphate acceptor/donor in intermediary energy metabolism
- biosynthetic processes
- active transport
- mechanical work (muscles)
- temperature regulation
- bioluminescence
gtp
protein synthesis and signal transduction
ctp
membrane and storage lipid synthesis
utp
carbohydrate synthesis and degradation
cyclic nucleotides
- second messengers in signal cascades
- relays a stimulus from an external first messenger
- typically results in cascade of events leading to amplification of first messenger
first messenger
hormones, neurotransmitters
second messenger
- Ca2+ ions
- inositol-Pi3
- diacylglycerol
- cyclic nucleotides
cyclic amp
- adenylate cyclase
- ATP -> cAMP + PPi
- cAMP involved in many signal cascades
- hormone signaling
- apoptosis
- disease reactions
- neuron function
cyclic gmp
- guanylate cyclase
- GTP -> cGMP + PPi
- cGMP is involved in nitric oxide (NO) signaling
- blood pressure homeostasis
- nerve impulse transmission
- stress response in plants
cAMP- mediated signal transduction
- hormone binds to membrane receptor
- GTP replaces GDP on inactive G protein on membrane
- this converts G protein to active form
- Active GTP-G protein complex activates adenylate cyclase
- adenylate cyclase produces cAMP
- cAMP activates protein kinase
- protein kinase phosphorylates and inactive enzyme to convert it to active form
flow of genetic info in a typical cell
replication (DNA) -> transcription (RNA) -> translation (protein)
primary structure of nucleotides
- sequence of nucleotides
- strand has 5’ to 3’ direction
secondary structure of nucleotides
- 3D arrangements of nucleotide residues with respect to one another
- short term folding interactions such as double helix
- usually DNA
tertiary structure of nucleotides
- longer range 3D interactions
- superhelical forms: overwinding and underwinding cruciforms
- protein and DNA interactions
structural characteristics of DNA
- 2 linear polynucleotide strands wound around each other to form double helix ladder
- DNA has a rise. if DNA were a spiral staircase, the rise would be the distance from one step to the next
- nucleotide monomers are composed of nitrogenous base, 2-deoxyribose sugar, phosphate group
- sugar phosphates form background
- bases form steps of ladder
- strands are antiparallel
- strands are held together via H bonding between bases
- A and T form double bonds
- C and G form triple bonds
base pairing in DNA
- purine ALWAYS pairs with pyrimidine
- A always pairs w T (2 H bonds)
- C always pairs w G (3 H bonds)
- H bond distances relatively constant
- paired bases in same plane
- paired bases have same total distance across
transcriptome
complete set of RNA molecules produced by a cell, tissue, or organism under specific physiological conditions
proteome
complete set of protein molecules produced by a cell, tissue, or organism under specific physiological conditions
metabolome
complete set of organic metabolites (sugars, lipids, amino acids) and macromolecules produced by a cell, tissue, or organism under specific physiological conditions
hershey and chase
- showed that DNA transferred from a virus to a bacterium contains sufficient info to direct synthesis of new virus
- DNA has a high phosphorous content so used p32 labels
- Proteins have lots of sulfur in them so they also used s35 labels
- Allowed phage to infect E. Coli
- Everything that had S35 did not infect bacteria
- but phosphorous was incorporated in next generation
chargaff
- Found that all organisms had a fairly equal amount of A ant T and G and C
- Hypothesized that A paired with T and G paired with C
- Created Chargaff’s Rules!
chargaff’s rules
- base composition of DNA varies from one species to the next
- DNA specimens from different tissues of same organism have same base components
- base composition of DNA in a given species doesn’t change with age, nutritional state, or environment
- in all cellular DNA molecules, A=T and G=C in concentration/number
Watson and Crick
-double helix structure of DNA
rosalind franklin
- x-ray fiber diffraction
- helped determine double helix structure
B-DNA spatial dimensions
- individual helices not equally spaced (form major and minor grooves)
- helices are right-handed
- double helix makes one complete turn every 3.4 nm
- 10.5 base pairs per turn.
- essentially no linear space between base pairs
- angle of base plane with ribose plane is perpendicular
- form characterized by watson and crick
A-DNA
- observed when DNA is extracted from ethanol
- more compact than B-form bc dehydrated
- angle of base plane with ribose plane no longer perpendicular
functions of major groove
- recognition sites for several transcription initiation factors
- specific domains of initiation factors lie here
- promote separation of DA strands
- allows proteins to interact with DNA
functions of minor groove
- not really known
- often bind smaller (non-protein) ligands, which then can have several effects:
1. inhibits some cancers
2. inhibits topoisomerases
3. antimicrobial activity
stabilizing forces in DNA
- hydrogen bonds between base pairs
- hydrophobic interactions between bases and H2o
- van der waals forces
- electrostatic interactions
hydrogen bonds between base pairs
- 2 between AT pairs
- 3 between CG pairs
- maintain correct complementary orientation (no slipping)
- have “zippering” effects (can sequentially form/separate)
- AT pairs separate easier than CG pairs
hydrophobic interactions between bases and H2o
- purine and pyrimidine bases are non-polar
- bases attract each other towards center of double helix while repelling/excluding water
- phosphates are at surface attracted towards water
van der waals forces
- flat/planar bases can stack closer together
- cumulative effect of van der Waals forces become significant
electrostatic interactions
- sugar-phosphate backbone has negatively charged phosphate groups (destabilizing via repulsions)
- repulsions are avoided by shielding
- charges improve solubility in h2o
Z-DNA structure
- zig zag appearance
- occurs in regions rich in alternating CGCG sequences
- left handed
- more elongated than B-DNA
- syn orientation
Z-DNA formation
- not completely known
- can occur at stretches of DNA with alternating G and C bases
- small amounts form in cell when DNA is transcribed
- may be important for controlling DNA replication
- a family of conserved Z-DNA binding proteins exists
- some viruses have Z-DNA binding domains-required for viral pathogenesis
cruciform DNA
- cross-like DNA structures that form when DNA contains a palindrome
- one-half of the palindrome in one strand is complementary to the other half
- double stranded region of palindrome separates
- single strands fold upon themselves to base pair in complementary regions
- cruciform DNA thought to be involved in protein binding to DNA
- palindromes also serve as recognition sites for restriction enzymes
triple stranded DNA
- discovered in 1957
- thought to form from partially unwound duplex DNA under “super-helical” conformational stress
- polypyrimidine segment folds back to interact with polypurine region of remaining duplex forming triplex
- third strand occupies major groove of original duplex
- possible role in reonmbination
- cannot be replicated! might have a role in preventing cancer
- 3rd strand is parallel to purine strand
linear dna
occurs in eukaryotic interphase chromosomes
circular dna
occurs in prokaryotic chromosomes, plasmids, chloroplasts, and mitochondria
super-coiled DNA
- maximal in eukaryotic metaphase chromsomes
- intermediate levels in prokaryotes and eukaryotes
- compacts DNA to occupy less space
- inaccessible (prevents replication and transcription)
- protects DNA when not being replicated or transcribed
- max coiling found in eukaryotic metaphase chromosomes during division
snRNA
involved in removing introns and splicing exons together to form functional mRNA
snoRNA
process rRNA, involved in ribosome biogenesis
siRNA
-involved in gene silencing and regulation
gRNA
- needed for RNA editing
- removal and insertion of bases into mRNA
tmRNA
disengages ribosomes from stalled translation of mRNA in bacteria
telomerase RNA
forms much of structure and all of template required by telomerase
hnRNA
function not really known (heterogeneous and nuclear RNA)
tRNA structure
- bases consistently occur in same positions
- 3’ end: amino acid attachment
- D loop: aminoacyl-tRNA synthetase recognition
- TYC loop: ribosome recognition binding
- anticodon loop: matching codon on mRNA during translation
tRNA function
- carry transfer amino acids to ribosome for assembly into polypeptides
- at least one tRNA molecule for each of the 20 diff amino acids
- anticodon base pairs with mRNA codons
- often described as adaptor molecule
