Nucleic acids Flashcards
Central dogma
- DNA is replicated and stores information
- DNA is transcribed to make RNA
- RNA is modified and translated to make proteins
What carbon position determines if it is ribose or deoxyribose?
Carbon position 2
What Bases are different between RNA and DNA
DNA has thymine
RNA has Uracil
What carbon position has the anhydride bonds that provide energy?
-carbon position 5
What are the building blocks of DNA and RNA?
- 5 carbon sugar
- nitrogenous base
Carbon 1 on sugar
- covalently linked to a base
- glycosidic bond
Carbon 2 on sugar
- hydroxyl group in RNA
- no oxygen in DNA
Carbon 3 on sugar
- hydroxyl group in both DNA and RNA
- required for polymerization of nucleic acid
- joined to the 5 carbon by phosphodiester bond
Carbon 5 on sugar
- liked to one or more phosphates
- joined to carbon 3 of an adjacent nucleotide through phosphodiester bond
Is DNA polar or non polar?
- POLAR
- free phosphate group at the 5’ end
- free hydroxyl group at the 3’ end
What kind of bonds join the nucleotides in DNA?
-phosphodiester bonds
What kind of bonds link bases in DNA?
-glycosidic bonds
if no end designation is made, you should assume DNA is going…
5’ to 3’
When writing a sequence backwards, how should DNA be written?
you have to specify 3’ to 5’
antiparallel
-the two strands of DNA are opposite in direction
complementary
- A matches with T
- C matches with G
- via hydrogen bonds
How many hydrogen bonds like the complementary bonds?
A:T has 2
C:G has 3
Chargaff’s rule
- A=T, C=G
- A+T+C+G=100%
If DNA has 10% G, what is the % of the others?
G=10%
C=10%
A=40%
T=40%
What kind of grooves are associated with the double helix?
- major and minor grooves
- important for regulatory proteins
- important for gene expression regulation
Which part of DNA is hydrophilic?
- sugar-phosphate backbone
- has a negative charge
- is on the outside of the helix
Which part of DNA is hydrophobic?
- hydrogen bonded base pairs
- perpendicular to the axis of symmetry
- form the stairs of the helix (on the inside)
DNA is…
Directional and amphipathic
What is a right handed helix called?
- watson-crick DNA
- B-DNA
- most common
Left handed helix
- less common
- high CG content
- Z-DNA
- function unknown
Denaturation and renaturation of DNA
- mechanical and chemical
- important for replication and transcription
Melting DNA
- heat denatures double stranded DNA
- Hydrogen bonds between base pairs are broken, but phosphodiester bonds linking nucleotides are not broken
Tm
Temperature required to melt 50% of the DNA in a sample
CG content and Tm
-high CG content means higher Tm
AT content and Tm
-high AT content means lower Tm
What happens if DNA cools?
-hydrogen bonds will reform and the DNA will renature
another word for renature
reanneal
What happens if DNA denatures and then reanneals in a way that is not the most stable?
-it will denature again and reanneal until it reaches the most stable form
Organization of DNA
- genomes are HUGE
- length of DNA in one cell is 2 meters
- DNA is thin and long
Supercoiling
-DNA gyrase does supercoiling in prokaryotes and mitochondrial DNA
Quinolones
- inhibit DNA gyrase
- toxic in high concentrations
DNA in the nucleus of eukaryotes
- associates with histone and non histone proteins to form nucleosomes
- nucleosomes are packaged tightly to form chromatin
Why package DNA ?
- protects DNA from denaturation
- but you have to have some DNA loose for gene expression
Histones
- rich in lysine and arginine(+charged basic amino acids)
- bind tight to negatively charged DNA
Histone octamer
- two units of EACH histone:H2A, H2B, H3, and H4 aggregate and form it
- DNA wounds around it to make a nucleosome
Beads on a string
- a group of free nucleosomes(without H1)
- sensitive to nuclease degradation
- necessary for gene expression
nucleofilament
-histone H1 associates with the DNA between the nucleosomes to further condense the DNA into a thick 30nm fiber
Condensation
- important for cell division
- condensation of nucleosomes forms chromatin and chromosomes
KEY RNA and DNA differences
- Sugar
- thymine/uracil
- DNA is DS and RNA is SS
- RNA can base-pair back on itself
- RNA is smaller
- DNA stores information and RNA expresses information
RBC
- no nucleus, so cant store DNA
- they have some mRNA that helps them
What are the three major types of RNA that act in conjunction with proteins to allow infor from DNA to be translated into proteins?
-mRNA, rRNA, tRNA
mRNA
- messenger RNA
- prepared in a way in which it can get into the cytosol and be recognized
- vary in size depending on the size of proteins encoded
Eukaryotic mRNA
5’ terminus contains a m7G-cap structure (contributes to getting recognized and not getting degraded)
-3’ terminus contains poly-A tail(helps ribosomes recognize the end and let it be released)
Prokaryotic mRNA
-DO NOT CONTAIN SPECIAL TERMINAL STRUCTURES
all mRNAs
- 5’ untranslated region
- 3’ untranslated region
- coding region
rRNA
- associates with proteins
- mostly structural to combine with proteins to form ribosomes
What are the different sizes associated with eukaryotes rRNA
80s
60s
40s
What are the different sizes associated with prokaryotes rRNA
70s
50s
30s
What are the sizes given in?
”s”
- Svedberg
- unit of sedimentation value
tRNA
- small(80 nucleotides)
- covalently linked to specific amino acid
- CCA-3’ terminus acts as amino acid attachment site
Anticodon loop
- on tRNA
- determines amino acid specifically by base pairing with mRNA during translation
CCA-3’ terminus
- amino acid attachment site on tRNA
- covalently attached
Anticodon form
-complimentary strand then put it back in 5’-3’ form
hnRNA
- heterogeneous nuclear RNA
- pre-mRNA
- represents mRNA in various stages of processing in the nucleus of eukaryotes
- in nucleus, just recently transcribed
snRNA
- small nuclear RNA
- only in nucleus of eukaryotes
- combine with certain proteins to form snRNPs
snRNPs
- used for splicing hnRNA to form mRNA
- splice out introns
- in eukaryotes
Ribozymes
-RNAs that act as enzymes
