Nucleic Acids Flashcards
Central dogma of molecular biology
- DNA stores info which is transcribed to make RNA
- RNA is modified and used as a template and translated to make a protein
Replication–DNA–transcription–RNA–translation–protein
Building blocks of DNA and RNA
5 carbon sugars
- ribose
- deoxyribose
What are the nitrogenous bases?
Purines
Pyrimidines
Purines
Adenine and guanine
-2 rings
Pyrimidines
Cytosine, thymine, and uracil
-1 ring
DNA contains what nitrogenous bases?
Adenine, guanine, cytosine, and thymine
RNA contains what nitrogenous bases?
Adenine, guanine, cytosine, and uracil
Nucleotide di- and triphosphates (such as ADP and ATP)
Are high energy compounds due to the energy associated with anhydride bonds
Where does the energy necessary for nucleus acid synthesis come from?
The high energy bonds in nucleotide triphsophates (NTPs)
ATP and GTP are also used as a source of energy for many reactions
Carbon 1 (1’) on the sugar residue
Covalently linked to a base (glycosidic bond)
Carbon 2 (2’) on the sugar residue
- Hydroxyl group in RNA
- no oxygen in DNA (deoxy-)
Carbon 3 (3’) on the sugar residue
OH group in both DNA and RNA, REQUIRED for polymerization of nucleic acids, joined to the 5’ carbon through a phosphodiester bond
Carbon 5 (5’) of the sugar residue
Linked to one or more phosphates, joined to carbon 3 of an adjacent nucleotide through a phosphodiester bond
Is DNA polar or non polar?
Polar
At what end of DNA is the free phosphate group
5’
At what end of the DNA molecule is the free OH group?
3’
What are the nucleotides joined together by in DNA?
Phosphodiester bonds
What are the bases linked together by?
Glycosidic bonds
DNA is always assumed to be written…
5’-3’
Can be written 5’-TACG-3’ or just TACG
Or 3’-GCAT-5’
Ways DNA can be written
- Sometimes written with the location of the phosphate groups PTpApCpG
- sometimes type of nuclei acid is indicated dTdAdCdG (DNA)
DNA structure
Antiparallel and complimentary
Antiparallel
The two strands are opposite in direction
Complementary
A always pairs with T
G always base pics with C
Via H bonding
How many H bonds does A::T have?
2H bonds
How many H bonds does G::C have?
3 H bonds
How do you indicate the complementary strand
You have to indicate that it is 3’ to 5’
Sometimes it will be reversed to 5’ to 3’ too
Chargaffs Rule
- A=T
- G=C
- A+T+G+C=100%
Using Chargaff’s rule, what percentage of T is in a sample of DNA with 10% G?
- G=C, so G=10% and C=10%
- G+C=20%
- 100-20=80%
- A+T=80%
- T=80%/2
- T=40%
What feature of DNA is important for regulatory proteins (gene expression)?
The major and minor grooves formed by the double helix
What is on the outside of the helix and contains a negative charge?
Hydrophilic sugar-phosphate backbone
-can interact with water
What forms the “stairs” of the helix, perpendicular to the axis of symmetry?
Hydrophobic hydrogen-bonded base pairs
Is DNA hydrophobic, hydrophilic, or amphipathic?
Amphipathic
What is the normal DNA structure?
Right handed or Watson and Crick DNA or B-DNA
Rare form of DNA
Contains higher GC content and a left handed helix, possibly important for gene regulation
-mammals don’t normally have this
Melting
Desaturation
Why is desaturation and repatriation important?
- important for regulation and transcription
- important for molecular biology techniques
What can “melt” dsDNA?
Heat
Alkali
Certain chemicals
How does desaturation work
Hydrogen bonds between base pairs are broken but phosphodiester bonds linking the nucleotides are not broken
- maintains integrity of the two strands
- results in a single stranded DNA (ssDNA)
Tm
Temperature required to melt 50% of the DNA in a sample
Tm for a high GC content
Higher because of triple bonds
Tm of high AT content
Lower because double bonds
Reannealing
The DNA is allowed to cool and the hydrogen bonds will reform and the DNA will renature
-temp falls below the Tm
How often does DNA associate/dissociate?
Until they find proper orientation so the complimentary strand is correct
Are genomes of most organisms big or small compared to the size of the cell?
Huge
What is the length of the DNA in a single human cell?
2m
How long is all the DNA end to end?
Would reach to the sun and back
What kind of DNA has lots of supercoiling
Prokaryotes and mitochondria
What is DNA gyrase (topoisomerase II) inhibited by?
Quinolones (norfloxacin/ciprofloxacin)
Why are quinolones toxic in high dosages?
Because it can target the mitochondrial DNA in humans
nucleosomes
DNA in the nucleus of eukaryotes associates with histones and nonhistone proteins forming these
-DNA wraps around his tones
Chromatin
Nucleosomes are packaged tightly to form this
Nucleosome packaging
- want the DNA accessible to do translation/transcription
- they are packed for protection, but leave parts exposed to do transcription/translation
What are histones rich in?
Lysin and arginine (+ charged basic AA)
What do histones bind tightly too?
Negatively charged DNA
How many types of histones are there?
4 (H2A, H2B, H3, and H4)
-there are two units to each his tone forming an octamer
What is the DNA tightly wound around to form nucleosome?
Histone octamer
histone sensitive to nuclease degradation
A group of fire nucleosomes (without H1) called “beads on a string”
-necessary for gene expression
Histone H1
Associates with the DNA between the nucleosomes to further condense the DNA into a thick 30nm fiber called a nucleofilament
Why is condensation important?
For cell division
-reverse-can see gene expression
What does further condensation of nucleosomes form?
Chromatin and chromosomes
What sugar does DNA contain
Deoxyribose
What sugar does RNA contain
Ribose
What base does DNA contain that RNA does not
Thymine
What base does RNA contain that DNA does not
Uracil
Can DNA or RNA base pair back on itself?
RNA (tRNA)
Which is smaller, DNA or RNA?
RNA
Why is RNA smaller than DNA?
DNA contains many units of information, RNA contains individual units of information
What does DNA store?
Genetic information (storage molecules)
What is RNA used for?
To express genetic information (transient expression molecules)
What are the 3 major types of RNA?
mRNA, rRNA, tRNA
What do the three major RNA types do?
Act n conjunction with proteins to allow the information contained in DNA to be translated into protein
mRNA
Processed in a way so that they can get in the cytosol. Recognized by molecules that use them
rRNA
Associate with proteins. From large molecules, ribosomes to make protein
-mostly structural
tRNA
No enzymatic activity but transfers AA to proper place
Size of mRNA
Very heterogenous in size, depending on the size of the proteins encoded
What does the 5’ terminus contain on the mRNA?
m7G-cap structure
-ribosome recognition
What does the 3’ terminus contain on the mRNA?
Poly A tail
- 50-200 adenine residues that are not part of the genomic sequence
- helps release from ribosomes
Do prokaryotic mRNAs contain the cap and poly A tail?
No
All mRNA’s contain:
- 5’ untranslated region
- 3’ untranslated region
- coding region
Eukaryotic ribosome size
80s ribosome
- 60S (large) subunit
- 40S (small) subunit
Prokaryotic ribosome size
70S ribosomes
- 50S (large) subunit
- 30S (small) subunit
What is the unit if size for ribosome?
S (svedberg)
- unit of sedimentation value
- how it passes through a medium such as a gel
How many nucleotides in tRNA
About 80
What is tRNA linked to?
- Covalently linked to a specific AA
- At least one specific tRNA for each of the 20 AA
What is specific for each of the AA?
At least one specific tRNA
Where is the AA attachment site on tRNA
CCA-3’ terminus
Structure of tRNA
- Cloverleaf like structure-extensive intrachain base pairing (similar to dsDNA)
- unusual bases , many modified bases, primarily methylated bases
What is the only RNA that contains thymine?
tRNA
Anticodon loop
On tRNA
Determines AA specifically by base pairing with mRNA during translation
hnRNA
Heterogenous nuclear RNA, also called pre-mRNA-represents mRNA in various stages of processing in the nucleus of eukaryotes
snRNAs
Small nuclear RNAs, only in the nucleus of eukaryotes, combines with certain proteins to form snRNPs, used for splicing hnRNA to form mRNA
Robozymes
RNAs that act as enzymes
