DNA & RNA Flashcards
What constitutes a nucleotide?
-What are they a part of?
Nucleotide = Phosphate, sugar & Base (Adenine, guanine, cytosine, thymine or uracil)
-DNA is made up of a large number of linked, repeating nucleotides.
Primary Structure of DNA
Sugar classification
-Primary structure refers to the nucelotides linked by phosphodiester bonds
- Sugar: either purine (double ringed - Guanine & Adenine) or pyrimidine (single ring - cytosine, thymine)
- deoxyribose in DNA (lacks an O atom on 2nd C) and Ribose sugar in RNA (extra O atom makes it more reactive & less chemically stable - DNA more suited to storing info in the long term).
Phosphate Group
What’s free on each end of chain
What makes up the DNA backbone?
- P atom bonded to 4 O atoms - found in very nucleotide and carry negative charge.
- 2 P cleaved when bonded to other nucleotides
- always bonds to 5’ end
- 5’ end = Free phosphate group
- 3’ end = Free OH group
-Backbone = Alternating Sugar and phosphates
Secondary Structure of DNA
Secondary Structure = 3D configuration (helical structure)
- Fundamental characteristic: 2 polynucleotide strands wound around each other (makes the double helix)
- bases stacked in interior of molecule
- polynucleotide strands run in opposite directions (ANTIPARALLEL) - held together by H bonding (weak compared to phosphodiester bonds)
*Precise 3D shape of DNA can vary depending on conditions its placed in (sometimes base sequence)
Alternate shapes of DNA
B-DNA:
-exists when there is plenty of water surrounding the molecule & no weird base sequences
-has right handed helical, clockwise twist
-approx. 10 bp per 360 degrees (bp = 0.34nm apart)
A-DNA
-Form if there is less H2O
-right helix, but shorter and wider
-bases tilted away from main axis
-Detected in spores of some bacteria
Z-DNA
-left handed helix (sugar-phosphate backbone zigzags back and forth)
-Can arise if lots of C & G repeats
How the bases pair up
Adenine - Thymine (2 H bonds)
Cytosine - Guanine (3 H bonds)
- Bond numbers are important - have practical applications (i.e. hybridization)
- Due to complementary base pairing, sequence of one strand always determines the sequence of the other
- if bases paired wrongly, creates kink in chain (allows enzymes to identify problem and fix)
Characteristics of DNA
Cruciform Structures
- double stranded (beneficial in case 1 strand gets damaged)
- antiparallel
- made up of nucleotides that are held together by phosphodiester bonds (P-O)
- two strands held together by H bonds
- Complementary base pairing
*Can get intrastrand base pairing in DNA - can mark import. signalling region (i.e. Origin of replication)
Cruciform Structures: Inverted repeated sequences (generally the loop they form gets deleted - DNA polymerase just bypasses it)
RNA characteristics
miRNA
- single stranded nucleic acid (but double stranded in character)
- loves to H bond (binds to itself and forms structures)
- structure is critical to function - i.e. tRNA needs to be clover leaf shaped to work)
miRNA (messenger inhibitory RNA)
- v. common across all kingdoms
- anneals to RNA transcript - destroys or inhibits translation (secondary structure crucial to functions)
2 Types of RNA
- Informational RNA: contains message of a.a. sequence of proteins (that will get translated into proteins)
- Functional RNA: not translated into proteins; used as they are (i.e. tRNAs & rRNAs)
RNA polymerase subunits
- 5 subunits = core enzyme
- sigma factor joins to core to form holoenzyme (capable of binding to promoter and initiating transcription)
- helps in recognising promoters (doesn’t actually help transcription)
subunits in core;
- 2 x alpha subunits (enzyme assembly, promoter recog.
- beta subunit (catalytic centre)
- beta prime subunit (catalytic centre)
- w subunit - stability of enzyme
*core enzyme is what makes the RNA!
Promoter on genes
-10 to 35 bases upstream = bases very similar (conserved)
Consensus sequences:
-10 bases upstream: TATAAT
-35 bases upstream: TTGACA
Promoter:
- part of DNA
- upstream of gene
- where RNA polymerase can bind to recognise where to start transcription
