Unit 4 - Nucleic Acid and Information Flow Flashcards
Name and describe DNA
Deoxyribonucleic acid - molecule by which hereditary info is transmitted from generation to generation.
What is DNA made up of
A double helix consisting of subunits called nucleotides, which is composed of; 5-carbon sugar, a base, and one or more phosphate groups
How is the carbon group illustrated
Indicated by a pentagon, in which 4/5 vertices represent the position of a carbon atom. They are numbered clockwise with primes (1’, 2’, etc)
describe the sugar found in DNA
It is deoxyribose (meaning minus oxygen) because the chemical group projecting downwards from the 2’ carbon is a H atom rather than an OH hydroxyl group
Describe the phosphate group attached to the 5’ carbon
It will have negative charges on two of its O atoms. Cellular pH 7 = ionization of the OH group (loss of proton, negative charge) therefore DNA is a mild acid
What bases are usually found in a nucleotide of DNA
Adenine, Guanine, Thymine, Cytosine
Distinguish between purines and pyrimidines
Purines (double ring) - A & G
Pyrimidines (single ring) - T & C
Difference between nucleoside and nucleotide
Nucleoside - the combo of sugar and base
Nucleotide - the combo of a nucleoside with one or more phosphate groups
What is important about nucleoside triphosphates
They are the molecules that are used to form DNA and RNA, and they’re carriers of chemical energy in the form of ATP and GTP
What bond connects nucleotides and what are they called
Covalent bond, called phosphodiester bond
Why are phosphodiester bonds good
They are relatively stable bonds that can withstand stresses such as heat and substantial changes in pH that would break weaker bonds.
What do the phosphodiester linkages give the DNA
polarity
How do we use the different ends of the molecule to write a sequence
where the nucleotide has a free phosphate (eg. 5’) will be known as the 5’ end and where the nucleotide has a free hydroxyl (eg. 3’) is known as the 3’ end.
sequence will be written as 5’-AGCT-3’ or 3’-TCGA-5’
What 3 pieces of information allowed researchers to build a molecular model of DNA
- results from X-ray crystallography of DNA (Rosalind Franklin & Maurice Wilkins)
- published results showing DNA extracted from various organisms cells showed: no. of base A=T and no. of base G=C (Erwin Chargaff)
- determined that if bases were to pair they’d pair: A-T and G-C (Jerry Donohue & John Griffith)
What was the final DNA structure that watson and crick came up with
Double helical structure, with the backbones on the outside, the bases pointing inwards, and A paired with T & G paired with C
How big is a DNA helix
In one complete turn of the helix, there are 10 base pairs, and the diameter of the molecule is 2nm
What are the major groove and minor groove in DNA
uneven pair of grooves formed by the outside contours of the twisted strands
Why are major and minor grooves important
Proteins that interact with DNA often recognise a particular sequence of bases by making contact with the bases by the major or minor groove
What is the main characteristic of the individual DNA strands
They are antiparallel - they run in opposite directions
What different models of the DNA structure are there
Watson-Crick Structure - each atom is represented as a color coded sphere
Ribbon Model - sugar phosphate backbones wind around the outside of the bases paired between the strands
what would happen if two purines/pyrimidines were paired
2 purines - the backbones would bulge
2 pyrimidines - the backbone would narrow
What causes the complementary bonding of bases
The H bonds that form between A & T (2 H bonds) and between G & C (3 H bonds)
How is stability maintained in the DNA molecule if H bonds are weak
Because they are added together, millions of the weak bonds along the molecule make the structure more stable.
The interactions between bases in the same strand also increase stability, due to base stacking. (the nonpolar, flat bases group together away from H2O molecules, hence the stacking as tightly as ppossible on top of each other)
What is the process of DNA creating exact copies of itself called
Replication
Give a brief description of replication
The 2 strands of the parental double helix unwind and separate into single strands, each of these strands serves as a template for the synthesis of a complementary daughter strand.
The synthesis of a new strand is then carried out by DNA polymerase.
At the end there are 2 molecules, each containing one parental and one daughter strand
What makes errors in replication rare
DNA polymerase’s proofreading function
What is a mutation
a change in the genetic information in DNA
what is the central dogma of molecular biology
DNA transcribed to RNA translated to proteins
What is the first step in decoding DNA
Transcription - genetic info in a molecule of DNA is used as a template to generate an RNA molecule.
What is the second step in decoding DNA
Translation - a molecule of RNA is used as a code for the sequence of amino acids in a protein
What is an example of an exception to the usual central dogma
Genetic info is transferred from RNA to DNA in the replication of HIV
What is gene expression
The production of a functional gene product, such as a protein
What is the difference in DNA replication of prokaryotes and eukaryotes
prokaryotes:
- transcription & translation occur in the cytoplasm
eukaryotes:
- transcription occurs in the nucleus & translation occurs in the cytoplasm
What is the advantage of the way that eukaryotes replicate DNA
The separation between transcription and translation allows for additional levels of gene regulation that aren’t possible in prokaryotic cells
Differences in RNA vs DNA
RNA:
- ribose sugar
- 2 OH groups
- uracil (U)
- uracil has a hydrogen attached to it
- 5’ is a triphosphate
DNA:
- deoxyribose sugar
- 1 OH group
- thymine (T)
- thymine has a methyl group attached to it
- 5’ is a monophosphate
What are the physical differences in RNA and DNA
- RNA molecules are much shorter than DNA molecules
- RNA is single stranded, as opposed to DNA double stranded
What characteristics do folded RNA structures have
Can have a 3D complexity similar to that of proteins, and can serve as catalysts in biochemical reactions
What is the RNA world hypothesis
the hypothesis that the earliest organisms relied on RNA for both catalysis and information storage
if RNA played a key role in the origin of life, why do cells now use DNA for information storage and proteins for other cellular processes
Because DNA is much more stable than RNA, and proteins are much more versatile, it is assumed that life evolved away from RNA-based, to DNA, RNA, and proteins with specialised functions
What is an RNA transcript
The RNA sequence synthesized from a DNA template
How is the RNA transcript produced
Produced by polymerization of ribonucleoside triphosphates
What is RNA polymerase
The enzyme that binds to DNA and carries out the polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript
How does RNA polymerase act
By adding successive nucleotides to the 3’ end of the growing transcript
What is the nontemplate strand
The strand of DNA that isn’t used as a template for RNA synthesis during transcription.
What else is the nontemplate strand known as and why
Coding, sense, and plus strand because it matches the RNA sequence
What are the 3 stages of transcription
- Initiation - RNA polymerase & other proteins are attracted to double-stranded DNA. The DNA strands are separated, and transcription begins
- Elongation - successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand
- Termination - RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released
What direction is the RNA synthesized in
They grow in a 5’-3’ direction, nucleic acids are synthesized by addition to the 3’ end (3’ direction)
What does it mean that the DNA template and RNA strand are transcribed are antiparallel
The DNA template runs in the opposite direction from the RNA. The RNA transcript is synthesized 5’-3’, and the DNA template is read in a 3’-5’ direction
What are promoters
A regulatory region where RNA polymerase and associated proteins bind to the DNA duplex in the process of transcription
What is the TATA box
a DNA sequence present in many promoters in eukaryotes and archaea that serves as a protein-binding site for a key general transcription factor
What is the terminator
a DNA sequence at which transcription stops and the transcript is released
What dictates which strand of DNA is transcribed
depends on the orientation of the promoter - when promoters are in opposite orientation transcription occurs in opposite directions because transcription can only proceed by successive addition of nucleotides to the 3’ end
What does transcription regulation depend on
Whether the RNA polymerase & associated proteins are able to bind with the promoter
What is a sigma factor
a protein that associates with RNA polymerase that facilitates its binding to specific promoters
How do sigma factors work
Once transcription is initiated, the sigma factor dissociates and the RNA polymerase continues transcription on its own
Where do sigma factors mediate promoter recognition
in bacteria
What proteins bind to the promoter in eukaryotes
At least 6 proteins known as general transcription factors
What is needed in addition to the assembly of the general transcription factors
Transcriptional activator proteins - each of which binds to a specific DNA sequence (known as an enhancer)
What do transcriptional activator proteins do
help control when and in which cells transcription of a gene will occur.
what do transcriptional activator proteins bind to
enhancer DNA sequences and with the proteins that allow transcription to begin
What do TAP do once they’re bound to enhancer DNA sequences
They attract a mediator complex of proteins
What is a mediator complex and what does it do
A complex of proteins that interacts with the Pol II complex and allows transcription to begin - the mediator complex recruits the RNA polymerase to the promoter
What RNA polymerase complex is responsible for transcription in eukaryotes
Pol II
What needs to be so that transcription can be initiated
The mediator complex and Pol II complex need to be in place
How large is the transcription bubble in bacteria
Transcription bubble - 14 base pairs
region of paired RNA DNA in the bubble - 8 base pairs
What provides the energy that drives the reaction to create new phosphodiester bonds attaching the incoming nucleotide to the 3’ end
The oxygen attacks the bond, seizes an electron and the phosphate bond breaks, releasing energy
What does the polymerization reaction release
a phosphate-phosphate group - has a high energy phosphate bond which is split by another enzyme
