Nucleic acids1+2

Question 1

monomers are built up into polymers using increasing lengths?

Answer 1

Dimer
Trimer
Up to short polymers of unspecified length= oligomers

Question 2

Are nucleic acids homo or hetero polymers?

Answer 2

heteropolymers

Question 3

Describe the role of DNA?

Answer 3

Universal information store across all 3 Domains of Life.
DNA is stable, repairable, easy to transcribe and to copy.
* Only role is information storage. Good for long-term storage.
* Double stranded (except in some viruses or in damaged cells).

Question 4

What bases are cytosine (C), thymine (T), uracil (U)?
What bases are guanine (G), adenine (A)?

Answer 4

Pyrimidine bases: cytosine (C), thymine (T), uracil (U).
Purine bases: guanine (G), adenine (A).
These are not monomers of the acid

Question 5

What is the structure of a nucleotide and order of formation?

Answer 5

A base bound to a pentose (C5) sugar = nucleoside
(sugar = ribose in RNA, 2-deoxyribose in DNA)
A nucleoside bound to a phosphate group = nucleotide
Nucleotides are the monomers of nucleic acids

Question 6

What are the bases for RNA?
What are the ribonucleosides?
What are the ribonucleotides?
What’s the name for CMP?

Answer 6

Bases: cytosine (C), uracil (U), adenine (A), guanine (G)
ribonucleosides: cytidine (C), uridine (U), adenosine (A), guanosine (G)
ribonucleotides: CMP, UMP, AMP, GMP
(e.g. cytidine 5′-monophosphate, CMP)

Question 7

What are the bases for DNA?
What are the deoxyribonucleosides?
What are the deoxyribonucleotides?
What’s the name for dCMP?

Answer 7

Bases: cytosine (C), thymine (T), adenine (A), guanine (G)
deoxyribonucleosides: deoxycytidine (dC), thymidine (dT), deoxyadenosine(dA), deoxyguanosine (dG).
deoxyribonucleotides: dCMP, dTMP, dAMP, dGMP
(e.g. deoxycytidine 5′-monophosphate, dCMP)

Question 8

Why do we use the prime (‘)

Answer 8

When there are two or more rings we can use the prime to distinguish which ring is which so the bigger ring is 1,2,3,4,5 whereas the smaller ring is 1’,2’,3’,4’,5’.

Question 9

What is the link/bond between the phosphate group and the sugar in a nucleotide?

Answer 9

3′-5′-phosphodiester link

Question 10

Base pairs are held by hydrogen bonds explain?

Answer 10

G and C pair with 3 hydrogen bonds but A andT(U) pair with 2 – thus, G-C pair is bound more strongly.

Heating a nucleic acid solution will unpair the bases by breaking the hydrogen bonds. Higher G+C fraction of the DNA molecule, the higher the melting
temperature.

Question 11

What do things living in a hotter environment tend to have more of in their DNA as an evolutionary advantage?

Answer 11

They contain more G’s and C’S as these form 3 hydrogen bonds so stronger to prevent strands from separating at a higher temperature.

Question 12

What is Chargaff’s Rule 1 and the unit used?

Answer 12

%A = %T and %G = %C
Conventionally we measure the G+C fraction (or G+C content) of DNA and it’s in the odd unit of mol% (percentage of the molecule aka % mol/mol)

Question 13

What are the 3 types of DNA and where are they found?

Answer 13

B-DNA (right-hand helix, 2.0 nm diameter), which is the
most abundant form in Nature.

A-DNA (right-hand helix, 2.6 nm diameter) – discovered by Franklin – forms when B-DNA is dehydrated. Found therefore in many Bacteria and Archaea at low water activity (e.g. in seawater, in hypersaline lakes). Also found in some viruses.

Z-DNA (left-hand helix, 1.8 nm diameter) – discovered by Mitsui et al. – found commonly in DNA of Eukarya when being transcribed into mRNA. Also found in
many H. sapiens cancers.

C-DNA (not found in Nature).
There are also triple-stranded forms important in some human pathologies.

Question 14

When two complementary strands of B-DNA are in solution around pH 7, they will spontaneously coil to form right-handed double helix. Explain characteristics of B-DNA?

Answer 14

2.0 nm diameter
BASES on the inside, paired PHOSPHATE on the outside
Distance from base to base along strand
= 0.34 nm (3.4 Å)
Distance of one wavelength of helix
= 3.4 nm (34 Å)
1 minor groove.
2 major grooves.

Question 15

Explain where the bonds are in a double helix of B-DNA

Answer 15

Hydrogen bonding between complementary bases on opposite strands and between sugars in backbone.

Hydrophobic interactions and some van der Vals interactions between rings of adjacent bases on same strand.

Ionic bonding between 3D-adjacent phosphate groups on the backbone.

Question 16

Describe structure and role of DNA in Bacteria and Archaea

Answer 16

Majority of taxa in these two Domains do not have membrane bound nuclei, the DNA is ‘naked’ in the cytosol.
* No histones/proteins associated to the DNA.
* DNA is circular (linear in Eukarya).
* Usually 1-2 chromosomes (all the core DNA).
* Often smaller replicons (i.e. plasmids, megaplasmids, chromids)
– also circular, contain non-critical DNA and are used in vitro for molecular biology, molecular ecology etc as cloning vectors.
* Circular DNA is often supercoiled – gives it structural stability
and helps it form a more compact shape. Organisms resistant to heat, radiation etc have very tight supercoiling into complex shapes.
* Mitochondria and plastids were once Bacteria, so have same DNA properties in their genomes as Bacteria have.

Question 17

When is B-DNA converted to Z-DNA in vivo?

Answer 17

During transcription.

Question 18

DNA organisation in Eukarya

Answer 18

• All Eukarya have membrane-bound nuclei where the
  DNA is contained.
• DNA is protein-associated to stabilise it.
• DNA is linear
• Chromosome number varies a lot.
• No non-chromosomal DNA in the nucleus.

Question 19

DNA packaging starting from DNA double helix to a chromosome.

Answer 19

Chromosomal DNA is packaged inside microscopic nuclei with the help of histones. These are positively-charged proteins that strongly adhere to negatively-charged DNA and form complexes called nucleosomes. Each nucleosome is composed of DNA wound 1.65 (2) times around eight histone proteins. Nucleosomes fold up to form a 30-nanometer chromatin fiber, which forms loops averaging 300 nanometers in length. The 300 nm fibers are compressed and folded to produce a wider fiber, which is tightly coiled into the chromatid of a chromosome.

Question 20

Explain chromatin
The key difference between chromatin and nucleosome is that chromatin is a whole structure of complex DNA and proteins while nucleosome is a basic unit of chromatin.

Answer 20

complex of DNA and proteins = chromatin contains an outer compact heterochromatin (stuff that isn’t used goes on outer edge as this).
inner areas contain euchromatin (active so less dense,)

Question 21

Explain further of nucleosomes and types of histone proteins

Answer 21

• Most of the protein content is histones (H1, H2a,
  H2b, H3 and H4).
• At 20 nm spacing along DNA strand are
  nucleosomes (DNA wound around hydrophobic
  histones).
• Nucleosomes are separated by linker DNA.
• Several nucleosomes and linker DNA are termed a
  polynucleosome.
• Polynucleosomes coil to form a fibre 30 nm in
  diameter.
• Fibre is supported by scaffold proteins to form a 300
  nm strand with looped domains.
• Strand folds further to form 700 nm diameter
  condensed active chromosome. The very family “Xshaped” chromosomes only form at metaphase and
  require additional scaffold proteins – they are about
  1,400 nm across the top of the “X”

Question 22

Ribonucleic acids (RNA)
mRNA
rRNA
tRNA

Answer 22

• Usually single stranded but can form hairpin loops etc with
  complementary sequences coming together.
• mRNA – messenger RNA, used in transfer of information from DNA
  to ribosome for protein synthesis.
• rRNA – ribosomal RNA, forms part of the structure of the ribosome and catalyses the formation of peptide bonds.
• tRNA – transfer RNA, traffics amino acids around the cell to the ribosome.

Question 23

Explain simply DNA transcription

Answer 23

• Information from DNA is copied into a strand of mRNA:
• mRNA encodes amino acid sequence in the form of triplets (groups of 3 bases –which form codons, each encoding an
  amino acid.
• Which amino acids each codon encodes is the genetic code. Note this is NOT universal.

Question 24

Explain start and stop codons.

Answer 24

mRNA translation happens on the ribosome
* Start codons usually encode methionine (Met/M) as the first amino acid in the protein strand.
* Stop codons don’t encode an amino acid, they just terminate
translation and make the mRNA fall off of the ribosome.

Question 25

What is a gene, operon and explain the diagram.

Answer 25

• A gene is a region of DNA that begins with a START codon and ends with a STOP codon.
• An operon is a region of DNA that is transcribed as a single mRNA strand.
  If a group of genes are just close together but we don’t have
  actual evidence of this, then they are a gene cluster (sometimes putative operon) until someone provides that evidence then it becomes an operon.
  These are normally shown in arrow diagrams – each arrow block is a gene for a single polypeptide note there are gaps because not all genes encode and switching genes off and on relies on space between them for coiling around a protein.
  they don’t always face the same way!

Question 26

Talk about introns and exons

Answer 26

Regions that actually encode the polypeptide are exons Regions of non-coding DNA are introns
the mRNA strand in the Eukarya has to undergo the process of
splicing in which the introns are cut out
* In the Bacteria and the Archaea, introns are found very rarely the intein is the equivalent structure: regions of the
finished polypeptide that actually cut themselves out of the strand to form the finished protein.

Question 27

What happens during splicing and what is the 5’cap modified nucleoside usually found and what are the roles?

Answer 27

initial primary transcript (mRNA) still contains the introns between the exons:
* There is a 5’ cap and a 3’ polyadenine tail (polyA tail).
* 5’ cap is usually a modified nucleoside (e.g. 7 methylguanosine, m7G) – this is recognised by the
ribosome and enables it to bind, but also protects this end of the mRNA from degradation by
enzymes.
* 3’ poly-A tail stops the mRNA being degraded by enzymes.
* Splicing is a highly complex process that removes the introns and produces an exon-only final

Question 28

Ribosomes are subcellular particles – they are
not organelles and don’t have a membrane. A ribosome can have different subunits with different subunits sizes.
What are ribosome in translation?
What is the non-additive unit used for sizes of subunits?

Answer 28

• About 60 % rRNA and 40 % protein within the ribosome
• Large and small subunits, each composed of many rRNA and protein pieces.
• Sizes of subunits are given in Svedberg (S)
• Bases on the rRNA interact with both the mRNA
  transcript and tRNA molecules.
• Free in the cytosol of the Bacteria and Archaea
  and in mitochondria and plastids (matrix).
• Bound to rough endoplasmic reticulum in the
  Eukarya.

Question 29

What is the structure of a tRNA molecule:
What does the 3’end contain and what binds to it?
What does the 5’end contain?
What does the TΨC loop have?
What are 5 names of the wobble bases?
What does the d-loop contain?

Answer 29

r-shaped RNA molecules
* Anti-codon loop carries the anti-codon sequence.
* 3’ end has a CCA tail, but the “A” is hydroxylated (-
OH) – this is where the amino acid binds. COOH of amino acid binds to OH and helps prevent enzymatic degradation
* 5’ end has a phosphate group on the last base to stop it getting attacked by enzymes.
* The TΨC loop has pseudouridine (Ψ).
* The anti-codon loop’s first base (the final codon
position) is usually a ‘wobble’ base that can bind to
different bases here e.g. if codons CUC and CUU both
code for leucine, the anti-codon loop would have GA_
where “_” represents an atypical base that binds both C
and U.
* anti-codon loop ‘wobble’ bases include: inosine (I),
queuosine, uridine 5-oxyacetic acid, 5-
methylaminomethyl-2-thiouridine and lysidine.
* The D loop contains dihydrouridine (D)
dihydrouridine and pseudouridine make sure tRNA aligns with ribosome.

Question 30

What is the process of translation

Answer 30

mRNA binds to rRNA, using the cap and start codon as recognition sites.
* Start codon binds anti-codon on e.g methionyl-tRNA. The tRNA stays bound to ribosome until 2nd AA binds.
* Using our example, the CUA codon on the mRNA binds lysinyl-tRNA via the anti-codon.
* rRNA catalyses peptide bond formation between methionine and lysine. tRNA for methionine now leaves and binds another methionine in cytosol.