1.5 Nucleic acids and their functions

as biology unit 1

What does DNA and RNA stand for and what type of molecules are they?

Deoxyribonucleic acid and ribonucleic acid. They are both macromolecules made up of nucleotides, making them both polynucleotides.

What are the parts of a nucleotide?

Phosphate group, pentose sugar and nitrogenous base

Features of a phosphate group

same in all nucleotides and it gives the nucleic acids their structure

features of a pentose sugar

in DNA it is deoxyribose sugar, in RNA it is a ribose sugar

features of a nitrogenous base

there are two types: pyramidine and purine

• pyramidine bases are thymine, cytosine and uracil (RNA). they have 1 ring structure
• purine bases are adenine and guanine. 2 ring structure

What does ATP stand for?

Adenosine triphosphate

What type of molecule is ATP and what is it used for?

A molecule that makes energy available when it's needed. It is a universal currency (involved when energy changes happen in living things). Humans make/break 50kg of ATP every day but the body only contains 5g at a time.

What are the parts of an ATP molecule?

Adenine base, ribose sugar and 3 phosphates (triphosphate)

What does adenosine mean?

Adenine + ribose sugar

What happens when energy is needed?

ATPase, an enzyme, hydrolyses the bond between the second and third phosphate of ATP. This leaves ADP- adenosine diphosphate. When this happens, 30.6 kJ/mol energy is released.

ATP reaction

ATP + Water --> ADP + Pi + 30.6kJ/mol. This reaction is exergonic (releases energy). The opposite reaction is condensation and endogonic - requires energy.

What is the addition of a phosphate to ADP called?

Phophorylation

Uses of ATP

• Metabolic processes = to build large complex molecules from small simple ones
• active transport = change shape of carrier proteins in membranes to allow movement against conc. gradient
• movement = muscle contraction
• nerve transmission = sodium/potassium pumps
• secretion = package and transport secretory products in vesicles

features of DNA (deoxyribonucleic acid)

It has a double helix structure.
Made from the polymerisation of many nucleotides

Structure of a DNA molecule

A condensation reaction joins the phosphate group of 1 nucleotide to the deoxyribose sugar of another. This forms the sugar-phosphate backbone. The bonds in the backbone are called phosphodiester bonds. The sugar, phosphate group and nitrogenous base are joined together with covalent bonds. The two strands of polynucleotides twist to form double helix, which makes it more stable as bases are on the inside and their sequences are protected from damage/mutations.

How are the 2 strands of polynucleotides in DNA anti-parallel?

one goes in the 3¹ to 5¹ direction and the other is 5¹ to 3¹. = anti-parallel

What is Chargaff's rule?

That Adenine must pair with Thymine and Guanine must pair with Cytosine.

How are the bases A, T, G, C bonded together?

Adenine and Thymine join together with 2 weak hydrogen bonds. Cytosine and Guanine join together with 3 weak hydrogen bonds

features of an RNA molecule

It is built up from 4 types of RNA nucleotides that each have a different base. These are purine: adenine and guanine, and pyramidine: cytosine and uracil.
RNA is similar to DNA but uracil replaces thymine and the pentose sugar ribose replaces deoxyribose.

What is RNA polymerised to produce?

Single nucleotide chains

What are the three types of RNA?

Messenger RNA (mRNA), Ribosomal RNA (rRNA), Transfer RNA (tRNA)

features of Messenger RNA

It is a single stranded molecule which is formed in the nucleus. It carries genetic code to ribosomes in the cytoplasm. Each mRNA molecule will have a different length. It has a short life and is involved in protein synthesis

features of Ribosomal RNA

It is found in the cytoplasm and is a large complex molecule. Makes up a ribosome along with protein (rRNA + protein = ribosome). It is involved in translation (protein synthesis)

features of Transfer RNA

It's made in the nucleolus and is a small, single stranded molecule. It is folded, which means base sequences form complimentary base pairs. It has a 3¹ end which a specific amino acid attaches to. The other end is the ANTI-CODON end. It transports specific amino acids to the ribosomes during protein synthesis.

What are the two main roles of DNA?

DNA replication and protein synthesis

Where and why does DNA replication happen?

It happens in interphase in the nucleus and it is for cell division and gamete division

What are the three possibilities of DNA replication?

Conservative, semi-conservative (what actually happens) and dispersive.

What is semi-conservative replication?

parental double helix separates, each strand acts as a template for synthesis of new strand

What did the Meselson and Stahl experiment prove?

Semi-conservative replication

What happened in the Meselson-Stahl experiment?

1. They cultured E.coli for several generations in a medium containing amino acids with a heavy isotope of nitrogen - N15
   -> the bacteria incorporated only N15 into their DNA so when centrifuged, the DNA settled low in the test tube as N15 was heavy
2. N15 bacteria were washed and transferred to medium with only lighter isotope N14 and allowed them to divide
   -> this was to prevent contamination of N14 medium with N14
3. DNA from this generation was centrifuged and had mid-point density
   -> this rules out conservative because no band shows heavy DNA but the other two were still possible
4. DNA from the second generation in N14 settled at mid and high points in equal amounts
   -> not dispersive as there would be one band only

Before DNA replication can start, what has to happen?

The molecule has to unwind from its double helix shape one section at a time, so the two strands have to be separated.

What is the enzyme that helps unwind DNA before DNA replication, and how does it work?

DNA helicase is responsible for breaking the hydrogen bonds between bases, causing the strands to separate from one end. This is called unzipping. It exposes the bases from both strands so that DNA replication can occur.

When the two strands of DNA separate, what is formed?

Y-shape known as the replication fork.

What happens at the start of DNA replication?

Each strand acts as a template for the formation of a new strand. The enzyme DNA polymerase attaches to each of the single strands and adds one new nucleotide at a time to the strand, which is called complementary base pairing.

How does DNA polymerase copy in the 5¹ to 3¹ direction?

It only copies in the 5¹ to 3¹ direction, which means for the new 5¹ to 3¹ direction, DNA polymerase catalyses joining of nucleotides all in one go to make the new strand, known as the "leading" strand. The nucleotides are held in place by hydrogen bonds.

How does DNA polymerase copy in the 3¹ to 5¹ direction?

For the 3¹ to 5¹ strand known as the "lagging" strand, DNA polymerase produces short segments of the strand but they have to be joined together by the enzyme DNA ligase to complete the new strand.

What does DNA ligase form?

It conencts neighbouring nucleotides with phophodiester bonds to form the sugar phosphate backbone of the new DNA molecule.

What are the characteristics of the Genetic code?

• Triplet code - 3 bases code for one amino acid
• Redundant/degenerate - 64 combinations possible but only 20 amino acids = meaning more than one tripet can code for the same amino acid
• Punctuated - triplets that do not code for an amino acid = in mRNA this is a stop codon
• Universal - each triplet codes for the same amino acid in all living things
• Non-overlapping - each base only occurs in one triplet
• Unambigous - single codon only codes for one amino acid

What is the proof that 3 bases code for 1 amino acid?

There are 4 different bases in DNA but 20 commonly occuring amino acids in proteins. Therefore:
if 1 base coded for 1 amino acid = only 4 a.a. made
if 2 bases coded for 1 amino acid = there would be 4x4= 16
if 3 bases coded for 1 amino acid= 4x4x4= 64 amino acids (more than enough)

What takes place during protein synthesis?

Transcription and Translation, where the intermediary molecule mRNA carries the information

How and where does transcription start?

It happens in the nucleus and DNA helicase breaks hydrogen bonds between the bases in a specific region of a DNA molecule, causing the strands to separate and unwind exposing the nucleotide bases

What happens in transcription after the DNA molecule has been unwound?

RNA polymerase binds to the template strand at the start of the sequence to be copied. Free RNA nucleotides align opposite the template strand to complementary base pairing.

What happens in transcription after RNA nucleotides have aligned with template strand?

RNA polymerase moves along the DNA forming hydrogen bonds with the complementary bases until it reaches a stop codon. Then, it forms phosphodiester bonds between nucleotides (between phosphate and ribose sugar groups) creating the sugar-phosphate backbone.

What happens in transcription after sugar phophate backbone is formed?

mRNA detaches from the strand and the 2 DNA strands joins back together into a double helix

What happens in transcription after DNA winds back together?

mRNA is modified before it leaves the nucleus. The initial sequence (pre-mRNA) is much longer than the final one as it contains sequences of bases that need to be removed called Introns (non-coding regions). These are cut out using endonucleases and leave behind Exons which do code for proteins. These exons are joined by ligase.

What happens last in transcription?

mRNA leaves the nucleus through the nuclear pores in the nuclear envelope, to the cytoplasm and attaches to a ribosome.

What is translation?

The process by which a sequence of bases in mRNA is converted into a sequence of amino acids into a polypeptide.

Where does transcription take place?

It takes place on a ribosome with 2 subunits. The larger has 2 sites for tRNA molecules to attach and the smaller binds to mRNA

In translation, what do the tRNA molecules carry on them?

A different amino acid on one end and on the other hand, 3 bases form an anticodon which is complementary to codon on mRNA.

What are the three stages of translation?

Initiation, elongation and termination

What happens during initiation stage of translation?

A ribosome attaches to a start codon at one end of the mRNA molecule. First, tRNA with an anticodon complementary to the first codon on the mRNA attaches to the ribosome. These bases are bonded together with hydrogen bonds. Because two tRNA molecules can fit into the ribosome at any one time, a second tRNA with an anticodon complementary to the 2nd codon on mRNA attaches with hydrogen bonds.

What happens during the elongation stage of translation?

The two amino acids are side by side and a peptide bond forms with a condensation reaction. The first tRNA leaves the ribosome leaving its attachment site vacant and returns to the cytoplasm to bind to another copy of its specific amino acid (for attachment ATP is needed known as amino acid activation. The ribosome moves one codon along the mRNA strand and the next tRNA binds.

What happens during the termination stage of translation?

The sequence repeats, forming a polypeptide until a stop codon is reached and the ribosome-mRNA-polypeptide complex separates.

What is a polysome?

Multiple ribosomes bind to a single mRNA strand, each reading the coded information at the same time. This means several polypeptides can be made at the same time.