Chapter 6.1 Flashcards
Nucleotide Structure
- Nucleic acids such as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are macromolecules (giant molecules)
- Like proteins (polypeptides) and carbohydrates (polysaccharides), these nucleic acids are polymers (‘poly’ meaning ‘many’)
- This means they are made up of many similar, smaller molecules (known as subunits or monomers) joined into a long chain -The subunits that make up DNA and RNA are known as nucleotides
- Therefore DNA and RNA can also be known as polynucleotides
Nucleotides
Nucleotides are made up of three components:
—-A nitrogen-containing base (also known as a nitrogenous base)
—-A pentose sugar (containing 5 carbon atoms)
—A phosphate group
Nucleotide structure table
ATP
- Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive many processes inside living cells
- ATP is another type of nucleic acid and hence it is structurally very similar to the nucleotides that make up DNA and RNA
- It is a phosphorylated nucleotide
Purines & Pyrimidines
- The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and RNA (A, U, C, G) occur in two structural forms: purines and pyrimidines
- The bases adenine and guanine are purines – they have a double ring structure
- The bases cytosine, thymine and uracil are pyrimidines – they have a single ring structure
DNA Structure
-The nucleic acid DNA is a polynucleotide
– it is made up of many nucleotides bonded together in a long chain -DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions
– the strands are said to be antiparallel
–The nitrogenous bases of each nucleotide project out from the backbone towards the interior of the double-stranded DNA molecule
Hydrogen bonding
- The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
- These hydrogen bonds always occur between the same pairs of bases:
—The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are formed between these bases
—The purine guanine (G) always pairs with the pyrimidine cytosine (C)
– three hydrogen bonds are formed between these bases This is known as complementary base pairing —These pairs are known as DNA base pairs
Double helix
- DNA is not two-dimensional
- DNA is described as a double helix
- This refers to the three-dimensional shape that DNA molecules form
Semi-Conservative DNA Replication
-DNA replication occurs in preparation for mitosis, when a parent cell divides to produce two genetically identical daughter cells
– as each daughter cell contains the same number of chromosomes as the parent cell, the number of DNA molecules in the parent cell must be doubled before mitosis takes place
- DNA replication occurs during the S phase of the cell cycle (which occurs during interphase, when a cell is not dividing)
- The hydrogen bonds between the base pairs on the two antiparallel polynucleotide DNA strands are broken -This ‘unzips’ the DNA double helix to form two single polynucleotide DNA strands
- Each of these single polynucleotide DNA strands acts as a template for the formation of a new strand
– the original strand and the new strand then join together to form a new DNA molecule
DNA Polymerase
- The extra phosphates activate the nucleotides, enabling them to take part in DNA replication
- The bases of the free nucleoside triphosphates align with their complementary bases on each of the template DNA strands
- The enzyme DNA polymerase synthesises new DNA strands from the two template strands
- It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands
- DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester bonds (between adjacent nucleotides)
- Hydrogen bonds then form between the complementary base pairs of the template and new DNA strands
Leading strand
-DNA polymerase can only build the new strand in one direction (5’ to 3’ direction) -As DNA is ‘unzipped’ from the 3’ towards the 5’ end, -This means the DNA polymerase enzyme can synthesise the leading strand continuously -This template strand that the DNA polymerase attaches to is known as the leading strand
The synthesis of the complementary strands occurs slightly differently on the leading and lagging template strands of the original DNA molecule that is being replicated
RNA Structure
- the nucleic acid RNA (ribonucleic acid) is a polynucleotide – it is made up of many nucleotides linked together in a long chain
- RNA nucleotides contain the nitrogenous bases adenine (A), guanine (G) and cytosine (C) -RNA nucleotides never contain the nitrogenous base thymine (T)
– in place of this they contain the nitrogenous base uracil (U)
- RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)
- RNA molecules are only made up of one polynucleotide strand (they are single-stranded)
-Adenosine (a nucleoside) can be combined with one, two or three phosphate groups
—-One phosphate group =
adenosine monophosphate (AMP)
—-Two phosphate groups = adenosine diphosphate (ADP)
—-Three phosphate groups = adenosine triphosphate (ATP)
-An example of an RNA molecule is
messenger RNA (mRNA),
which is the transcript copy of a gene that encodes a specific polypeptide.
Two other examples are transfer RNA (tRNA) and ribosomal RNA (rRNA)
what form phosphodiester bonds
- These bonds form what is known as the sugar-phosphate backbone of the RNA polynucleotide strand
- The phosphodiester bonds link the 5-carbon of one ribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the ribose sugar molecule of the next nucleotide in the strand
-Each DNA polynucleotide strand is made up of alternating
deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone. These bonds are covalent bonds known as phosphodiester bonds
—The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand
activated triphosphates
-In the nucleus, there are free nucleotides to which two extra phosphates have been added (these free nucleotides with three phosphate groups are known as nucleoside triphosphates or ‘activated nucleotides’)
why does semi conservative replication have such name
semi-conservative replication because half of the original DNA molecule is kept (conserved) in each of the two new DNA molecules
what does DNA ligase do
is needed to join these lagging strand segments together to form a continuous complementary DNA strand
-DNA ligase does this by catalysing the formation of phosphodiester bonds between the segments to create a continuous sugar-phosphate backbone
lagging strand
- The other template strand created during DNA replication is known as the lagging strand -On this strand, DNA polymerase moves away from the replication fork (from the 5’ end to the 3’ end)
- This means the DNA polymerase enzyme can only synthesise the lagging DNA strand in short segments (called Okazaki fragments)
The numbers represented in DNA
—-Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon on the pentose sugar could be bonded with another nucleotide)
—-As the strands run in opposite directions (they are antiparallel), one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
-Each RNA polynucleotide strand is made up of alternating
ribose sugars and phosphate groups linked together, with the nitrogenous bases of each nucleotide projecting out sideways from the single-stranded RNA molecule
-The sugar-phosphate bonds (between different nucleotides in the same strand) are covalent bonds known as phosphodiester bonds
