2.1.3- Nucleotides and Nucleic Acids

2.1.3- Nucleotides and Nucleic Acids

elements that make up a nucleotide

• Carbon

• Hydrogen

• Oxygen

• Pi (Phosphate)

• Nitrogen

nucleotide definition

monomer of nucleic acids (deoxyribose and ribose)

three components of a nucleotide

• nitrogenous base (C1)

• pentose sugar (ribose or deoxyribose)

• phosphate group (C5)

whats the difference between ribose and deoxyribose pentose sugars

deoxyribose only has H on C2 but ribose has OH on C2

what are the nitrogenous bases

• adenine

• thymine (or uracil for RNA)

• cytosine

• guanine

what is the difference between purines and pyrimidines and which are which

• purine= two carbon rings; A and G

• pyrimidine= one carbon ring; C and T

what is a polynucleotide

multiple nucleotide monomers bonded together

how do nucleotides bond together

• phosphodiester bond between C5 and C3 of two nucleotides

• phosphodiester bonds covalent

• condensation reaction as water is released

how are complementary nitrogenous bases held together

hydrogen bonds between the two

how many H bonds do each different pair have

• C and G= 3

• A and T= 2

structural properties of DNA

• anti-parallel= strands parallel but run in opposite directions

• double helix shape= stable and allows it to remain unchanged as much as possible in nucleus

• sugar-phosphate backbone on outside and nitrogenous bases in the middle

• very long; many millions of nucleotides

• H bonds between bases= means that it can easily unzip as H bonds are weak

where is DNA found

inside the nucleus

differences in RNA structure compared to DNA

• RNA shorter; only few 100 nucleotides

• RNA found in the cytoplasm while DNA in nucleus

• RNA has ribose while DNA has deoxyribose

• RNA single stranded while DNA double stranded and antiparallel

• RNA has base uracil instead of DNA’s thymine

what are the three types of mutation

• substitution

• addition

• deletion

how are mutations caused

random; can be from carcinogens, sun etc

what type of mutation is the most harmful and why

• deletion/addition as it impacts all of the next codons as all the subsequent codons are misplaced by one and so changes the sequence

• this then changes all of the AA’s that they code for, which then changes the primary structure, tertiary structure and therefore the protein itself

what type of replication does DNA do and what does it mean

semi-conservative= one original parent strand and one new offspring strand together in each offspring DNA

what are the three enzymes involved in DNA replication and what is their function

• DNA helicase= unzips the DNA by causing the H bonds between bases to break

• DNA polymerase= catalyses the formation of phosphodiester bonds between the free nucleotides

• DNA ligase= joins together the okazaki fragments through formation of phosphodiester bonds along the lagging strand

stages of DNA replication

1. DNA helicase attaches to DNA molecule causing the H bonds to break and the two polynucleotides separate from one another

2. free nucleotides line up with their complementary bases and H bond

3. DNA polymerase attaches; moves along and catalyses phosphodiester bonds between the activated nucleotides

4. DNA polymerase can only act from 5’-3’ of new stand so one side fine but other not and so DNA ligase connects fragments

what is an activated nucleotide

the free nucleotides found in the nucleus, contain three phosphates

how do the activated nucleotides become unactivated

condensation reaction; loses the two extra phosphate groups which provides energy for the reaction

what are the names of the two strands in relation to the use of DNA ligase

leading strand and lagging strand (ligase works on this one)

whats the name of the place where DNA replication occurs

replication fork

what type of DNA replication did scientists originally believe occurred and what is it

conservative DNA replication; where DNA replicated contains two new strands and no oiriginal

gene definition

part of DNA strand that code for a nucleotide sequence, which codes for amino acid sequence, therefore coding for the primary structure of proteins and the specific shape and function of proteins

what are the two stages of protein synthesis

transcription and translation

what enzymes are involved in transcription and what do they do

• DNA helicase= breaks H bonds between the two strands

• RNA polymerase= joins RNA nucleotides together with phosphodiester bonds

transcription stages

1. DNA helicase breaks H bonds between the two strands

2. complementary RNA nucleotides move in and H bond with exposed nucleotides of one DNA strand

3. RNA polymerase joined RNA nucleotides together with phosphodiester bonds, which is a strand of mRNA

4. mRNA detaches, DNA returns to normal and mRNA moves out of the nucleus through nuclear pores and travels to ribosomes where translation occurs

what is the structure of tRNA

• amino acid binding site at the top

• two unpaired bases sections

• anticodon at the bottom

what is an anticodon

complementary to mRNA codon of the AA that it attaches to

what part of the tRNA does the mRNA and the AA attach to

• mRNA= the anticodon of the tRNA attaches to the mRNA codon as they are complementary to one another

• AA= attaches at the AA binding site at the top of the tRNA molecule

what enzymes are involved in translation and what do they do

• peptidyl transferase= part of the rRNA and catalyses the formation of peptide bonds between the AA’s brought by the tRNA

what is rRNA

• main part that makes up ribosome

• helps to catalyse different parts of the translation process by providing ATP as energy

• helps with the formation of peptide bonds between AAs, the bonding of mRNA to the ribosome ete

stages of translation

1. mRNA binds to small site at the ribosome, at the start codon

2. tRNA complementary to start codon binds to it with H bonds; the second tRNA complementary to the next bonds to it as well

   1. each of these tRNA bring its complementary AA with it

3. the two AAs then bind together with peptide bond, catalysed by petidyl transferase which is part of the rRNA

4. ribosome moves to next mRNA codon and the above is repeated

5. this continues down the mRNA and detaches at the stop codon and polypeptide chain released

6. then travels to SER and golgi to be folded and adapted and then released

how are proteins able to be produced rapidly

multiple ribosomes can work on mRNA at once meaning multiple identical proteins can be formed at the same time for the body to use

whats the full name for ATP

adenosine triphosphate

why is ATP used and not just glucose

• glucose releases too much energy at once, making it inefficient and not useful to the body

• ATP releases smaller amounts that are more useful to the body to then use

• one glucose= 30 ATP

what is ATP used for

immediate energy source, not for storage; provides energy to the metabolic reactions of the body so they can therefore be carried out

what are the different parts of ATP

• ribose

• adenine base

• three phosphate groups (triphosphate)

• makes it a phosphorylated nucleotide

what is adenosine

the ribose and adenine base together

how does ATP release energy

• one of the phosphate molecules is broken off

• this requires a small amount of energy to break but releases a large amount of energy

• this energy is then used by processes in the body

what type of reaction is the removal of the phosphate

hydrolysis reaction, meaning it requires water

what is the equation for the ATP reaction

ATP + water → ADP + Pi

what enzyme catalyses this reaction

ATPase (or ATPhydrolase)

when does the ATP reaction that produces energy happen

during cellular respiration

what is Pi

inorganic phosphate; not attached to a carbon containing molecule so is inorganic after it is released from the ATP molecule

what is ATP required for (name 3)

• anabolic reactions

• moving substances across cell membrane

• muscle contraction

• DNA replication

• cytokinesis

• nerve impulse conduction

• thermoregulation

• endocytosis and exocytosis

• mitosis and meiosis

• lipid synthesis

what are the properties of ATP

• small

• polar; water soluble

• phosphate bonds immediate energy

• easily reenergised

what are the characteristics of the genetic code and what they mean

• degenerate= more than one codon can code for the same AA

• non-overlapping= no base is read more than once

• universal= same triplets code for same AAs in all organisms

• stop codons= codons that code for no AA, meaning the sequence stops and protein is released

what is a start codon

AUG- methionine; means the DNA sequence is starting