biology module 2 section 3 (nucleic acids and nucleotides)

what are nucleotides

• the building blocks of nucleic acids such as DNA and RNA

• monomers that can join together to form dimers (dinucleotides) and polymers (polynucleotides)

what are nucleic acids

a functional molecule made of one or more polynucleotide chains

what are nucleotides made up of

• a pentose sugar (contains 5 carbon atoms)

• a nitrogenous base (contains carbon and nitrogen)

• a phosphate group (contains phosphate)

what are polynucleotides and how do they form and break

nucleotides that are joined together via condensation reactions

the phosphate group of one nucleotide forms a covalent bond with the sugar of another forming a phosphodiester bond which can form a chain known as the sugar-phosphate backbone

bonds can break by hydrolysis reactions releasing nucleotide monomers

what is DNA

a type of nucleic acid that contains the instructions needed to make proteins

what is DNA made up of

• deoxyribose (pentose sugar)

• nitrogenous base (A,T,C or G)

• a phosphate group

who discovered DNA structure

1953 James Watson and Francis Crick were credited with working out the structure of DNA.

with the help of other scientists like Rosalind Franklin, they found that DNA is made up of two polynucleotide strands wound around each other to form a double helix

describe the purposes of the structure of DNA

• sugar phosphate backbone (protects bases)

• double stranded (allows strands to act as template in replication)

• double helix (compact)

• complimentary base pairing (for DNA replication)

• weak hydrogen bonds (can separate in DNA replication)

• large molecule (to store lots of info)

what is the difference between purines and pyrimidines

purines - larger bases that contain 2 carbon ring structures ( A and G)

pyrimidines - smaller bases that contain 1 carbon ring structure ( T and C )

how do the bases pair together

• adenine pairs with thymine with 2 hydrogen bonds

• cytosine pairs with guanine with 3 hydrogen bonds

smaller pyrimidine always binds to a larger purine to maintain a constant distance between the 2 sugar-phosphate backbones

what is RNA

a type of nucleic acid that uses information from DNA to synthesise proteins

what is RNA made up of

• ribose (a pentose sugar)

• A, U, C or G base

• a phosphate group

describe the structure of RNA

• contains ribose rather than deoxyribose

• has uracil instead of thymine

• single stranded polynucleotide which is shorter than DNA strands

describe the process of DNA (semi-conservative) replication

1. a DNA molecule that is ready to be replicated unwinds by the enzyme DNA helicase which breaks hydrogen bonds between complimentary bases separating the strands

2. each strand acts as a template as free nucleotides attract to their complementary bases

3. enzyme DNA polymerase joins the free nucleotides together via condensation reactions in the 5' to 3' direction forming phosphodiester bonds to create the sugar-phosphate backbone of the new DNA strand

4. two identical copies of DNA are made. each copy is made up of one original DNA strand and one new DNA strand (semi-conservative replication)

how did meselson and stahl investigate DNA replication

1. bacteria was grown in a medium containing 15N, so all their DNA is ‘heavy’.

1. bacteria was transferred to a medium with 14N for one round of replication, so the lighter nitrogen was incorporated into any new DNA strands they made.

2. DNA was extracted and centrifuged.

3. steps 2-3 were repeated for another round of replication.

4. distribution of heavy and light DNA was analysed to track how the DNA was replicating:

• the heavier bands sink lower in the test tube.

• the intermediate bands, made of DNA with one heavy strand and one light strand, are in the middle of the test tube.

• the lighter bands are higher up in the test tube.

what were the results of meselson and stahls experiment

• showed that DNA replicates through a semi-conservative process

because in the first replication each resulting DNA molecule consists of one old, heavy strand and one new, light strand

and then in the second replication the other half were completely made of light strand

how is DNA condensed into chromosomes

• they are wound around proteins as histones to form DNA-histone complexes

• they then coil further to form chromatin which helps pack the DNA into chromosomes which each contain just a single molecule of DNA

what is genetic code

genetic codes are summarised into a table

each amino acid is coded for by a sequence of 3 mRNA bases known as codons

it is universal (codons for the same amino acid are the same in all organisms), non-overlapping (each base is only read once), degenerate (most amino acids are coded for by more than one triplet)

what is mRNA

a type of RNA that is synthesised during the process of transcription

used to carry genetic info from DNA to ribosomes

what are the features of mRNA

• single-stranded, linear

• contains a base sequence complementary to a DNA sequence

• contains codons, which are sets of three bases that code for an amino acid

• small enough to leave the nucleus

what is tRNA

a type of RNA used in the process of translation

used to transport amino acids to ribosomes to build up a polypeptide chain

what are the features of tRNA

• single-stranded molecule folded into a clover-leaf shape.

• hydrogen bonds between complementary base pairs to hold it in shape

• contains a specific sequence of three bases at one end, known as the anticodon

• contains an amino acid binding site at the opposite end

what is transcription and where does it take place

the initial step of synthesis of proteins by creating an mRNA copy of a gene from the DNA template

in eukaryotic cells, occurs in the nucleus where it exits into the cytoplasm for translation

what are the steps of transcription

1. RNA polymerase enzyme binds to DNA

2. hydrogen bonds between the DNA bases break so the two strands of the double helix separate

3. free RNA nucleotides align with the DNA template through complementary base pairing

4. in the RNA molecule, uracil pairs with adenine, while adenine pairs with thymine, and cytosine pairs with guanine

5. RNA polymerase catalyses the formation of phosphodiester bonds between adjacent RNA nucleotides.

6. complementary mRNA strand is formed, carrying the same base sequence as the DNA sense strand

7. the process ends when RNA polymerase reaches a stop codon, detaches from DNA and terminates transcription

8. mRNA is released, detaches from DNA, and DNA rewinds into its double helix structure

what is translation and where does it occur

process of decoding the information in mRNA to synthesis a polypeptide chain with the help of tRNA folding into a functional protein

occurs in the cytoplasm, specifically on the ribosome

what are the steps of translation

1. ribosome attaches to the mRNA strand at a start codon

2. tRNA molecule, carrying a specific amino acid and with an anticodon that is complementary to the start codon, binds to the mRNA.

3. second tRNA molecule with an anticodon complementary to the next mRNA codon, and also carrying a specific amino acid, attaches to mRNA.

4. amino acids carried by the first two tRNA molecules are linked together via a peptide bond using ATP

5. first tRNA molecule detaches from mRNA and is free to collect another amino acid for future use

6. ribosome moves along mRNA, allowing another tRNA molecule, which carries the next amino acid, to bind to the next codon on mRNA

7. process is repeated elongating the polypeptide chain.

8. sequence continues until the ribosome reaches a stop codon on mRNA

9. completed polypeptide chain detaches from the ribosome

what is the structure of ATP

• nitrogenous base (adenine)

• ribose (5-carbon sugar)

• phosphates (3 phosphate groups

what is ATP used for in the body

• movement (eg muscle contraction or for sperm cells to swim)

• active transport (eg ions entering plant roots)

• synthesis of large molecule (eg DNA and proteins)

• secretion of substances from cells (eg releasing hormones from glands)

describe hydrolysis of ATP to release energy

• when water is added to ATP, it breaks down into ADP and inorganic phosphate (Pi)

• catalysed by the enzyme ATP hydrolase

• releases energy for use in cells

describe condensation reaction of ATP

• when a phosphate group and ADP join, a water molecule is released

• reaction is catalysed by the enzyme ATP synthase

• process requires energy and traps chemical energy in the bond

how do the properties of ATP relate to its function

1. hydrolysis releases a small amount of energy, little energy is lost as heat

2. broken down quickly so energy is released quickly

3. rapidly re-synthesised so is always readily available

4. inorganic phosphate from ATP hydrolysis can phosphorylate other compounds, makes them more reactive

5. bonds between the phosphate groups are unstable, have a low activation energy and are easily broken

6. soluble, can be easily transported around cells