Bio Topic 2 -> DNA

Structure of mononucleotides

DNA nucleotide → deoxyribose sugar + a phosphate group + nitrogenous base (ATCG)

RNA nucleotide → ribose sugar + a phosphate group + nitrogenous base (AUCG)

Phosphodiester bond

Nucleotides join via condensation reactions and make a phosphodiester bond to form polynucleotides like DNA and RNA

Phosphate group of one nucleotide binds to the OH group of the pentose sugar of the next

Ester bond → between an OH group and an acid group (phosphate group acts as the acid)

What is the structure of DNA

DNA molecule → made of 2 polynucleotide strands running in opposite directions → each strand is held tg by phosphodiester bonds

• The 2 strands are held tg by hydrogen bonding between the complimentary nitrogenous bases (A → T and C → G)

What is the structure of RNA

RNA molecule → 1 polynucleotide strand made of a ribose sugar, a phosphate group and nitrogenous base (AUCG) → shorter than DNA

What is a gene

A sequence of nucleotide bases that codes for the production of a specific sequence of amino acids that makes up a protein

How is a protein formed

1. Transcription → DNA is transcribed and an mRNA molecule is produced

2. Translation → mRNA is translated and an amino acid sequence is produced

transCription before transLation

C is before L

What is the process of transcription

1. Part of the DNA molecule unwinds and the Hydrogen bonds between the complimentary base pairs break

2. Exposes the gene to be transcribed

3. A complimentary copy of the code from the gene is made called the mRNA → Free RNA molecules pair up via hydrogen bonds with their complementary bases on the template strand → phosphodiester bonds form between the RNA molecules to form the sugar - phosphate backbone of the mRNA which is catalysed by RNA polymerase

4. When the gene has been transcribed → the mRNA and DNA template strands’ hydrogen bonds break

5. Double stranded DNA molecule reforms

6. mRNA molecule leaves the nucleus via a pore in the nuclear envolope

What is the process of translation

1. After leaving the nucleus via a pore in the nuclear envolope, mRNA attaches to a ribosome

2. There are free tRNA molecules in the cytoplasm, each with a complementary anticodon to the codon on the mRNA (triplet of bases) and a region for a specific amino acid to bind to → tRNA is already binded to the specific amino acid and when it reads the complementary codon on the mRNA it attaches to the ribosome

3. At the beginning of the mRNA, there is a start codon which codes for a specific amino acid → starts translation

4. 2 tRNA molecules fit onto the ribosome at one time → amino acids form a peptide bond

5. Repeats until the stop codon is read

6. Polypeptide chain folds to from a protein

What is the nature of the genetic code

Triplet code → A triplet of bases code for one amino acid

Non overlapping → Each base is only read once so the adjacent codons dont overlap → the same base is not used to make another codon

Degenerate → There are 4 bases on the mRNA (AUCG) → 4³ (64) combinations of codons possible → but only 20 amino acids exist → so multiple codons can code for the same amino acid → limits the effect of mutations

What is a peptide bond

Forms between amino acids

What is the primary structure of a protein

• Specific to each protein

• The sequence of amino acids is the primary structure of a protein

• Gene codes for the primary structure of a protein

• Primary structure → affects the shape + function of the protein

What is the secondary structure of a protein

• Secondary structure refers to the hydrogen bonds that form between peptide bonds

• Hydrogen bonds can form these 2 shapes :

  • Alpha helix → hydrogen bonds form between every 4th peptide bond

  • Beta pleated sheet → forms when the protein folds so that 2 parts of the polypeptide chain are parallel so hydrogen bonds form between parallel peptide bonds

What is the tertiary structure of a protein

Aditional bonds forming between the R groups in the amino acids after secondary structure → creates a 3D structure

What is the quarternary structure of a protein

• Proteins with more than 1 polypeptide chain

What is the structure of a globular protein

• Compact

• Spherical → non polar hydrophobic R groups are in the centre of the protein away from the aqeuous surroundings + polar hydrophillic R groups are on the outside of the protein

• Have specific shapes

What is the function of a globular protein

• Due to the polar hydrophillic R groups on the outside → globular proteins are soluble in water → can be easily transported around the body

What is an example of a globular protein

• Haemoglobin → has a quarternary structure (4 polypeptide chains) → each polypeptide chain contains a haem group

• If there are changes to the sequence of amino acids (primary structure) → protein would fold differently → sickle cell anaemia

• The haem group in each subunit contains an Fe 2+ ion → binds to oxygen reversibly → useful because oxygen is not soluble in water so transported around the body in haemoglobins

What is the structure of a fibrous protein

Long polypeptide chains that have cross linkages due to hydrogen bonding

→ repeafting structure → creates an organised structure

What is the function of a fibrous protein

Due to large no of hydrophobic R groups → not soluble in water

• Strong + insoluble → structural proteins eg collagen

What is the structure of collagen

• Formed from 3 polypeptide chains held tg by hydrogen bonding to form a triple helix

• Covalent bonds form cross links between R groups of amino acids → holds collagen molecules tg to form fibrils → have staggered ends → not in a perfect line → stronger

What is the function of collagen

• Structural protein

• Many hydrogen bonds within the triple helix → strong

• The fibrils have staggered ends → strong

• Insoluble → high no of hydrophobic R groups

What is the role of an enzyme

• Biological catalyst → speeds up the rate of reaction by finding an alternate pathway with a lower activation energy for the reaction to occur

Structure of enzymes

Globular protein → highly specific → active site has a specific shape for a specific substrate

Enzymes 3D structure is determined by the tertiary structure → if altered → active site changes shape → substrate no longer fits → enzyme cant carry out its function

High pH or temp → denatures the enzyme by changing the shape of the active site