Biology - Nucleic acids

Structure of a nucleotide (3)

1. Pentose sugar (deoxyribose in DNA, ribose in RNA)

2. Phosphate group

3. Nitrogenous base

How is a DNA nucleotide formed?

Condensation reaction where a link between the phosphate and sugar is formed

How are polynucleotides formed? (2)

• Nucleotides join together to form a polynucleotide by a covalent phosphodiester bond

• Condensation reactions occur between the phosphate group attached to the 5’ carbon on one nucleotide pentose sugar and the 3’ carbon of the next pentose sugar

How is a DNA molecule arranged? (2)

• DNA consists of 2 polynucleotide strands joined together by hydrogen bonding

• The two strands run antiparallel to eachother where where one strand runs 5’ to 3’ and the complementary strand runs 3’ to 5’

Complementary base pairing (2)

Purines pair with pyrimidines:

• Adenine always pairs with thymine

• Guanine always pairs with cytosine

What are the important features of DNA? (5)

1. Sugar phosphate backbone - provides structural stability and protects nitrogenous bases

2. Double stranded helix - provides stability and each strand acts as a template in semi-conservative replication

3. Hydrogen bonds between bases - provides stability and allows strands to separate easily for replication + transcription

4. Complementary base pairing - ensures genetic info is replicated accurately

5. Large molecule - large amounts of genetic code can be stored

How is DNA packaged into chromosomes in eukaryotic cells? (3)

1. DNA associates with histone proteins to form nucleosomes, providing structural stability

2. The DNA helix coils into a super helix (chromatin), remaining as indistinct chromatin in the nucleus to compactly store genetic info during most of the cell cycle

3. During mitosis, chromatin condenses and coils further into visible chromosomes

(Prokaryotic DNA is circular with no associated histones and no nuclear structure)

How did the Meselson and Stahl experiment provide evidence for semi-conservative replication? (5)

1. E. coli cells were grown in a medium containing the heavy isotope ¹⁵N

2. The cells divided until the entire DNA contained the heavy nitrogen

3. Bacteria were transferred to a medium containing the normal isotope ¹⁴N and allowed to divide

4. Samples of bacteria were taken after each generation and the DNA was extracted and separated in a centrifuge

5. DNA containing ¹⁵N is denser than DNA with the normal isotope ¹⁴N

What were the DNA compositions observed in each generation after replication in the Meselson and Stahl experiment? (3)

1st generation - all DNA molecules contained one ¹⁵N strand and one ⁴N strand

2nd generation - 50% of DNA molecules contained one ¹⁵N strand and one ¹⁴N strand, the other 50% contained two normal isotope ¹⁴N strands

3rd generation - 25% of DNA molecules contained one ¹⁵N strand and one ¹⁴N strand, 75% of DNA molecules contained two ¹⁴N strands

Describe the semi-conservative mechanism of DNA replication (6)

1. The enzyme helicase breaks the hydrogen bonds between the two polynucleotide strands and separates them

2. Each original strand acts as a template to form new complementary strands

3. DNA nucleotides align by complementary base pairing (A-T C-G)

4. The enzyme DNA polymerase joins nucleotides together to form two new complementary strands

5. The strands are joined together by hydrogen bonds, forming two identical DNA molecules

6. Each DNA molecule contains one original strand and one newly-synthesised strand, making the replication semi-conservative

Describe the process of continuous replication (5)

1. DNA strands are antiparallel, so the two strands are copied differently

2. DNA polymerase can only synthesise DNA in the 5' → 3' direction

3. The template strand running in the 3' → 5' direction can be copied continuously as DNA unwinds

4. A complete complementary strand is synthesised as one long length

5. This produces the leading strand and is known as continuous replication

Describe discontinuous replication (5)

1. The template strand running in the 5' → 3' direction is copied in small sections as new 3' ends become available

2. These short DNA sections are called Okazaki fragments

3. DNA ligase joins the Okazaki fragments by forming bonds in the sugar-phosphate backbone

4. This produces a continuous polynucleotide strand

5. This process is known as discontinuous replication

What are the structural differences between DNA and RNA? (4)

• RNA contains the pentose sugar ribose, whereas DNA contains deoxyribose

• RNA contains uracil instead of thymine (bases in RNA: A, U, C, G)

• mRNA, tRNA and rRNA are usually single-stranded, whereas DNA is double-stranded

• RNA molecules are generally shorter and have a lower molecular weight than DNA

What is the role of rRNA? (3)

• rRNA is synthesised from genes on DNA in the nucleolus

• rRNA leaves the nucleus through nuclear pores and associates with proteins to form ribosomes

• Ribosomes are the site of protein synthesis where the mRNA code is translated into a sequence of amino acids

What are the characteristics of mRNA? (4)

• mRNA is a single-stranded molecule produced from DNA during transcription

• The base sequence of mRNA is complementary to the single DNA strand being copied

• mRNA has a variable length depending on the gene transcribed, which reflects the length of the polypeptide it codes for

• mRNA is short-lived and is degraded after its role in protein synthesis is complete

What is the function and structure of tRNA? (7)

Function - tRNA acts as an intermediate between mRNA codons and amino acids, transferring amino acids to the ribosome

Structure - all tRNA molecules have a characteristic cloverleaf shape

• The 5' end always ends with guanine (G)

• The 3' end always ends with the base sequence CCA, where the amino acid attaches

• The anticodon is located on the bottom loop and has a triplet base sequence complementary to an mRNA codon

• The anticodon determines the specific amino acid carried by the tRNA molecule

• The base sequence of the rest of the tRNA molecule is variable

Genes and chromosomes definitions (5)

Gene - a region of DNA whose nucleotide base sequence codes for a specific polypeptide/protein

Chromosome - contains many genes located along its length

Locus - the position of a gene on a chromosome

Alleles - different forms of genes which occupy the same locus on homologous chromosomes and code for similar polypeptides

Homologous chromosomes - carry genes for the same characteristics but may contain different alleles

What are the features of the genetic code? (6)

Genetic code - a sequence of three nucleotide bases (base triplet in DNA, codon in mRNA) that code for a specific amino acid

• Four nucleotides produce 64 possible codons (4³) which code for the 20 common amino acids

Main features:

• Degenerate - different codons can code for the same amino acid

• Stop codons - signal the end of polypeptide synthesis

• Non-overlapping - codons are read as separate triplets

• Universal - the same codons code for the same amino acids in all organisms

Describe the stages of transcription (7)

1. The DNA unwinds and uncoils and the hydrogen bonds between complementary base pairs are broken by DNA helicase, separating the two DNA strands

2. The template strand is used to produce an mRNA strand

3. Free RNA nucleotides align alongside the template strand by complementary base pairing (A-U, C-G)

4. RNA polymerase joins the RNA nucleotides together by phosphodiester bonds, producing a strand of pre-mRNA

5. Introns are removed and exons joined together by a spliceosome to produce mature mRNA

6. The mature mRNA leaves the nucleus through a nuclear pore and attaches to a ribosome for translation into a polypeptide

7. The two DNA strands re-form hydrogen bonds and recoil, reforming the double helix

What is splicing and alternative splicing? (6)

Splicing - the removal of introns (non-coding sequences) from pre-mRNA, leaving the exons (coding sequences)

• Introns are removed after transcription before translation can occur

• A spliceosome recognises splice sites, removes introns and joins exons together

• This produces a continuous strand of mature mRNA

Alternative splicing - allows different introns/exons to be removed or joined in different cells

• This enables one gene to produce different but similar proteins

How is transcription regulated? (7)

1. Transcription requires specific transcription factors that move from the cytoplasm into the nucleus

2. Transcription factors bind to specific DNA sequences upstream of the gene

3. They stimulate RNA polymerase to begin transcription, producing mRNA

4. The mRNA can then be used in translation to produce a protein

5. When a gene is not expressed, an inhibitor blocks the DNA-binding region of the transcription factor

6. This prevents transcription and therefore prevents gene expression

How does oestrogen regulate gene expression? (7)

Oestrogen - a steroid hormone and is lipid-soluble so it can diffuse through the cell membrane

1. Oestrogen binds to a specific receptor protein that forms part of a transcription factor

2. The transcription factor enters the nucleus

3. Oestrogen binding changes the shape of the transcription factor, allowing it to bind to the promoter region of a specific gene

4. This enables RNA polymerase to bind and begin transcription

5. mRNA is produced and then translated into a protein

6. As a result, oestrogen increases the expression of specific genes

How does siRNA regulate translation? (7)

1. RNA interference (RNAi) regulates gene expression by preventing translation

2. Double-stranded RNA is hydrolysed into short siRNA (small interfering RNA) molecules

3. The siRNA separates into single strands

4. siRNA binds to an enzyme that can hydrolyse mRNA

5. The siRNA binds to a specific target mRNA by complementary base pairing

6. This guides the enzyme to the target mRNA, which is then hydrolysed and broken down

7. As the mRNA is destroyed, translation cannot occur and the protein is not produced

How do histones and epigenetics regulate gene expression? (7)

Epigenetics - refers to changes in gene expression without changes to the DNA sequence, causing a change in phenotype without a change in genotype

• Gene expression can be altered by DNA methylation and by histone modification

Nucleosome - consists of DNA wrapped around eight histone proteins

• Histones have amino acid tails that can be chemically modified (acetylation, methylation and phosphorylation)

• These modifications are added or removed by specific enzymes

• Some histone modifications increase gene expression, while others decrease gene expression

• Environmental factors can affect gene expression through changes in histone modification

How does increased DNA methylation affect gene expression? (4)

1. DNA methylation occurs when a methyl group (CH₃) attaches to DNA

2. The methyl group attaches to a cytosine (C) base next to a guanine (G) base, forming a CpG site

3. Increased methylation prevents transcription factors from binding to the promoter region

4. This inhibits transcription, so the gene is not expressed

How does decreased histone acetylation affect gene expression? (6)

1. DNA is wrapped around histone proteins to form chromatin

2. Histones can be modified by the addition or removal of acetyl (COCH₃) groups

3. When histones are acetylated, chromatin becomes less condensed, making genes more accessible to transcription factors

4. Decreased acetylation causes chromatin to become more condensed

5. This reduces access of transcription factors to the DNA and inhibits transcription

6. As a result, gene expression decreases

What are gene mutations and what causes them? (7)

Gene mutations - changes in the DNA base sequence that can result in a different polypeptide being produced

• The altered base sequence can lead to a different amino acid sequence

• Mutations create new alleles of genes

• Mutations occur randomly and may arise from errors during DNA replication

• Mutagenic agents increase the frequency of mutations

Examples - high-energy radiation (X-rays, gamma rays, UV light), alpha and beta particles, chemicals such as nitrous oxide and benzene

What are the different types of gene mutations? (6)

Substitution - the replacement of one or more bases with different bases; it may have no effect, produce a different amino acid, or create a stop codon

Deletion - the removal of one or more bases; deletion of 1 or 2 bases causes a frameshift mutation, altering all codons after the mutation

• Deletion of three bases removes one amino acid but does not alter the reading frame

Addition - the addition of one or more bases and usually causes a frameshift mutation

Duplication - occurs when one or more bases are repeated, resulting in a frameshift

Inversion - occurs when a sequence of bases is reversed

Translocation - occurs when a sequence of bases is moved to a different location in the genome; the effect depends on where it is moved from and to

Explain why not all gene mutations affect the order of amino acids (3)

• Some mutations only change 1 codon which could still code for the same amino acid

• The genetic code is degenerate so a specific amino acid can be coded for by more than one codon

• Some mutations occur in introns which do not code for amino acids and they are removed during splicing

Explain why a change in amino acid sequence is not always harmful (2)

• May not change tertiary structure of the protein as the different bondings don’t change (ionic, disulphide, hydrogen)

• May give the organism a selective advantage by changing the properties of the protein and making it more beneficial

Explain what is meant by a frameshift (2)

Frameshift - occurs when mutations change one or two bases in a triplet/codon

• This shifts the way the genetic code is read so all DNA triplets/ mRNA codons downstream from the mutation change

How can gene mutations affect proteins and enzymes? (5)

• Deletions and additions are usually more harmful than substitutions because they often cause a frameshift, altering the amino acid sequence from the point of mutation

• A mutation can alter the amino acid sequence of a polypeptide, producing a non-functional protein

• If the mutation changes amino acids at the active site, the substrate may be unable to bind, making the enzyme non-functional

• If the substrate can still bind, enzyme activity may be reduced

• A mutation away from the active site can alter the enzyme's tertiary structure, changing the shape of the active site and affecting function