Topic 7 - Nucleic acids HL revision list

7.1 DNA structure and replication

DNA structure

• Part of DNA supercoiling are structures called Nucleosomes.

• DNA structure gives a clue to the mechanism of DNA replication.

• Non-coding regions of DNA have other important functions, limited to regulators of gene expression, introns, telomeres and genes for tRNAs.

Essential Questions

• How does DNA coil up in chromosomes?

• What is a histone protein and what is its purpose in a nucleosome?

• What are the functions of DNA which does not code for proteins?

DNA replication (in prokaryotes only)

• DNA polymerase enzymes can only add nucleotides to the 3’ end of a primer.

• Continuous DNA replication occurs on the leading strand and discontinuous on the lagging strand.

• A complex group of enzymes do DNA replication including; helicase, DNA gyrase, single strand binding proteins, DNA primase and DNA polymerases I and III.

Essential Questions

• What are the main steps in DNA replication?

• Which enzymes are involved in DNA replication?

• What is the 'leading strand' and the 'lagging strand'?

Crossing over

• DNA replication makes a second chromatid in each chromosome in interphase before meiosis.

• Crossing over exchanges pieces of DNA between non-sister homologous chromatids and forms new combinations of alleles on the chromosomes formed in meiosis.

Essential Questions

• When does DNA replication take place?

• What are non-sister chromatids?

• How does crossing over change the structure of DNA molecules (Link to topic 11)

Student skills and applications

• To realise that Rosalind Franklin’s and Maurice Wilkins’ X-ray diffraction work gave insights into the structue of DNA.

• Awareness that the Sanger method of base sequencing uses nucleotides containing dideoxyribonucleic acid (DNA with deoxyribose missing 2 oxygen molecules) to stop DNA replication at a specific base which allows sequencing using fluorescent markers and computers. (Sanger chain termination. Video here)

• Awareness that in DNA profiling Tandem repeats are used as these vary greatly from person to person.

• Ability to analyse of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material.Graphic

• Skill to use of molecular visualization software to analyse the association between protein and DNA within a nucleosome

7.2 Transcription

• The direction of Transcription is in a 5’ to 3’ direction as RNA polymerase adds the 5´ end (phosphate) of the free RNA nucleotide to the 3´ end of the growing mRNA molecule.

• Transcription is partly regulated by Nucleosomes in eukaryotes.

• Eukaryotes modify mRNA after transcription.

• Splicing of mRNA increases the number of different proteins an organism can produce.

• Gene expression is regulated by proteins that bind to specific base sequences in DNA. - eg. methylation

• Gene expression is affected by the environment of a cell and of an organism.

Essential Question(s)

• How is the DNA used as a template for a mRNA molecule?

• How does the cell control which genes to use for making mRNA molecules (transcription)?

• What is the difference between gene expression and transcription?

• mRNA has introns sliced out of it after transcription, what other splicing can occur?

• What can no longer happen to a gene after 'methylation'?

• In what ways do you think the environment can affect gene expression?

Student skills and applications

• Awareness that the promoter region is an example of non-coding DNA.

• The skill to analyse changes in the DNA methylation patterns in connection with gene expression

7.3 Translation

Three stages of translation

• Initiation is the assembly of the components (large and small ribosome subunits, mRNA and tRNA molecules) that carry out the process.

• Synthesis of the polypeptide involves a repeated cycle on a ribosome where tRNA binds to the A (aminoacyl), P (peptidyl) and E (exit) sites in turn. Polypeptide molecule is produced.

• (examples of start and stop codons not needed)

• Termination of translation is followed by disassembly of the components.

Essential Question(s)

• The central dogma described by Francis Crick in the 1950s explains how DNA makes mRNA which in turn makes protein. Which molecule is missing?

• How can a mRNA molecule be used as a template for a polypeptide?

Ribosomes

• Free ribosomes synthesize proteins for use primarily within the cell.

• Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes.

• Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.

Essential Question(s)

• What is the difference between free ribosomes in the cytoplasm and ribosomes attached to the rER?

• What advantage do prokaryotes have over eukaryotes in the way transcription links to translation?

• The sequence and number of amino acids in the polypeptide is the primary structure.

• The secondary structure is the formation of alpha helices and beta pleated sheets stabilised by hydrogen bonding.

• The tertiary structure is the further folding of the polypeptide stabilised by interactions between R groups. (Polar and non-polar amino acids are relevant to the bonds formed between R groups.)

• The quaternary structure exists in proteins with more than one polypeptide chain. and may involve the binding of a prosthetic group to form a conjugated protein.

Essential Question(s)

• What are the four levels of protein structure?

• Which two secondary structures are stabilized by hydrogen bonding?

• Interactions between R-groups leads to complex folding in which level of protein stucture?