1. Topic 7: Nucleic Acids and Proteins
Biology HL
Mrs.Ragsdale
Topic 7: Nucleic Acids and Proteins

2. Topic 7.1 DNA Deconstructed
The function, structure and secret details about the blueprints essential to every form of life!

3. Review DNA= deoxyribonucleic acid
Primary components: 5-carbon sugar (deoxyribose), phosphate group, nitrogen base
Monomer = nucleotide
4 Nucleotides
Adenine + Thymine
Cytosine + Guanine

4. Purines and Pyrimidines
Purines – Adenine and Guanine
A purine has two rings in its molecular structure
Pyrimidines – Thymine and Cytosine
A pyrimidine has one ring in its molecular structure
Purines always match to a pyrimidine
Held together by Hydrogen bonds

5. Notice how the nucleotides are bonded, N-H and O-H

6. Sugar-Phosphate “Backbone”
Support structure made up of alternating Phosphate groups and Sugars
At the end of each sugar is a “hydroxyl” which consists of an –OH
5’ is always a phosphate group
3’ is always a hydroxyl group

7. These strands are antiparallel to each other

8. Problem! DNA replication can only occur in a 5’ – 3’ direction
What about the antiparallel strand?
A different solution is necessary!

9. DNA Coiling
Nucleosomes – DNA wrapped around eight histone proteins and held together by an additional histone
Allows DNA to supercoil
Aides with DNA transcription as well
Nucleosomes can be tagged with histone proteins to promote or repress transcription

11. DNA MakeUp Unique or single copy genes
Contain the protein coding sequences
Highly repetitive sequences or satellite DNA
Once known as “junk” DNA
Large pieces of DNA that contain repetitive base sequences which are not translated
Anywhere between 5 and 300 bases long
Repeated up to 10,000 times
Constitutes 5 -45% of typical eukaryotic DNA

12. Introns and Exons Introns – DNA that is transcribed but not translated
Eventually removed from the mRNA sequence before leaving the nucleus – Posttranscriptional modification
Prokaryotes typically do not have introns
Exons – DNA that is both transcribed and translated
Contain sections of protein building DNA sequences

13. 7.2 DNA Replication
The process by which DNA copies itself inside of the nucleus

14. Enzymes Involved in Replication
Helicase – Uncoils and “unzips” the DNA helix into two template strands
RNA Primase – acts as a primer for DNA replication by adding a short length of RNA
DNA Polymerase I – removes the RNA primer
DNA Polymerase III – adds nucleotides in a 5’ to 3’ direction
DNA ligase – seals cuts made in the template

16. DNA Replication Details
Free nucleotides are produced by the cell so that they are available for DNA replication
Deoxyribonucleoside triphosphates are located on each nucleotide. Two phosphate are removed during replication to release energy.
Helicase unzips the DNA into two template strands
DNA polymerase III adds the nucleotides in a 5’ – 3’ direction.

17. DNA Replication Details
Leading strand – moves in the same direction as the replication fork
Lagging strand – moves in the opposite direction
RNA primase adds a short length on the template to act as a primer
DNA polymerase III initiates replication next to the primer
DNA polymerase I releases (excises) the RNA primer and replaces it with DNA

18. Lagging Strand
Occurs in pieces and not all at once like the leading strand
Okazaki fragments – short lengths of DNA formed between the RNA primers
Fragments are sealed together using DNA ligase by making another sugar-phosphate bond

20. Final Thoughts
DNA replication occurs in multiple points all at the same time in a eukaryotic chromosome
DNA replication produces two identical copies that are semi-conservative
Always in a 5’ – 3’ direction

21. 7.3 Transcription of DNA
Prokaryotic and Eukaryotic DNA Transcription

22. Transcription of DNA First step in protein synthesis
Goal is to copy segments of DNA “protein recipe”
Eukaryote – occurs in nucleus
Prokaryote – occurs in cytoplasm

23. Process of Transcription
RNA Polymerase splits DNA into two strands
Sense – has the correct sequence to form a protein (except U’s are T’s)
Antisense – has the complimentary sequence. This way it can act as a template for the copying RNA
Free nucleotide triphosphates are again used by RNA polymerase to create the chain of mRNA using two phosphates to create energy
mRNA is always copied in a 5’ – 3’ direction

24. Promoter and Terminator Regions
Promoter – a short sequence of nucleotides that essentially tell the RNA polymerase where to begin coding
Terminator – a short sequence of nucleotides that tell the RNA polymerase when to stop

25. Introns and Exons Introns – “junk” DNA Exons – coding DNA
Prokaryotes typically do not have “junk” or non-coding DNA so once transcription has completed the mRNA is mature
Eukaryotic mRNA must remove the introns in order for it to mature and leave the nucleus

26. Codons
mRNA is broken up into 3 nucleotide long sequences known as codons
Used in translation to match up nucleotides to amino acids

27. 7.4 Translation
Creation of Protein

28. Process of Translation
Once the mRNA leaves the nucleus it enters the cytoplasm
Ribosomes form around the mRNA
mRNA is fed through the Ribosome and each codon is matched up to the corresponding tRNA anticodon
The tRNA brings the amino acids, a chain is formed
Occurs in a 5’ – 3’ direction

29. Transfer RNA (tRNA)
A strand of RNA that has turned into a double loop by base pairing
Each amino acid has a specific tRNA activating enzyme that binds a specific amino acid to the tRNA
20 different tRNA enzymes, each matching up to a specific amino acid
Energy from ATP is needed to attache the amino acid to the tRNA
Contains the anti-codon used to match up to the mRNA template

30. Structure of Ribosomes
Ribosomes are made up of rRNA and protein
Two subunits – large and small
Three binding sites for rRNA on the surface of the ribosomes
Two tRNA molecules can bind at the same time to the ribosome.
Also a binding site for mRNA

32. 4 phases of Translation Initiation – translation begins (Start codon)
Elongation – chain of amino acids grows
Translocation – newly formed protein is folded
Termination – sequence ends (Stop codon)

33. Polysomes
Sometimes, one strand of mRNA can be translated by more than one ribosome at a time
This results in a polysome

34. Free and Bound Ribosomes
Free ribosomes – located in cytoplasm
Typically synthesize proteins made for use within the cell itself
Bound ribosomes – located on the RER
Synthesize proteins primarily for secretion or for lysosomes

35. Draw and label – Peptide bond between 2 amino acids

36. 7.5 Proteins

37. Protein Review Long chains of amino acids Functions: Blood
Muscle, tissue, hair, nails
Antibodies
Hormones
Enzymes

38. 4 Levels of Protein Structure
Primary Structure
The number and sequence of amino acids in a polypeptide
Typically anywhere between 50 – 1,000 peptides long
Secondary Structure
The regular repeating structures
Α-helix
Β-pleated sheets

39. 4 Levels of Protein Structure
Tertiary Structure
The three dimensional conformation of a polypeptide
Essentially, the 3-dimensional folded formation of a protein
Includes the intramolecular bonds formed between amino acids
Quaternary Structure
How two or more polypeptides link together to form a single protein
Prosthetic group – non-polypeptide structure that some polypeptides contain
Conjugated protein – Proteins with a prosthetic group

42. Fibrous Proteins Long, narrow shape Insoluble in water Examples:
Collagen – structural protein
Strengthens bones, tendons, skin
Causes these tissues to create long tough fibres
Myosin – movement
Myosin + actin cause contraction in muscle fibres
Results in muscle movement

43. Globular Proteins Round shaped proteins Typically soluble in water
Examples:
Haemoglobin
Binds with oxygen in the bloodstream and transports to tissues
Immunoglobulin
Antibodies

44. Structure of an Amino Acid

45. Polar and Non-Polar Amino Acids
Polarity based on the R group
Hydrophilic R groups = polar
Hydrophobic R groups = non-polar
Polarity determines the location and distribution of proteins located in the cell and what function it might have
Creation of hydrophilic channels through the cell membrane
Influences specificity of active sites in enzymes

46. Polar amino acids are forced to stay on the internal/external of the cell wall
Non polar amino
Acids are able to
Cross the cell membrane
And make channel proteins

47. Enzyme Active Sites
Polar amino acids act within the active site of an enzyme initiates a chemical reaction
Substrate and enzyme interact to form an activated complex
Weakened state allows for transitions to occur

48. 4 Functions of Proteins Hormones – Insulin Immunoglobulin – Antibodies
Regulates glucose uptake in cells
Immunoglobulin – Antibodies
Immune response
Enzyme – Lipase
Breaks down glucose
Gas transport – Haemoglobin
Brings oxygen to the tissues

49. 7.6 Enzymes

50. Enzyme Review Made of protein or RNA
Enzyme specificity – only one substrate per enzyme
Lock and Key
Affected by temperature and pH levels

51. Metabolic Pathways Chains and cycles of enzyme-catalysed reactions
Each stage of the reaction features its own enzymes
Metabolic pathways are chains of chemical reactions carried out in a particular sequence
Anabolic pathways – build up organic compounds
Catabolic pathways – break down organic compounds

53. Induced Fit Model Lock and Key method incomplete
Does not explain how substrate binds to the active site
Until a substrate binds to the active site, it does not actually fit precisely
Induced Fit Model states that the substrate induces the active site to change
The bonds within the substrate weaken
Lowers the activation energy
Allows the reaction to occur

55. Enzymes and Activation Energy
Enzymes work by lowering activation energy
The energy required for the reaction to take place
Exergonic or exothermic reactions

56. Enzyme Inhibition Competitive Inhibition
Substrate and Inhibitor are similar in shape
Inhibitor is able to bind to the active site and thereby block the substrate
Only slows down the rate of the reaction, not stop it completely
Increasing the concentration of the substrate would allow the substrate to out compete the inhibitor
Noncompetitive Inhibition
Substrate and inhibitor are different in shape
Inhibitor binds to a region on the enzyme other than the active site
Causes structural changes to the enzyme allowing the active site to change shape
Prevents substrate from being able to bind – results in a decrease in activity

58. C0mpetitive Inhibition Example
Methanol poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness.
Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol.
Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.

60. Noncompetitive Inhibition Example
Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator.

61. End-Product Inhibition
Enzyme pathways can be controlled by concentration of products from the end of the pathway.
The enzyme that is inhibited by the end-products is an example of an allosteric enzyme.
Allosteric enzymes have two non-overlapping binding sites – active site and allosteric site.
Also, typically they are the end product
Once bound at the allosteric site, the structure of the enzyme is altered so that the substrate is less likely to bind to the active site
Essentially, this limits and inhibits the end-product.
Reversible change – allosteric site is detachable
Allows for the management of metabolic pathways – able to switch off when an excess of product is made