Biochemistry Notes

Biochemistry

Explain the importance of specific intermolecular bonds and intermolecular forces in a glyceride fat molecule.

• Glycerol molecule and fatty acid held together by Ester bonds
• Covalent bonds present for Fatty acids and Glycerol molecules
• LD forces present, hold the fat together
• Saturated fatty acid and glycerol (fats) are solid due to more LD forces
• Unsaturated (oils) are liquid due to less LD forces present

Explain the importance of specific intermolecular bonds and intermolecular forces in a protein molecule.

• The amino acids are held together by peptide bonds
• The secondary structure created through hydrogen bonds between the Carboxyl and amino group
• The tertiary structure  created through bonds between R groups – included covalent bonds and ionic (disulphide bridge)
• Structure relates to function, therefore the different bonds result in different protein with different functions.

Explain the importance of specific intermolecular bonds and intermolecular forces in a cellulose molecule.

• Cellulose is made up of glucose molecules
• Glucose consists of covalent bonds (LD and HB- for hydroxyl group)
• Glucose chain made up of glycosidic bonds
• Every other glucose is inverted
• Hydrogen bonds present in-between the stands of glucose.

By referring to the molecular structure of enzymes and how they function, explain each of the following observations

1. Chemical reactions occur faster in the presence of an enzyme

• Enzymes lower the activation energy of reactants
• The lowered energy allows for more molecules to reach the transition state more easily
• The more reactants that proceed to the transition state, the faster the reaction becomes

1. Amylase will only catalyze the decomposition on starch

• Enzymes have a specifc chemical make up
• Each type of enzyme (protein) is unique due to their molecular make up
• Different enzymes created through different amino acid sequence
• And different secondary and tertiary structure lead to different structure –function
• An enzyme has an active site in which reactants can bind to
• Induced fit & lock and key models (specific to a reactant)
• Therefore each enzyme has its own specific function
• Hence why amylase will only catalyze starch.

Using a simple diagram explain how the properties of a phospholipid molecules allow it to form a bilayer.

•  The polar head is faced out due to the fact it is hydrophilic. It can withstand the water surrounding the membrane[pic 1]
• The polar head facing outwards allows for the flow of water across the membrane
• The non polar (hydrophilic) tail is on the inside. The opposite positioning of the bilayer allows the tails to isolate themselves from water.
• Water can sneak passed it once it enters

Compare and contrast how the phospholipid bilayer assists in the process of endocytosis and exocytosis

• Exocytosis and endocytosis are membrance assisted transport methods.
• Materials that are too large to diffuse through or be sent through proteins are transported this way
• The bilayer fuses with a vesicle inside the cell and the vesicle becomes part of the membrane. The substances are then dumped out of the cell (exocytosis)
• When taking substances in there are two ways

• Pinocytosis – the membrane engulfs a large body of liquid and the liquid enters inside the cell in form of a vesicle
• Phagocytosis – The membrane engulfs a particle or another cell. The engulfed object is enclosed within a membrane-bound vacuole 

Molecular Genetics

A fictional species of bacteria, containing the iso-operon, has genes that code for the proteins that produce isoleucine, an amino acid. The bacterium uses these proteins to synthesize isoleucine when it is not readily available in its environment.

1. Is this operon likely to be repressible or inducible? Explain

• Repressor
• Similar to trp-operon
• When the concentration of isoleucine is high, the bacterium does not need to synthesize it. Therefore the presence of the molecule would bind with a repressor protein and repress the promoter.
• When concentration is low, the bacterium needs to create it. The conformation of the repressor protein changes and cannot bind with promoter – allows for gene expression

1. Sketch and annotate a diagram that illustrates how the presence isoleucine regulates the expression

Same concept as trp-operon, however it would be with isoleucine molecule as a co-repressor [pic 2]

Describe how a DNA molecule’s structure allows it perform replication

• DNA replication is semi conservative (one daughter one parent strand)  
• Double helical structure allows that.
• DNA is unzipped (Helicase) and replication fork is created
• Due to fact DNA is anti parallel, one strand runs 5-3 while other runs 3-5
• DNA polymerase begins to synthesize DNA in a 5 – 3 direction with assist of primers
• Leading strand created towards replication fork
• Lagging strand creates okazaki fragments away from replication fork
• The fragments put together through ligase and primers removed by RnaseH

Explain, using the 4 steps required to make a GMO, how a plant that is resistant to pesticides can be created

• Identify gene of interest – Find a DNA sample that has the genes to resist the pesticide. Use restriction enzymes and cut the genes out at the recognition sites.
• Create/design a vector – Find a vector would carry the gene of interest. Agro bacterium is common bacteria that invades plants, the plasmid of this bacterium could be used. The gene would be added into the plasmid (again with the aid of the same restriction enzyme)
•  Transform Gene – Introduce plasmid to host cell.
• Express Gene – Host cell will divide and make copies of DNA

Compare and contrast the three types of RNA in terms of structure and function

• mRNA (messenger RNA) – This is the end product of transcription in the nucleus. This RNA resembles one strand in the DNA except it contains Uracil not Tymine. The purpose of this RNA is to allow for the DNA sequence to be read by the ribosomes without the actual DNA needing to leave the nucleus.
• tRNA (transport RNA) – This is a clover leaf shaped RNA that consists of an anti codon arm for a specific amino acid codon. The purpose of this is to deliver specific amino acids to the ribosomes that translate the mRNA.
• rRNA – This is an RNA that makes up a ribosomal unit. The rRNA is crucial ad ribosomes are needed for the translation of mRNA. They read the mRNA sequence and synthesize the appropriate amino acid chain, which will then later become a protein.

Compare and contrast the process of transcription and translation.

Homeostasis

By referring to a specific set of hormones covered in this course, explain how negative feedback is useful in maintaining homeostasis. Include an explanation of why that particular hormone system requires regulation in the human body.