MGC: Semester 1

Life and Cells:

Define Life
The unique ability of an organism to use metabolic activity to reproduce, react to stimuli, adapt,
etc To impose negative entropy on a system.
Describe the difference between Prokaryotes and Eukaryotes
Prokaryotes: No localized nucleic acid, no organelles, no nucleus, usually single celled, blue
green algae and bacteria, rapid growth. Eukaryotes: DNA localized to nucleus, organelles,
multicellular, flora and fauna, cytoskeleton.
Describe structure and function of Viruses
Viruses have a body (Nucleocapsid) and tail end (tail + end plate). Viruses have nucleic acids of
their own but are not considered cells / life. Can be lytic = use host cell which will eventually
lyse, or provirus = viral progeny buds at the surface, cell survives.
Describe the structure and function of the cell membrane
Phospholipid bilayer. Fluid mosaic and dynamic. Rigidity is regulated by proteins, saturation of
the phospholipids and presence of cholesterol. Phospholipids can move laterally but rarely
between layers. Forms a selectively permeable membrane.
What are the main three types of cell membrane proteins, and where they sit?
Receptor proteins, transport proteins, enymes. Can sit, peripheral, anchored or intergrally.
Why are eukaryotic cells compartmentalized?
An increase of compartmentalization means increased cell efficiency due to the ability of cells to
specialize and localize certain processes.
Structure and function of the nucleus.
Double layered membrane within cytosol. Site of main genome. Site of most rna and dna
synthesis. Contains nuclear pores for diffusion to and from the nucleus. Contains the nucleolus
which is the site of rRNA synthesis.
What is contained within the Cytosol?
The cytosol houses the organelles and many ions, nutrients.
What are the roles of the cytoskeleton?
Overall structure of the cell, motility within the cell (organelles), movement of the cell, cell
division.
Explain what microtubules, microfilaments and intermediate filaments do.
Microtubules involved with cell division, microfilaments involved in contraction, intermediate
filaments involved with cell strength.
Function of the mitochondria
Double layered organelle, site of cellular respiration (aerobic).
Function of the endoplasmic reticulum
Site of synthesis of peptides (rough), synthesis of lipids, detoxification of lipid soluble drugs.
Function of the Lysosomes
Contain hydrolytic enzymes which dissolve unwanted molecules.
Function of Golgi Apparatus
Stacks of cisternae, transport and packaging of glycoproteins and polysaccharides. Cis faces and
receives things from ER, trans associated with packaging.
Function of Transport Vesicles
Import and export from cell
Function of Ribosomes
NOT an organelle, RNA protein complex associated with synthesis of polypeptides / proteins.
Function of Microbodies
Remove unwanted compounds from cells. Ex. Peroxisomes break down AAs and uric acids
(oxidation)
Carbon Chemistry:
What bonds form carbohydrates?
Covalent glycosidic bonds. Condensation reactions, ie. Water produced.
What are the types of lipids?
Phospholipids, glycerol, triaglycerol, Fatty Acids, Steroids,
What do lipids function as?
Long term energy stores for organisms
Proteins
Draw the structure of the monomer of a protein.
What is this unit called?
Amino Acids
What bonds form polypeptides?
Polypeptides formed by peptide bonds, amide bonds
What is the structure of protein hierarchy, and what are the bonds involved in each step?
1 Chain of amino acids joined by peptide bonds
2 Hydrogen bonding between polypeptide to form folding, repeated patterns, a-helix, b-
pleated sheets, or random coil
3- 3D globular structure of the protein, driven by hydrophobic interactions and S-S- bonds.
4- Association of multiple protein subunits and can contain prosthetic groups
What is the structure and consequence of Glycine?
R-H therefore achiral, very flexible
What is the structure and consequence of Alanine?
R-CH3, non polar and uncharged
What is the structure and consequence of Phenyalanine?
R-CH2-Benzene, same as alanine
What is the structure and consequence of Tyrosine?
R-CH2-Benzene-OH, likes forming H-Bonds, polar, uncharged.
What is the structure and consequence of Cysteine?
Only protein that readily forms covalent bonds, in the form of disulfide bonds.
What is the structure and consequence of Proline?
Proline forms an internal ring structure and therefore very inflexible.
Explain denaturation
Denaturation is the change in regular conformation of a protein due to disruption in the 2,3,4
heirarchical stages. As structure is closely linked with function, denaturation is generally
associated with a lack of functioning of the protein. Some proteins may renature.
Explain the various agents that can cause denaturation
Heat, reducing agents, salts, chaotropes, detergents,
Explain sickle cell anaemia, what it causes, and its relationship to proteins.
Sick cell results from the change in polarity as a result in the change of one protein, glutamic
acid -> valine. Can cause kidney failure, infection and thrombosis. In Hb
Explain Creutzfeldt-Jakob disease and its relationship to proteins
Creutzfeldt Jakob disease results from the conformational change in a protein under certain
conditions and is linked with brain damage.
Describe some of the functions of proteins in Eukaryotes
Storage, transport, enzymes, receptors, defense, structural, movement.
Explain how enzymes function
Enzymes are biological catalysts which greatly reduce the activation energy of a reaction
occurring. They do not get used up and do not change the equilibrium of a reaction therefore
cannot cause reactions to occur which otherwise would not have. They bind substrates at an
active site and form products. They can assist reactions by increasing the local S concentration,
altering the shape of S, strain S, or maintain precise S orientation.
Explain what inhibitor molecules do to enzymes
Inhibitor molecules are molecules which bind the same or better to an active site of a protein
and thus inhibit it from working on its substrates. The object of many pharmaceutical drugs is to
act on enzyme activity sites in pathogens and not in human cells.
Chromosomes and Nucleic Acids
Draw the structure of a chromosome from Double Helix -> Metaphase Chromosome
Consists of a double stranded DNA helix, this wraps around a histone octamer, which is
associated with an H1 histone (this subunit is called a nucleosome). Nucleosomes are arranged
in hexagonal structures named solenoids. Solenoids are bound to protein scaffolds in looped
domains which, in total greatly reduces the amount of space taken up by DNA. A chromosome is
a protein/DNA complex which houses part of the genome.
Define a gene
A gene is the functional unit of hereditary, which consists of a specific nucleotide, encoding
instructions for various proteins and regulatory factors.
What are introns, exons , promoter region and 3 UTR
Introns are areas of mRNA that are spliced out, exons are spliced together, promoter region 5
area which initiates translation and the 3 UTR is an untranslated area which can contain
regulatory information.
Draw the structure of a nucleotide
What is the difference between a nucleotide and nucleoside?
A nucleoside is a nucleotide without the phosphate.
What is the bonding involved in between a nitrogenous base and a ribose?
Glycosidic bonds
Draw the structure of a nucleic acid, which way is it running?
Always runs 5 to 3
What is the bonding between nucleotides?
Phosphodiester bonds
What are the differences between the nitrogenous bases (A,C,G,T,U)?
CTU are pyrimidine, single circle, AG are purine, double circle. GC bond together with 3
hydrogen bonds, AT bond together with 2 hydrogen bonds.
What are the differences between RNA and DNA
RNA is single stranded, oxyribose, contains uracil instead of Thymine, relatively more unstable.
DNA is double stranded, deoxyribose, contains thymine instead of Uracil and relatively more
stable.
The Central Dogma: Replication
Explain the steps in the central dogma.
DNA is transcribed to RNA, RNA is translated to proteins. DNA is also replicated.
What is the significance of the DNA as an antiparallel double helix?
Double helix means that the Hydrophobic interactions of the nitrogenous bases creates stability
in the helix and that it is protected by the polar charged phosphate backbone. Double helix also
allows for semiconservative replication and the ability to correct errors in replication.
Describe the process of replication
Helicase splits the double stranded DNA, one leading strand, this is continually replicated via
DNA polymerase III. On the lagging strand, replicated strand must be made in blocks. First RNA
primase makes a primer, secondly, DNA polym III elongates the strand past the primer with
complementary base pairing nucleotides, thirdly DNA polym I replaces the primer with DNA, and
lastly the ligase protein joins the two okazaki fragments together via a phosphodiester bond.
Energy to make new DNA strands comes from cleaving phosphate groups from nucleotide
triphosophate.
Explain the various proteins of the replisome
Helicase, topoisomerase, ligase, primase, dna polymerases
Draw a diagram to illustrate replication on the lagging strand
Explain how DNA can detect errors and repair them?
DNA polymerase has a proof-reading ability which can detect errors and repair them by
synthesizing DNA which is complementary to the adjacent DNA strand.
Explain Nucleotide excision repair
If an error is detected, the area around the lesion is cut out and filled by DNA polymerase and
ligase.
The Central Dogma: Transcription
Describe the mechanism of gene transcription
3------------------------5 <- coding strand
5------------------------3 <- template strand
RNA polymerase synthesizes new immature mRNA strand from the template strand. Synthesizes
in 5 3 direction. Differences are now it is RNA, so Uracile instead of Thymine.
The Central Dogma: Translation
Describe the basic structure of the various types of RNAs and their roles in gene expression in
eukaryotic cells.
mRNA: messenger RNA, the coding for proteins and RF. tRNA: transport AAs. rRNA: form
ribosomal complexes where translation occurs. snRNPs: form spliceosomes with associated
proteins. snoRNP: Associated with the modification of NTs
What is a Codon? How many are possible?
A codon is a 3 nucleotide sequence that codes for an amino acid. There are 64 codons.
Explain the meaning of Degenerative and Unambiguous
Degenerative means that more than one codon encodes for the same AA. Unambiguous means
that any one codon only encodes for a single AA.
What is the code for the Initiation of transcription?
AUG, methionine
What is the code for the termination of transcription
UAA, UGA, UAG
The 5 -> 3 mRNA translates to which termini of the AA chain?
NH3+ -> COO-
Explain the 4 steps of translation
Amino Acid Activation: Amino Acid + tRNA + Aminoacyl tRNA synthetase+ atp = activated Amino
Acid.
Initiation: methionine tRNA binds its anticodon to AUG within ribosome and translation is
begun. Elongation: Ribosome moves 3NT along mRNA, and each associated tRNA binds its
anticodon to codon and AAs form peptidebonds to eachother forming polypeptide.
Termination: When codon = UAA UGA or UAG then ribosome dissociates, and newly formed
polypeptide has formed.
Describe the structure of a tRNA protein, to which area does the AA bind?
3
The Central Dogma: Gene Expression
Which is the primary level of gene expression?
Transcriptional control
Explain transcriptional control
Controlling promoters to make sure that the right proteins are made in right amounts.
Promoters are molecules which determine the start of transcription and direct the binding of
RNA polymerase II.
Explain pre-mRNA processing
5 cap and polyadenylated tail, processing to produce mRNA.
Explain the function of the ribosome and spliceosome and the role of RNA within them
Spliceosome is snRNPs and proteins which bind around introns via H-Bonds and catalyse them,
allowing them to be removed from immature mRNA.
Explain RNA transport and localization
Before mRNA is moved to cytosol, series of checkups are engaged to make sure it is mature
(until all uneeded RNA is degraded) Furthermore, RNA may be localized to increase
concentration and production of proteins
Explain Translational control
If a protein is not needed, separate proteins will bind to the 3 and 5 ends which will initiate
negative translational control. For normal development to occur, translational control and rna
transport and localization are needed.
Explain mRNA degradation
Removal of methylated guanine cap and polyadenylated tail will greatly reduce the stability of
RNA, allowing it to degrade and thus, not function.
The Central Dogma: Mutation
Describe the different types of mutation at the DNA level
Point shift: A single change in nucleotide pairs. Can be transitional, from purine to purine, or
transversional, from purine to pyrimidine or vice versa.
InDel: An insertion or deletion of a nucleotide. Alters the reading frame.
Frameshift: A shift in the reading frame.
Describe the impact of mutation on DNA structure: Silence, missense, nonsense, frameshift
Silence: Where a different codon occurs, but still ends up with the same AA, therefore, no
change.
Missense: A different AA ; can result in no change ie. Non important area of the protein, can
result in big change, ie. At the active site or area of directional change in the protein. Depends
on characteristics of AAs being changed, polarity, charged, etc..
Nonsense: Resulting in stunted protein. An AA insertion that results in UAA, UGA or UAG
therefore STOP codon. More effective if closer to 3 end, but still stunted.
Frameshift: Change in the reading frame, very unlikely that protein will function correctly. Often
occurs at repeated bases; base slippage.

Cell Energy: Metabolism
Draw a picture outlining the three steps of metabolism and the cell compartments involved.
Explain the relationship between anabolic and catabolic reactions in the cell
Catabolic reactions break down macromolecules which yield ATP, which can be used for fueling
metabolic processes and the simple molecules that are formed can be used to build up different
macromolecules for the cell and body.
What are the main high energy compounds in a cell?
ATP, acetyl CoA, NADH, FADH2
Draw a diagram explaining the oxidation and reduction of NADH
Describe the energy yield of the glycolytic pathway.
1 glucose molecule yields 38 ATP
D-Glucose + 602 + 38ADP + 38Pi + 38H+ 6CO2 + 6H20 + 38ATP
Explain how different cell types use different metabolic pathways.
Hb does not have mitochondria therefore rely on anaerobic respiration.
Cell Energy: Glycolysis
What is produced by the glycolytic pathway?
Glycolytic pathway results in pyruvate which can be converted into acetyl-coa via TCA, or lactate
depending on mitochondria and presence of O2.
What happens in the investment stage of Glycolysis?
Breakdown of glucose (phosphorylated) into 2 triose pentose molecules, 2 ATP are invested in
this stage.
What happens the second stage of Glycolysis
2 x Glyceraldehyde-3 phosphate are oxidative conversion into 2 x pyruvate, which yields net 2
ATP, 2 NADH
What is yielded via Glycolysis?
Net yield of 2 ATP, 2 NADH
What are the irreversible reactions in Glycolysis?
Phosphofructokinase, pyruvate Kinase and Hexokinase: These three reactions produce large
free energy changes, not close to equilibrium and therefore are irreversible , the driving force
for the glycolytic pathway.
What is the Pentose Phosphate Pathway?
Using intermediates of the glyolytic pathway to form pentose for nucleotides and NADPH which
is important in the synthesis of fatty acids
Cell Energy: TCA Cycle
What is the significance of the TCA cycle in Oxidative Metabolism?
Whilst TCA cycle itself only produces 2 GTP, it produces many high energy carrier molecules, 6x
NADH, 2x FADH2 which are used in the electron transport chain to produce large amounts of
ATP.
Explain the cyclic nature of the TCA cycle and how this provides energy carrier molecules
Pyruvate enters matrix of mitochondrion, oxidative carboxylation to form Acetyl CoA (via
pyruvate dehydrogenase), Acetyl CoA joins with 4C oxaloacetate, CoA is removed, Acetyl-
Oxaloacetate goes through 8 stages, twice through (one per pyruvate) and yields 6x NADH, 2x
FADH2, GTP, QH2. Oxaloacetate is reformed.
Draw a picture illustrating the TCA cycle.
Explain the regulatory mechanisms that control the TCA cycle.
Irreversible reactions with alpha citrate sythase, isocitrate dehydrogenase, alpha ketoglutarate
dehydrogenase. Inhibited by build up of succinyl coa, citrate and NADH. Up-regulated by ADP
and Ca2+
Describe the importance of FADH2 and NADH.
Every NADH yields 3 ATP, FADH2 yields 2 ATP.
Cell Energy: Oxidative Phosphorylation
Draw a picture to illustrate the processes of the electron transport chain.
Explain how energy is produced in the presence of O2 during oxidative phosphorylation.
NADH and FADH2 donate electron which is passed through the electron transport chain. The
electron transport chain is a series of electron carriers which contain 3 specialised carriers which
act as proton pumps. As the electron passes through the carriers, it falls to lower energy levels
which allows the pumps to transfer protons into the intra-membranous space generating a
proton gradient. The protons pass through an ATP synthase pump, energy derived from this
movement synthesizes ATP from ADP and Pi. The electrons are transported to oxygen which
converts them to water.
Cell Energy: Anaerobic Respiration
When does Anaerobic respiration occur?
In the absence of oxygen, or in cells without mitochondria.
Explain the mechanism of anaerobic respiration
In the glycolytic pathway, after pyruvate has been formed, it is then converted into lactate, this
is to reoxidize NADH enabling them to be able to produce more ATP from glucose molecules via
the glycolytic pathway.
Explain the Cori Cycle
Lactate produced by cells, appears in blood stream, converted by the liver to glycogen or
glucose via gluconeogenesis, which re-enters the muscle
Cell Transport: Membranes
Explain simple passive diffusion
Explain carrier mediated transport
Explain Endo and Exocytosis
Explain osmolarity and hydrostatic pressure
Explain the concept of tonicity
Explain Diarrhea and Hyponatremia
Cell Transport: Carrier Mediated Transport
Explain the principles of Carrier Mediated Transport
Explain the role of pumps in uphill transport and the role of metabolic energy
Explain the concepts of primary and secondary active transport
Describe Endo and Exocytosis
Describe Familial Hypercholesterolemia
Cell Activity: Electrical Phenomena
Describe the resting membrane potential
Describe an action potential (basic)
Describe synaptic transmission (basic)
Explain the basis of typical cell resting potential
Explain significance of the Na-K pump
Are cells in equilibrium or steady state? Why?
Explain how ion diffusion generates voltages across cell membranes
Cell Activity: Action Potentials
Describe action potential generation in nerve and muscle cells.
What are the determinants of an action potential velocity
Explain action potentials in cardiac muscle
Explain action potentials in sensory neurons
Describe ways in which Action Potentials can travel from cell to cell
Cell Activity: Synaptic Transmission
Describe synaptic transmission and the transmission of Action Potentials
Draw a diagram of synaptic transmission at the synaptic cleft
Distinguish between chemical and electrical synaptic transmission
Explain the recycling of Acetycholine in chemical synapses.
Explain different problems that can arise at synapses.
Cell Activity: The Central Nervous System
Describe the difference between the CNS synapses and neuromuscular junctions.
Explain the concept of synaptic integration.
Explain the action potential firing code
Cell Activity: Neurotransmitters
Introduce more complex actions of neurotransmitters
Identify key excitatory and inhibitory neurotransmitters
Describe the differing behavior of Acetylcholine on nicotinic and muscarinic receptors.
Muscle: Skeletal Muscle
Be able to describe the gross anatomy and structure of skeletal muscle
Draw the structure of a sarcomere
Understand the structure of thin filaments
Understand the structure of thick filaments
Define twitch in muscle
Explain tetanus
Explain the length-tension relationship in striated muscle
Muscle: Smooth Muscle
Describe the features of phasic and tonic smooth muscle
Explain and draw a picture illustrating the smooth muscle contractile apparatus
Describe the organization of contractile units within smooth muscle
Explain smooth muscle contraction (difference vs. skeletal muscle)
Explain the role of Ca2+ in the activation of smooth muscle contractile apparatus
Explain smooth muscle relaxation
Muscle: Cardiac Muscle
Explain the length-tension relationship in cardiac muscle
Explain excitation-contraction coupling in cardiac cells

Cell Regulation: Cell Cycle
Recognize the importance of the cell cycle
Draw a diagram to illustrate the steps of the cell cycle
Explain the proceedings in G1 phase
Explain the proceedings in G0 phase
Explain the proceedings in S phase
Explain the proceedings in G2 phase
Explain the proceedings in M phase
Describe the relationship of cell regulation with cancers
Cell Regulation: CDK Cyclins
Define a CDK Cyclin
Describe the relationship of CDK cyclins to phases of the cell cycle
Describe the basic function of CDK cyclins
Explain process of the G1 CDK Cyclin complex
Describe the attributes of each subunit
Outline the targets of CDK Cyclin complexes
Illustrate the example of CDK2-Cyclin A and Rb-E2F
When is the primary regulation of the cell cycle
What can influence CDK Cyclin regulation?
What are cell cycle checkpoints?
Checkpoint example: CDK2 Cyclin A p53
Main checkpoints within the cell cycle
Describe how Apoptosis occurs
Genetics: The Chromosome
Explain the structure of a chromosome
Explain Diploid cell behavior with respect to mitosis and meiosis
Describe the basic overview of meiosis
Outline the differences between mitosis and meiosis
Define bivalency
Explain the significance of division and bivalency in genetics
Explain genetic recombination
Define the following
Oogonia
Oocyte
Spermatocyte
Gamete
Allele
Heterozygous
Homozygous
Semi-Dominant
Genotype
Phenotype
Consanguinous Mating
Dihybrid
Epistasis
Expressivity
Hypostatic Gene
Linkage
Penetrance
Pleiotropy
Polygenic
Polymorphism
Polyploidy
Trisomy
Understand that a 9:3:3:1 involves two genes, located on separate pairs of homologous
chromosomes, separating independently of eachother, in which the alleles have complete
dominance.
MGC Lab Manual:
Draw a dipeptide, indicating separate amino acids and peptide bond
Is Copper Sulphate a useful solution in determining if a protein is denatured or not?
What is restriction enzyme/endonuclease?
What two forces hold the strands of DNA together?
Why does DNA carry a charge and what is that charge?
What are plasmids?
What does a T test prove?
Why do red blood cells NOT change volume in 0.15mol NaCl?
What is the difference between heterochromatin and euchromatin?
Which of two stimulating wires excites a nerve and why?
What is the site of action of pancuronium and other curare like compounds and why?
Explain effects of Na+ and K+ concentration changes of Vm peak
Provide explanation for the effects of Saxitoxin and TEA on Action Potentials
Explain the molecular mechanism underlying the summation of muscle tension with repeated
stimuli
Explain why a nerve trunk is not an all or none action potential
What is the conduction speed of a human nerve