BIOCHEMISTRY
Biomolecules 1, 2, 3
1. Differentiate anabolism and catabolism. (anabolism make up synthetic reactions and catabolism are the
degradation reactions)
2. What are the three main reaction sites for metabolism? (mitochondria, cytosol and ER)
3. What determines function of a protein? (structure and 3D folding)
4. What is the nucleotide pairing? (A-T [2] and C-G [3] )
5. Why are the basic biological atoms the backbone of biomolecules? (because they can form strong
covalent bonds)
6. What does molecular polarity result from? (uneven distribution of charge)
7. How does electronegativity change on a periodic table? (up and to the right increases)
8. What is a dipole? (a charge seperation)
9. What determines polarity? (geometry, structure, charge)
10. Name the three types of interactions and two types of bonds that are non-covalent. (hydrogen bonds,
ionic bonds, salt bridges, electrostatic interactions, van del waals interactions, hydrophobic interactions)
11. What are salt bridges? (electrostatic interactions between permanently charged residues)
12. What are the van der waals interactions? (based on induced assymetric distribution of electrons)
13. What is coloumb’s law? Why is it important? (E = [Kqq]/[Dr2] energy of an ionic bond is given by it)
14. Who generally forms ionic bonds? (atoms having widely varying electronegativities)
15. Draw an ATP molecule.
16. Differentiate steroisomers and constitutional isomers in
a. Names (stereoisomers have identical names except for the cis and trans prefix; constitutional
isomers have different names)
b. Functional groups (constitutional isomers can have same or different functional groups and
stereoisomers have the same functional group)
c. Chemical and physical properties (constituional isomers have different chemical and physical
properties. Stereoisomers, as in enantiomers have the same chemical and physical properties and
diastereomers have different chemical and physical properties)
17. Differentiate enantiomers and diastereomers. (enantiomers are mirror images that are nonsuperimposable. Diastereomers are non-mirror image stereoisomers)
18. _______ acids and bases dissociate completely and ______ acids and bases do not. (strong, weak)
19. The _____ the pKa, the ____ the acid. (larger, weaker)
20. Derive the HH equation from Ka = [HA] [H+] / [A]
21. List the four types of lipids and types of each. (fatty acids – saturated and unsaturated, glycerides –
neutral and phosphoglycerides, complex lipids – lipoproteins and glycoproteins, non-glycerides –
sphingolipids, waxes and steroids)
22. Saturated fatty acids have ___ double bonds and unsaturated fatty acids have ____ double bonds. (no,
one or more)
23. ______ fatty acids pack better and thus have a high melting point. (Saturated)
24. Basic hydrolysis of triacylglycerols yields what? (salts of carboxylic acids and glycerol)
25. Where is the connect point for for lipids? (only at carboxyl group)
26. How can carbohydrates be defined? (polyhydroxy aldehydes or ketons or substances that can yield such
things)
27. What is a glycosidic bond? (the bond between the anomeric carbon or a carbohydrate and some other
group or molecule)
28. What is van’t hoff rule? (2n = number of steroisomers)
29. What is an epimer? (one or two opital isomers that differ from each other only in the configuration about
one assymetric carbon atom)
30. What do benedict’s or Tollen’s reagants test for? (they test positive for aldoses and ketoses. Aldose
gives a blue color to a benedicts solution and ketose gives a brick red)
31. Hemiacetals test _____ in Tollen’s and benedict’s because _______ (positive; they are reducing sugars)
32. What is mutarotation? (change in optical rotation as an equilibrium mixture of anomeric forms)
33. What is the difference between an α and β configuration? (together they are called anomers. Α is carbon
is above the plane and β is below the plane)
34. Sucrose is made up of ____ and it will test ____ for Tollen’s/benedict’s because _____ (glucose and
fructose, negative; it is a acetal linkage)
35. Maltose is made up of ___ and it will test ___ for tollen’s/benedict’s because _____ (glucose in an α
linkage; positive; reducing sugar)
36. Cellobiose is made up of ___ and it will test ___ for tollen’s/benedict’s because ______ (glucose in a β
linkage; positive; reducing sugar)
37. Difference between amylose and amylopectin. (amylose is made up of 1-4 linkages and anylopectin is
made up of 1-6 linkages)
38. Glycogen is stored in _____ and it has a ___ backbone with ____ branches which are broken by _____
and _____, respectively. (liver and muscles, 1-4; 1-6; glycogen phosphorylase; debranching enzymes)
39. Starch has ___ linkages while cellulose has ___ linkages (α; β)
Enzymes
1. How is an enzyme named? (substrate + reaction performed + ase)
2. What are:
a. Oxidoreductases? (catalyze the transfer of electrons, hydride ions or hydrogen atoms between
molecules)
b. Transferases? (catalyse the transfer of functional groups between molecules)
c. Hydrolases? (catalyse the transfer of functional groups to water)
d. Lyases? (form double bonds by removing functional groups from a molecule)
e. Isomerases? (transfer functional groups within a molecule)
f. Ligases? (use the chemical energy of ATP-hydrolysis to form C-C, C-O, C-N, or C-S bonds)
3. What are the three phases of a chemical reaction? (steady, non-steady and depletion state)
4. What does it mean by catalytic perfection? (if the rate [ratio of Kcat/Km] is under a certain number, then
the enzyme can handle substrate as fast as it is delivered from the solution)
5. What is the relaxed and tense state? (a empty enzyme as opposed to a filled enzyme correlating with
cooperativity)
6. What are the two types of allosteric inhibition? (K type and V type. K type means the K50% is changed.
V type means the Vmax is changed)
7. What is a medical use of competitive inhibitors? (giving ethanol to someone to reduce the body’s uptake
of methanol. Both are gotten rid of eventually)
8. What is a medical use of non-competitive inhibitor? (Dianox is used as a diuretic because it inhibits
carbonic anhydrase)
9. Be able to plot the different types of reversible inhibitors both on a MM plot and a LB plot.
10. What are the two types of irreversible inhibitors? (specific and unspecific: specific means that the
enzyme is protected in the presense of substrate; unspecific means that protein structure is destroyed)
11. What is a suicide substrate? (A competitive inhibitor that is converted to an irreversible inhibitor at the
active site of the enzyme.)
12. What are coenzymes usually derived from? (vitamins)
13. Whose analogs are coenzymes usuallys? (RNA-analogs)
14. What’s the difference between co-substrates and prosthetic groups? (co-substrates are soluble molecules
that bind to and dissociate from enzymes during turnover; they become chemically changed during the
reaction. Prosthetic groups are permanently bound to the enzyme and if they undergo chemical changes
during turnover, they are re-generated)
Receptors and Second Messengers
1. Describe receptor binding. (it is stereospcific, saturable, can be inhibited selectively and triggers
intracellular signalling cascade)
2. How do steroid hormones work? (they can enter the cell by passive diffusion. Binds to it’s receptor in
cytoplasm or nucleus; complex binds to receptor elements in the promoters and enhancers of genes
which stimulate transcription)
3. What other hormones use the same method as the steroid hormone? (thyroid, retinoic acid, calcitriol)
4. How do ligand-gated ion channels work and give an example of it. (The channel is closed in the resting
state. It opens when the neurotransmitter binds. Opening of sodium channels depolarizes the membrane.
Opening of chloride and potassium channels hyperpolarizes the membrane. An example of it is GABA
and it’s inhibitory effects on chloride channels)
5. What is the structure of G protein? (and α, β, and gamma subunit. Β and gamma stay together when
activated. Un-activated version has GDP attatched to the α subunit)
6. Describe the steps of G protein activation and deactivation.
a. Activation of G protein (ligand attatches to G protein receptor and activates it. The gamma and β
portion break off and α switches out it’s GDP with a GTP.)
b. Possible enzymes that can interact with G protein (adenylate cyclase with ATP to make cAMP;
guanlyl cyclase with GTP to make cGMP and PLC with PIP2 to make IP3 and DAG)
c. Post actions enzyme-G protein interaction of adenylate cyclase (cAMP activates PKA which
activates CREB which attatches to DNA using CBP)
7. What actions does the cAMP do in these spots? Also, what hormone does each spot use for this action.
a. Liver (glycogen breakdown; glucagon)
b. Adipose tissue (fat breakdown; epinephrine)
c. Bronchial smooth muscle (relaxation; epinephrine)
d. Vascular smooth muscle (relaxation; epinephrine)
e. Thyroid gland (proliferation, hormone synthesis; TSH)
f. Adrenal cortex (proliferation, hormone synthesis; ACTH)
g. Melanocytes (melanin synthesis; MSH)
h. Kidney (water retention; Vasopressin)
i. Intestine (diarrhea; pancreatic polypeptide)
8. State which parts of the body these hormones help inhibit cAMP and what the response is.
a. Opioid peptides (intestine, brain - constipation)
b. Epinephrine – α receptors (brain - hypotension)
c. Dopamine (brain - euphoria)
d. Somatostatin (pituitary gland – inhibition of GH secretion)
e. Melatonin (melanocytes – inhibition of melanin synthesis)
9. What is PTH? (raises the blood calcium level by raising cAMP)
10. What is pseudoparathyroidism?
a. Symtpoms (Patient has signs of chronic PTH deficiency: hypocalcemia, tetany. But the PTH
level is normal or elevated.)
b. Causes (Some patients have mutations in the PTH receptor. Others have an abnormal Gs protein
that makes inefficient coupling with adenylate cyclase)
11. What is TSH? (from the pituitary gland stimulates hormone production and cell proliferation in the
thyroid gland by raising cAMP.)
12. What is the toxic thyroid nodules?
a. Problems (These are benign tumors in the thyroid gland that overproduce the hormones.)
b. Causes (Some patients have an activating somatic mutation in the gene for the TSH receptor.
Others have an activating mutation in the Gs protein that keeps it constitutively active, usually by
blocking its GTPase activity.)
13. What is cholera? (This is an intestinal infection by vibrio cholerae. The bacteria do not invade the
tissues, but cause watery diarrhea through a secreted protein toxin.)
a. Mechanism (The toxin enters the cells, and catalyzes the covalent modification of the α-subunit
of the Gs protein. This abolishes the GTPase activity of the Gs protein, leaving it in the active
state permanently.)
14. What causes whooping cough? (Caused by Bordetella pertussis, which lives on the respiratory
epithelium. One of its virulence factors is pertussis toxin.)
a. Mechanism (Pertussis toxin enters the cell. In a reaction similar to that of cholera toxin it
modifies the α-subunit of the Gi protein. This inactivates the Gi protein.)
15. What is the function of IP3? (Calcium regulation coming out of ER)
16. How does NO work? (Calcium activates Arginine into Citrate which activates NO which goes from
endothelial cell into the vascular smooth muscle and activates GTP into GMP which induces relaxation)
17. How does a GH receptor work? (The receptor oligomerizes. The receptor autophosphorylates. Signaling
proteins containing an SH2 domain bind to the autophosphorylated receptor. The signaling proteins
become activated allosterically, or tyrosine-phosphorylated by the receptor)
18. How is insulin different from GH? (The unstimulated receptor is a disulfide-bonded tetramer. Most
effects are mediated by IRS-1 and IRS-2.)
19. What is the Ras protein? (small G-protein that is activated by growth factor receptors)
20. Describe the three GH cascades.
a. Formation of IP3 (The autophosphorylated receptor phosphorylates and activates phospholipase
C-γ.)
b. Acitvation of protein kinase B (Akt) (The autophosphorylated receptor activates the lipid kinase
PI3K (phosphoinositide 3-kinase).This produces PIP3 and other 3-phosphorylated inositides. The
3-phosphorylated inositides activate protein kinase B.)
c. Activation of MAP kinase (The autophosphorylated receptor activates the small G-protein Ras.
Ras activates protein kinases. These protein kinases phosphorylate and activate the MAP
kinases.)
Eukaryotic Gene Expression
1. What causes the opening of the DNA coils? (acetylation by HATs reduces the charge of the histone
lysine side chains and thus weakens the nucleosomal glue that holds the coils together)
2. What are the two results of HAT acetylation? (chromatin remodelling; activation of transcription after
transcription factor binding)
3. What is a CpG island? Where are they located usually? (unmethylated CpG’s, at 5’ regulatory regions of
genes)
4. What is the significance of CpG islands in cancer? (gene promoter CpG islands acquire abnormal
hypermethylation which results in heritable transcriptional silencing)
5. What is generally the most important determinant of the amount of functional gene expression which
results? (control of the rate of transcription initiation at the promoter of every gene)
6. What are enhancers and where can they be located? (A short piece of DNA which interacts with proteins
to produce a molecular assembly which increases the rate of transcription of a gene. They can be
located thousands of base-pairs upstream from the start site of transcription, thousands of base-pairs
downstream from the start site and even have been located within introns (non-coding) segments of the
genes.)
7. What are promoters? (sites where gene transcription is controlled and initiated. Normally, a eukaryotic
promoter contains a “TATA” box, so named for its unique DNA sequence.)
8. What is a promoter element? (promoter elements are within the promoter. Promoter elements are short
DNA sequences which recruit proteins that act to increase or decrease transcription rates. These
transcription factors are proteins which have important regulatory roles, in sensing extracellular or
intracellular cues, to modulate rates of transcription initiation)
9. What are proximal promoter elements? (found within a couple of hundred base pairs of the TATA
sequence, and provide binding sites for transcription factors which increase or decrease transcription
rates after binding. Normally, important genes are carefully regulated by several of these proximal
promoter element sites)
10. What are exons? (the part of the gene which carries information about which amino acid should be
present in a protein sequence, or what a functional RNA (rRNA, snRNA, tRNA) sequence should be)
11. What are introns? (the intervening DNA sequences of a gene which are non-coding. These introns are
not removed before transcription is complete, but are removed before the RNA moves to the cytosol for
translation)
12. What are silencers? (just like enhancer sequences, but they slow down existing rates of transcription
initiation)
13. What is a cis-acting mutation? (the mutation affecting transcription rates is in the DNA near the TATA
box, or in a proximal promoter element.
14. What is a trans-acting mutation? (change transcription initiation rates by altering the interaction of
proteins with their DNA binding sites at the promoter. will lower transcription rates, but in some rare
cancers, up-regulated transcription rates can lead to unimpaired cell growth)
15. Describe these eukaryotic RNA polymerases:
a. RNA Polymerase I: (Transcribes Pre-rRNA)
b. RNA Polymerase II: (Transcribes Pre-mRNA)
c. RNA Polymerase III: (Transcribes tRNA and 5S rRNA)
d. Mitochondrial RNA Polymerase: (Transcribes Mitochondrial Genes)
16. What is the mechanism for initiation of transcription at the simplest of eukaryotic promoters? (Proteins
called general transcription factors assemble into a “pre-initiation complex” at the site of the TATA box.
This allows for the binding of RNA polymerase II, and its eventual phosphorylation by one of the
kinases within the initiation complex (TFIIH). This phosphorylation event leads to formation of the
transcription bubble (short denatured segment of DNA) and transcription initiation. Strangely, it is
believed that all of this needs to start over from scratch for every initiation event. A “constitutive”
promoter will act using only these general transcription factors and will not be subject to any other
regulation, up or down.)
17. What causes rubinstein-taybi syndrome? (Characterized by broad thumbs, facial dysmorphism and
mental retardation. The cause is a mutation in a gene coding for CBP, the transcriptional coactivator
CREB-binding protein. Patients have a significantly higher rate of neuronal cancers. chromatin is
maintained in a tightly wound state during development and this results in inappropriate developmental
transcription of genes)
18. Do all eukaryotic genes have an upstream TATA sequence? (no)
19. What three steps are involved in RNA processing? (poly A tail, 5’ cap and splicing)
20. What disease is related to mutations in the splicing area? (cystic fibrosis)
21. Describe RNA transport. (this is an ATP driven transport of mature mRNA. It is presumed that the
“nuclear cage” is involved in capture of mature mRNA for translocation to the cytoplasm. Not much
regulation of gene expression occurs here.)
22. What is transferrin? ( a serum iron binding protein)
23. What is ferritin ( a cellular iron storage protein)
24. What is a transferrin receptor? ( membrane bound receptor which captures iron bound to tranferrin and
ferries it into acidic compartments for release)
25. What do eIFs do? (Assemble initiator tRNA 40S and 60S ribosomal subunits into an 80S ribosome at
the initiation codon of mRNA.)
26. What is EF-2 inhibited by? (diphtheria toxin)
27. What is the most common chemical modification of polypeptides by enzymes after translation?
(phosphorylation of serines)
28. What goes through glycosylation? (Glycosylation is a common modification, but only for proteins
destined for membrane compartmentation or the extracellular space.)
Prokaryotic Gene expression
1. What is conjugation? (mechanism of DNA transfer between bacteria by plasmids.)
2. What is transformation? (uptake of DNA from the medium and incorporation into the bacterial
chromosome.)
3. What is transduction? (Movement of DNA from one bacterial cell to another, mediated by bacterial
viruses – bacteriophages)
4. What is an operon? (a group of genes under a common mechanism of control. Genes are either
expressed together when needed, or turned off together when not of use)
5. Differentiate constitutive and inducible genes. (Constitutive: Genes are “on” all the time, or an activity
is present all the time. Housekeepers. Inducible: Genes can be switched on when all necessary
“inducer” signals are present. These inducers signal that the gene products are needed.)
6. What is a polygenic RNA transcript? (A single RNA transcript which encodes multiple protein products)
7. How do repressor proteins control activity? (by negatively regulating the rate of transcript initiation)
8. What is the lac operon schematic? (cap site, promoter, operator: region for protein binding to control
transcription; lac Z, lac Y, lac A: region transcribed into RNA)
9. Describe what role each part of the lac operon schematic plays (cap site is the cap activator binding site
which requires cAMP; promoter is the RNA polymerase binding site; the operator is the lac repressor
binding site and Z, Y, A are structural genes that encode proteins utilized into lactose catabolism)
10. How does the level of lactose effect the lac operon? (High lactose results in high allolactose; Allolactose
binds to the lac repressor protein; The lac repressor undergoes a conformational change; The lac
repressor-allolactose complex dissociates from the operator; Transcription is stimulated by increased
access of RNA polymerase to the promoter)
11. When is lac operon transcription
a. Highest (low glucose, high lactose)
b. Less (high glucose, high lactose)
c. Least (high glucose, low lactose)
12. The lac and ara operons are _______ while the trp operon is a ______ operon. (catabolic, biosynthetic)
13. When does attenuation happen? (occurs when ribosomes do not “stall” during translation.)
14. What is the schematic for the trp operon? (promoter and operator: trp repressor binding site; Leader with
attenuator at the end of it – ribosome stalling happens at the attenuator when TRP is scarce; EDCBA –
structural genes which encode enzymes utilized in tryptophan biosynthesis)
15. What is the ara operon schematic? (Ara C gene; operator site – ara C protein binds here when Ara C is
abundent which leads to autoregulatory regulation; second operator site – Ara C protein binds here when
Ara C is bound to arabinose which leads to activation; promotor – RNA polymerase binds here; Ara B,
Ara A, Ara D – struuctural genes which encode enzymes utilized in arabinose catabolism)
16. What are the 4 mechanisms by which bacteria find to gain resistance to a drug? (Destroy or inactivate
the drug; Decrease the amount of drug that reaches the receptor by altering entry or increasing drug
elimination; Alter the receptor for the drug (the molecule on which it exerts its effect); Develop resistant
metabolic pathways)
Mutations
1. What is a Single-base substitution?
a. What is another name for it? (Also called point mutations)
b. Two types: (Transition: purine is replaced by another purine. Transverstion: purine is replaced by
a pyrimidine)
2. What is Insertion, deletion? ((“indel”): come in all sizes. Single base pair (most common) or few base
pairs)
3. What is Translocation? (movement of whole genes)
4. What is Inversion? (breakage of chromosome and invereted.)
5. What is Duplication? (Mis-alignment during mitosis and there is crossing over. Then one gets a deletion,
one gets a duplication)
6. What is a missense mutation? (one base change causes different amino acid to be made)
7. What is a nonsense mutation? (premature truncation of protein due to production of stop codon)
8. Differntiate somatic and germline mutations. (Somatic mutations - Accumulate with increasing age ;
Germline mutations - Risk increases with paternal age)
9. What is an induced mutation? (caused due to exposure to something)
a. Tautomeric shift: (Spontanous shifts of atoms in some bases)
b. Ionizing radiation – like X rays (energy rich radtiation that can penetrate the whole body but also
knocks electrons off. Hits the DNA directly or causes a formation of free radicals. Most
consequential mutation is a breaking of DNA.)
c. UV radiation (cannot penetrate whole body. No germ line mutations. More selective type of
DNA damage)
10. Cells are most suscepptible to mutagens during the ___ phase. (S)
11. DNA repair systems: where do they take place?
a. 3’-exonuclease activities: (Replication errors)
b. Post-replication mismatch repair: (Replication errors)
c. Direct repair: (Some methylated bases, pyrimidine dimers in bacteria)
d. AP endonuclease: (Baseless (“apurinic”) sites)
e. Base excision repair: (Abnormal bases)
f. Nucleotide excision repair: (Bulky lesions. 2 types: Genome-wide and Transcription-coupled)
g. Repair of double-strand breaks: (Non-homologous end joining and Homologous end joining)
12. DNA repair defects:
a. Xeroderma pigmentosum
i. Where is the defect? (Defect of genome-wide nucleotide excision repair)
ii. Symptoms (Sunburn, skin cancer)
iii. Inheritance pattern (Autosomal recessive)
b. 2. Cockayne syndrome
i. Defect? (Defect of transcription-coupled nucleotide excision repair)
ii. Symptoms (Poor growth, neurological problems, early senility)
iii. Interitence pattern (Autosomal recessive)
c. . Hereditary non-polyposis colon cancer (HNPCC)
i. Defect? (Defect of post-replication mismatch repair)
ii. Risk of colon cancer? (80%)
iii. Inheritance pattern? (Autosomal dominant inheritance)
d. Ataxia-telangiectasia
i. Cause? (Mutations in the ATM protein kinase, a signaling protein required for the repair
of DNA double-strand breaks)
ii. Inheritance pattern? (Autosomal recessive inheritance)
e. Abnormalities?( Cerebellar ataxia, Immunodeficiency, Lymphoreticular malignancies,
Chromosome breakage, Median survival 20 years, most die from lung infections)
Viruses
1.
2.
3.
4.
5.
6.
What do viruses not posess? (cellular structure, ribosomes, ATP synthesis)
What are the three things that make up a virus? (nucleic acid, capsid, envelope)
What does the capsid of a polio virus look like? (icosahedral made up of 4 sub units)
What does the adenovirus look like? (hexon with penton fibers coming out of it)
DNA viruses replicate through the _____ cycle (lytic)
Describe the lytic pathway. (Adsorption to a virus receptor on the cell surface; Injection of the viral
DNA into the bacterial host cell; Timed expression of the viral genes; Synthesis of viral mRNA and
proteins; Destruction of host cell DNA; Replication of viral DNA; Assembly of new virus particles;
Destruction of host cell envelope, release of about 200 new virus particles)
7. Describe the lysogenic pathway. (After entering the host cell, λ phage DNA becomes circular. An
integrase enzyme, encoded by one of the viral genes, integrates the viral DNA into the host cell
chromosome. The λ repressor is formed at the same time. This protein prevents the transcription of all
viral genes except its own. The integrated λ phage DNA is replicated as part of the host’s chromosome.
When the cell suffers DNA damage, the λ repressor gets degraded. The viral genes become active, the
viral DNA is cut out of the chromosome, and the host cell is destroyed.)
8. What two options does the lambda bacteriophage have when it enters the cell.(Lytic infection or
Lysogenic infection)
9. What is a prophage? (The integrated phage DNA)
10. Why are bacteriophages not used for cure for bacterial infections? (frequent mutations and an abundance
of resistant bacterial strains; Occasionally, a defective phage carries DNA from cell to cell, thus
spreading drug resistance)
11. What are three differences from the bacteriophage and animal/human virus? (human/animal viruses:
Most animal viruses do not kill their host cell. They bud out of the cell without killing it. Many animal
viruses are enveloped. Viruses have to battle the immune system)
12. Which cells can HIV effect? (Only those cells that contain CD4 and a chemokine receptor on their
surface)
13. What are three alternative ways to enter the cell for a virus? (uncoating at the plasma membrane,
uncoating with endosomes, uncoating at the nuclear membrane)
14. Describe what each type of virus has and needs.
a. (+)RNA viruses (have a single-stranded RNA that can serve as mRNA.)
b. (-)RNA viruses (have a single-stranded RNA that is complementary to the viral mRNA. This
genomic RNA needs to be replicated before the virus can make its proteins.)
c. (ds)RNA viruses (have a double-stranded RNA that needs to be made single-stranded or
replicated before. The viral mRNA is transcribed from one of the strands by a virus-encoded
RNA replicase.)
15. Describe the structure of retroviruses according to:
a. Genome: (gag for capsid proteins, pol for reverse transcriptase and integrase, and env for the
spike proteins.)
b. Long terminal repeats (required for integration in the host cell genome, and they contain the
promoter)
c. Enzymes (reverse transcriptase and integrase)
16. What are the nine steps in a retrovirus life cycle? (Fusion of the viral envelope with the plasma
membrane; Uncoating in the cytoplasm; Reverse transcriptase turns the genomic RNA into a doublestranded cDNA; The viral integrase inserts the retroviral cDNA into the host cell DNA; Viral RNA is
transcribed from the integrated retroviral cDNA; Viral RNA is translated into viral proteins.; Viral spike
proteins appear in the plasma membrane; New virus particles are assembled under the plasma
membrane; The new virus particles bud out of the host cell.)
17. Why is it hard to develop vaccines for viruses? (high mutation rate and adaption - can jump species)
Neurotransmitters
1. Name some of the features of neurotransmitters (Synthesized in the presynaptic cell (always a neuron);
Stored in synaptic vesicles; Released in response to membrane depolarization; Release is calciumdependent; Action on postsynaptic cell; Rapid inactivation)
2. What are the four types of nuerotransmitters? (Acetylcholine, Biogenic amines (catecholamines,
serotonin), Peptides, Amino acids)
3. What are the two effects of neurotransmitters? (Excitatory neurotransmitters increase sodium
(sometimes calcium) permeability. Inhibitory neurotransmitters increase chloride or potassium
permeability.)
4. What are two types of receptors that these effects can be mediated by? (Ligand-gated ion channels
mediate the fast effects of neurotransmitters: nicotinic cholinergic, GABA-A, NMDA... G-protein linked
receptors: adrenergic receptors, dopamine receptors, muscarinic cholinergic, opiate...)
5. What are nicotinic receptors? What drug could block this? (Ligand-gated sodium channels in
neuromuscular junction, autonomic ganglia & brain. Curare)
6. What are muscarinic receptors? What drugs could block this? (G-protein linked receptors forming IP3 or
lowering cAMP. In parasympathetically innervated tissues, sweat glands, brain. Atropine and
scopolamine)
7. What do organophosphates inhibit? (acetylcholinesterase irreversibly by reacting with the serine residue
in its active site.)
8. What are biogenic amines made up of? (made from aromatic amino acids by decarboxylation)
9. What are biogenic amines used for? (not only as neurotransmitters, but also as paracrine messengers or
hormones)
10. Describe the steps of catecholamine biosynthesis? (Tyrosine to L-dopa to dopamine to norepinephrine to
epinephrine)
11. Describe inactivation of catecholamines. (Catecholamines are first taken up back into the nerve terminal
by high-affinity uptake (sodium cotransport). Enzymatic inactivation: Oxidative deamination by
monoamine oxidase (MAO) in the nerve terminal. and Methylation by catechol-O-methyltransferase
(COMT).)
12. Name two indoleamines. (5-HT, serotonin)
13. What forms from 5-HT? (melatonin)
14. How do you inactivate 5-HT? (high-affinity uptake into the nerve terminal, and oxidative deamination
by MAO)
15. Name the two isoforms of MAO and what they both degrade. (- MAO-A for 5-HT; - MAO-B for
dopamine. norepinephrine)
16. What are MAO inhibitors used for? (antidepressants)
17. What is the treatment for parkinson’s disease? (L-DOPA (+ carbidopa), deprenyl (an MAO-B inhibitor),
and/or anticholinergics.)
18. What do the following do?
a. Tricyclic antidepressants (inhibit the high-affinity uptake of norepinephrine and 5-HT.)
b. Serotonin-specific reuptake inhibitors (SSRIs) (inhibit the high-affinity uptake of 5-HT only.)
c. Cocaine and methylphenidate (inhibit the uptake of dopamine in addition to norepinephrine and
5-HT.)
d. Amphetamine (releases dopamine, 5-HT and norepinephrine from nerve terminals)
19. Describe the following relating to peptide neurotransmitters.
a. Where are they Derived from? (precursor proteins that are synthesized in the perikaryon)
b. Where are they Transported to? (the nerve terminals in vesicles, using fast axoplasmic transport.
c. What are they formed from? (the precursor protein by proteases during transport.
d. Give some examples. (Endorphins, TRH, cholecystokinin, substance P)
20. Peptide neurotransmitters are mostly found in ________ while amino acid neurotransmitters are most
important in the __________. (short internuerons, central nervous system)
21. What are three important features of amino acid neurotransmitters? (No biosynthetic and inactivating
enzymes needed. Accumulation in synaptic vesicles. High-affinity uptake from synaptic cleft.)
22. Name the important amino acid neurotransmitters. (Glutamate, aspartate (excitatory); Glycine
(inhibitory))
23. What effect does GABA have? (Enhanced GABA neurotransmission in the brain has sedative, hypnotic,
anxiolytic and anticonvulsant effects)
Genetics
Genome and Genome project
1. What is the difference between genomic health care and genetic health care? (genetic health care is
based on understanding the impact of single genes on disease. Genomic health care is based on the
understanding the impact of entire genome and environmental factors on disease and health)
2. Describe the levels of organization of DNA to chromosome and the size differences. (DNA, about 2nm
wide is packed around histones which are about 11nm in diameter. Those are coiled into a 30nm
solonoid fiber and the coils can be up to 300 nm in height of coil. The coil gets coiled into 700 nm
lengths and the diameter of a chromosome is about 1400 nm)
3. What makes up a histone? (two H3’s and two H4’s make a C shape into which H2A and H2B fit into.
H1 holds DNA onto the histone)
4. What’s the difference between mitotic chromosome and interphase chromosome? (Interphase chromatin
is usually much less condensed than that of mitotic chromosomes)
DNA structure and replication
1. Why does DNA have a major groove and a minor groove? (simply a consequence of geometric pairing)
2. In what three forms can DNA exist? (right handed A and B; left handed Z)
3. Compare and contrast the organization and expression of the genetic material in prokarotes and
eukaryotes. (prokaryotes: no membrane bound nucleus, transcription and translation are coupled; in
eukaryotes, DNA is in nucleus and transcription and translation are seperated by time and space)
4. Compare and contrast the similarities and differences between prokaryotic and eukaryotic DNA
replication. (similarities: chains are made in the 5-3 direction, both require an RNA primer, DNA
polymerase active and tertiary site are similar in structure. Differences: eukaryotic replication is much
slower, it has many origin points, associated with histones, DNA Pol is much more specialized and their
interactions are much more complex, chromosomal DNA is linear and it requires special processing of
the ends)
5. When in the cell cycle does DNA replication occur? (S phase)
6. How do eukaryotes manage to replicate their genome “quickly enough”? (have multiple origins of
replication)
7. Be able to match the prokaryote and eukaryote protein equivalents that are involved in DNA replication
(Bacteria matching with eukaryotes: SSB matches with RPA; Primase matches with Pol a; Pol III
polymerase matches with Pol d; β2 sliding clamp subunit of Pol III matches with PCNA; 3’ exonuclease
of Pol I matches with RNaseH + FEN1; g subunit of Pol III (sliding clamp loader) matches with RFC).
8. How is DNA “melted” at the origin of replication? (dnaA binds to a set of 4 repeats of a 9bp sequence,
which melts the origin at the A=T)
9. What is gene amplification and why does it occur? (over-replication of specific chromosomal regions)
10. How can gene amplification contribute toward drug resistance? (it can amplify a good gene?)
11. Explain the structure and function of DNA helicase. (DNA helicase is composed of 6 identical subunits.
It binds to the single strand that is the lagging strand template and unwinds the DNA duplex ahead of
DNA polymerase creating single stranded DNA)
12. Explain the significance of helicase in the synthesis of the lagging strand. (Because the helicase is on the
lagging strand DNA template and because of how the helicase contacts the DNA pol holoenzyme, the
leading strand polymerase is held to the DNA and the lagging stand polymerase remains free to cycle)
13. Explain how SSBs bind to DNA. (bind to the sugar phosphate back bone leaving the bases exposed)
14. What are four functions of RPA? (binds and stabilizes ssDNA, facilitates the unwinding of dsDNA,
regulates DNA-damage-induced cell cycle arrest, is needed to supress DNA synthesis in response to
DNA strand breaks, required for genomic stability)
15. What does a defeciency of RPA cause? (spontaenous DNA damage, apoptosis, and ATM dependent
check point)
16. What is the best explanation of how DNA and DNA polymerase move with respect to one another?
(DNA moves through the replication factory which contains DNA Pol)
17. What does processivity mean? (ability of polymerase to hold onto the DNA)
18. What makes DNA polymerase processive? (-sliding clamp keep the polymerase attatched to the DNA)
19. ***Compare and contrast the prokaryotic and eukaryotic -clamp. (in eukaryotes, a trimer of PCNA)
20. What is necessary for the -clamp to be loaded onto the DNA? (The -sliding clamp loader binds to the
two polymerases and helicase. It also binds to the -sliding clamp to open it so it can be put onto the
DNA.)
21. Why do all polymerases polymerization nucleotides at the 3’ end only (never at the 5’ end)? (the energy
needed to add a new nucleotide is only available if polymerization occurs at the 3’ end.)
22. ***How can an incorrect nucleotide be incorporated into DNA during DNA replication?
23. How does DNA polymerase proof-read its own polymerization? (it has a exonuclease active site where
it checks the newly formed strand)
24. What three mechanisms assure that the error rate remains in the range of 1 error/109-1010 dNTPs added?
(base pairing specificity at the active site, proofreading activity by 3-5 exoncluease, mismatch repair
system)
25. What is the general relationship between DNA repair activity and life span? (linear, direct relationship)
26. What are 6 diseases that are a result of defects in DNA repair or replication?
a. Xeroderma pigmentosum (mutations in genes involved in nucleotide excision repair – associated
with a 2000-fold increase of sunlight-induced; skin cancer and with other types of cancer such as
melanoma)
b. Ataxia telangiectasia (mutations in ATM, a gene that detects DNA damage - increased risk of
X-ray; associated with increased breast cancer in carriers)
c. Fanconi anemia (Ubiquitin ligase defect - increased risk of X-ray; sensitivity to sunlight)
d. Bloom syndrome (DNA helicase gene mutations - increased risk of X-ray; sensitivity to sunlight)
e. Cockayne syndrome (a defect in transcription-linked DNA repair - sensitivity to sunlight)
f. Werner’s syndrome (DNA helicase gene mutations - premature aging)
27. How is the supercoiling that results from replication and transcription relieved? (Type I topoisomerases:
Make nicks in one DNA strand - Can relieve supercoiling; Type II topoisomersases: Make nicks in both
DNA strands (double strand break) - Can relieve supercoiling and untangle linked DNA helices. Both
types of enzyme form covalent intermediates with the DNA)
28. What are three drugs that target topoisomerases? (camptothecin, doxorubicin, ciproflaxacin)
29. Which topoisomerase does these drugs target? (camptothecin – I, doxorubicin – II, ciproflaxacin –
topoisomerase gyrase)
30. How does a cell deal with the “end replication” problem? (telomerase ends it with tandem repeats)
31. Explain how telomerase extends the telomeric sequence. (telomerase binds, telomerase extends 3’ end,
translocation, repeat extension and translocation, release telomerase, completion of lagging strand by
DNA polymerase)
32. What two kinds of structures are possible within the telomere? (a G-4 structure or a T-loop structure)
33. What are some of the importances of the telomere? (apoptosis, aging, cancer, plants)
34. What is one of the functions of nucleosomes? (keep DNA negatively coiled)
35. How do nucleosomes help in DNA replication? (keeping them negatively coiled helps store the energy
required for strand seperation)
36. What are 5 kinds of disorders that result from DNA replication errors during the copying of trinucleotide
repeats? (myotonic dystrophy, Fragile X, huntington’s, SCA, friedreich ataxia)
37. What enzyme is defective in Bloom syndrome and Werner’s syndrome? (Bloom’s and Werner’s is due
to a mutation in DNA helicase gene)
38. What is the difference between Bloom and Werner’s? (bloom’s – sensitivity to sunlight, short stature;
Werner’s – premature aging)
Chromosome structure and diseases
1. One DNA strand can act as a _______ while the other has to utilize a _____ (template for replication all
the way to the end, RNA primer)
2. What is telomerase? (enzyme that has integrated the template in the form of a RNA molecule)
3. Describe telomere structure. (always has one repeat unit that is single stranded at the tip of the 3’ strand
which takes the form of a fold-back triple-strand structure)
4. Anhidrotic dysplasia
a. Inheritance pattern (X linked recessive)
b. Symptoms (stippled areas have decreased electrical conductance due to absent sweat glands)
5. A chromatid is _______ (the name of either left or right half of the metaphase chromosome)
6. Describe the steps in karotype-ing. (blood taken, phylohematogluttin added, kept at 37 for three days,
colchicine and hypotonic saline added, cells fixed, spread on slide, digested with trypsin, and giemsa
stain, metaphase spread analyzed)
7. Decribe the three positions the centromere can be in. (meta- in the center; submeta – towards the top;
acro – all the way in the top forming a satellite)
8. Differentiate heterochromatin and eurochromatin. (not active, active)
9. Structural abnormalities
a. Inversion (you have a chromosome, a part in the middle got flipped, but nothing is added or
deleted)
b. Duplication (could be two normal chromosomes, but you have extra copy of that area into
another place)
c. Insertion (something is pulled out of a chromosome and inserted somewhere else)
d. Ring (chromosome loses the telomeres at both ends)
e. Translocation
i. Reciprical (exchange or either two acentric fragments or exchange of centric and acentric
fragments)
ii. Robertsonian (exchange of proximal short arms)
f. Isochromosome (??)
10. Down’s syndrome:
a. Cause: (trisomy 21)
11. Differentiate Edward’s and Patau’s syndrome (trisomy 18 and trisomy 13)
12. Cause of turner’s syndrome (Monosomy X)
13. ______ is given to turner’s females to induce secondary sexual characteristics. (estrogen)
14. What causes kleinfelter’s syndrome? (XXY male)
15. Cri-du-chat syndrome:
a. Cause : (deletion of the terminal part of chromosome 5 – short arm)
b. Symptoms: (distinctive cry, hypotonia, microcephaly)
16. Cause of DiGeorge’s syndrome. (region of chr. 22 deleted)
17. Differentiate FISH and chromosome painting. (purified DNA clone, heterogenous collection of many
DNA clones with inserts derived from many different regions of a SINGLE chromosome)
18. Describe the philadelphia chromosome and what does it cause? (the abl gene on chromosome 9 inserts
itself into the bcr gene on the 22 chromosome. CML)
19. Describe the three phases of CML. (initial – can last for month to years; accelerated – fever, bone pain,
and splenomegaly; last phase – blast crisis, bone marrow failure)
20. Which plasma protein is indicative of CML? (low level of leukocyte ALP)
21. STI571 is designed ____________ (to inhibit bcr-acl activity)
22. Presense of SRY gene leads to ______ (male gonad)
23. Hallmark of a true hermaphrodite is ____________ (presense of both ovarian and testicular tissue)
24. Definition of mixed gonadal dysgensis is __________ (testis and streak ovary)
25. Differentiate a female and a male pseudo hermaphrodite. (female – only ovary but virilized phenotype;
male – externall and psychosexually female, no uterus and fallopian duct, non-descended testes in
abdomen)
26. Describe the symptoms of adrenogenital syndrome and how you treat it. (hyperplasia of adrenal cortex,
hyponatremia and hyperkalelima in servere cases. Treatment with cortisol)
Transcription
1. List at least 4 kinds of RNA produced by a cell and describe their function. (mRNA: encodes the amino
acid sequence of a polypeptide; tRNA: transports amino acids to ribosomes during translation; rRNA:
forms ribosomes; snRNA: forms complexes with proteins used in eukarotic RNA processing)
2. In what direction does the RNA polymerase read the template? (3-5)
3. In what direction does the RNA polymerase polymerize the new RNA strand? (5-3)
4. How does the polymerization of deoxynucleotides compare to the polymerization of ribonucleotides?
(there is no primer, no proofreading and uses an RNA polymerase)
5. What are the three steps of translation? (initiation, elongation, termination)
6. Describe the elements of a typical E. coli promoter. (there is a 10 base pair 5’-TATAAT-3’ sequence
and a 35 base pair 5’-TTGACA-3’ sequence)
7. What is the composition and purpose of the Shine-Dalgarno sequence? (The Shine-Dalgarno sequence
base-pairs with a pyrimidine-rich sequence in 16S rRNA to facilitate the initiation of protein synthesis)
8. ***What recognizes the Shine-Dalgarno sequence during protein translation? (a purine rich sequence
before the initiation site…I think)
9. What is the difference between RNA polymerase enzyme and RNA polymerase holoenzyme? (RNA
polymerase combines with  factor (a polypeptide) to create RNA polymerase holoenzyme)
10. Explain the physical location of the following with respect to their location on a stretch of DNA:
a. +1 initiation nucleotide
b. +1 initiation codon
c. Pribnow box
d. -35 region
e. Promoter
f. Shine-Dalgarno sequence
g. Coding region
h. Stop codon
i. Termination of transcription signal
11. Compare and contrast function of the components of the E. coli RNA polymerase.
a. Αlpha (there are 2 and they interact with other factors that bind upstream of the -35 box)
b.  (there is 1 and forms phosphodiester bonds)
c. ’ (there is 1 and it binds the DNA template)
d.  (there is 1 and it recognizes promoter and facilitates initiation)
12. What is the function of the  factor? (to ensure that RNA polymerase binds stably to DNA only at
promoters.)
13. What is the function of NusA? (take the place of  factor and aids in transcription termination)
14. What is the function of the  protein with regard to translation? (termination factor that catalyzes the
dissociation of the RNA and polymerase)
15. What structure is involved with transcription termination in E. coli? (Type I (rho ()-independent):
Inverse repeat forms a hairpin loop followed by a poly U stretch which destabilize the DNA-RNA
hybrid. Type II (-dependent): Involves  factor proteins which breaks the hydrogen bonds between the
template DNA and RNA. -dependent terminators lack the poly U stretch after the hairpin)
16. What is rifampicin and how is it used medically? (it is a lipophilic drug that inhibits RNA polymerase in
bacterial cells by binding to the β-subunit of RNA polymerase. It is used to treat TB, leprosy, MRSA)
17. What is the potential drug interaction that has to be considered with using rifampicin? (dilutes heart
medication effects)
18. Compare and contrast the similarities and differences between prokaryotic mRNA and eukaryotic
mRNA. (Eukaryotic mRNA is not mature and must be processed; transcription and translation is not
coupled; they contain amino acid sequence for just one gene. Prokaryotic mRNA is the opposite)
19. ***Compare and contrast the differences between prokaryotic and eukaryotic gene expression.
20. What are the functions of the three eukaryotic RNA polymerases? (RNA polymerase I, transcribes three
major rRNAs - 28S, 18S, 5.8S; RNA polymerase II, transcribes mRNAs and some snRNAs; RNA
polymerase III, transcribes tRNAs, 5S rRNA, and snRNAs)
21. What three RNA processing events occur in generating a eukaryotic mRNA? (poly A tail is put on, 5’
cap is put on, introns are spliced out)
22. What elements “boxes” are often found within a eukaryotic promoter? (Eukaryotic promoters have two
parts to it: a basal element TATA box and a proximal element CAT box which is located upstream)
23. What is the function of the transcription factors? (similar to sigma factor [Q#12]; assembled basal
promoter elements)
24. How are transcription factors named? (they are numbered to match their RNA polymerase)
25. What is a PIC? (RNA polymerase + TFs)
26. Explain the physical location of the following with respect to their location on a stretch of DNA:
a. +1 initiation nucleotide
b. +1 initiation codon
c. Enhancer
d. Proximal control elements
e. Promoter
f. Cap
g. Coding region
h. Exons
i. Introns
j. Stop codon
k. Poly A tail
l. 5’ UTR
m. 3’ UTR
n. Poly A signal sequence
o. Termination of transcription signal
27. Which of the above are retained in a mRNA? (5’ cap, 5’UTR, Star codon, stop codon, 3’UTR, Poly A
tail)
28. What is the order of assembly of TFs at a Pol II promoter? (IID + IIB + RNA pol II + IIF +IIE +IIH)
29. **What two “promoter” factors are involved in Hemophilia B Leyden and Hemophilia B Brandenburg?
(AR and HNF4)
30. **What would the position where these factors bind to DNA be considered?
31. Which Hemophilia B improves during puberty? (Leyden)
32. ***Why? Explain with respect to the utilization of the Factor VIII promoter.
33. ***How many proteins (approximately) make up RNA polymerase II?
34. How does RNA polymerase and DNA interact? (DNA passes through the RNA polymerase tunnel)
35. Which is really moving, the DNA or the RNA polymerase? (DNA)
36. Compare and contrast enhancers and activators. (Activators bind to enchancers which induce high level
transcription. They’re both located upstream, can be several kB from the gene, single or multiple copies
in either orientation)
37. ***Compare and contrast silencers and repressors.
38. What is a UTR? (untranslated region)
39. Are 5’ UTRs and 3’ UTRs considered exons? (yeah)
40. What is the function of the C-terminal domain of RNA polymerase with regard to the RNA processing
events that are needed to make a mature mRNA? (modifying mRNA – capping, slicing, polyadenylation
factors)
41. What the structure and function of the 5’ cap that is put on mRNA? (guanine nulceotide. Stabilizes
mRNA)
42. What is the consensus polyadenylation signal? (AAUAAA)
43. How is the 3’ end of an eukaryotic mRNA generated? (poly A polymerase catalyzes cleavage of primary
transcript and 200 adenylate residues are added)
44. What is the function of a poly A tail? (stabilize mRNA)
45. What proteins bind to the poly A tail? (PBP)
46. To what other proteins do the PBPs bind? (cap binding protein)
47. Compare and contrast introns and exons. (Intron - non-coding DNA sequences between exons in a gene.
Exon - expressed DNA sequences in a gene, code for amino acids (plus 5’ UTR and 3’ UTR).)
48. ***What 5 nucleotides are always present in an intron?
49. What is a splicosome composed of and what is its function? (complexes of small nuclear RNAs and
proteins that cleave the intron at the 3’ end and join the exons.)
50. What is a lariat? (a loop of introns)
51. How is it formed and what is its structure? (Cleavage occurs first at the 5’ end of an intron.The now free
5’ G joins with an A at a specific branch point sequence in the middle of the intron, using a 2’ to 5’
phosphodiester bond)
52. When does splicing occur with respect to when transcription occurs? (before transcription finishes)
53. How do the snRNAs assist in splicing? (they help cut the lariat off the exons)
54. What two diseases are caused by mutations in the pre-mRNA splicing factor genes? (retinitis
pigmentosa and spinal muscular atrophy)
55. What disease is caused by an expansion of a trinucleotide repeat within an intron that interferes with
splicing? (myotonic dystrophy)
56. Where are the splicing recognition proteins located with respect to the RNA polymerase? (associating
with exons and CTDs)
57. What is the most common result from a mutation in the conserved nucleotides of an intron? (skipping
the entire exon)
58. What are four diseases that are known to be caused by a splice site mutation? (Familial Isolated Growth
Hormone Deficiency Type II mutations in the GH-1 gene, Fraser Syndrome mutations in the WT-1
gene, Frontotemporal Dementia and Parkinsonism on Chr.17 (FTDP17) mutations in the Tau gene,
Atypical Cystic Fibrosis mutations in the CFTR gene)
59. ***What is a cryptic splice site?
60. ***How is a cryptic splice site activated?
61. ***Why are some splice site mutations cause o thalassemia while other cause + thalassemia?
62. ***What is alternative splicing?
63. ***How does alternative splicing affect the number of proteins produced in a cell?
64. Compare and contrast the prokaryotic and eukaryotic ribosome. (prokaryotic ribosome has a 50 and 30 S
subunits and a eukaryotic ribosome has a 60 and 40S subunit)
65. Compare and contrast the -amanitin sensitivity of the three eukaryotic RNA polymerases. (Pol I and II
are relatively sensitive and Pol III is moderately sensitive)
66. Where are ribosomes assembled? (nucleolus)
67. Where is rRNA trasnscribed? (nucleolus)
68. ***What is the organization of ribosomal genes?
69. Where are the rRNA genes located in the human genome? (ribosomal genes are located on the short arm
of 5 chromosomes: 13, 14, 15, 21 and 22.)
70. What are the two sequence components of a Pol I promoter? (upstream promoter element and a core
promoter)
71. What is the sequence of events that allows a RNA pol I to start transcribing rRNA genes? (UBF binds to
upstream promoter elements, core-binding factor binds to core, RNA polymerase I binds at start point)
72. ***Why is one polymerase dedicated to transcribing rRNA only?
73. ***What kinds of RNA processing events occur in the generation of a tRNA?
74. What part of the tRNA binds to the amino acid and what part binds to the mRNA? (anti-codon binds to
the mRNA )
75. What polymerase(s) transcribe snRNAs? (Pol II or Pol III)
76. Compare and contrast the three types of RNA polymerase III promoters. (All three types of genes
terminate with a run of T residues; Type I and Type II are internal control region, I being 5S and II being
tRNA. Type III is U6 and is the 5’ control region)
77. What kinds of diseases are caused by tRNA mutations? (Maternally Inherited Diabetes and Deafness;
Mitochondrial Encephalopathy, Lactic Acidosis, Stroke-Like Episodes)
78. What is the underlying reason that the tRNA mutations cause these diseases? (reduce the amount of
complex I which effects the amount of ATP made)
Translation
1. What is the central dogma of molecular biology? (DNA to mRNA to protein)
2. How often does an aminoacyl-tRNA synthetase incorporate an incorrect amino acid into tRNA? (1 per 10100 thousand proteins)
3. What is the start codon? (AUG - Met)
4. What are the stop codons? (UAA, UAG, UGA)
5. Which amino acid is usually “degenerate”? (third one)
6. What usually determines the codon usage by an organism? (relative amount of tRNA that are expressed)
7. What three nucleotides are always added to the 3’ end of all tRNAs? (ACC)
8. Be able to match the modified nucleotide structures with their correct name. (m2G is two methyl groups
added to Guanine; de-amination of Guanine gives you inosine; two Hydrogens added to Uracil gives you
UH2; 4-thiridine is when sulfur replaces oxygen in Uracil)
9. Which is the most important step in protein synthesis? (charging tRNA’s)
10. What is an activated amino acid? (amino acid bound to AMP)
11. What is a charged tRNA? (amino acid attatched to tRNA)
12. How many ATP equivalents are used up in charging a tRNA? (1)
13. How does the aminoacyl-tRNA synthetase know which tRNA to charge? (recognizes key shapes and bases)
14. What happens to a mischarged tRNA? (acylation sites rejects amino acids that are too large and editing sites
hydrolyze amino acids that are too small)
15. Compare and contrast Class I and Class II aminoacyl-tRNA synthetases. (Class I is monomeric and acylates
the 2’OH and Class II is dimeric and acylates the 3’OH)
16. What are the two levels of control to ensure that the proper amino acid is incorporated into a protein?
(charging of the proper tRNA and matching the cognate tRNA to the messenger RNA)
17. Where does protein synthesis take place? (on ribosomes)
18. Compare and contrast the prokaryotic and eukaryotic ribosome? (prokaryotic – 50 [5 and 23] and 30 [16] S ;
eukaryotic – 60 [5, 28, 5.8 ] and 40 [18] S)
19. Which ribosome is the mitochondrial ribosome more like? (prokaryotic)
20. What is the basic organizational scaffold for the ribosome? (rRNA molecules)
21. Where are ribosomes assembled? (nucleolus)
22. ***In what part of the nucleolus is the ribosome generated? ()
23. Describe the synthesis of the rRNA that is generated in the nucleolus. (The 45S precursor is processed and
cleaved into mature rRNAs; Ribosomal proteins then bind to generate the large and small ribosomal
subunits)
24. ***What is really the most important part of the ribosome, the RNA or the protein? (RNA)
25. Explain how the prokaryotic ribosome finds the start codon of a mRNA. (The alignment of the 16S rRNA
with the Shine-Delgarno sequence positions the start codon in the P site of the ribosome)
26. What is the function of the three initiation factors involved with starting translation? (IF1 and IF3 keep the
small and large subunits apart and help to guide the “tertiary complex” into the P site; The tertiary complex
consists of a fMet, initiator tRNA, IF2, and GTP)
27. What high energy molecule is involve with translation initiation? (GTP)
28. How many high energy molecules are used up to get the initiator tRNA set up in the P site of the ribosome?
(1)
29. What are the two parts of the complete ribosome called? (large and small subunits)
30. Compare and contrast the eukaryotic and prokaryotic ribosomes with respect to size. (answered earlier - 18)
31. What three tRNA binding sites are there and what is their function? (A site = amino-acyl tRNA binding site;
P site = peptidyl-tRNA binding site; E site = exit site)
32. How does the newly synthesized protein exit the ribosome? (There is a tunnel through the large subunit that
allows the growing polypeptide chain to pass out of the ribosome)
33. Where is the P site which contains the growing peptide located on the ribosome? (below the tunnel)
34. What catalyzes the formation of the peptide bond? (large subunit rRNA)
35. What does wobble mean when it comes to translation? (the last amino acid as it’s not that important)
36. Which “unusual” nucleotide is often involved with the wobble base pairing? (inosine)
37. What elongation factor guides the acylated tRNA into the A-site? (EF-Tu (eEF-1))
38. In order for this elongation factor to leave the tRNA in the A-site, what high energy molecule must be
hydrolyzed? (GTP)
39. What is EF-G (eEF-2)? (elongation factor is required to “translocate” the mRNA so that the P and the A
sites are positioned correctly so that the A site can accept another charged-tRNA)
40. What high energy molecule is hydrolyzed during the translocation step? (GTP)
41. How many high energy molecules are necessary to incorporate 1 amino acid into a peptide chain? (Include
charging the tRNA, entry into the A site and the translocation step)? (3)
42. What is a polysome? (multiple ribosomes translating one mRNA strand as it goes through each one)
43. What interactions usually occur between the 3’ and 5’ end of a message? (eIF-4G on the 3’ end interact with
eIF-4E on the 5’ end)
44. What does it mean by “transcription and translation” are coupled? (as one is happening, the other is
happening simultaneously)
45. ***What would happen to the expression of a gene if a mutation occurred where an frequently used codon
was replaced by an infrequently used codon?
46. What triggers termination of translation? (stop codons)
47. What high energy molecule needs to be hydrolyzed so that the various components of the translation
machinery can dissociate? (GTP)
48. How does a release factor recognize the stop codon? (eRF1 is a mimic but different enough from a tRNA)
49. Does the release of the protein from the ribosome require the hydrolysis of GTP? (no)
50. ***How many high energy (ATP equivalents) are needed to generate a protein 100 amino acids long? (7 X
100? )
51. What is usually necessary for a ribosome to recognize the 5’ end of mRNA? (5’ cap)
52. What is the complex of proteins called that binds to the cap structure? (cap binding proteins)
53. With what complex does the small ribosomal subunit interact before it binds to the cap binding proteins?
(eIF-2/tRNA/Met/GTP – tertiary complex)
54. Compare and contrast the translational control of ferritin and transferrin. (Ferritin is a cytosolic iron binding
protein expressed when iron is abundant in the cell. Transferrin receptor is a plasma membrane receptor
important for the import of iron into the cytosol. They are coordinately regulated, in opposite directions, by
control of protein synthesis)
55. What TCA cycle intermediate is the protein that binds the mRNA secondary structures to regulate ferritin
and transferrin translation? (aconitase)
56. What is the general effect of having a low concentration of amino acid in the serum? (down-regulates
translation)
57. ***How is the feast/famine phenomena exert its control over translation? ()
58. How does phosphorylation of eIF-2 stop translation? (keeps the eIF-2 complex inactive)
59. How is translation controlled by eIF4E? (it’s availability controls translation)
60. What two viruses modify the translational machinery as part of their life cycle? (Polio virus;
Encephalomyocarditis virus)
61. How does poliovirus interfere with cellular protein translation? (viral protease 2A cleaves the translation
initiation factor eIF4G so that it can no longer function as a bridge between the methyl cap binding subunit
and the 40S subunit.)
62. Why are the polio virus messages translated when cellular translation is inhibited? (due to the presence of
an internal ribosomal entry site (IRES). This acts like a bacterial initiation site to allow cap-independent
initiation from internal AUG codons)
63. What is an internal ribosome entry site? (a structure in the mRNA itself that can bind to the remaining
fragment of eIF4G.)
64. When does the cell tend to use IRES elements? (During G2/M phase of the cell cycle, translation is
generally down-regulated by activation of 4E-BPs. Many proteins expressed during this period bypass this
control by using IRES elements.)
65. What is ribosomal frameshifting? (Because translation uses a triplet code, there are three potential reading
frames in each mRNA)
66. What kind of virus will induce ribosomal frameshift as part of its life cycle? (retrovirus)
67. How do the following antibiotics inhibit translation:
a. Streptomycin (inhibits initiation and cause misreading of mRNA in prokaryotes)
b. Tetracycline (binds to the 30S subunit and inhibits binding of amino-acyl-tRNA in prokaryotes)
c. Chloramphenicol (inhibits the peptidyl transferase activity of the 50S ribosomal subunit in
prokaryotes)
d. Cycloheximide (inhibits the peptidyl transferase activity of the 60S ribosomal subunit in
eukaryotes)
e. Erythromycin (binds to the 50S subunit and inhibits translocation in prokaryotes)
f. Puromycin (causes premature chain termination by acting as an analog of aminoacyl-tRNA in
prokaryotes and eukaryotes)
DNA technology
1. What is a restriction enzyme? (cleaves the incoming phage DNA at recognition sites)
2. To what does the “restriction” part of the name refer? (specific recognition sites restrict it)
3. How does a bacterium protect itself from its own restriction enzymes? (methyl groups at the restriction
sequence block the restriction enzyme and protect the bacterial DNA from being cleaved)
4. ***What kind of sequence does a restriction enzyme recognize?
5. How do you identify the size of a restriction fragment? (gel electrophloresis)
6. In a electrophoretic gel, what electrical pole do DNA fragments migrate? (to the positive end)
7. Given a set of markers and a picture of a electrophoretic separation of DNA fragments, be able to determine
what size of DNA fragments are present on a gel.
8. How is a Southern blot performed? (gel is placed in a basic solution that denatures DNA, nylon filter picks up
the DNA from the gel to cleat a blot, the filter is placed in a solution and a radioactively labelled singlestranded DNA probe is added; the proble hybridiezes to its unique target sequence on the denatured DNA)
10. What is a “sticky end” when it comes to a restriction fragment digestion? (staggered cuts in the two strands
of DNA, creating "sticky ends" with unpaired bases. These sticky ends can be used to create recombinant
DNA if DNA molecules from different species are cut with the same restriction enzyme.)
11. What is a vector? (Newly introduced DNA must be part of a replication unit if it is to be propagated in host
cells. One way to make sure that the transfected DNA is part of such a unit is to insert it into a vector)
12. What are the feature that make a vector so useful for cloning? (The cutting of DNA by a restriction enzyme
produces many fragments that can be individually and randomly combined with a vector and inserted into a
host to create a gene library)
13.*** What kinds of vectors exist and how much DNA can each vector contain?
14. How does one clone a piece of DNA? (dna sample and plasmids are cleaved with the same restriction
endonucleases; fragments and plasmids are mixed and spliced with DNA ligase; a mixture of plasmids, all
with different fragments inserted, results. Bacterial take up the plasmids and are grown in a nutrient medium
that selects for recombinant clones. Colonies containing clones of each fragment of the original DNA are
seperated and maintained as a pure culture. Each such culture is a volume in the gene library.)
17. How do you make a cDNA library? What does a cDNA library really represent? (take mRNA and make
DNA backwards. Represents a gene?)
18. What is a knockout mouse? (gene is inactivated and its effect is examined)
19. How is a knockout mouse created? (the targeted gene is inactivated by insertion of the marker gene, vector
is inserted into a mouse stem cell where the targetted genes on the vector and mourse genome line up.
Recombnation occurs. The inactivated gene is now in the mouse genome and vector is lost during cell
division. Stem cell is transplanted into an early mouse embryo and resulting mouse is examined)
20. For what are microarrays and DNA chips used? (screening of thousands of sequences of DNA at the same
time)
21. How does antisense interfere with gene expression? (interfering RNA complementary to a specific mRNA
can prevent translation of the mRNA by hybridizing with it)
22. How does siRNA interfere with gene expression? (breaks down target mRNA)
23. How does the two hybrid system work? (allow scientists to determine which proteins interact in cells)
24. What are the advantages of DNA biotechnology when it comes to making new products that are useful to
mankind. (large scale production of gene products, useful in agriculture)
25. What are 5 new “drugs” that have been created by DNA biotechnology methods? (growth hormone, insulin,
vaccines, platelet derived growth factor etc)
26. How can DNA techniques be used in forensic science? (DNA fingerprint)
28. What components must be in a reaction to do “Sanger” sequencing or “dideoxy” sequencing? (pieces of
DNA and primer)
29. How do dideoxynucleotides stop DNA synthesis? (lack the 3'-hydroxyl group necessary for chain extension)
30. What are the steps to dideoxy sequencing? (DNA is purified from the cells of the organism of interest, and
placed into cloning vectors, which allow the DNA to be multiplied by bacterial hosts. Each clone is then
individually sequenced.)
31. What is the principle that makes capillary electrophoresis a valuable tool for DNA sequencing? (you can
sequence very long strands of DNA)
32. What is the difference between hierarchical sequencing and shot-gun sequencing? (H - specifically track the
DNA from just one of the 23 pairs; Shotgun - DNA is broken up randomly into numerous small segments,
which are sequenced using the chain termination method to obtain reads. Multiple overlapping reads for the
target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer
programs then use the overlapping ends of different reads to assemble them into a contiguous sequence.)
33. What is a STS? (serve as chromosomal landmarks)
35. What are the steps in PCR? (yeah not writing all that down)
36. What is Taq polymerase? From what organism was it derived? (Taq polymerase is derived from hot springs
bacteria and can tolerate the intense heat of a PCR reaction)
37. How many DNA molecules exist after 1, 2, 3, 4, 5, 6, and 25 cycles of a PCR reaction? (2n , n = number of
cycles)
38. What is a restriction fragment length polymorphism? (a variation in the DNA sequence of a genome which
can be detected by gel electrophoresis.)
39. ***How frequently would one expect to find a 4 bp, 6 bp and a 8 bp restriction enzyme site in DNA? ()
40. Be able to determine if a person has a disease by looking at a RFLP gel result.
DPS
Culture
1. Define the following: Cultural group, ethnic group and race. (Cultural Group: The integrated pattern of
human behavior that includes communication, actions, customs, beliefs, values and institutions of a
group. Ethnic Group: Belonging to a common group, often linked by race or nationality with a common
cultural heritage. Race: A socially defined population that is derived from distinguishable physical
characteristics that are genetically transmitted)
2. Culture is ____ not inherited. It derives from ______. It represents a _____ . It is shared by _______. It
has no absolute criteria for _____. (learned, one’s social environment; collective phenom; shared by the
people that live in the same social environment; judging)
3. What is cultural competence? (A set of congruent behavior, attitudes and policies that come together and
enable to work effectively in “cross-cultural” situations.)
4. What is accultaration? (THE PROCESS OF CULTURAL AND BEHAVIORAL ASSIMILATION
INTO THE CULTURAL CHARACTERISTICS OF THE HOST COUNTRY)
5. What are the four degrees of accultaration? (BICULTURAL: Maximum degree of adaptation while
maintaining similar degrees of acculturation to ones culture. ASSIMILATED: Maximum degree of
acculturation to the host country while resisting social, cultural or familial ties to with home culture.
TRADITIONAL: A person with low level of acculturation to the host country, maintaining traditions of
the original country and restricting participating in most aspects of host country. MARGINAL: Losing
one’s contacts and practices with the country of origin while resisting the culture of the host country)
6. What are three levels of accultaration can happen at? (INDIVIDUAL: Acculturation of oneself in
relation to a society (Independent of family). FAMILY. Levels of acculturation may vary for different
individuals and different generations. SOCIETY: When cultural characteristics of one society diffuse
into another society in a massive scale. Whether acculturation takes place or not depends on the
relationships between the two cultures.)
7. What are the four steps in accultaration curve? (euphoria with positive indication, culture shock with
negative indication, accultaration with going toward neutral and steady state)
8. Define the following accultaration continums:
a. SEPARATION.(Holding to own culture, refusing to interact with other groups)
b. MARGINALIZATION (Low interest in maintaining culture but low interaction with other
cultures)
c. INTEGRATION. (Maintain cultural integrity while participating in larger social network)
d. ASSIMILATION. (Do not wish to maintain original culture active in dominant culture)
ANATOMY
ANS
1. What is a ganglion? (Ganglia are collections of cell bodies somewhere outsidee the CNS.)
2. What kind of cells do you find in ganglia? (contain either sensory or motor cells.)
3. Where do you find sensory ganglia? (Sensory ganglia are found on dorsal roots of spinal nerves, and
cranial nerves.)
4. What is another name for sensory ganglia? (Dorsal root ganglia)
5. Where do you find autonomic ganglia?
6. Are both sensory and autonomic ganglia the same?
7. Describe ANS in terms of control, origin, sensory or motor components. (ANS is part of the Visceral or
involuntary nervous system. It arises from Brain and Spinal Cord; It has 2 neurons from center to
Periphery; It must have a sensory component)
8. First order neurons are in _____ and second order neurons are in _____. (brain or spinal cord; peripheral
ganglia)
9. Name the location for the following receptors: *** do we need to memorize?
a. Nm (neuromusclular endplate, skeletal muscle)
b. Nn (ganglionic neurons, adrenal medulla)
c. M1 (gastric parietal cell, ganglionic neurons, CNS)
d. M2 (myocardium, presynaptic sites)
e. M3 (smooth muscle, exocrine glands, vascular endothelium)
f. Α-1 (vascular and visceral smooth muscle, radial muscle of the iris)
g. Α-2 (some pre-synaptic terminals, platelets, pancreatic β cells)
h. Β-1 (myocardium, juxtaglomerular cells)
i.
j.
k.
l.
Β-2 (visceral smooth muscle, vascular smooth muscle and liver)
Β-3 (adipocytes)
D1 (renal and mesenteric vasculature)
D2 (brain)
Vertebral column and Spinal cord
1. Describe the four curvatures. (Thorasic and sacral are concave anteriorly and are the primary curvatures.
Cervical and lumbar: concave posteriorly and are the secondary curvatures)
2. Differentiate kyphosis, lordosis, and scoliosis. (Kyphosis – increase in thorasic, lordosis –increased
lumbar and scholiosis is curved back)
3. What are the distinctive features of the cervical vertebrae? (transverse foramen for the vertebral arteries
and veins. Spinous processes are bifid for ligamentum nuchae; transverse processes have an anterior and
posterior tubercle)
4. Describe C1. (Atlas: no body, no spinous processes, carries the skull, rotates on C2)
5. Describe C2. (Axis: strongest cervical vertebrae, dens for rotation)
6. C6 have the ______ and C7 is the _______. (carotid tubercle; vertebral prominens)
7. What is the jefferson burst fracture? (fracture and dislocation of the atlas; vertical compression of the
vertex of skull, no spinal injury)
8. What is hangman’s fracture? (fracture and dislocation of the axis; quadriplegia)
9. What is the distinctive feature of the thorasic vertebrae? (costal facets for articulation of ribs)
10. ______ have cervical features, _____ have lumbar features. (T1-T4; T9-T12)
11. Where does the anterior longitudinal ligament travel to and from? (from the Sacrum to C1 and the
occipital bone anterior to foramen magnum)
12. What is it’s job? (prevents hyperextension)
13. Where does the posterior longittudinal ligament travel to and from? And what is its job? (from C2 to
Sacrum. Prevents hyperextension and disc prostrusion)
14. What are the joints of the vertebral arches? (zygapophyseal)
a. What do they let you do? (allow gliding movements between vertebrae, limit range of
movement)
b. What are they innervated by? (articular branches of the dorsal primary ramii)
15. Describe the ligament:
a. Nucal ligament (occiput to C7 and joins spinous processes)
b. Ligamenta flava (C1/C2 to L4/L5 and joins laminae)
c. Intratransverseal ligaments (joins transverse processes)
d. Interspinous ligaments (joins spinous processes)
e. Supraspinous ligament (C7 to S1 and joins spinous processes)
16. Where are the atlanto-occipital joints? (between the C1 lateral masses and occipital condyles)
a. What do the joints help you do? (neck flexion and extension; sideways tilting)
b. Which parts of the this joint help prevent excessive movements? (anterior and posterior)
c. What type of joint is the atlanto-occipital joint? (synovial of the condyloid type)
17. What are the two categories of atlanto-axial joints you have? (lateral and medial)
a. Where are each of them? (the 2 lateral are between the C1 lateral masses and C2 superior facets.
The medial is between the C2 dens and the C1 anterior arch)
b. What does the joint help you do? (moving the head from side to side)
c. Which ligament prevents excessive rotation? (alar ligament)
d. Describe the three parts of the cruciate ligament. (superior longitudinal band, transverse band,
inferior longitudinal band)
e. What covers over the cruciate ligament? (membrana tectoria)
18. Describe the movements allowed by each region of the vertebra. (cervical region allows
flexion/extension, lateral bending, rotation, movement of the head. Thorasic region allows rotation, little
flexion, Lumbar region allows flexion/extension, no rotation, help increase abdominal pressure)
19. Name the vessels in the four parts of the vertebra. (Cervical part contains the ascending cervical artery
and vertebral artery. The thorasic part contains the intercostal arteries. The lumbar part contains the
subcostal artery and the lumbar artery. The sacral part contains the iliolumbar artery and the medial and
sacral artery)
20. List the number of spinal nerves each section of the vertebra has. (8 cervical, 12 thorasic, 5 lumbar, 5
sacral, 1 cocygeal)
21. How many denticulate ligaments do we have and what do they do? (21 from T12-L1 and they anchor the
lateral surfaces of pia mater to the dural sac)
22. Name the arteries in the following parts of the vertebral column.
a. Superior spinal cord (1 anterior spinal artery and 2 posterior spinal arteries)
b. Enlargements (Anterior and posterior segmental medullary arteries)
c. Inferior thorasic and superior lumbar (great anterior radicular artery of Adamikiewicz)
d. Roots of spinal nerves and coverings (anterior and posterior radicular arteries)
Moore’s Blue Box Questions:
Back
1. Describe the prominence of back pain and how it can be made wose. (10% of population comes in with
back pain problems and typically occurs between 30-70 years of age. If you make a person with a spinal
injury flex their neck or sit up, you can make it worse)
2. What is a laminectomy? (surgical excision of one or more spinous processes at the pedicle or the
lamina)
3. What are three reasons to do a laminectomy? (tumors, herinated intervertebral discs and bone
hypertrophy)
4. How likely and dangerous is it for dislocation of a cervical vertebrae? (because they are more horizontal
and they have the large vertebral canal, slight dislocations aren’t a problem. Dislocation-fractures can
injure the spinal column but things tend to slip back in place is there is no “facet jumping”)
5. How could you cause a fracture of an atlas? (blow to the top of head by something)
6. What happens in this instance? (compression of the lateral masses between the occipital condyles,
fracturing one or two of the arches)
7. What is a jefferson or busrt fracture? (the atlas ruptures)
8. What makes a jefferson fracture worse? (when the transverse ligament ruptures)
9. What is the most common cervical vertebra injury? (fractures of the vertebral arch)
10. What is the bony column formed by the sup. and inf. Articular processes? (the pars interarticularis)
11. What happens when you hyperextend your neck? (traumatic spondylolysis of C2/hangman’s fracture)
12. What is subluxation? (incomplete dislocation)
13. How can you rupture the dens? (horizontal hit to the head)
14. What is surgical treatment of lumbar spinal stenosis? (laminectomy)
15. What is the sacral hiatus closed by ? (sacrococcygeal ligament)
16. Where is the sacral hiatus located? (between the sacral cornua and inferior to the S4 spinous process or
medial sacral crest)
17. Which nerves does the caudal epidural work on? (S2 – Co spinal nerves)
18. What is coccygodynia? (syndrome that follows coccygeal trauma)
19. What problems can a cervical rib cause? (thorasic outlet syndrom when the protuberance from C7 is a
complete rib)
20. Differentiate spondylosis and osteoarthrosis (development of osteophytes in the vetebral column versus
in the zygapophisial joints)
21. What is spina bifida occulta? (lamania of L5 and/or S1 fail to develop normally and fuse posterior to the
vertebral canal)
22. What are the two types of spina bifida cystica? (meningoceole to do with a meningeal cyst and a
meningomyoceole to do with the spinal cord)
23. How can you rupture an intervertebral disc? (hyperflexion of the vertebral column)
24. If the L4-L5 IV disc is protrudes, which nerve does it compress? (L5)
25. What is atlantoaxial subluxation? (dens is set free because transverse ligament of atlas ruptures)
26. What is the Steele Rule of thirds? (One third of atlas ring is occupied by the dens, one third by the
sspinal cord and one third by the fluid-filled space and tissues surrounding the cord. Explains why some
patients with anterior displacement of the atlas may be relatively asymptomatic until a large degree of
mocement occurs)
27. Why is a tear in alar ligament significant? (increase 30% in the range of movement to the controlateral
side)
28. What are the five sources back pain? (fibroskeletal structures, meninges, synovial joints, muscles,
nervous tissue)
29. How can you tell a pain of a fracture versus dislocation ? (sharp pain following a fracture is mostly
periosteal in origin, wheras pain from dislocations is ligamentous.)
30. What is the difference between back sprains and back strains? (back sprain is an injury in which only
ligamentous tissue or the attatchment of ligament to bone is involed without dislocation or fracture.
Back strain is a common problem from overly strong contraction. It involed some degree or microscopic
tearing of muscle fibers. The muscles usually involed are those producing movements of the lumbar
intervertical joints, especially eherector spinae columsns)
31. What is a spasm? (sudden involuntary contraction of or more muscle groups)
Scapular region
1.
2.
3.
4.
5.
6.
What does the pectoral girdle include? (scapula and clavicle)
Point out the acromial end and the sternal end of this bone: Sternal
Acromial
Which surface of the clavicle would you be able to see the conoid tubercle? (The inferior end)
What are the muscle attatchments on the clavicle? (Two insertions and three origins: the trapezius and
subclavius insert themselves, and sternocleidmastoid, pec major and deltoid originate at the clavicle)
7. What happens to your arm when you have a mid-clavicular break? (arm pulls in and drops down)
8. What happesn due to cleido-cranial dystosis? (you’re missing your clavicle so your shoulders touch each
other)
9. Point out the spinoglenoid notch, the two processes, and the three fossas on this bone:
a. Coracoid process
b. Spinoglenoid notch
c. Acromion process
d. Subscapular fossa
e. Supra and infrascapular fossa
10. What is Klippel Fiel syndrome? (congenital fusion of any 2 of the 7 cervical vertebrae.)
11. What are the three main divisions of muscles for the scapular region? (superficial extrinsic, deep
extrinsic and instrinsic)
12. What happens when you injure your serratus anterior muscle? (winged scapula)
13. Be able to draw out the anastomosis of the scapular region.
14. Table things to memorize: scapular region muscles, rotator cuff muscles, deltopectoral triangle, spaces
and intervals.
Breast and scapular region
1. What are the borders to the breast region? (Midaxxilary line to parasternal line; 2nd to 6th rib)
2. Where does the greater and smaller part of the mammary gland lie? (greater part lies in the superficial
fascia and smaller part pierces the deep fascia and extends to the axilla [axillary tail of spence])
3. What is the retromammary gland? (loose CT seperating mammary gland from deep fascia of underlying
muscles)
4. What is the blood supply to the mammay gland? (Internal thorasic artery coming from the Subclavian
artery, the lateral thorasic artery coming from the axillary artery and the thorasic aorta gives rise to the
posterior intercostal arteries)
5. Name the important nodes of the mammary gland? (the brachial or lateral axillay nodes; the central
axillary nodes, the parasternal nodes, pectoral nodes or anterior axillary nodes; apical or subclavian
nodes)
6. What is Poland’s syndrome? (missing one or both pectoral muscles)
7. Table things to memorize: Breast muscles
Axilla and brachial plexus
1. What are the contents of the axilla? (axillary vein, axillary artery, brachial plexus and lymph nodes.
Muscles that pass through it: shord head of biceps, corachobrachialis, pec minor)
2. The bones that border the axilla? (clavicle, upper border of scapula and 1st rib)
3. State which nerve is damaged and thus causes this:
a. Winged scapula (long thorasic)
b. Claw hand (ulna)
c. Weakened opposition of thumb (median at wrist)
d. Ape hand (median)
e. Papal hand (median)
f. Drop wrist (radial nerve)
g. Weak supination of radioulnar joint (musculocutaneous)
h. Hard to start shoulder abduction (supraspinatous)
i. Difficult abducting arm to horiozontal (deltoid)
j. Loss of shoulder roundness (deltoid)
4. Give the symptoms of:
a. Erbs palsy (loss of abduction, flexion and rotation at shoulder; weak shoulder extension;
“waiter’s tip” position)
b. Klumpke’s palsy (ulnar and median nerve muscles damaged)
Moore’s blue boxes
Pecs, breast, scapular regions
1. What is the triangle of auscaultation? (good place to examine posterior segments of the lungs with a
steth. Superior horizontal border of the Lats, the medial border of the scapula and the Traps make the
borders)
2. What happens as a result of the injury to the accessory nerve? (ipsilateral weakness when the shoulders
are elevated against resistance. So you can’t shrug if someone puts their arms on your shoulder)
3. What happens as a result of the thoracodorsal nerve? (causes paralysis to the lats. Person is unable to
raise the trunk with the upper limbs. So you can’t climb or swim. Person can’t use axillary crutch
because the shoulder is pushed superiorly by it. Active depression of scapula is lost. )
4. What happens as a result of injury to the dorsal scapular nerve? (scapula is located farther from the
midline than that on the normal side)
5. What happens as a result of the injury to the axillary nerve? (deltoid atrophies.gives shoulder a flattened
appearnence and produces a slight hollow inferior to the acromion. Loss of sensation over the lateral
side of the proximal part of the arm.)
6. What are three ways you can injure the axillary nerve? (using crutches wrong, injury to the surgical neck
of the humerus, dislocation of the glenohumeral joint)
7. What tends to break on a humerus when there is a shot to the shoulder? (surgical head, not the epiphysis)
8. Where can you palpate the axillary artery? (inferior part of the lateral wall of the axilla)
9. Why are arterial anatomoses important around the scapula? (they make collateral circulation possible so
if and when the axillary artery is ligated or occluded [slowly] there is no ischemia and blood can still get
around)
10. What happens to the axillary vein when the arm is fully abduted? (overlaps the axillary artery anteriorly)
11. What’s the danger of axillary vein puncture? (air embolism)
12. When does the axillary vein become the subclavian vein? (when the first ribs is crossed)
13. Which nerves are at risk during axillary node dissection? (long thorasic nerve, thoracodorsal)
14. What happens as a result when you injure the
a. Superior part of the brachial plexus? (waiter’s tip hand, Erbs-duchenne palsy, paralysis of the
shoulders and arm muscles supplied by C5 and C6 – deltoid, biceps, brachialis, brachioradialis.
Adducted shoulder, medially rotated arms and extended elbow. Loss of sensation in the lateral
aspect of the upper limb)
b. Compression of the cords of the brachial plexus (pain radiating down the arm, numbness,
parasthesia, erythma, weakness of hands)
c. Inferior parts of brachial plexus (claw hand)
15. What are the symptoms of lymphedema of the breast? (deviation of the nipple, thickened leather like
appearance of the skin, puffy skin between dimpled pores giving an orange appearance)
16. What can cause inversion of the nipple? (subareolar breast cancer)
17. What is the most common site of metastasis from a breast cancer ? (axillary lymph nodes)
18. What might it mean when your breast elevates when the muscle contracts? (cancer might have spread to
the retromammary space, attach to or invade the deep pectoral fascia overlying the pec major, or
metastasize to the interpectoral nodes. Advanced breast cancer)
HISTOLOGY
Cytoplasm
1. How are antibiotics useful? (kill bacterial things that have no eukaryotic component or things that are
different enough from the eukaryotic counter parts)
2. Mitchondria have their own ___ and ___ . (DNA and ribosomes)
3. What is phospholipid composition? (glycerol backbone, two long non-polar fatty acid chains and
variable phosphate containing polar group)
4. Name the choline containing phospholipids. (sphingomyelin, phosphatidycholine)
5. Name the non-choline containing phospholipids. (phosphatidylserine, - ethanolamine and - inositol)
6. What is the E face and P face? (P face is closer to the protoplasm and the E face is closer to the
extracellular space)
7. Define integral proteins and the three types of integral proteins. (integral span the whole membrane and
can only be removed with detergent; transmembrane, partially spans the bilayer and covalently bonded)
8. Define peripheral proteins. (do no penetrate the bilayer, are no covaltently linked and form ionic links to
membrane structures)
9. How do you produce glycolipids or glycoproteins? (add a carbohydrate group to a lipid or protein)
10. Where do you find carbohydrates? (outerleaflet of the plasma membrane)
11. What are lipid rafts? (small, specialized areas in membranes where sphingolipids and cholesterol and
proteins are concentrated)
12. What are four ways to restrict lateral mobility of membrane proteins? (proteins can self-assemble into
large aggregates, they can be tethered either on the inside or outside of the cell, interact with proteins on
the surface of another cell)
13. Describe the three types of filaments. (intermediate filaments (composed of a variety of IF proteins)provide mechanical strength (10 nm) *intermediate in size; microtubules (tubulin)(25 nm)-determine the
position of intracellular organelles and direct intracellular transport. Form cilia and flagella. *biggest
filament; microfilaments (actin)(5-9 nm)-determine the shape of the cell’s surface and are necessary for
whole cell locomotion *smallest filament)
a. Where are they in the cell? (intermediate are everywhere; microtubules are around the nucleus
and microfilaments are in the periphery)
14. Describe each:
a. Keratins (cell type – epithelium; both keratinizing and non-ker)
b. Vimentin (cell type – mesenchymal; fibroblasts, chondroblasts, macrophages, endothelial,
vascular smooth muscle)
c. Demin (muscle; smooth and straited)
d. Glial fibrillary acidic proteins (glial cells; astrocytes)
e. Neurofilaments (neurons; nerve cell body and processes)
f. Nuclear lamins (found everywhere)
15. How do MT’s grow and shrink? (by the addition or loss of tubulin heterodimers at + end)
16. Describe basal bodies. (anchor cilia and flagella in the cell membrane; have the same structure (nine sets
of triplets MT’s) as the centrioles found in centrosomes)
17. Structure of cilia and flagella bodies. (nine doublets of MT’s plus two central MT’s)
18. Cilia and flagella use _____ to bend (dyenin and ATP)
19. What is a lamellipodia? (sheet like extension of a cell which helps it crawl)
20. What are the two types of actin? (G actin and F actin: G is unassembled Globular actin dimers and the F
is the assembled actin filaments)
Nucleus
1. What is chromatin? (a complex of DNA, histones, proteins, and non-histone proteins found in the
nucleus of a eukaryotype. It is the material that chromosomes are made up of)
2. The nulclear lamina is composed of ______ filaments. (intermediate)
3. In the nucleus, the three types of RNA that are produced are ____. (tRNA, mRNA, rRNA)
4. Differentiate euchromatin and heterochromatin. (heterochromatin is the highly condensed,
transcriptionally inactive part and euchromatin is the active part of a nuclues)
5. What is a nucleosome? (basic unit of DNA packing. Consists of the core histones and DNA)
6. What are the core histones? (H2A, H2B, H3 and H4)
7. What three DNA sequences are required for a chromosome to be replicated and then segregated?
(telomere, replication origin and a centromere)
8. What is the nuclear matrix? (a nucleoskeleton that functions in the nucleus much like the cytoskeleton in
the cytoplasm)
9. What are the two ways a sorting signal can be built into a protein? (the signal is in a single stretch of
amino acid sequence that can be either at the ends or inside the protein. A signal patch can be done
putting a bunch of sequences together)
10. Describe a NLS. (signal for nuclear import. Usually contains basic amino acids)
11. Describe a NES. (signal for nuclear export. Usually contains hydrophobic amino acids)
12. What regulates cargo importins and exportins? (Ran – a small GTPase)
13. What’s so special about HIV and influenza viruses? (viruses whose proteins contain NLSs that are used
to import the viral genome into the nucleus and then viral mRNAs made in the nucleus are exported
from the nucleus by the host cell export machinery for translation on cytoplasmic ribosomes)
Mitochondria, peroxisomes, and lysosomes
1. What is the main function of the mitochondria? (converts glucose in a cell via pyruvate to ATP and
breakdown of fatty acids)
2. Why do the contents of the intermembrane space resemble the cytosol? (porins are always open)
3. Describe cristae. (covered with granular units of ATP synthase. Contains ATP transporters that pump
the new ATP molecules into the matrix to the intermembrane space where they then move through
porins into the cytosol)
4. What is cardiolipin? (the main reaction of lipid biosynthesis catalyzed by the mitochondria themselves is
the conversion of imported lipids to cardiolipin)
5. What is the difference between peroxisomes and lysosomes? (peroxisomes oxidize organic molecules
and hydrogen peroxide)
6. Describe peroxisomes. (single membrane bound; do no contain DNA, must import all their proteins, use
a lot of oxygen, rids body of toxic substances, numerous in the liver. Break down fatty acids through β
oxidation)
7. Which signal tells the cell to take something to the peroxisome? (PTS signal)
8. Describe Zellweger’s syndrome. (have a defect importing proteins into peroxisomes, have “empty”
peroxisomes and die soon after birth. defect is two mutant (non-functional) copies of the PTS receptor
on the peroxisomal membrane)
9. Describe three properties of lysosome membranes. (a ATP proton pump, a glycoprotein coat and a
transporter channels)
10. What’s wrong in Tay Sachs’ disease? (results from an absense of hexosminidase A, swollen lysosomes)
ER, Golgi and Membrane trafficking
1.
2.
3.
4.
5.
6.
What are chaperones? (prevent aggregation of unfolded proteins and aid in folding)
What are two types of chaperones? (hsp70 and GroEL)
What are the two ways types of protein targetting signals? (post-translational and co-translational)
What is the major function of the smooth ER? (lipid biosynthesis, sequestering Ca)
Where do the initial steps in cholesterol biosynthesis occur? (peroxisome)
Where does phospholipid synthesis occur? (exclusively on the cytosolic leaflet of the smooth ER
membrane by enzymes in the ER membrane that have their active sites facing the cytosol and then it
gets flipped by flippase)
7. How do the lipids produced by the smooth ER get to the other membranes in the cell? (by vescicles that
bud off and are moved to other membranes with which they fuse; Diffuse to the rough ER which is
continous to the smooth ER, take lipid to organelles like mitochondria that don’t receive vescicle traffic
from the ER by transfer proteins)
8. Where do you see cells with a lot of smooth ER? (in cells engaged in steroid synthesis and lipid
metabolism and in the liver)
9. What function does smooth ER have in the liver? (detox)
10. What are ER signal sequences? (stretches of 20 hydrophobic amino acids)
11. What is the function of SRP? (pauses translation by the ribosome and allows time for the complex to
find the SRP receptor on the rough ER membrane)
12. **Ways protein is threaded through plasma membrane
13. What are five possible ways a protein can be modified as it enters the lumen of ER? (N-terminal signal
peptides are usually cleaved by signal peptidase, most proteins in ER lumen receive N-linked
glycosylation, formation of disulfide bonds, some membrane proteins lose their transmembrane domain
and gain a GPI anchor, protein folds)
14. What is cystic fibrosis? (due to protein misfolding: caused by a mutation in the CFTR gene which codes
for a protein that transports chloride ions out of epithelial cells into the lumen. Chloride imbalance
causes cell to secrete less water and the cells swell)
15. What is the most common mutation in cystic fibrosis? (Phe508 deletion from CFTR which slightly
misfolds the protein, trapping it. It would work fine if it escaped but it can’t)
16. Describe the three types of coat proteins. (COP II – mediates anterograde transfer of vescicles from RER
to the cis-golgi, COP I – mediates retrograde transport from the trans to medial, Clathrin – mediates
transfer of vescicles)
17. What are SNARES? (target vescicles to correct membrane and dock them, also aid in fusion.)
18. What are RABS? (contribute to specifity of docking)
19. Where are glycolipids formed? (in the golgi)
20. What happens to proteins as they go through the golgi? (their n-terminal carbohydrate is trimmed and
they receive additional O-linked sugars, sialic acid is added)
21. What tells a protein to go to a lysosome? (M6P)
22. What is adaptin? (bind both clathrin and cytoplasmic tails of certain receptors)
23. What are primary and secondary lysosomes? (primary lysosome – a cytoplasmic cell organelle that buds
off from the golgi complex. A primary lysosome becomes a secondary lysosome when it fuses with
vesicles that contain matter to be ingested.)
24. What are residual bodies and lipofuscin granules? (debris filled vacoule, lipofuscin granules are what
residual bodies are called in neurons)
25. What are caveolae? (specialized lipid rafts. They are thought to be where signal transduction events can
take place very efficiently)
Mitosis
1. What is the G0 phase? (an inactive phase after G1 that all cells enter but only few stay for long periods of
time)
2. Which phases are considered to be interphase? (G1, S, G2)
3. DNA replication is confined to the __ phase. (S)
4. What are the two major cell cycle checkpoints? (before the cell replicates DNA and before the cell
divides at mitosis)
5. Describe what happens at each phase of mitosis.
a. Preprophase (intra-nuclear condensation of chromosomes)
b. Prophase (individualization of chromosomes, initiation of mitotic spindle and rupture of nuclear
envelope)
c. Metaphase (chromosomes arranged in equatorial plane, spindle completed, disappearance of
nuclear envelope and nucleolus)
d. Anaphase
i. Early (longitudinal splitting of chromosomes and migration to poles)
ii. Late (Aggregation of chromosomes at the poles, beginning of cell division, initiation of
cleavage furrow)
e. Telophase (nuclear restitution, nuclear envelope and nucleolar formation, end of cell division)
6. Describe the structure of cohesins and condensins. (have two identical DNA- and ATP-binding domains
at one end and a hinge region at the other, joined by two, long, coiled-coil regions)
7. Differentiate the functions of cohesins and condensins. (cohesins cross link two adjacent sister
chromatids, gluing them together. Condensins mediate intra-molecular cross-linking to coil DNA in the
process of chromosome condensation)
8. What happens to cohesins during mitosis and which phase does it happen in? (degraded in anaphase)
9. Microtubules form the _______ (mitotic spindle)
10. What is anaphase A and anaphase B? (A: chromosomes move to the poles. B: seperation of poles
themselves)
11. Anaphase A depends on _________________, which anaphase B depends on ____________. (A
depends on motor proteins at kinetochore ; b depends on motor proteins at the poles that pull the poles
apart and motor proteins at the central spindle that push the poles apart)
12. What are the plus and minus ends thought to do? (plus ends help in pushing the poles apart and minus
end helps in pulling the poles apart)
13. What does Taxol do? (binds tightly to MT’s and stabilizes them and the cell arrests at mitosis. Widely
used as a anti-cancer drug)
14. What is the danger in Taxol? (taxol kills ALL diving cells, not just cancer cells)
15. What do actin filaments do during mitosis? (form contractile ring during cytokinesis)
16. What do intermediate filaments do during mitosis? (control the breakdown and reassembly of the
nuclear envelope)
17. What triggers disassembly of of nuclear lamina? (phosphorylation of lamins)
18. What happens to each of the following organelles during mitosis?
a. ER and Golgi (vesiculate and reform at telophase)
b. Mitochondria, lysosomes, peroxisomes (nothing, just not part of the spindle process)
19. What processes halt during mitosis? (translation, transcription, endocytosis, exocytosis, all vesicular
transport)
Apoptosis
1. What’s the difference between apoptosis and necrosis? (apoptosis is planned cell death, all the
organelles vesiculate and are then eaten, no danger to surrounding cells, is sometimes needed for
development. Necrosis is cell death due to damage, can be dangerous to surrounding cells, everything
just spills out of the cell)
2. What is BCL2? (is a family of pro or anti effectors that can signal a cell to either die or stay alive)
3. What is caspases? (the executionary effector of the apoptotic machinery)
4. How can cells be activated to die from:
a. Inside the cell: (The relative ratios of the various bcl-2 proteins can often determine how much
cellular stress is necessary to induce apoptosis. Cellular stress may occur from exposure to
radiation or chemicals or to viral infection. It might also be a consequence of growth factor
deprivation or oxidative stress caused by free radicals. Most importantly, in general, intrinsic
signals initiate apoptosis via the involvement of the mitochondria and release of cyt C)
b. Outside the cell: (binding of death inducing ligands to cell surface receptors called death
receptors)
c. What kind of signals trigger cytochrome C release from mitochondria? (withdrawal of survival
factors ; receptor ligand interactions (example tumor necrosis factor TNF); cellular damage;
aging and mitochondrial DNA damage)
5. What is the “eat me” signal on apoptotic cells that attracts phagocytic cells? (phosphatidylserine or PS is
exposed by scramblase to the outside of the cell)
Epithelium
1. Draw out concept Map. (Powerpoint presentation)
2. What are the five principle functions of epithelia? (barrier, secretion, absorption, transport and detection
of sensations)
3. Where is basal lamina present? (epithelia, muscle, adipose cells and schwann cells)
4. What are the functions of basal lamina? (physical support, limits contact, selective barrier, cell to cell
interaction, location and movement during embryogenesis and polarity)
5. What is the function of Collagen IV in the basal lamina? (acts as a filter and the negative charges of
heparan sulfate restricts negatively charged molecules)
6. What does a mutation in collagen VII result in? (dystrophic epidermolysis bullosa)
7. Match:
Characteristic
Stomach, small intestines, gall bladder
Parietal layer of Bowman’s capsule
Epithelium
Simple Columnar
Skin
Bladder
Lining of blood vessels
Ducts of large glands
Kidney tubules
Esophagus
Trachea
Ducts of sweat glands
Sites for fluid, gas and metabolite exchange
Epididymis
Nucleus is spherical and centrally located
Ureter
Nucleus is ovoid and basally located
Urethra
Lining of alveoli
Covering of ovary
Simple Cuboidal
Simple Squamous
Pseudostratified Columnar
Stratified Squamous Keratinized
Stratified Columnar
Transitional
Stratified Sqamous non-keratinized
Stratified Cuboidal
8. Microvilli have a ________ core which are attatched to the plasma membrane by ______. (actin, myosin
I)
9. The terminal web contains ____________. (actin, intermediate filaments and spectrin)
10. An axoneme has a ____ pattern (9+2)
11. What is the function of nexin? (connects adjacent doublets)
12. What is the role of dyenin in cilia? (dyenin contains ATPase, hydrolyses ATP thus releasing energy for
Ciliary movement(bending))
13. What is the function of Occludin and claudins? (interact with actin filaments via ZO-1 to form a seal in
the intercellular space)
14. What do CMV and cholera toxins target? (ZO-1 and ZO-2 and result in permeable junction)
15. Where is the zonula adherens located? (zonula occludens)
16. What is the function of zonula adherens? (forms a continuous lateral adhesive band that encircle &
hold cells together)
17. Describe the structure of zonula adherens? (E-cadherins are Ca2+ dependent transmembrane extension
proteins that bind to catenin, vinculin and α-actinin and also to actin microfilaments of the terminal web.
The actin filaments are also bound by α-actinin)
18. What is the difference between macula adherens and zonula adherens? (macula means spot and zonula
means band)
19. What’s another name for macula adherens? (desmosomes)
20. Describe the structure of desmosomes. (The attatchment plaque has tonofilaments coming out of it
which go through the plasma membrane and anchor the desmocoilin and desmoglein)
21. What does the attatchment plaque consist of ? (desmoplankins and pakoglobins)
22. Auto-antibodies produced against desmosomal proteins cause _____________ resulting in
____________. (skin disease called pemphigus vulgaris resulting in blistering of skin)
23. Where do you find desmosomes? (simple and stratified squamous epithelium)
24. What are gap junctions made up of ? (conexons which consist of conexins)
25. Focal adhesions anchor _______ filaments while hemidesmosomes anchor ________ filaments of the
cytoskeleton to the basement membrane (actin, intermediate)
Connective Tissue
1. What are the functions of Connective tissue? (structural support, medium for exhange, defense and
protection by phagocytic, immune and mast cells)
2. What are tendons? (cord like structure that joins muscle to bone, composed of parallel bundles of type I
collagen fibers and rows of tendinocytes)
3. Where is the vasculature of tendons? (tendon is surrounded by a C.T. capsule,the epitendineum and is
subdivided into fascicles by endotendineum – an extension of the capsule. This endotendineum contains
small blood vessels and nerves.)
4. What are ligaments? (join bone to bone)
5. What are aponeuroses? (broad flat tendons)
6. What are collagen fibers made up of? (fibrils which are made up of tropocollagen which is made up of
three α polypeptide chains wrapped around each other to form a triple helix)
7. What amino acids make up collagen? (glycine, proline and hydroxyproline, hydroxylysine)
8. Reticular fibers:
a. Function: (provide supporting framework for tissues and organs)
b. Found where? (around nerves, blood vessels, in hemopoetic organs)
c. Where is not found? (thymus)
d. What does a defeciency of collagen III result in? (EDS-IV)
9. What is fibrillin? (acts as the organizer center. It forms first and elastin materials are deposited on
surface of microfibrils to form elastic fibers)
10. What is the amino acid make up of elastic fibers? (rich in glycine and proline , poor in hydroxyproline
and lacks hydroxylysine)
11. What is Marfan’s syndrome? (disease due to lack of resistance in tissues rich in elastic fibers.)
12. What is the function of ground substance? (act as both lubricant and a barrier to microorganisms)
13. What are GAGs? (long chain polysaccharides made up of repeating disaccharide units, negatively
charged)
14. What do multi-adhesive glycoproteins do? (stabilize extracellular matrix by binding to cell surface,
collagen, proteoglycans, and GAGs)
15. What role does hyluronic acid play? (helps act as an anchor for many proteoglycans to sit on)
16. What is structure of a fibroblast cell? (spindle-shaped cell with tapering eosinophilic cytoplasmic
extensions)
17. Why are mast cell granules metachromatic? (high levels of heparin)
Meiosis
1. What are the two stages of meiosis? (reductive division – involves seperation of homologous
chromosomes and equitational division – involves seperation of chromatids in each chromosome)
2. What are stages of Prophase? Describe them. (leptotene – condensation of chromatin, sister chromatids
become connected by meiosis-specific cohesion complexes called Rec8p and pairing of homologous
chromosomes is initiated; zygotene – synapsis of homologous chromosomes and it continues in
pachytene, Synapsis involves formation of a synaptonemal complex and they forma tetrad; pachytene –
crossing over of different chromatids; diplotene – condensation still occurs and homologous
chromosomes starts to separate from each other and chiasmata appears; diakinesis – condensation of
chromosomes, nucleolus disappears and nuclear membrane disintegrates)
3. What is the most common form of polyploidy? (triploidy)
4. When does spermatogenesis begin? (puberty)
5. How long does spermatogenesis take? (64 days)
6. What are the three phases of spermatogenesis? (spermatogonial – spermatogonia differntiate into
primary spermatocytes, spermatocyte – to reduce chromosome # and amount of DNA, spermiogenesis –
spermatids differentiate into spermatozoa)
7. List the steps of spermatogenesis in detail. (Stem cells become progenitor cells which go through
mitosis. Primary spermatocytes are formed due to the first meiotic division of the mitotically divided
cells. Secondary spermatocytes are formed due to the second meiotic division. Residual bodies form
with the spermatids as spermiogenesis phase begins. The residual bodies separate out and you have
spermatozoa)
8. Describe the number changes in as primary spermatocytes become spermatids. (Chromosom # - 46
double  23 double  23 single; DNA – 4n  2n  1n)
9. What is the acrosome? (acrosome is what forms the head of the sperm. Starts off as a granule and
eventually becomes a cap/coat over the head of the sperm)
10. What steps of oogenesis take place before the girl is born? (primitive germ cells or oogonia undergo
mitosis and form primary oocytes with 7th month and arrest at the diplotene stage of meiosis I by OMI.
At 5th month, atresia begins for oogonia and primary oocytes)
11. What is OMI and where is it produced? (Oocyte maturation inhibitor and it is made by follicular cells of
primordial follicles)
12. How many eggs will a female ovulate over her time? (400-500)
13. How many eggs has the female lost before puberty? (goes from 600 thousand/2 million to about
400,000)
14. What are the layers of the uterus? (endometrium which has a basal and functional, myometrium,
perimetrium)
15. Describe the following (or draw it out)
a. Primordial follicle (oocyte surrounded by stromal cells)
b. Unilaminar primary follicle (oocyte with a zona pellucida forming surrounded by a follicular cell
surrounded by a basal cell surrounded by stroma cells)
c. Multilaminar primary follicle (oocyte with a zona pellucida surrounded by granulosa cells
surrounded by a theca folliculi)
d. Antral follicle (oocyte containing antrum surrounded by granulosa cells surrounded by a theca
interna and externa)
e. Mature graafian cell (Antrum with a in-protruding corona radiata and cumulus oophorus
connecting radiata to the granulosa cells surrounded by a theca interna and externa)
16. What is the order of release and effect of the hormones related to ovulation? (hypothalamus releases
gonadotropin-releasing hormone which influences the pituatary gland to secrete gonadtropin which
leads to the release of FSH and LH)
17. What does FSH do? (influences the development of follicular cells of growing and maturing follicles;
secrete estrogenl cause repair of endometrium of uterus)
18. What does LH do? (stimulates final formation and release of secondary oocyte at ovulation at 14 days
and causes formation of corpus luteum; secretes progesteronel influence endometrial glands for zygote;
stimulates theca interna cells which produce androstenedione; High estrogens during proliferative phase
cause an LH surge that results in ovulation and formation of corpus luteum.)
19. What are the three phases of menstruation? (menstrual, proliferative, secretory)
20. What does each phase correspond with as related to hormones? (menstrual – constant release of FSH
which keeps a constant amount of estrogen in the blood which helps the oocyte morph; proliferative – a
spike in LH causes a increase in estrogen and small spike in FSH and corpus luteum is starting to form;
secretory – slow spike in progesterone as LH levels decrease and FSH levels off)
21. Go through the steps of sperm piercing through the egg. (Sperm passes through corona radiata; Sperm
penetrates zona pellucida (Acrosomal reaction); Sperm head attaches to surface of secondary oocyte;
Sperm plasma membrane fuses with oocyte plasma membrane; Fast block (up to 1 min.) –
depolarization of plasma membrane; Slow block - Cortical reaction causes high Ca++ stores to trigger
cortical granules to migrate to plasma membrane; Zonal reaction –released enzymes from cortical
granules alter plasma membrane receptors and nature of zona pellucida; Polyspermy is prevented and
secondary oocyte completes meiosis II)
22. What is the zona pellucida composed of? (glycoproteins)
23. What is the female pronucleus? (nucleus of ovum)
24. What is the male pronuclues? (sperm nucleus)
EMBRYOLOGY
First three weeks, embryonic folding
1. Recall the process and stages of cleavage including compaction . (zygote goes through divisions till it
goes past the 8 cell stage which is then called a morula [3 days] and then a blastocyst which eventually
implants [6 days] )
2. Distinguish between a morula and a blastocyst. (morule is a 16 cell ball going through compaction and a
blastula is a hollow ball of cells and a blastocyst is a hollow ball of cells that have a growth of cells
invaginating the hollow)
3. Recall the formation of the blastocyst (cells start forming into the hollow to form the embryoblast which
is the inner cell mass and trophoblast which is the surrounding cell mass)
4. Identify the derivatives of the inner cell mass and the outer cell mass (inner cell mass is the emrbyoblast
and outer cell mass is the trophoblast)
5. Define the process of implantation including the decidual reaction (trophoblast inavginated the
endometrium)
6. Distinguish between the two layers of the trophoblast. (cytotrophoblast and syncytiotrophoblast –
cytotrophoblast is the fast dividing inner layer compared to the syncytiotrophoblast which is the
invaginating layer)
7. Identify the two layers of the bilaminar germ disc. (Hypoblast – an internal layer of small cuboidal cells
adjacent to the blastocyst cavity (primitive endoderm). Epiblast – an external layer of high columnar
cells adjacent to the amniotic cavity (primitive ectoderm))
8. Recall the formation of the amniotic cavity (a small cavity within the epiblast which is the primordium
of the amniotic cavity. This new cavity forms as fluid begins to collect between the cells of the epiblast.)
9. Recall the formation of the primitive yolk sac (a membrane that lines the inner surface of the
cytotrophoblast called the exocoelomic (Heuser) membrane . The exocoelomic membrane together with
the hypoblast forms the lining of the exocoelomic cavity, or primitive yolk sac)
10. Describe the formation of the uteroplacental circulation (trophoblast invaginate the maternal sinusoids
and form lacunae which interconnect to form a network – beginning of placental development)
11. Recall the formation of the definitive (secondary) yolk sac (By day 13, additional cells from the
hypoblast migrate out to line the exocoelomic cavity (primitive yolk sac) which still exists at this time
within the newly formed chorionic cavity. Proliferation of these cells gradually forms a new cavity
within the primitive yolk sac called the secondary or definitive yolk sac)
12. Recall the formation of the chorionic cavity (called the extraembryonic mesoderm forms between the
cytotrophoblast and the outer surface of the exocoelomic cavity (primitive yolk sac). Soon, coelomic
spaces (cavities) form within the extraembryonic mesoderm. These spaces rapidly join together to form
a new cavity called the extraembryonic coelom or chorionic cavity)
13. Distinguish between different abnormal sites of implantation. (Implantation in the inferior segment of
the uterus near the internal os (opening) of the cervix results in placenta previa; In the abdominal cavity,
the blastocyst most commonly attaches to the peritoneal lining of the rectouterine pouch (of Douglas)
but it can implant at any place covered by peritoneum; if implantation occurs in the ovary, a primary
ovarian pregnancy results.)
14. Describe the process of gastrulation to form the three germ layers (Gastrulation establishes axial
orientation and all three germ layers, ectoderm, mesoderm and endoderm. During this process, the
bilaminar germ disc formed during the second week is transformed into a trilaminar embryonic disc.)
15. Recall formation of the notochord (Some of the earliest cells to migrate through the primitive pit and
rest in the midline will give rise to a dense midline tube called the notochord. The notochord underlies
the neural tube and serves as the basis for the developing axial skeleton)
16. Recall the layers of the buccopharyngeal and cloacal membranes (The buccopharyngeal membrane
represents the future opening of the oral cavity and the cloacal membrane corresponds to the openings of
the anus and urogenital organs. These membranes are first evident in the third week as two small
depressions in the ectoderm at the cranial and caudal ends of the embryo, respectively. At these sites,
the ectoderm adheres tightly to the endoderm to form a bilaminar membrane without any intervening
mesoderm. The buccopharyngeal membrane breaks down in the fourth week and the cloacal membrane
in the seventh week.)
17. Identify the epiblast fate map and the respective mesodermal sub-populations derived from each region
of the primitive streak. (paraxial - dermatome – forms the dermis of the skin, myotome – forms muscle
cells, sclerotome – forms vertebrae and ribs, intermediate - kidneys and gonads and lateral plate
mesoderm - 2 pleural cavities, pericardial cavity, peritoneal cavity)
18. Recall the derivatives of the ectodermal germ layer (Neural crest cells; Central nervous system;
Peripheral nervous system; Sensory epithelium of the sense organs (inner ear, retina, lens); Epidermis
including hairs, nails, cutaneous and mammary glands; Anterior pituitary gland; Enamel of the teeth)
19. Recall derivatives of the mesodermal germ layer (Connective tissue, cartilage and bone (except in the
head and neck); Striated (skeletal) muscle, smooth and cardiac muscle; Blood cells, walls of the heart,
blood vessels, lymph vessels; Kidneys; Gonads and their ducts; Cortex of the adrenal gland; spleen)
20. Recall derivatives of the endodermal germ layer (epithelial lining of the respiratory tract; parenchyma of
thyroid gland, parathyroid glands, liver, pancreas and stroma of tonsils and thymus; epithelial lining of
urinary bladder and urethra; epithelial lining of tympanic membrane and auditory tube; epithelium and
glands of gut)
21. Describe embryonic folding (Tube-within-a-tube body plan established; Embryo undergoes folding in:
cranial (head), caudal (tail) and lateral directions; Embryonic folding is responsible for: incorporating
the endoderm into the center of the embryo, establishing ventral body wall, connection point for the
umbilical cord and establishing recognizable vertebrate body form)
PHYSIOLOGY
Pores and Channels
1. Compare the intracellular and extracellular relative concentrations of Na+, K+, H+ (pH), HCO3-, Cl-,
Ca++, and glucose.
2. Describe how transport rates of certain molecules and ions are accelerated by specific membrane
transport proteins (pores, channels and transporters).
3. Write Fick’s Law of diffusion, and explain how changes in the concentration gradient, surface area,
time, and distance will influence the diffusional movement of a substance.
4. Differentiate the following terms based on the source of energy driving the process and molecular
pathway for: diffusion, facilitated diffusion, secondary active transport, and primary active transport.
5. Describe how energy from ATP hydrolysis is used to transport ions such as Na+, K+, Ca++, and H+
against their electrochemical differences.
6. Explain how energy from the Na+ and K+ electrochemical gradient across the plasma membrane can be
used to drive the net “uphill” (against a gradient) movement of other solutes (e.g., Na+/glucose cotransport; Na+/Ca++ exchange or counter-transport).
Regulation of Cell Volume
1. Identify major routes for water intake and loss, and predict how changes in intake or loss
affect the distribution of total body water
2. Given the body weight, estimate the a) total body water, b) extracellular fluid volume, c)
intracellular fluid volume, d) blood volume, and e) plasma volume. Identify normal
extracellular fluid (plasma) and intracellular fluid (red blood cell) osmolarity.
3. Demonstrate the ability to use the indicator dilution principle to measure plasma volume,
blood volume, extracellular fluid volume, intracellular fluid volume, interstitial fluid volume, and
total body water, and identify compounds used to measure each volume.
4. Differentiate between the terms osmole, osmolarity, osmolality and tonicity. List the typical
value and normal range for plasma osmolality.
5. Define the Donnan equilibrium and list the resulting characteristics.
6. Using the membrane as an example, define a reflection coefficient, and explain how the
relative permeability of a cell to water and solutes will generate an osmotic pressure. Contrast
the osmotic pressure generated across a cell membrane by a solution of particles that freely
cross the membrane with that of a solution with the same osmolarity, but particles that cannot
cross the cell membrane.
7. Given the composition and osmolarity of a fluid, identify it as hypertonic, isotonic, or
hypotonic. Predict the change in transcellular fluid exchange that would be caused by placing
a red blood cell in solutions with varying tonicities.
8. Using the volumes/compartments, contrast the movement between intracellular and
extracellular compartments caused by increases or decreases in extracellular fluid osmolarity.
9. Predict the changes in extracellular volume, extracellular osmolarity, intracellular volume, and
intracellular osmolarity caused by infusion of three liters of 0.9% NaCl, 0.45% NaCl, and 4.5%
NaCl.