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Exam 1 Week 2 Flashcards

1
Q

Describe the terms Sense Strand and Antisense Strand:

A
  1. Antisense Strand: The template strand of DNA being used to transcribe RNA.
  2. Sense Strand: The strand of DNA not being transcribed that will be identical to the RNA transcript.
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2
Q

4 Differences between DNA synthesis and RNA synthesis:

A
  1. RNA Polymerase vs. DNA Polymerase
  2. RiboNTP’s vs. DeoxyriboNTP’s
  3. RNA Polymerase DOESN’T require a Primer, while DNA Polymerase 1 lays down a primer.
  4. Uracil vs. Thymine
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3
Q

Role of MicroRNA’s:

A

Silencing/Enhancing genes during transcription

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4
Q

Difference in RNA Polymerase in Prokaryotes vs. Eukaryotes:

A
  1. Prokaryotes: Only 1 RNA Polymerase
  2. Eukaryotes: THREE different ones:
    - RNA Pol. 1: rRNA transcription
    - RNA Pol. 2: mRNA transcription (+snRNA and miRNA)
    - RNA Pol. 3: tRNA transcription (+snRNA)
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5
Q

Describe the regions of a prokaryotic gene:

A
  1. Promoter: Upstream of the coding region, initial binding site of transcriptional machinery.
  2. Coding Sequence: The DNA SEQUENCE that is transcribed into RNA.
  3. Terminator: Downstream, where transcription will stop.
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6
Q

How can we tell if a base lies in the promoter region, rather than the coding region?

A

It will be given a (-) designation

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7
Q

Describe Prokaryotic Promoter Sequences vs. Eukaryotic Promoter Sequences:

A
  1. Prokaryotic: Only 2 main sequences ensure proper initiation site…
    a. ) -10 consensus sequence
    b. ) -35 consensus sequence (Pribnow Box)
  2. Eukaryotic: High variability in multiple consensus sequences….(allows fine-tuning of transcription).
    a. ) GC Box: -70 to -200
    b. ) TATA Box: -20 to -35
    c. ) CAAT Box: -80
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8
Q

Describe Prokaryotic Transcription: (5)

A
  1. (RNA Polymerase + Sigma Factor) binds to -10 and -35 regions of promoter.
  2. DNA is unwound in the -10 region
  3. After transcription of 8 or 9 nucleotides, Sigma Factor dissociates from the core polymerase.
  4. Polymerization proceeds as RNA Polymerase unwinds the DNA molecule.
  5. Termination sequence is transcribed and transcription stops.
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9
Q

Function of Rifampin:

What is it used to treat?

A
  1. Inhibits Initiation of transcription
  2. Binds to PROKARYOTIC RNA Polymerase and blocks formation of 1st phosphodiester bond.
  3. Used to treat TUBERCULOSIS.
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10
Q

5 Factors Required For Transcription Initiation in Eukaryotes:

A
  1. TF2D: Distorts the helix, recruitment of other factors.
  2. TATA Box-Binding Protein: Subunit of TF2D
  3. TF2B: Recognition of initiation site
  4. TF2E: Recognition of initiation site
  5. TF2H: Helicase that unwinds the DNA, also has kinase activity to phosphorylate RNA Polymerase and activate it.
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11
Q

When will transcription factors dissociate from the Basal Transcriptional Machinery?

A

After they have stabilized and activated RNA Polymerase at the promoter region and initiation site, but PRIOR to initiation itself.

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12
Q

What specifically makes up the Basal transcriptional Machinery?

A
  1. RNA Pol. TWO

2. Transcription Factors

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13
Q

Activators/Repressors:

A
  1. PROTEINS that bind (with Adaptor Molecules) to enhancers/suppressor gene sequences in the promoter.
  2. When bound, they increase/decrease transcription of certain genes as DNA folds and is able to interact with them more.
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14
Q

What is Amanita Phalloides and how does it function?

A
  1. Death Cap Mushroom
  2. It produces a toxin called Alpha Amanitin that inhibits RNA Pol. TWO.
  3. So as it moves through your body, it stops mRNA synthesis and therefore protein synthesis along the way.
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15
Q

How is Alpha Amanitin poisoning treated?

A

High doses of penicillin can inhibit its function in the liver

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16
Q

Give the 2 types of antibiotics (and examples) that can inhibit Topoisomerases:

A
  1. Courmarins: Novobiocin
  2. Quinolones: Nalidixic Acid and Ciprofloxacin
    i. e. “C.N.N.” stops supercoiling
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17
Q

Describe Intrinsic vs. Extrinsic termination:

A
  1. Intrinsic: Terminator possesses palindromic sequences with internal complementarity that form HAIRPIN loops. These are G-C RICH structures that destabilize the transcription complex and cause it to dissociate.
  2. Extrinsic: Hairpin loops aren’t sufficient to destabilize, so Rho Protein follows the transcriptional machinery and separates RNA from DNA to pull the machinery off.
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18
Q

How is Rho protein recruited for Extrinsic termination?

A

It binds to the recognition site at the beginning of transcription and is following the RNA Pol. the entire time, so when RNA Pol. stalls at the terminator hairpin loops, Rho is able to catch up and pull the RNA off of the DNA.

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19
Q

What is the function of Actinomycin D?

A
  1. (Anti-Cancer) Inhibits DNA strand separation in both prok. and euk.
  2. It INTERCALATES between and binds too tightly to double stranded DNA and therefore inhibits BOTH TRANSCRIPTION AND DNA REPLICATION.
    * And therefore cell division too*
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20
Q

Describe the general structure of mRNA: (5)

A
  1. The 5’-UTR
  2. Start Codon (AUG)
  3. Protein Coding Sequence
  4. Stop Codon (UGA, UAG, UAA)
  5. The 3’-UTR
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21
Q

How is eukaryotic mRNA different from prokaryotic mRNA?

A

Eukaryotic mRNA has:

  1. A 7-methyl Guanasine CAP on the 5’ end.
  2. A Polyadenylated Tail at the 3’ end.
  3. Splicing of Introns
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22
Q

How is bacterial mRNA Polycistronic?

A

Bacterial mRNA’s can have MULTIPLE coding sequences with spacer sequences in between. This way they can coordinate transcription of multiple proteins for the same pathway/enzyme/mechanism all at once.

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23
Q

How does eukaryotic mRNA come into contact with the proteins responsible for its post-transcriptional modification?

A

RNA Polymerase 2 POSSESSES a set a pre-mRNA processing proteins on its tails and they are transferred to the mRNA after about 25 bases have been transcribed
i.e. Capping factors, Poly-A factors, Splicing Factors

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24
Q

4 Steps of 5’-Capping Mechanism:

A
  1. Phosphatase: Removes a phosphate from the 5’ end of the mRNA.
  2. Guanylyl Transferase: Adds a GMP to the 5’ end.
  3. Guanine-7-methyl Transferase: Adds a methyl group to position 7 of the terminal guanine.
  4. 2’-O-Methyl-Transferase: Adds another methyl group to the 2’-O position of the NEXT TO LAST base on the 5’ end.
    * i.e. P.G.G.2*
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25
Q

4 Functions of the 5’ Cap:

A
  1. Protection from degradation
  2. Recognition by the Ribosome
  3. Cap-Binding Complex to Exit Nucleus
  4. Recognition by Spliceosome
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26
Q

What must happen to mRNA before it can be Polyadenylated and what 3 things accomplish this?

A
  • ***IT MUST BE CLEAVED FIRST:
    1. Cleavage/Poly-A Specificity Factor (CPSF) binds to Polyadenylation signal (before cleavage site).
    2. Cleavage Stimulating Factor F (CstF) binds to the GU-Rich element BEYOND the cleavage site.
    3. Cleavage Factors bind the CA sequence AT the cleavage site.
  • i.e. Bind 1.Before–2.After–3.AT…cleavage site*
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27
Q

After cleavage of the mRNA has occurred, describe the 3 steps of Polyadenylation:

A
  1. Poly-A-Polymerase (PAP) adds about 200 A nucleotides to the 3’ end produced by the cleavage.
  2. Poly-A-Binding Proteins (PABP) bind the tail and direct translation by the ribosome.
  3. The cleaved fragment of the mRNA is degraded in the nucleus.
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28
Q

4 Functions of Polyadenylation:

A
  1. Protects the mRNA from degradation in the cytoplasm.
  2. PABP’s stimulate translation of the mRNA.
  3. Facilitates transcription termination.
  4. Aids in export of mRNA from nucleus.
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29
Q

Where are splice junctions located?

Which is the Splice Donor and Splice Acceptors site respectively?

A
  1. On the 5’ and 3’ ends of the INTRON
  2. Splice DONOR = 5’ (the 1st one)
    Splice ACCEPTOR = 3’ (the 2nd one)
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30
Q

How are the Splice Donor and Acceptor sites recognized?

A
  1. Splice Donor: GU

2. Splice Acceptor: AG

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31
Q

What is a Conserved Branch Point Sequence?

A

A sequence denoted by an “A” that is in between the Splice Donor and Splice Acceptor Sites

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32
Q

Describe the 4 Basic Steps of Intron Removal (Splicing):

A
  1. Cleavage at the Splice Donor Site
  2. The 5’ end “G” is released and the intron folds to form a 5’ to 2’ bond with the “A” of the branch point (PRODUCING A LARIAT).
  3. Cleavage at the Splice Acceptor Site
  4. Ligation of the two exons
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33
Q

Describe the 5 more detailed steps of intron removal by the spliceosome:

A
  1. U1 snRNP binds the Splice Donor Site while U2 binds the branch point site.
  2. U4/U6 and U5 snRNP’s BINDS the first two together to form a loop.
  3. U4 dissociates from the spliceosome, thereby signaling it to cleave.
  4. Spliceosome cleaves at the 5’ end, which is then free to bind to the branch point (FORMS LARIAT).
  5. Spliceosome cleave at the 3’ end, the two exons are ligated, and the snRNP’s are released.
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34
Q

Systemic Lupus Erythematosis:

A
  1. (Auto-Immune Disease) Possession of antibodies that attack U1 snRNP of the spliceosome, as well as histones and topoisomerases.
    i. e. Splicing cannot occur properly
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35
Q

Describe Alternative Splicing:

A

Inclusion or exclusion of certain exons to yield many different proteins from different isotopes of the same mRNA, ultimately increasing biological diversity.

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36
Q

How is alternative splicing controlled?

A
  1. Activators/Repressors: Proteins that bind to splice sites and either repress or activate them.
  2. Intron sequence ambiguity (weak splice sites)
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37
Q

Beta Thalassemia:

A
  1. Improper Splicing of B-Globin

2. Changes an AT to an AG, inserting a NEW SPLICE SITE in the 3rd intron–> LONGER B-globin protein

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38
Q

Limb girdle Muscular Dystrophy:

A
  1. Improper Splicing of Calpain-3

2. Changes a GT to a GG in THE MIDDLE of Exon 16, so half of the exon is lost–>Defective, shorter protein

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39
Q

Describe RNA Editing:

A
  1. CHEMICALLY changing an RNA after transcription to yield a different protein
  2. “The process by which information changes at the level of mRNA”
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40
Q

How would you determine if RNA editing has occurred?

A

The RNA coding sequence would be different from the DNA sequence from which it was transcribed

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41
Q

Describe the main example of mRNA editing in humans:

A
  1. (Apo-B) Apolipoprotein-B encodes 2 different forms of the protein:
    a.) Apo-B100 in Liver
    b.) Apo-B48 in Intestine
  2. Intestinal mRNA for Apo-B is EDITED so that
    CAA–>UAA (a stop codon) and truncates synthesis.
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42
Q

What enzyme causes the truncation of Apo-B in the intestine?

A

Cytidine Deaminase (CAA–>UAA)

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43
Q

What is another common example of mRNA editing in humans (besides Apo-B)?

A
  1. Glutamate Receptor in the BRAIN
  2. Editing changes CAG–>CIG (Glutamine–>Arginine)
  3. Normal receptor conducts both Na+ and Ca2+ inward when activated by glutamate. Mutated receptor ONLY conducts Na+ in response.
    * Gives ABNORMAL BRAIN DEV.*
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44
Q

What enzyme causes the mutation in the Glutamate receptor in the brain?

A 
Adenosine Deaminase (CAG-->CIG)
*I = Inosine*
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45
Q

What organisms accomplish more complex RNA editing and where do they do it?

A
  1. a. )Trypanosomes (Chagas Disease)
    b. )Leishmania (Leishmaniasis)
  2. BOTH IN MITOCHONDRIAL mRNA
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46
Q

4 Steps of Trypanosome RNA editing:

A
  1. “Guide RNA” forms complimentary base pairs with target RNA.
  2. Endonuclease CLEAVES RNA at regions of mispairing bases.
  3. Terminal Uridyl Transferase (TUTase) adds a “U”
  4. RNA Ligase joins the substrate RNA together.
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47
Q

How many “U”s are added to Trypanosome edited RNA?

A

The number of bases in each loop formed by mispairing bases will be the number of “U”s added by the TUTase

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48
Q

Why would such extensive RNA editing be useful to Trypanosomes?

A

They are parasites that invade a host, so when that host develops antibodies against their proteins they are able to alter the structure of those proteins slightly to prevent being targeted by the host.

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49
Q

Differentiate between Unique Single Copy Genes and Multi-gene Families:

A
  1. Unique Single Copy Genes: Only codes for a single protein (receptor/enzyme/etc.)
  2. Multi-Gene Families: Genes that code for multiple proteins that have similar functions. There are 2 Types…
    a. ) Classic Gene Familes: Also have HIGH sequence homology
    b. ) Gene Superfamilies: LOW sequence homology
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50
Q

Extragenic DNA:

A

The remaining 98% of our DNA that is non-coding, but may be regulatory of transcription and gene expression
Ex: Shorter tandem repeats = MORE polymorphic

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51
Q

4 Types of Polymorphisms:

A
  1. (SNP) Single Nucleotide Polymorphism: Only a single base pair changes.
  2. (SSR) Simple Sequence Repeat: Short tandem repeat sequence of 2-4 tandem repeats.
  3. (VNTR): Variable # = Any more than 4 tandem repeats
  4. (LCR) Low Copy Repeat: Very large sequences that only need 1 repeat to elicit effects.
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52
Q

Why don’t some SNP’s exhibit a different phenotype?

A

The single base pair change may not code for a different amino acid, so it might have no effect.

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53
Q

Define LINE’s/SINE’s:

A
  1. Long/Short Interspersed Nuclear Elements
  2. Able to make RNA, and ALSO have reverse transcriptase ability.
    i. e. Makes a DNA copy from the LINE/SINE mRNA and integrates it into the genome.
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54
Q

How do LINE’s/SINE’s create genetic diversity?

A

They can lead to unequal crossover during meiosis

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55
Q

SNP’s versus Rare Variants:

A
  1. SNP: Commonly found in people, but only a limited number of them that are all identified.
  2. Rare Variants: Very rarely found in people, but there are billions of them and most are unidentified.
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56
Q

Pseuodgenes:

A

Sequences that look like real genes but don’t code for any protein (i.e. Not functional)

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57
Q

How are pseudogenes most likely created?

A

Reverse Transcriptases of viruses copy their mRNA back into DNA and a mutation arises before the DNA is re-inserted into their genome

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58
Q

The _______ is the constricted region of the chromosome.

A

Centromere

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59
Q

The centromere divides the chromosome into a ______ and a ______.

A
  1. Short Arm: “P”
  2. Long Arm: “Q”
    * EACH sister chromatid has a branch of the “P” and “Q” arms respectively*
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60
Q

Differentiate between the 3 types of chromosomes:

A
  1. Metacentric–>Centromere is at Chrom. #1, so P/Q arms are equal length.
  2. Submetacentric–>Centromere is at Chrom. #4, so P arm is SHORTER than Q arm.
  3. Acrocentric–>Centromere is at Chrom. #13-22, so P arm is MUCH SHORTER and contains almost no info.
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61
Q

What do we call a visualization of the chromosomes during metaphase?

A

A Karyotype

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62
Q

How are chromosomes ordered?

A

According to size, so #1 is the LARGEST and #21 is the smallest.

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63
Q

Uniparental Disomy:

A

When both of the chromosomes in a homologous pair are derived from the same parent

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64
Q

Describe X-inactivation:

A

One of the X-chromosomes is condensed to form a Barr Body, and that SAME X-chromosome will be inactivated in all of the cells in its lineage (FIXED INACTIVATION)

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65
Q

How is X-inactivation regulated?

A

The X-inactivation center (Xic) has the gen XIST: Codes for RNA that coat one of the X-chromosomes and prevent its transcription by CAUSING IT TO CONDENSE into heterochromatin.

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66
Q

Females with X-inactivation will have a _______ genotype , meaning: ______.

A
  1. Mosaic

2. Their cells will express various different genotypes

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67
Q

How specifically does XIST cause condensation of the X-chromosome?

A
  • —->It causes:
    1. Methylation of the CG islands (cytosine bases)
    2. Histone De-acetylation
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68
Q

Alleles:

A

Different forms of the same gene

i.e. Even though homologous chromosomes have identical genes, they may express different forms

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69
Q

What is a Locus?

A

The locus OF A GENE refers to its location in the chromosome.
Ex: Huntington Gene Locus is on Chromosome 4p (the small arm of chromosome 4)

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70
Q

Describe Mendelian Inheritance in Man (MIM):

A
  1. Each genetic trait has a unique 6-digit number
  2. Diff. Disorders Begin with Diff. Numbers:
    a. ) Autosomal Dom. = 1
    b. ) Autosomal Rec. = 2
    c. ) X-Linked = 3
    d. ) Mitochondrial = 5
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71
Q

Describe the 3 types of cells with respect to the cell cycle:
Give examples of each…

A
  1. Labile cells: Multiply throughout life. Have SHORT G1 phases (i.e. Skin, GIT, epithelial cells, etc.)
  2. Stable Cells: Quiescent cells in the G0 Phase that can still divide if stimulated (i.e. Hepatocytes)
  3. Permanent cells: CAN’T divide, have lost the capacity. Stuck in G0 Phase forever. (i.e. Neurons, cardiac muscle)
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72
Q

What is still occurring in a stable cell or permanent cell even though it is in the G0 Phase?

A

Protein Synthesis, since that is characteristic of the G1 Phase which it is essentially limited to forever.

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73
Q

G1 Phase is characterized by 2 things:

A
  1. Protein Synthesis

2. Cell Differentiation

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74
Q

G2 Phase is characterized by 2 things:

A
  1. More cell growth

2. Post-replication DNA repair mechanisms

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75
Q

What signals cells to move from the G0 to G1 phase and from G1 to S?

A

Growth Factors

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76
Q

What 2 proteins are important at the G1 Checkpoint?

A
  1. p53 protein

2. Rb Protein

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77
Q

Prophase: (4)

A
  1. Nuclear Envelope Dissolves
  2. Mitotic Spindle Forms
  3. Chromosomes Condense
  4. Chromosomes start binding to spindle
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78
Q

Metaphase: (3)

A
  1. Maximally condensed chromosomes
  2. NOW visible by karyotyping
  3. Microtubules attach to kinetochores of centromeres
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79
Q

Anaphase: (2)

A
  1. Sister chromatids move to centrioles

2. Non-disjunction may occur

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80
Q

Telophase: (3)

A
  1. Sister chromatids move to opposite poles
  2. Nuclear Envelope starts forming
  3. Chromosomes De-condense
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81
Q

How many chromosomes and chromatids are there at the end of S-phase?

A
  1. 46 Chromosomes

2. 92 Chromatids

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82
Q

What is produced by meiosis in males? In females?

A
  1. Males = 4 gametes: Each with only 23 chromosomes

2. Females = 1 Ovum (23X or Y) and 3 Polar bodies

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83
Q

When does homologous recombination (meiotic crossover) occur?

A

During Prophase-1 of Meiosis

Reason that each gamete is unique!

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84
Q

Describe what is generally accomplished from Meiosis 1 and 2:

A
  1. Meiosis 1: Chromosomes separate (reduction division)

2. Meiosis 2: Sister chromatids separate

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85
Q

Effects of Nondisjunction during Meiosis 1 versus Meiosis 2:

A
  1. Meiosis 1: Aneuploidy–>An extra or lost chromosome (45 or 47)
  2. Meiosis 2: Trisomy or Monosomy (An extra or lost ENTIRE set of chromosome)
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86
Q

Describe Uni-parental Disomy and its effect:

A
  1. Both copies of homologous chromosomes in a pair are derived from a single parent.
  2. Only NOT IMPRINTED genes will exhibit a phenotype.
    i. e. Imprinted = Silenced
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87
Q

What are the TWO possible phenotypes of non-disjunction in Meiosis 1 of males?

A
  1. Turner Syndrome: 45X —> So only an X from the mother, NOTHING from the father.
  2. Klinefelter Syndrome: 47XXY –>So a normal X from the mother, and an XY (BOTH) from the father.
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88
Q

What are the THREE possible phenotypes of non-disjunction in Meiosis 2 of males?

A
  1. Turner Syndrome: 45X —> So a normal X from the mother, NOTHING from the father.
  2. 47XYY: So a normal X from the mother, and YY from the father.
  3. 47XXX: So a normal X from the mother, and XX from the father.
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89
Q

Describe the process of Ovum development and Meiosis:

A
  1. Oogenesis begins during prenatal dev. (Not Meiosis 1)
  2. Primary Oocytes (prod. of Meiosis 1) are ARRESTED at birth at Prophase-1.
  3. At Puberty: COMPLETION of Meiosis 1, and ovulation of mature oocytes once a month.
  4. After Fertilization: Meiosis 2 Completion
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90
Q

Does male or female gametogenesis have a higher number of mitoses?

A

MALE: Because each cell gives rise to 4 haploid cells, while female oocytes only give rise to one ovum.

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91
Q

Does gametogenesis begin earlier in males or females?

A

FEMALES: Because it begins before birth, even though it is halted at birth at prophase 1.

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92
Q

What are the increased risks of fertilization with a mother or father of increased age?

A
  1. Mother: Risk of non-disjunction (trisomy, monosomy)

2. Father: Risk of New Dominant Single Gene Mutations

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93
Q

Difference between a Polymorphism and a Mutation:

A
  1. Polymorphisms have NO PHENOTYPIC presentation, and do not result in a disorder.
  2. Mutations change the phenotype expressed.
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94
Q

Difference between Proband and consultand:

A
  1. Consultand: Person who may or may not be affected

2. Proband: Person who IS affected with the disorder

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95
Q

Consanguinity:

A

Inbreeding

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96
Q

Difference between Monozygotic and Dizygotic twins:

A
  1. Monozygotic: Result from ONE ovum (identical genes)

2. Dizygotic: Result from TWO ova (share only 50% of genes)

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97
Q

What is the difference between Mendelian and Non-Mendelian Inheritance?

A
  1. Non-Mendelian: Mitochondrial Inheritance

2. Mendelian: Everything Else with nuclear DNA

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98
Q

4 Main Characteristics of Autosomal Dominant Inheritance:

A
  1. VERTICAL inheritance (No skipped Generations)
  2. Children receive it from an AFFECTED parent
  3. Equal Male:Female frequency
  4. SHOWS Father:Son transmission
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99
Q

How do you differentiate between Autosomal Dominant and X-Linked Dominant?

A

Autosomal Dominant disorders show Father to Son transmission, X-linked disorders can only be passed to sons from their mothers.

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100
Q

List the 8 Autosomal Dominant Disorders Discussed in Class:

A
  • FMH MOANA*
    1. FH (Familial Hypercholesterolemia)
    2. Myotonic Dystrophy
    3. Huntington’s Disease
    4. Marfan Syndrome
    5. Osteogenesis Imperfecta
    6. Achondroplasia
    7. Neurofibromatosis Type 1
    8. Acute Intermittent Porphyria
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101
Q

What is unique about Acute Intermittent Porphyria?

A

It is a disorder affecting an enzyme, most of which are recessive disorders. But it is autosomal dominant.

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102
Q

Describe Myotonic Dystrophy: (4)

A
  1. Autosomal Dominant
  2. Mutation in DMPK gene
  3. Causes:
    a. ) Muscle Wasting
    b. ) Cataracts
    c. ) Heart Conduction Defects
    d. ) Myotonia
  4. Pleiotropic Phenotype: Affects multiple organ systems
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103
Q

Describe Achondroplasia: (5)

A
  1. Autosomal Dominant
  2. Mutation in FGRF3: Codes for a transmembrane receptor involved in DIFFERENTIATION of cartilage to bone.
  3. GAIN of abnormal function mutation
  4. HIGH number of “Mutation Hot Spots” (new mutations without familial history)
  5. Causes: Severely stunted bone growth
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104
Q

Describe NeuroFibromatosis Type 1: (6)

A
  1. Autosomal Dominant
  2. Mutation in NF-1: Codes for neuro-fibromin protein, involved in TUMOR SUPPRESION.
  3. Caused by Alelic Heterogeneity: Diff. mutations of the same gene in diff. people.
  4. HIGH number of “Mutation Hot Spots”
  5. Variable expressivity, but HIGH penetrance: Those affected have PHENOTYPIC expression most often.
  6. Causes:
    a. ) Tumor growth (Neurofibromas, i.e. Swellings on Skin)
    b. ) Cafe-au-lait spots (brown)
    c. ) Lisch Nodules on the Iris
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105
Q

Define Haplo-Insufficiency:

What types of disorders cause this?

A
  1. Loss-of-function mutations in which only 50% of the gene product is functional. The other 50% are non-functional to due mutation.
  2. Autosomal Dominant Disorders
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106
Q

Define Dominant Negative Mutations:

Give an Example…

A
  1. Mutant gene product interferes with the NORMAL product’s function.
  2. Multimeric Protein assembly is often hindered.
    Example:
    a.) Osteogenesis Imperfecta
    b.) Marfan Syndrome
    Both still Autosomal Dominant
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107
Q

Define Gain of Function Mutations:

Give an Example…

A 
1. Increased levels of expression of gene product OR development of NEW function of product. 
Example: 
a.) Huntington's Disease
b.) Achondroplasia
*Both still Autosomal Dominant*
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108
Q

Most oncogene mutations are ________ mutations.

A

Gain-Of-Function

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109
Q

What percentage of proteins are functional in Dominant Negative Mutations?

A
  1. Only 1/3 or 33%
    Example: One form of the protein will be normal, but because they’re multimeric, 2 other forms could both be abnormal (so 2/3 are non-functional).
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110
Q

Describe the normal function of the neurofibromin protein and what the mutation causes:

A
  1. Normal: Breaks down GTP to GDP in the RAS signal transduction pathway to inactivate it. (Tumor Suppressor)
  2. Mutation: RAS signaling stays activated and tumor proliferation is permitted.
111
Q

Give 3 examples of how being a HOMOZYGOTE for an autosomal dominant mutation can exhibit different effects than being a heterozygous affected mutant:

A
  1. Familial Hypercholesterolemia (FH): Homozygous mutation is more severe, and has earlier age of onset.
  2. Huntington’s Disease: Same as FH description
  3. Achondroplasia: Homozygous mutation is LETHAL
112
Q

4 Main Characteristics of Autosomal Recessive Disorders:

A
  1. Horizontal Inheritance: ALL affected seen in DAME generation.
  2. Both parents are typically carriers, but not affected (IT SKIPS GENERATIONS).
  3. Equal frequency in males and females.
  4. Can be the result of Consanguinity
113
Q

When do Autosomal Recessive disorders typically present?

A

Early in life

114
Q

What is different about the calculation for recurrence risk for being a carrier of autosomal recessive disorders?

A

The “aa” fraction is DISREGARDED because, if the person has both mutant alleles then they are not a carrier, they are affected. So the risk would be 2/3.

115
Q

List the 11 Autosomal Recessive Disorders discussed in class:

A

“CC,HH,AA,SS GTP”

  1. Cystic Fibrosis (CF)
  2. Congenital Deafness
  3. Hemachromatosis (late onset)
  4. Homocystinuria
  5. Alkaptonuria (late onset)
  6. Alpha-1 Antitrypsin Deficency
  7. SCID (“Severe Combined Immune Deficiency”)
  8. Sickle Cell Anemia
  9. Galactosemia
  10. Tay-Sachs Disease
  11. Phenylketonuria
116
Q

List the 2 autosomal recessive disorders that exhibit late onset:

A
  1. Hemachromatosis

2. Alkaptonuria

117
Q

What are most autosomal recessive disorders associated with? More Specifically?

A
  1. Loss-of-Function disorders

2. Enzyme Deficiency

118
Q

How do carrier genotypes affect phenotype differently in autosomal recessive disorders than they do in autosomal dominant disorders?

A
  1. Autosomal Dominant: Haplo-insufficiency
  2. Autosomal Recessive: The 50% normal functioning gene products are sufficient to carry out normal function, so carriers are ASYMPTOMATIC.
119
Q

Describe Hemachromatosis: (4)

A
  1. Autosomal Recessive
  2. Mutation of the HFE gene–>”High Iron”
    a. ) C282Y = (most common) Cysteine–>Tyrosine
  3. Exhibits Allelic Heterogeneity: Multiple mutations
    a. ) Other: H63D = Histidine–>Aspartate
  4. Causes:
    a. ) Iron Uptake Overload
120
Q

Describe SCIDS:

A
  1. Autosomal Recessive
  2. Deficiency of Adenosine Deaminase (ADA): An enzyme that degrades PURINES. (“A” and “G”)
  3. Without it, the purines have AMP added to them and become dAMP–>dATP.
  4. Accum. of dATP is TOXIC to B-cells/T-cells.
  5. Causes:
    a. ) Respiratory Infections
    b. ) Diarrhea
    c. ) Eczema
121
Q

Describe PseudoAutosomal Dominace: (2)

A
  1. Autosomal Recessive disorders that appear Autosomal Dominant.
  2. Doesn’t skip generations as often as normal recessive.
    i. e. Exhibits Vertical Transmission
122
Q

Explain the 2 explanations for PseudoDominant Disorders:

Give examples of each…

A
  1. High Carrier Frequency
    Ex: Sickle Cell Anemia
  2. High Consanguinity
    Ex: Isolated Populations
123
Q

What are the most common genotypes of the parents of a child affected with a PseudoDominant Disorder?

A

Homozygote Mutant and Heterozygote Mutant

i.e. Aa and aa

124
Q

Describe an give an example of Codominance:

A
  1. Equal expression of both dominant gene products

Ex: Blood Type Genotypes

125
Q

Hemizygous:

A

Males only have one copy of the X chromosome, so females have twice as many of each gene on that chromosome.

126
Q

What is a PseudoAutosomal Region?

A

The region of a pair of sex chromosomes (X and Y) that match perfectly.

127
Q

4 Characteristics of X-Linked Recessive Disorders:

A
  1. More common in MALES (Hemizygous = They only need one mutant copy to express it).
  2. Skips generations commonly
  3. Mother transmits to Sons = All AFFECTED
    Father transmits to Daughters = All CARRIERS
  4. NO male-male transmission
128
Q

What is unique about Red/Green Color-Blindness?

A

It is the only (rare) X-linked recessive disorder where a female can become as a Homozygote Mutant (i.e. Both parents donated a mutant allele.

129
Q

List the 6 X-Linked Recessive Disorders:

A
  • LRG DHS*
    1. Lesch-Nyhan Syndrome (HGPRT Deficiency)
    2. Red/Green Color-Blindness
    3. Glucose-6-Phosphate DeHase (G6PD) Deficiency
    4. Dystrophin assoc. Muscular Dystrophy
    a. ) Duchenne: SEVERE
    b. ) Becker: More Mild Form
    5. Hemophilia A and B
    6. SCID (X-Linked): Defect in SCIDX1 gene
130
Q

Describe Duchenne Muscular Dystrophy:

A
  1. X-Linked Recessive
  2. Mutation of Dystrophin gene
  3. Lethal (Males die before 30 y.o.)
  4. Causes:
    a. ) Muscle Wasting
    b. ) Large Calves/Tongue (replacement of muscle with fat)
    * called Pseudohypertrophy*
131
Q

What is meant by “the genetic code is degenerate”?

A

It is REDUNDANT: Multiple codons form the same amino acid.

132
Q

How many reading frames are there for mRNA and DNA respectively?

A
  1. mRNA = 3 reading frames

2. DNA = 6 reading frames (for DOUBLE stranded DNA)

133
Q

Frame-Shift Mutation:

Give an example….

A
  1. Insertion/Deletion of a single base pair or two base pairs that causes a shift in the reading frame and possibly CHANGES an amino acid.
    Example: Cystic Fibrosis mutation in DeltaF508
134
Q

How many codons code for amino acids?

A

61 out of 64

135
Q

Which amino acids are only encoded by a single codon?

A

Methionine (AUG) and Tryptophan (UGG)

136
Q

How do we know the genetic code is universal? Give 2 examples….

A
  1. Genes can be transcribed AND translated after being transplanted from one species to another.
    Ex. 1: Tobacco Plant expressing a Firefly Gene to glow
    Ex. 2: Pig expressing a Jellyfish gene
137
Q

5 Components Required for Translation:

A
  1. mRNA
  2. Ribosomes
  3. Charged tRNA
  4. Initiation Factors
  5. GTP
138
Q

Describe the 3 binding sites of the ribosome:

A
  • APE*
    1. A Site: (Aminoacyl) Holds the tRNA that carries the next Amino Acid to be added to the chain.
    2. P Site: (Peptidyl) Holds the tRNA that carries the growing polypeptide chain.
    3. E Site: “Exit Site” Where discharged tRNA leaves the ribosome.
139
Q

What other binding site does the ribosome have and where is it located?

A
  1. mRNA-binding site: In the small ribosomal subunit

2. The A,P, and E sites are part of the large ribosomal subunit.

140
Q

What base of a charged tRNA is known as the wobble position?

A

The 5’ position of the anticodon

So it will pair with the 3’ base of the CODON in the mRNA*

141
Q

To what codon does the amino acid of a charged tRNA bind at the 3’ end?

142
Q

Compare the secondary and tertiary structure of tRNA:

A 
2' = Stem loop, clover structure
3' = CHARGED tRNA
143
Q

How is Inosine involved in the wobble hypothesis?

A

Inosine BASES can be at the 5’ position of the anticodon and allow it to pair with 3 different Amino Acids
Ex: Anticodon = IGC
CODON = GCA, GCC, GCU

144
Q

5 Steps of Translation:

A
  1. Activation of the monomer (charging tRNA)
  2. Initiation
  3. Elongation
  4. Termination
  5. Processing of the polymer
145
Q

Describe Charging of tRNA:

A
  1. Aminoacyl-tRNA Synthetase is BOUND to ATP and hydrolyzes it to attach the amino acid to itself (i.e. The Product = (Enzyme-AMP) bound to Amino Acid at 3’-OH.
  2. tRNA comes in and binds the complex, so AMP and the Enzyme dissociate.
146
Q

What is the FIRST amino acid translated in mRNA of prokaryotes AND in mitochondria?

A

fMET: N-formylmethionine

147
Q

Describe the 2 ways that Prokaryotes use Met-tRNA:

i.e. 2 different tRNA recognize AUG differently

A
  1. As 1st tRNA: (fMet) Recognized as 1st codon

2. Normal Met-tRNA is simply recognized as internal Methionine.

148
Q

How is translation initiated differently in prokaryotes vs eukaryotes (with respect to “finding the AUG start sequence”):

A
  1. Prokaryotes: Ribosome binds to the SHINE-DELGARNO sequence that lies slightly upstream of the AUG codon.
  2. Eukaryotes: Ribosome binds near the 5’-cap and scans until it encounters the AUG codon.
149
Q

Describe the 1st step of protein synthesis after charging of tRNA:

A
  1. Initiation Factors (IF) form the initiation complex (WITH GTP and the 30S SUBUNIT) that brings the first tRNA to the P site
150
Q

Describe the 2nd step of protein synthesis after charging of tRNA:

A
  1. Formation of the 70S subunit: GTP on IF-2 is hydrolyzed and IF’s are released WHEN the 50S subunit arrives to accomplish this
151
Q

Describe the 3rd step of protein synthesis after charging of tRNA:

A
  1. Elongation Factor (EF-Tu-GTP) brings the next charged tRNA into the A site, and GTP is hydrolyzed
152
Q

Describe the 4th step of protein synthesis after charging of tRNA:

A
  1. Peptidyltransferase (a Ribozyme) activity of the 50S subunit forms a Peptide Bond between the two, adding the P site amino acid to the end of the A site amino acid
153
Q

Describe the 5th step of protein synthesis after charging of tRNA:

A
  1. EF-G-GTP moves the RIBOSOME to the next mRNA codonin the 5’-3’ direction by hydrolyzing GTP, so the codon that was in the P site is now in the E site
154
Q

Describe the 6th step of protein synthesis after charging of tRNA:

A
  1. Steps 3, 4, and 5 are repeated until a termination codon (UGA, UAG, UAA) enters the A site.
    i. e. Steps involving EF-Tu-GTP, Peptidyltransferase, and EF-G-GTP
155
Q

Describe the 7th step of protein synthesis after charging of tRNA:

A
  1. A termination codon is recognized BY either release factor 1 or 2 (RF-1/RF-2), and the hydrolysis of GTP on RF-3 allows the polypeptide chain (protein) to be released and the complex to synthesizing dissociate
156
Q

What is EF-G called in Eukaryotes?

157
Q

Why do the termination codons stall translation?

A

They have no tRNA, so a peptide bond cannot be formed

158
Q

When does protein folding occur? How is it accomplished?

A

DURING translation by chaperones the ensure proper folding orientation

159
Q

4 Major Differences between Prokaryotic and Eukaryotic Translation:

A
  1. fMET vs Met (not formylated in eukaryotes)
  2. Polycistronic vs Monocistronic
  3. Prokaryotes: MAY select an internal AUG to start at, instead of fMET. Eukaryotes start at FIRST AUG always.
  4. Translation/Transcription are coupled in prokaryotes, but in eukaryotes on occurs in the cytoplasm while the other occurs in the nucleus.
160
Q

What does Polycistronic mean?

A

Prokaryotic mRNA code for multiple proteinsof similar function, while in eukaryotes one mRNA codes for one protein

161
Q

How are proteins named?

A

In the same order they are synthesized: From the N-terminus (5’) to the C-terminus (3’).

162
Q

List the 7 compounds discussed in class that disrupt protein synthesis (translation):

A
  • DCT PECS*
    1. Chloramphenicol
    2. Cyclohexamide
    3. Diphtheria Toxin
    4. Puromycin
    5. Erythromycin
    6. Tetracycline
    7. Streptomycin
163
Q

Mechanism of Chloramphenicol:

A

Inhibits PeptidylTransferase activity in PROKARYOTES, possibly mitochondrial translation in eukaryotes

164
Q

Mechanism of Cyclohexmide:

A

Inhibits PeptidylTransferase activity in EUKARYOTES (do not use on human patients)

165
Q

Mechanism of Diphtheria Toxin:

A

Inhibits EF-2 by ADP-Ribosylation, preventing translocation of ribosome along mRNA

166
Q

Mechanism of Puromycin:

A

Causes Premature Termination in both prokaryotes and eukaryotes

167
Q

Mechanism of Erythromycin:

A

Inhibits translocation of the ribosome by binding to the 50S subunit of the completed (70S) ribosome

168
Q

Mechanism of Tetracycline:

A

Its 4 ring structure blocks aminoacyl-tRNA from entering the A site

169
Q

Mechanism of Streptomycin:

A

Inhibits INITIATION by binding to 30S subunit and preventing ribosome assembly

170
Q

List the 6 types of Post-Translational Modification discussed in class:

A
  • NOT SZL
    1. N-linked glycosylation
    2. O-linked glycosylation
    3. Tyrosine Phosphorylation
    4. Serine/Threonine Phosphorylation
    5. Zymogen Activation
    6. Lipid Anchoring
171
Q

What are caspases? Give 3 examples of when they are used:

A
  1. Enzymes used in Zymogen Activation
  2. Examples:
    a. ) Protein Digestion in intestines
    b. ) Activation of Apoptosis
    c. ) Blood Coagulation
172
Q

What is the most common form of protein phosphorylation as modification and how is it accomplished?

A
  1. Serine/Threonine Phosphorylation

2. Kinases use ATP to transfer a phosphate

173
Q

Give an example of a common Tyrosine Kinase:

A

The Insulin Receptor

174
Q

Differentiate between O-linked and N-linked glycosylation:

A
  1. O-Linked: Added to the -OH groups of Serine and Threonine–>Typically become Extracellular proteins or transmembrane proteins with glycans facing the EXF.
  2. N-Linked: Added to the Asn residue (NOT Gln)
175
Q

What 2 different ways can glycosylation occur?

A

Either as a LINKAGE, or with BOTH on the same protein

176
Q

Describe Lipid Anchoring:

Give an example of how it is used….

A
  1. Adding a Farnesyl group to Cysteine at C-15

Example: Farnesylation of Ras anchors it to the inner leaflet of the plasma membrane.

177
Q

Describe the packaging and processing of mRNA for Insulin:

A
  • **PrePro-mRNA TRANSCRIBED in Nucleus and exported in a secretory vesicle……
    1. First called PreProInsulin when translated into R.E.R. lumen and contains:
    a. ) C-Peptide: For proper folding
    b. ) Signal Sequence: Ensures targeting to the Rough E.R. to be translated into its lumen.
    2. Atfter translation, signal sequence dissociates and it is now called ProInsulin.
    3. Proinsulin moves to the Golgi, where C-Peptide is cleaved and it is now called Insulin.
    4. Insulin is packaged WITH C-peptide in secretory granules and released by exocytosis.
178
Q

Why is the C-Peptide of Insulin so important?

A

It has a much longer half life than insulin so it can be used to measure production and secretion of insulin

179
Q

Describe Hemophilia A/B: (4)

A
  1. X-Linked Recessive
  2. Mutation of Clotting Factor 8–>Increased tendency to bleed after minor trauma.
  3. Typically an inversion of an intron sequence
  4. Exhibits ALLELIC heterogeneity: Many different mutations of the same gene cause it.
180
Q

Describe X-Linked SCID: (4)

A
  1. X-linked Recessive
  2. Mutation in SCIDX1 gene–>Caused by defect in gamma chain of the IL2RG (Interleukin-2-Receptor-Gamma).
  3. IL2RG is necessary for T/B-cell maturation, hence why it is a severe COMBINED immune deficiency (SCID).
  4. Exhibits LOCUS heterogeneity: Many different mutations of different genes can cause it.
181
Q

Who are the obligate carriers of X-linked recessive disorders?

A

Daughters of affected fathers

182
Q

Describe Skewed Lyonization:

A

(Asymmetric X-Inactivation) When a female is a carrier for an X-linked recessive mutation and X-inactivation results in more of the mutant gene being expressed than the normal gene.

183
Q

Describe Manifesting Heterozygotes:

Give 2 common examples of this presenting….

A
  1. A heterozygote for an X-linked recessive disorder that is showing phenotypic symptoms of the disorder, most likely females due to skewed lyonization.
  2. Examples:
    a. ) Hemophilia A/B
    b. ) Duchenne Muscular Dystrophy
184
Q

Give an example of an X-linked recessive disorder that shows different manifestation between males and females:

A
  1. Red/Green Color-blindness
    a. ) Males: Hemizygous, so if affected will manifest every time (more common in males for this reason)
    b. ) Females: RARELY homozygous for the mutation, so manifestation is much less common.
185
Q

5 characteristics of X-Linked Dominant disorders:

A
  1. VERTICAL inheritance: NO skipping of generations
  2. More females than males affected
  3. NO male to male transmission
  4. Affected males = ALL affected daughters
  5. Variable Expression in females (due to x-inactivation)
186
Q

List the 3 X-Linked Dominant disorders discussed in class:

A
  • VIR*
    1. Vitamin D Resistant RICKETS
    2. Incontinentia Pigmenti
    3. Rett Syndrome
187
Q

Describe Rett Syndrome: (3)

A
  1. X-Linked Dominant
  2. Mutation in the MECP2 gene–>Essential for nerve cell function via activation/repression of transcription, so leads to improper brain development and is LETHAL.
  3. Results in…
    a.) Males: Die in utero typically
    Females: Affected more commonly, but may survive
188
Q

Describe Incontinentia Pigmenti: (4)

A
  1. X-Linked Dominant
  2. Mutation in the IKBKG gene
  3. Leads to rashes and blisters early in life, and later patches of hyperpigmentation + learning disability.
  4. Variable expression in females due to X-inactivation
189
Q

Describe “Female Mosaics” with respect to Incontinentia Pigmenti:

A

Heterozygote females will have dark patchy pigmentation where the mutant X is active and normal pigmentation where the normal X is active.

190
Q

Describe Y-Linked Inheritance:

Give 3 examples….

A 
1. ONLY males are affected, so all male-male transmission
Examples:
a.) SRY gene mutations
b.) H-Y Histocompatibility Antigen
c.) Hairy Ears
191
Q

Differentiate between Incomplete Penetrance and Variable Expression:

A
  1. Incomplete Inheritance: ALL or NONE presentation of phenotype in affected individuals (BUT incomplete, so some affected still have NO manifestations)
  2. Variable Expression: Graded level of manifestation in females due to skewed lyonization, some affected individuals will show more manifestations than others.
192
Q

Describe Age-Dependent Penetrance:

Give 3 examples….

A
  1. Penetrance may have a delayed onset so the disorder doesn’t exhibit complete penetrance until around the age of 70 or 80 years old.
  2. Example:
    a. ) Huntington’s Disease (Autosomal Dominant)
    b. ) Familial Breast Cancer
    c. ) Hemochromatosis (Autosomal Recessive)
193
Q

How do you calculate recurrence risk for incompletely penetrating disorders?

A

Multiply the:

(R.R.% x Penetrance) / 100

194
Q

3 Explanations for Variable Expression:

Give 3 Examples…..

A

REM
1. Random Chance
2. Environmental Exposure
3. Modifier Loci (other genetic factors)
Examples:
a.) Hemochromatosis: Autosomal Rec. (Iron overload) More severe in males because females menstruate and lose some iron.
b.) Xeroderma Pigmentosum: Autosomal Rec. (Defective Pigment) More severe in individuals exposed more frequently to UV radiation.
c.) Osteogenesis Imperfecta: Autosomal Dom. (Bone fractures and blue sclera/deafening) Random chance for variable expression.

195
Q

Describe the Penetrance of Neurofibromatosis Type-1:

A

HIGH penetrance, but VARIABLE expression

196
Q

Define Pleiotropy:

Give 3 examples…..

A
  1. Affecting multiple ORGAN SYSTEMS
  2. Examples:
    a. ) Marfan Syndrome
    b. ) Osteogenesis Imperfecta
    c. ) Waardenburg Syndrome
197
Q

Describe Marfan Syndrome: (3)

A
  1. Autosomal Dominant
  2. Mutation in the Fibrillin-1 gene
  3. Results in:
    a. ) Skeletal Abnormalities
    b. ) Ocular Abnormalities
    c. ) Cardiovascular Disease
    d. ) Arachnodactyly (long, thin fingers)
    e. ) Concave Chest/Improper Heart dev.
198
Q

Describe Osteogenesis Imperfecta: (3)

A
  1. Autosomal Dominant
  2. Mutation in the COL1A1/COL1A2 genes–>Defect in the structure of COLLAGEN.
  3. Results in:
    a. ) Blue Sclera
    b. ) Bone Fractures
    c. ) Deafness
199
Q

Differentiate between Allelic and Locus Heterogeneity:

A
  1. Allelic: Different mutations in the SAME gene can cause the same mutation.
  2. Locus: Different mutations in DIFFERENT genes can cause the same mutation.
200
Q

Describe Gene Complementation:

A

For a disorder exhibiting Locus Heterogeneity, heterozygotes for both mutations (i.e. AaBb) will NOT manifest any phenotypic symptoms.

201
Q

What disorder is an example of locus heterogeneity? What else is it an example of?

A
  1. Charcot Marie Tooth Disease

2. Incomplete Penetrance

202
Q

Give 3 Examples of Allelic Heterogeneity:

A
  1. Neurofibromatosis
  2. Hemochromatosis
  3. Cystic Fibrosis
203
Q

What becomes more likely in the offspring of older fathers and mothers respectively?

A
  1. Fathers: New Mutations (De Novo)

2. Mothers: Nondisjunction (Trisomy)

204
Q

What do Nondisjunction in the Spermatocytes during Meiosis 1 and Meiosis 2 lead to respectively?

A
  1. Meiosis 1: Turner (X), Klinefelter (XXY)

2. Meiosis 2: XYY, XXX

205
Q

Explain Germline Mosaicsm:

A

When a disorder is present in a PORTION of the spermatocytes of the father who is not himself affected, but he therefore passes it on to some of his children.

206
Q

Differentiate between Germline Mosaicism and De Novo Mutations:

A

De Novo Mutations would likely only occur in ONE offspring, whereas germline mosaicism could appear in multiple offspring.

207
Q

How is Glycine different from the other 19 amino acids?

A
  1. It is symmetric

2. It is NOT Chiral

208
Q

How is Proline different from the other 19 amino acids?

A

It has a SECOND amino group in its side chain that forms a ring structure

209
Q

Define Aliphatic:

A

Only bonded to “C” and “H”

i.e. NON-Polar

210
Q

List the only amino acids with aliphatic (non-polar) side chains: (6)

A
  1. Alanine
  2. Proline
  3. Glycine
  4. Valine
  5. Leucine
  6. Isoleucine
211
Q

List the only amino acids with aromatic side chains:

A
  1. Tryptophan
  2. Tyrosine
  3. Phenylalanine
212
Q

Of the aromatic amino acids, which absorbs light the best?

A

Tryptophan > Tyrosine > Phenylalanine

213
Q

Which amino acids contain sulfur?

A
  1. Cysteine

2. Methionine

214
Q

List the only Polar, but uncharged amino acids:

A
  • STAG*
    1. Serine
    2. Threonine
    3. Asparagine
    4. Glutamine
215
Q

What determines the charge of the amino acid at physiological pH?

A

The possible charge of the side chain

216
Q

Define Zwitterion:

A

When an amino acid is at neutral pH and the side chain carries no net charge

217
Q

List the (+) and (-) charged amino acids:

A
  • -> Positive:
    1. Lysine
    2. Arginine
  • -> Negative
    1. Aspartate
    2. Glutamate
218
Q

Define Isoelectric Point:

A

The pH at which an amino acid has NO NET charge

219
Q

3 Main Blood Buffer Systems:

A
  1. Phosphate Buffer System
  2. Hemoglobin Buffer in RBC’s
  3. Bicarbonate Buffer in Plasma
220
Q

How are GABA, Histamine, and Serotonin formed?

A
  1. GABA = DECARBOXYLATION of Glutamate
  2. Histamine = DECARBOXYLATION of Histidine
  3. Serotonin:
    a. ) 1st = Hydroxylation of Tryptophan
    b. ) 2nd = DECARBOXYLATION of Hydroxytryptophan
221
Q

Describe the mechanism of Prozac (Fluoxetine):

A

Prozac = (SSRI: Selective Serotonin Re-Uptake Inhibitor)

It blocks the elimination of Serotonin from the synaptic cleft, acting as an anti-depressant.

222
Q

What other drug increases the effects of Serotonin?

A

LSD (Lysergic Acid Diethylamide)

223
Q

Describe the 4 steps of Epinephrine formation:

A
  • ->1. Tyrosine Hydroxylase:
    a. ) Tyrosine–>3,4-DOPA
  • ->2. DOPA Decarboxylase:
    b. ) 3,4-DOPA–>Dopamine
  • ->3. Dopamine-B-Hydroxylase:
    c. ) Dopamine–>NE
  • ->4. Phenylethanolamine-N-MethylTransferase
    d. ) NE–>Epinephrine
224
Q

4 Functions of Epinephrine:

A

INCREASE ENERGY

  1. Release of Glucose from Liver
  2. Release of F.A.’s from Adipose
  3. Increase B.P.
  4. Increase C.O.
225
Q

Define Peptide Bond:

A

A bond between the Carboxyl group of one amino acid and the amino group of another amino acid

226
Q

Peptide bonds are _______, but ______. They are also in the _____ configuration.

A
  1. UNCHARGED
  2. POLAR
  3. Trans-configuration
227
Q

Where is rotation possible with respect to peptide bonds?

A

Around the alpha-carbon only

228
Q

Describe the location of polar and non-polar amino acid SIDE CHAINS in a protein respectively:

A
  1. Polar: Cluster on the SURFACE of the protein structure

2. Non-Polar: On the INTERIOR of proteins (hydrophobic)

229
Q

What stabilizes secondary structure of proteins?

A

H-Bonds between the PEPTIDE BONDED atoms

i.e. H-bonds within the alpha helix or beta pleated sheet

230
Q

3 Things that Disrupt the Alpha Helix:

A
  1. Charged R-Groups
  2. Bulky R-Groups
  3. Proline And Glycine
    a. ) Proline: Causes bends/kinks
    b. ) Glycine: Allows too much rotation
231
Q

What stabilizes the TERTIARY structure of a protein?

A
  1. R-GROUP Interactions:
    a. ) H-bonds (btwn uncharged chains, OR one charged and one uncharged chain)
    b. ) Disulfide bonds
    c. ) Ionic interactions (oppositely charged side chains)
232
Q

Differentiate between Van der Waals Forces and Ion Dipole Forces:

A
  1. Van der Waals: H-bonds between two uncharged, polar side chains.
  2. Ion Dipole: H-bonds between one charged, polar side chain and one uncharged, polar side chain.
233
Q

What is a Cystine residue?

A

Two Cysteine amino acids LINKED by a disulfide bond

234
Q

Describe the structure of Insulin:

A

Two polypeptide chains (A and B chain) held together by 2 INTER-chain disulfide bonds, with the A chain folded by an additional INTRA-chain disulfide bond

235
Q

What is the C-Peptide of Insulin necessary for?

A

The proper formation of disulfide bonds in Insulin

236
Q

Compare the structures of Myoglobin and Hemoglobin:

A
  • —->1. Myoglobin:
    a. ) Tertiary Structure (single polypeptide)
    b. ) ALL alpha helices, no Beta sheets
  • —->2. Hemoglobin:
    a. ) Quaternary Structure (multiple polypeptides)
    b. ) 2 alpha/2 beta subunits
237
Q

What holds each subunit (polypeptide chain) of a quaternary protein together?

A

NON-COVALENT forces

i.e. Everything except disulfide bonds

238
Q

What are Heat Shock Proteins?

A

(Hsp60) CHAPERONES that facilitate proper folding of proteins via ATP HYDROLYSIS

239
Q

What is done with mis-folded proteins?

A
  1. Tagged with Ubiquitin
  2. Degraded by the Proteasome
    (VIA ATP HYDROLYSIS)
240
Q

Give 2 example of mis-folded proteins accumulating instead of being degraded by the proteasome:

A
  1. Alzheimer’s Disease: Mis-folded protein is very stable

2. (TSE) Transmissible Spongiform Encephalopathy

241
Q

What are the 3 forms of TSE’s discussed in class?

A
  1. Humans: Creutzfeldt-Jacob Disease
  2. Sheep: Scrapie
  3. Cows: Mad Cow Disease
242
Q

Describe Prions:

A
  1. Proteinaceous Infectious Agent
  2. Two Types:
    a. ) Normal = PrPc (in neurons): HIGH Alpha Helical
    b. ) Mutant = PrPsc (“sc” for scrapie) HIGH Beta Pleated
  3. Contain NO nucleic acid
243
Q

Define Denaturation:

A
  1. Changing the 3-D structure of a protein

2. BUT primary structure remains intact

244
Q

4 Methods of Denaturation:

A
  1. Heat
  2. Strong Acids/Bases
  3. Detergents
  4. Thiol-containing Compounds
245
Q

Describe Mitochondrial Inheritance:

A

Maternal Mitochondrial DNA is always passed down to offspring, so ALL offspring off an affected female will be affected

246
Q

Define Heteroplasmy:

A
  1. Essentially “Variable Expression” for Mitchondrial Disorders ONLY
  2. A severely affected individual is simply expressing MORE mutant DNA than normal DNA.
247
Q

Define MELAS:

A
  1. “Mitochondrial Encephatlopathy, Lactic Acidosis, and Stroke-like Episodes”
  2. A mitochondrial disorder showing only mild symptoms in offspring of mildly affected mothers.
248
Q

Mitochondrial disorders are said to be _______, and 3 examples of this are: ________ and _______.

A
  1. Pleiotropic: Affecting multiple organ systems
  2. Examples:
    a. ) MELAS
    b. ) MERRF (Myoclonic Epilepsy with Ragged Red Muscle Fibers)
    c. ) LHON: Leber Hereditary Optic Neuropathy
249
Q

3 Types of Non-Mendelian Inheritance:

A
  1. Digenic Disorders
  2. Imprinting
  3. Triplet Repeat Disorders
250
Q

Describe Digenic Inheritance:

A

Must have mutation in BOTH genes to manifest mutation
i.e. AaBb = AFFECTED
But, AABb and AaBB are normal phenotype

251
Q

Define Imprinting:

A

Altering the methylation pattern (EPIGENETIC) of genes to affect their expression

252
Q

Describe the normal imprinting on Chromosome 15:

A
  1. PATERNAL = SNRPN active

2. MATERNAL = UBE3A active

253
Q

Describe the 2 ways Prader Willi Syndrome can be caused:

A
  1. Microdeletion of PATERNAL chromosome 15, so the only active copy of SNRPN is deleted.
  2. Maternal Uniparental Disomy, so both copies of chromosome 15 (silenced SNRPN) have come from the mother.
254
Q

Describe the 2 ways Angelman Syndrome can be caused:

A
  1. Microdeletion of MATERNAL chromosome 15, so the only active copy of UBE3A is deleted.
  2. Paternal Uniparental Disomy, so both copies of chromosome 15 (silenced UBE3A)have come from the father.
255
Q

How can you determine which of the two possible modes of transmission was responsible for an individual’s Prader Willi syndrome?

A
  1. If Microdeletion: There will be only one functional copy of UBE3A from the mother.
  2. If Maternal Uniparental Disomy: There will be TWO functional copies of maternal UBE3A present.
256
Q

Since Trisomy 15 is a lethal disorder, how do our cells correct for this disorder and result in Angelman or Prader Willi syndrome rather than death?

A
  1. Either Mother’s or Father’s Chromosome 15 must be destroyed.
  2. TWO different pathways:
    a. ) ANGELMAN Syndrome = Trisomy with 2 paternal copies, so the only MATERNAL is destroyed.
    b. ) PRADER WILLI Syndrome = Trisomy with 2 maternal copies, so the only PATERNAL copy is destroyed.
257
Q

Describe Methylation Analysis with respect to Chromosome 15:

A

Female Chromosome 15 is methylated at slightly different points than male chromosome 15, so ONLY MALE copies will be cleaved by a restriction enzyme at methylation sites to determine if phenotypes will develop severely in young children not yet showing manifestations.

258
Q

How can you test to determine whether or not Maternal or Paternal Uni-parental Disomy has occurred on chromosome 15?

A
  1. Look for SNP’s (single nucleotide polymorphisms) from BOTH parents DNA
  2. Compare them to the SNP’s in the offspring DNA
  3. This will show which 2 chromosomes (2 paternal or 2 maternal) have achieved “trisomy rescue” by the cell to cause the child’s condition.
259
Q

Where specifically on chromosome 15 are the UBE3A and SNRPN genes?

260
Q

Describe Angelman Syndrome:

A
  1. “Happy Puppet Syndrome”
  2. Severe Intellectual Disability
  3. Innapropriate Laughter
  4. Puppet-Like Posture of Limbs
261
Q

Describe Prader Willi Syndrome:

A
  1. Obesity
  2. Mental/Developmental Delay
  3. Underdeveloped Genitalia
  4. Hypotonia (Failure to Thrive) in Infancy
262
Q

Describe the 4 Classes of Triplet Repeat Disorders and give an example for each:

A
  1. (5’-UTR) Promoter Region: Reduces expression of gene
    a. ) Repeat = (CGG) Easily Methylated (silenced)
    b. ) Fragile X Syndrome
  2. Intron Region: Reduces expression of gene
    a. ) Repeat = (GAA) Too tight, forms heterochromatin
    b. ) Friedrich’s Ataxia
  3. Exon Region: Accumulation of Glutamine
    a. ) Repeat = (CAG) Forms too many glutamine in product
    b. ) Huntington’s Disease
  4. 3’-UTR: Affects Post=Translational Modification
    a. ) Repeat = (CTG) High number of repeats affects mod.
    b. ) Myotonic Dystrophy
263
Q

Describe Anticipation:

A

Disorders that get more severe manifestations with each generation due to increasing (unstable) repeats

264
Q

What specific gene mutation causes Fragile X Syndrome?

265
Q

The human body only utilizes _______ amino acids and ______ sugars.

A
  1. (Levo) L-Amino Acids

2. (Dextro) D-Sugars

266
Q

List the 6 Cytosolic Metabolic Pathways:

A

“Go Crazy For The Pretty Girls”

  1. Glycolysis
  2. Cholesterol Synthesis
  3. F.A. Synthesis
  4. TriacylGlycerol Synthesis
  5. Pentose-Phosphate Pathway (PPP)
  6. Gluconeogenesis
267
Q

List the 5 Mitochondrial Metabolic Pathways:

A

“Fat Kids Eat Plenty of Cake”

  1. F.A. Beta-Oxidation
  2. Ketone Body Synthesis
  3. E.T.C.
  4. Pyruvate Dehydrogenase Complex
  5. C.A.C. (Citric Acid Cycle)
268
Q

Give an example of an enzyme optimal at Acidic, Neutral, and Basic pH respectively:

A
  1. Acidic: Pepsin in Stomach
  2. Neutral: Trypsin in Duodenum
  3. Basic: Alkaline Phosphatase
269
Q

Give the Michaelis-Menten Equation:

A

Vo = Vmax[S] / Km + [S]

270
Q

What does the Km represent? What do higher and lower Km’s mean?

A
  1. When the substrate CONCENTRATION is at 1/2 Vmax

2. HIGHER Km = More substrate needed to reach 1/2 Vmax, so it’s WORSE.

271
Q

Describe how the lecture example of a “classic Competitive Inhibitor” functions:

A
  1. Enzyme = HMG-CoA Reductase
  2. Substrate: CoA, Competitor: Statin Drugs
  3. Complex formed is EI instead of ES, so Km increases
272
Q

What is the result of a Non-competitive inhibitor on a reaction?

A

An APPARENT decrease in Vmax

273
Q

What values are used to construct a Lineweaver-Burk Plot

A 
Y-Intercept = 1/Vmax
X-Intercept = -1/Km

Term 1 (8 decks)

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