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1
Q

Griffith’s experiment

A
  • When a mouse was injected with virulent bacteria, it died of pneumonia.
  • When a mouse was injected with non-virulent vacteria, it remained healthy.
  • When a mouse was injected with heat-killed virulent bacteria, it remained healthy.
  • When a mouse was injected with heat-killed virulent bacteria mixed with live non-virulent bacteria, it died of pneumonia.

This experiment revealed that some type of molecule in the heat-killed debris was capable of carrying the genetic information of virulence to the live bacteria.

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2
Q

Avery-MacLeod-McCarty experiment

A
  • When virulent bacteria extract was added to non-virulent bacteria alone, the bacteria were virulent and non-virulent.
  • When virulent bacteria extract was added to non-virulent bacteria with RNase (breaks down RNA), the bacteria were virulent and non-virulent.
  • When virulent bacteria extract was added to non-virulent bacteria with protease (breaks down proteins), the bacteria were virulent and non-virulent.
  • When virulent bacteria extract was added to non-virulent bacteria with DNase (breaks down DNA), the bacteria were solely non-virulent.

This experiment revealed that DNA carries genetic information.

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3
Q

nucleotide structure

A
  • a negatively charged phosphate group, with ionized hydroxyl groups
  • a deoxyribose sugar
  • a nitrogenous base (A, G, T, or C)
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4
Q

the four bases

A
  • adenine (A)
  • guanine (G)
  • thymine (T)
  • cytosine (C)
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5
Q

purines

A

adenine and guanine

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6
Q

pyrimidines

A

thymine and cytosine

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7
Q

nucleoside structure

A
  • a deoxyribose sugar
  • a nitrogenous base (A, G, T, or C)
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8
Q

three types of nucleotides

A
  • nucleoside monophosphate (1 phosphate group)
  • nucleoside diphosphate (2 phosphate groups)
  • nucleoside triphosphate (3 phosphate groups)
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9
Q

phosphodiester bond

A

the connection between nucleotides via phosphate groups

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10
Q

5’ vs. 3’ end of DNA

A
  • free 5’ phosphate group marks the beginning of the DNA strand
  • free 3’ ribose sugar marks the end of the DNA strand
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11
Q

what winds around the outside of the DNA molecule

A

the sugar-phosphate backbone

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12
Q

The two strands of DNA are…

A

antiparallel; they run in opposite directions

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13
Q

base pairing

A
  • A=T
  • C≡G
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14
Q

two things that contribute to the stability of DNA

A
  • hydrogen bonding
  • base stacking
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15
Q

these types of interactions hold the shape of DNA

A

hydrophobic interactions

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16
Q

DNA is packaged with proteins called…

A

histones

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17
Q

histone composition

A

positively charged amino acids (e.g. lysine, arginine)

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18
Q

these two things make complexes that form chromatin

A

histones and DNA

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19
Q

the number of chromosomal pairs in a regular human being

A

23 pairs; one homolog/parent

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20
Q

the phase at which DNA replication occurs

A

S phase

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21
Q

the two hypothetical models for replication, and the one that’s true

A
  • semi-conservative: the new DNA duplex consists of one old strand (parental) and one new strand (daughter)
  • conservative: the new DNA duplex consists of two newly synthesized daughter strands, leaving the parental duplex intact

The semi-conservative model is the true one.

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22
Q

Meselson-Stahl Experiment

A
  1. Both strands of DNA are labeled with heavy nitrogen (heavy/heavy). The DNA molecules forms a band of heavy density.
  2. After one round of replication, the parent and daughter strands are heavy/light. The two DNA molecules form a band of intermediate density.
  3. After another round of replication, half of the DNA molecules are light/light, forming a light density, and the other half are heavy/light, forming an intermediate density.

This experiment revealed that DNA is indeed semi-conservative.

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23
Q

the steps of DNA synthesis

A
  1. Helicase unwinds the DNA molecule, resulting in a replication fork. Topoisomerase II relieves the stress of unwinding, whilst single-stranded binding proteins stabilize single strands of DNA.
  2. RNA primase lays down an RNA primer.
  3. DNA polymerase III extends the RNA primer by elongating eh end of existing DNA. The 3’ hydroxyl end of the growing strand emits a pyrophosphate (two phosphate groups) as nucleotides are accepted.
  4. Replication occurs in the 5’ to 3’ direction. The daughter strand on the top elongates from left to right, whereas the daughter strand on the bottom elongates from right to left.
  5. Replication of the top strand (leading strand) is discontinuous - leaving Okazaki fragments (gaps) - whereas replication of the bottom strand (lagging strand) is continuous.
  6. DNA polymerase I removes the RNA primer and replaces it with DNA.
  7. DNA ligase joins Okazaki fragments.
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24
Q

the trombone model of DNA replication

A

DNA synthesis between the leading and lagging strands occurs at the same time and rate. The lagging strand is looped around to maintain contact between the polymerase complexes.

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25
Q

proofreading

A

DNA polymerase removes and replaces incorrect nucleotides during DNA synthesis. Though very rare, without proofreading, mutations may occur.

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26
Q

origins of replication in eukaryotes vs. prokaryotes

A

Eukaryotes (linear DNA) have many origins of replication, whereas prokaryotes (circular DNA) have one origin of replication.

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27
Q

telomeres

A
  • a region of repetitive nucleotide sequences (1,500-3,000 repeats) capped at each end of a chromosome
  • act as buffers, ensuring genetic information isn’t lost in DNA replication
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28
Q

the shortening of DNA, and the role of telomerase

A

After DNA replication, after the RNA primer is removed, there is a section of template DNA that remains unreplicated. After every round of replication, the template would get shorter and shorter, resulting in a shorter chromosome.

Telomerase contains an RNA template that allows the shortened 3’ end of the template strand to be restored via the addition of more telomere repeats.

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29
Q

the effect of the shortening of DNA on aging

A

Telomerase activity differs between different cells; stem cells have fully active telomerase, whereas in other adult cells (e.g. skin, liver), telomerase is inactive.

When telomers shorten to about 100 copies of telomere repeats, cell division stops; resulting in aging.

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30
Q

two forms of DNA manipulation

A

polymerase chain reaction (PCR) and gel electrophoresis

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31
Q

three steps of PCR

A
  1. denaturation: a solution containing double-stranded template DNA is heated to separate the DNA into two individual strands
  2. annealing: the solution is cooled, causing two DNA primers (20-30 nucleotides) to anneal to their complementary sequence on the two DNA strands; lots of primers are used to ensure they bind to DNA before the strands themselves come back together
  3. extension: DNA polymerase synthesizes new DNA strands - complementary to the template DNA strands - by extending primers in a 5’ to 3’ direction
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32
Q

four components of PCR

A
  • template DNA
  • DNA polymerase (e.g. Taq DNA polymerase)
  • the four deoxyribonucleoside triphosphates (dNTPS) (A, T, G, or C)
  • forward and reverse primers
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33
Q

the number of copies of the template sequence after PCR

A

2n copies, after n cycles of amplification

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34
Q

Taq DNA polymerase

A
  • derived by the bacteria thermus aquaticus
  • often used in PCR due to its heat-resistance (it’s a thermophile) and presence of DNA polymerase
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35
Q

a common number of cycles of amplication for PCR

A

30 cycles

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36
Q

steps of gel electrophoresis

A
  1. DNA samples are inserted into wells at one end of the agarose gel (the gel controls the speed at which DNA travels).
  2. An electric current is applied, resulting in the movement of DNA toward the anode (positive electrode).
  3. DNA is separated by size (kilobases (kb)), with smaller molecules moving farther than longer molecules.
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37
Q

steps of CRISPR/Cas9

A
  1. Guide RNA (gRNA) combines with the Cas9 protein.
  2. gRNA brings Cas9 to the target DNA and the target is cleaved.
  3. An exonuclease widens the gap in the target DNA.
  4. The editing template is used to repair the gap in the target DNA.
  5. The result is an edited DNA with an altered sequence.
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38
Q

possibilities of CRISPR

A

CRISPR has been used to fix monkeys with cystic fibrosis.

It could possibly be used to not only fix mutations, but edit human embryos.

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39
Q

risks of CRISPR

A
  • ethical issues (especially for the editing of human embryos)
  • risk of changing genes other than the intended ones (must be highly specific)
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40
Q

CFTR acronym

A

cystic fibrosis transmembrance conductance regulator

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41
Q

how cystic fibrosis works

A

CFTR is a chloride ion channel.

  • Normal CFTR channels move chloride ions to the outside of the cell; water following the movement of ions.
  • Mutant CFTR channels dont move chloride ions, causing sticky mucus to build up on the outside of the cell. Airways and intestines are dehydrated, gut absorption is compromised, and frequent (usually fatal) bacterial infections arise.
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42
Q

DNA editing in cystic fibrosis

A

Organoids (cell clusters made in petri dishes; “mini-guts”) are used to test CRISPR.

  • In mutated organoids (CFTR F508Del), CFTR activation doesn’t occur.
  • However, in mutated organoids with CRISPR activated cells (CFTR 508Del-Corrected clone (S1-c1 and S1-c2), CFTR can be activated with a chemical called forskolin, allowing for salts and fluid to fill the organoid.
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43
Q

mutation in cystic fibrosis patients

A

CFTR F508DEL
deletion (DEL) of phenylalanine (F) at position 508 (508)

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44
Q

eugenics

A

the scientifically inaccurate theory that humans can be improved through selective breeding of populations (CRISPR)

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45
Q

the Central Dogma

A

replication → transcription → translation

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46
Q

four differences between RNA and DNA

A
  • RNA has a ribose sugar (hydroxyl group on carbon 2), whereas DNA has a deoxyribose sugar (hydrogen group on carbon 2)
  • one of RNA’s bases is uracil (hydrogen), rather than thymine (methyl group) in DNA
  • RNA has a 5’ triphosphate end, where DNA has a 5’ monophosphate end
  • RNA is much smaller than DNA
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47
Q

RNA world hypothesis

A

many scientists believe RNA molecules were the first nucleic acids because

  • RNA is involved in many cellular processes (i.e. all the steps of the central dogma)
  • RNA has enzymatic properties
  • it is thought that DNA is used by cells because it is more stable than RNA
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48
Q

DNA transcription

A

DNA serves as the template for RNA production by the cell

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49
Q

initiation of DNA transcription

A
  1. Initation begins at a promoter sequence known as a “TATA box”; an A=T rich sequence present in almost every gene.
  2. General transcription factors bind to the promoter.
  3. Enhancer sequences are located near the gene.
  4. Transcriptional activator proteins bind to enhancers.
  5. Proteins bound to enhancers recruit a mediator complex.
  6. RNA polymerase II adds nucleotides, via a process called “elongation”; the 3’ hydroxyl end of the growing strand emits a pyrophosphate (two phosphate groups) as ribonucleotides are accepted.
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50
Q

The first nucleotide transcribed is positioned about ____ base pairs from the TATA box.

A

25

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51
Q

the four separate channels for RNA polymerase in prokaryotes

A
  • the entry for RNA nucleotides (trinucleotides)
  • the entry for DNA to be transcribed
  • the exit for the RNA transcript
  • the exit for the transcribed DNA
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52
Q

DNA transcription and translation in prokaryotes

A
  • these two processes occurc simultaneously within the cytoplasm of prokaryotic cells
  • mRNA can contain the information for more than one gene, leading to the synthesis of multiple proteins; these primary transcrips are called polycistronic mRNA
  • there are no post-translational modifications in prokaryotes
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53
Q

an other name for “primary transcripts”

A

mRNA

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54
Q

post-translation modifications in eukaryotes

A
  • a 5’ cap is a modified base linked by its 5’ carbon to the 5’ end of mRNA by a bridge composed of three phosphates; it contributes to mRNA stability
  • via polyadenylation, a poly(A) tail (approx. 250 A-bearing nucleotides) is added to the 3’ end of mRNA; it contributes to the export for mRNA into the cytoplasm and mRNA stability
  • via spliceosomes (composed of RNA and proteins), splicing occurs within mRNA; exons are protein-coding regions kept with the transcript, however, a lariat (containing non-coding introns and the 3’ splice), is broken down into individual nucleodies
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55
Q

alternative splicing

A

certain exons may be treated as introns, leading to different proteins, and different cell functionality

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56
Q

amino acid structure

A
  • amino group
  • α carbon
  • R group
  • carboxyl group
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57
Q

hydrophobic amino acids

A

these acids tend to be buried in the interior folds of proteins

  • alanine (Ala, A)
  • valine (Val, V)
  • leucine (Leu, L)
  • isoleucine (Ile, I)
  • methionine (Met, M)
  • phenylalanine (Phe, F)
  • tryptophan (Trp, W)
  • tyrosine (Tyr, Y)
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58
Q

hydrophilic amino acids

A

polar
* asparagine (Asn, N)
* glutamine (Gln, Q)
* serine (Ser, S)
* threonine (Thr, T)

basic
* lysine (Lys, K)
* histidine (His, H)
* arginine (Arg, R)

acidic
* aspartic acid (Asp, D)
* glutamic acid (Glu, E)

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59
Q

three special amino acids

A
  • glycine (Gly, G) is small and flexible
  • proline (Pro, P) creates kinks
  • cysteine (Cys, C) forms disulfide bridges within and between proteins
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60
Q

formation of a peptide

A

the synthesis of two amino acids via a dehydration reaction (water is expelled as a product)

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61
Q

alternative nomenclature for “protein” and “amino acid”

A
  • protein = polypeptide
  • amino acid = residue
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62
Q

directionality of proteins

A
  • N terminal (amino) to C terminal (carboxyl)
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63
Q

protein structure

A
  • Primary structure is the linear sequence of amino acids.
  • Secondary structure results from interactions of nearby amino acids (i.e. α helix or β sheet).
  • Tertiary structure is the three-dimensional shape, determined by the distribution of hydrophilic and hydrophobic R groups, and the chemical bonds and interactions between said R groups. It is the final structure for most proteins.
  • Quarternary structure results from the combination of multiple polypeptide subunits (e.g. hemoglobin is made up of two α subunits and two β subunits).
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64
Q

α helix

A
  • each carbonyl group forms a hydrogen bond with an amide group four amino acids away
  • the polypetide chain is twisted tightly in a right-handed coil
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65
Q

β sheet

A
  • hydrogen bonds form between carbonyl groups in one polypeptide and amide groups in a different part of the polypeptide
  • adjacent strands can run in the same direction (parallel) or in opposite directions (antiparallel)
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66
Q

the determination of protein function

A

protein function is determined by protein shape, which is determined by a protein’s primary structure

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67
Q

chaperones

A
  • proteins that bind newly made proteins and help them fold
  • can help protect against denaturation
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68
Q

components of DNA translation

A
  • mRNA
  • ribosome
  • tRNAs
  • aminoacyl tRNA synthethases
  • initiation, elongation, and release factors
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69
Q

ribosome

A
  • made up of proteins and ribosomal RNAs
  • moves down the mRNA from 5’ to 3’ and reads individual codons to incorporate the appropriate amino acids
  • contains a large and small subunit
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70
Q

the three functional sites of the ribosome

A
  • The A site accepts the aminoacyl tRNA.
  • The P site is where peptide bond formation occurs.
  • The E site is where the tRNA exits the ribosome.
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71
Q

initiation of DNA translation in prokaryotes

A
  • ribosomes bind to the Shine-Dalgarno sequence - a sequence preceding every start codon
  • one mRNA can code for several polypeptides
  • elongation and termination are similar to eukaryotic translation
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72
Q

tRNA’s 3’ end

A
  • has the nucleotide CCA at its 3’ end
  • the 3’ hydroxyl of the A is the attachment site for the amino acid
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73
Q

tRNA synthetases

A

charge tRNAs by attaching the respective amino acid

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74
Q

the start codon

A

AUG (Met, M)

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75
Q

the stop codons

A
  • UAA
  • UAG
  • UGA
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76
Q

three stages of translation

A

initiation
* Initiation factors recruit the small ribosomal subunit and tRNAMet scans the mRNA for the AUG start codon.
* When the complex reaches an AUG, the large ribosomal subunit joins, and initiation factors are released.

elongation
* A tRNA complementary to the next codon binds to the A site.
* A reaction transfers the Met to the amino acid on the tRNA in the A site, forming a peptide bond.
* The ribosome moves down one codon, which puts the tRNA carrying the polypeptide into the P site, and the now-uncharged tRNA into the E site, where it is release.
* A new tRNA complementary to the next codon binds to the A site.
* The polypeptide transfers to the amino acid on the tRNA in the A site.
* The polypeptide is elongated as this process repeats.

termination
* When a stop codon is encountered, a release factor enters the A site.
* The polypetide is released from the tRNA in the P site, and the ribosome dissociates.

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77
Q

locations of the Central Dogma in eukaryotes

A
  • DNA synthesis occurs in the nucleus
  • DNA transcription occurs in the nucleus
  • DNA translation occurs in the cytoplasm
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78
Q

folding domains

A

small regions of 3D structure shared by members of a protein family, independent of the rest of the protein

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79
Q

mRNA travels through ____________ into the cytoplasm.

A

nuclear pores

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80
Q

protein sorting

A

the first few amino acids of the polypeptide dictate where it will be transported after translation

81
Q

DNA translation in the rough endoplasmic reticulum (RER)

A
  1. The signal-recognition particle (SRP) binds to a signal sequence in the amino-terminal end of the growing polypetide; translation is paused.
  2. The SRP binds to the SRP receptor on the ER membrane.
  3. The SRP receptor brings the ribosome to a transmembrane channel; the SRP dissociates, protein synthesis resumes, and the growing polypeptide chain travels through the channel.
  4. The protein ends up in the lumen of the ER, where it may remain, be trasported to the lumen of another organelle, or be secreted out of the cell.
82
Q

cap-dependent translation vs. cap-independent translation

A
  • Cap-dependent translation occurs in most host proteins in the cell; ribosomes and translation initiation factors scan from the cap to find the start codon.
  • Cap-independent translation (e.g. poliovirus mRNAs) use an internal ribosome entry site (IRES).
83
Q

chromatin remodeling

A
  • histone tail modification (histone code) repositions nucleosomes and exposes DNA to transcription machinery
  • occurs during development and in response to environmental cues
84
Q

DNA methylation

A
  • cytosine bases on CpG islands (a C≡G rich sequence) in DNA are methylated via enzymes
  • heavy methylation inhibits transcription
85
Q

Epigenetic adaptations are passed on…

A

generationally

86
Q

epigentics and stress

A
  • In normal development, when stressed, glucocorticoid receptor in the hippocampus suppresses stress.
  • In early-life adversity (e.g. childhood anxiety), there are lower levels of glucocorticoid receptor due to methylation, resulting in less stress suppression.
87
Q

the three germ layers

A
  • ectoderm: outer skin layer, brain, spinal cord, peripheral nerve cells, pigment cells
  • mesoderm: inner skin layer, muscle, bone, blood
  • endoderm: inside lining of the gut and lung, liver, pancreas
88
Q

development of an embryo

A
  1. A fertilized human egg is totipotent; it can give rise to all cell types in a complete organism, along with extraembryonic structures, and placental cells.
  2. Embryonic stem cells (cells of the inner cell mass) are pluripotent; they can give rise any body cell.
  3. Cells of the germ layer are multipotent; they can give rise to a limited number of specialized cells.

Totipotent, pluripotent, and multipotent cells are all stem cells.

89
Q

induced pluripotent stem (iPS) cell therapy

A

there is a 1 in 1 billion chance of success that iPS cells - resemblind embryonic stem cells - can be differentiated into any type of human cell type

90
Q

regulation of the X chromosome

A
  • the level of expression of X-linked genes is the same in both sexes
  • if both chromosomes were active, females (XX) would have two times the X dosage as males (XY); this isn’t possible as we are the same species
91
Q

X-inactivation

A

embryonic X-inactivation occurs at the time of implantation in the uterine wall; itonly occurs in females

  1. The Xist gene is transcribed and Xist RNA binds with the X-chromosome inactivation center (XIC).
  2. Transcription of Xist continues; the entire chromosome becomes coated with Xist RNA.
  3. Xist RNA triggers DNA methylation and other changes, associated with reduced transcriptional activity.
92
Q

translational regulation

A
  • one strand of small regulatory RNAs is incorporated into a RISC complex that targets complementary mRNA sequences
  • in small interfering RNA (siRNA), there are no mismatches between the siRNA and the target mRNA, resulting in RISC cutting up mRNA
  • in micro RNA (miRNA), there are some mismatches between the miRNA and the target mRNA, resulting in translational inhibition
93
Q

the winners of The Nobel Prize in Physiology or Medicine 2024, “for the discovery of microRNA and its role in post-transcriptional gene regulation”

A

Victor Ambros and Gary Ruvkun

94
Q

translational regulation and untranslated regions (UTRs)

A

proteins can bind to UTRs to impact mRNA stability

95
Q

iron metabolism and gene regulation

A
  • Humans use iron to make new red blood cells, however, too much free iron is toxic.
  • mRNA for ferritin (the iron-sequestering protein) forms a hairpin at the iron response element (IRE).
  • mRNA for transferrin receptor, needed to transport iron into the bloodstream, also has an IRE, but also includes instability elements; specific sequences which bind proteins that target the mRNA for destruction.
  • The iron-response element binding protein (IRE-BP) binds IREs in the absence of iron. In the presence of iron, there’s a conformational change that disallows it to bind to IREs.
96
Q

reasons for cell division

A
  • growth
  • replacement
  • healing
  • reproduction
97
Q

four phases of interphase

A
  • G1 phase
  • S phase
  • G2 phase
  • G0 phase
98
Q

stages of mitosis

A
  1. prophase: chromosomes condense; centrosomes form microtubules (mitotic spindle), and migrate to opposite poles
  2. prometaphase: microtubules of the mitotic spindle attach to the kinetochores of chromosomes
  3. metaphase: chromosomes align in the center of the cell
  4. anaphase: sister chromatids separate and travel to opposite poles
  5. telophase: the nuclear envelope re-forms, and chromosomes decondense
  6. cytokinesis: the cytoplasm splits, resulting in two identical, diploid daughter cells
99
Q

stages of meiosis

A

MEIOSIS I
1. prophase l: homologous chromosomes condense and cross over, forming bivalents; when fully condensed, chiasmata become distinct, and the nuclear envelope breaks down
2. prometaphase I: spindles attach to kinetochores on chromosomes
3. metaphase I: homologous pairs line up in the center of the cell, with bivalents oriented randomly with respect to each other
4. anaphase I: homologus chromosomes separate (sister chromatids don’t)
5. telophase I and cytokinesis: daughter cells are ready to move into prophase II

MEIOSIS II (equational division)
1. prophase II: the nuclear envelope breaks down and the chromosomes condense
2. prometaphase II: spindles attach to kinetochores on chromosomes
3. metaphase II: chromosomes align in the center of the cell
4. anaphase II: sister chromatids separate
5. telophase II and cytokinesis: the nuclear envelope re-forms and the cytoplasm divides, resulting in four unique, haploid daughter cells

100
Q

cytoplasmic division in germline cells

A
  • for males, the second meiotic division is equal; resulting in four equal sperm cells
  • for females, most of the cytosol is passed onto one of the four daughter cells after the second meiotic division; the biggest cell is the oocyte, and the other three smaller cells are the polar bodies
101
Q

ovoviviparous

A

animals that produce eggs inside their body, but then give birth to live young (e.g. timber rattlesnakes; Crotalus horridus)

102
Q

genetic sex determination in mammals vs. birds/reptiles

A
  • in mammals, males have a Y chromosome (XY), whereas females don’t (XX)
  • in birds and reptiles, females have a W chromosome (ZW), whereas males don’t (ZZ)
103
Q

transmission (Mendelian) genetics

A
  • the manner in which genetic differences among individuals are passed generationally
  • doesn’t apply to humans much, due to many other factors (e.g. more than two alleles, epigenetics)
104
Q

Mendel and pea plant crossing

A
  1. The anthers (sperm-producing structures) of female parents were cut off to prevent self-fertilization.
  2. Pollen is collected from the male, and deposited into the stigma of the female.
  3. After fertilization, a cloth bag is tied around the flower to prevent entry of stray pollen.
105
Q

P1 generation (parental 1 generation)

A

true-breeding strains that are crossed

106
Q

F1 generation (fileal 1 generation)

A
  • only the dominant trait appears
  • all cells are heterozygous
107
Q

F2 generation (fileal 2 generation)

A
  • the recessive trait reappears
  • the genotypic ratio (AA:Aa:aa) is 1:2:1
  • the phenotypic ratio (dominant:recessive) ratio is 3:1
108
Q

the principle of segregation

A

the equal separation of alleles of a gene into different gametes

109
Q

incomplete dominance

A
  • the phenotype of the heterzygote is an intermediate; neither allele is dominant
  • e.g. red snapdragons (CRCR) cross with white snapdragons (CWCW) to form pink snapdragons (CRCW)
110
Q

co-dominance

A
  • each allele produces a distinct phenotype that can be detected in heterozygous individuals
  • e.g. both A-type and B-type modifications are present in AB blood
111
Q

the multiplication rule

A
  • used when outcomes can occur simultaneously, and the occurrence of one doesn’t impact the likelihood of the other
  • e.g. the probability of rolling two fours with two separate die is 1/36 (1/6 × 1/6)
112
Q

the addition rule

A
  • used when possible outcomes cannot occur simultaneously
  • e.g. the probability of rolling a seven with any combination of two die is 1/6 (1/36 + 1/36 + 1/36 + 1/36 + 1/36 + 1/36)
113
Q

principle of independent assortment

A

segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles of a different gene pair

114
Q

the genotypic ratio for an F2 generation and two traits

A

9:3:3:1

115
Q

epistasis

A

two genes interacting to affect the same trait

116
Q

pedigree symbols

A
  • circle = female
  • square = male
  • uncoloured = unaffected
  • coloured = affected
117
Q

pedigree of a dominant allele vs. pedigree of a recessive allele

A
  • a pedigree of a dominant allele appears in every generation
  • a pedigree of a recessive allele doesn’t appear in every generation
118
Q

genetic testing

A

identifying the genotype of an individual, who might be at risk for a certain trait

119
Q

benefits and risks of genetic testing

A

benefits:
* personalized medicine
* better understanding of risks/behaviours
* feeling less anxious; better quality of life

risks:
* limited answers
* physiological/emotional impact
* privacy concerns (life/health insurance)

120
Q

number of genes on sex chromosomes

A
  • approx. 1,000 genes on X chromosomes
  • approx. 50 genes on Y chromosomes
121
Q

lining up of sex chromosomes

A

the tips of the arms of the X and Y chromosomes share a small region of homology, which allow them to line up as homologs in meiosis

122
Q

X-linked disorders

A
  • affected males will have carrier daughters and unaffected sons
  • carrier females can have carrier daughters ad affected sons
123
Q

Human males receive their X chromosome from their…

A

mother

124
Q

nondisjunction in Morgan’s fruit flies

A

in non-disjunction, white-eyed females (w-w-) and red-eyed males (w+Y) can give way to white-eyed females (w-w-Y) and red-eyed males (w+)

125
Q

non-disjunction of sex chromosomes in humans

A
  • XXX (Triple X syndrome)
  • XO (Turner syndrome)
  • XXY (Klinefelter syndrome)
  • OY (embryonically lethal; non-viable)
126
Q

Trisomy 21

A

Down syndrome

127
Q

products of crossing over between two genes

A
  • two recombinant chromosomes
  • two non-recombinant chromosomes
128
Q

recombination frequency

A
  • a measure of the genetic distance between the two genes
  • genes that are linked have a recombination frequency between 0-50%)
129
Q

Y-linked genes

A
  • only males exhibit the trait
  • affected males will have affected sons
130
Q

inheritance of mitochondrial DNA

A
  • genes move with the organelles during cell division
  • both males and females exhibit the trait
  • males don’t transmit the trait, however, all offspring of affected mothers show the trait (only maternal mitochondria remain in the fertilized egg - uni-parental inheritance of mitochondria)
131
Q

genome

A
  • the transmissable genetic material of a cell, organism, organelle, or virus; its sequence is the order of bases along the DNA/RNA
  • the size of a genome and number of genes doesn’t correlate to the complexity of an organism
132
Q

C-value paradox

A

contradiction between genome size and organismal complexity

133
Q

composition of the human genome

A
  • retrotransposons (transpose by means of an RNA intermediate)
  • protein-coding genes (introns, untranslated ends of mRNA)
  • DNA transposons (replicate and transpose via DNA replication and repair)
  • α satellites
  • other (unrecognized, ambiguously annotated, or non-functional gene duplicates)
134
Q

mutation

A
  • any heritable change in the genetic material
  • tend to be spontaneous and at random, though some places are more prone to mutation than others)
  • can take place in reproductive cells (germ-line mutations) or non-reproductive cells (somatic mutations)
135
Q

how breast cancer works

A

The BRCA1 gene on chromosome 17 repairs breaks in DNA. It’s found in all cells, but is expressed in breast and ovarian cells. When non-functional due to a mutation, damaged DNA will not be repaired, leading to an increased risk for breast and ovarian cancers.

136
Q

mutagens

`

A

cause mutations

137
Q

point mutation

A

change in a single nucleotide

138
Q

three types of point mutations

A
  • silent mutations (synonymous mutations) are when a nucleotide substitution doesn’t change the amino acid
  • missense mutations (non-synonymous mutations) are when a nucleotide substitution changes the amino acid
  • nonsense mutations are when a nucleotide substitution creates a stop codon
139
Q

how sickle cell anemia works

A
  • a missense mutation (Val instead of Glu) causes hemoglobin to form long, inflexible chains instead of a bundle
  • sickled red blood cells get stuck in small capillaires, whereas normal red blood cells are flexible and can squeeze through
140
Q

insertions and deletions

A

the addition or deletion of three nucleotides, leading to an extra or missing amino acid

141
Q

frameshift mutation

A

an insertion or deletion that is not an exact multiple of three nucleotides, leading to a change in the reading frame of translation

142
Q

genetic variation

A

genetic differences that exist among individuals in a population at a particular point in time

143
Q

the main source of genetic variation

A

mutations

144
Q

singlue nucleotide polymorphisms (SNPs)

A

common genetic differences that exist between individuals, at single nucleotides

145
Q

variable number of tandem repeats (VNTRs)

A

different numbers of repeated sequences in particular locations between individuals’ chromosomes (i.e. DNA fingerprinting)

146
Q

complex traits

A

quantitative traits that are measured along a continuum, with only small intervals between similar individuals (e.g. height, blood pressure)

147
Q

environmental factors and complex traits

A
  • environmental factors can affect the variation in phenotype between individuals
  • e.g. corn crops are inbred (completely identical genotypes), however crops closer to the edge are shorter due to environmental factors (e.g. weeds, competition)
148
Q

genetics and complex traits

A

multiple genes act cumulatively to determine the intensity of the traits

149
Q

the percentage of genetic and environmental differences amongst human height variation

A
  • 80% genetic differences
  • 20% nutrition/environmental differences
150
Q

genotype-by-environment interactions and perfection

A
  • no one genotype is ideal for all environments
  • no one environment is ideal for all genotypes

an intersection between genotype and environment is what affects the trait

151
Q

Galton’s data for height

A
  • tall parents produce averagely tall offspring that are shorter than their parents (moving down towards the mean)
  • short parents produce averagely short offspring that are taller than their parents (moving up towards the mean)
  • Galton’s data indicates that 60% of the height variation is due to genetic variation, whereas 40% of the height variation is due to environmental variation
152
Q

why regression towards the mean occurs

A
  • in meiosis, recombination and segregation break up combinations of genes that result in extreme phenotypes (e.g. very tall, very short)
  • environmental effects are not inherited
153
Q

heritability

A

the proportion of the variation between individuals that can be attributed to genes alone

154
Q

identical vs. fraternal twins

A
  • Identical twins (monozygotic twins) have the same genotype, as they arise from a single fertilized egg.
  • Fraternal twins (dizygotic twins) have related genotypes, as they are the result of two separate egss fertilized by two different sperm; they are like a normal pair of siblings.
155
Q

concordance

A
  • the percentage of cases in which both members of a twin pair show a trait when it is known that at least one twin shows the trait
  • the difference in the concordance between monozygotic (MZ) twins and dizygotic (DZ) twins is a measure of the relative importance of the genotype
156
Q

twin studies on diseases

A
  • higher concordance rates in MZ twins means genes play an important role
  • similar concordance rates for MZ twins and DZ twins means the environment plays an important role
157
Q

Most common birth anomalies are…

A

complex traits (e.g. levels of serum cholesterol)

158
Q

pleiotropy

A

a single gene that has multiple effects (think: epistasis)

159
Q

gene number and effect on complex traits

A

as the number of genes decrease, the effect the genes have increases

160
Q

personalized medicine

A
  • identifying the patieny’s genotype and tailoring the treatment to the individual’s genetic risk factors and lifestyle; different people can have the same disease for different reasons
  • treating the patient, not the disease
161
Q

viruses

A
  • microscopic infectious agents that replicate when nucleic acid is delivered into the host cell
  • every living organism has a virus that can infect it
162
Q

virus composition

A
  • DNA or RNA as genetic material
  • genome surrounded by a capsid protein coat
  • some have an envelope; an outer membranous layer containing glycoproteins
163
Q

estimated number of viruses

A

1031

164
Q

specificity of viruses

A
  • a host range (host tropism) is the specific species a virus can infect
  • a cellular tropism is a specific number of cell types a virus can infect
165
Q

four reasons why viruses are on the boundary of what’s considered “life”

A
  • viruses contain genetic material
  • viruses cannot replicate outside of a living host cell
  • viral proteins exist (i.e. the Central Dogma?)
  • large viruses possess many of the molecules needed for translation (e.g. mimivirus)
166
Q

mimivirus (giant virus)

A
  • contains 7 of the 67 universal genes that are shared across the 3 domains of life
  • encodes various proteins needed for translation and protein modification
  • contains translation factors, tRNAs, and enzymes
  • “relics of a more complete ancestral protein-translation apparatus, gradually lost through a genome reduction process”
167
Q

the chance that viruses are from a 4th domain of life (origin, prediction, observation, and hypothesis)

A
  • origin: viruses evolved by stealing genes from other organism and encapsulating them in protective capsids
  • prediction: important enyzmes in viruses should resemble those of their hosts
  • observation: DNA-replicating enzymes in many viruses have no relationship whatsoever to the host cell enyzmes
  • hypothesis: viruses evolved from an ancient fourth domain of life, that has since disappeared
168
Q

virus classification via capsids

A
  • head-and-tail (e.g. T4 bacteriophage)
  • helical capsid (e.g. tobacco mosaic virus)
  • icosahedral capsid (e.g. adenovirus)
  • enveloped with spikes (e.g. coronavirus)
169
Q

virus classification via envelopes

A

naked virus vs. enveloped virus

170
Q

virus classification via genomes

A
  • double stranded vs. single stranded
  • DNA vs. RNA
  • (+) (same sequence as mRNA) vs. (-) (complementary strand needed)
171
Q

bacteriophage

A

virus that infects bacteria

172
Q

lytic pathway of bacteriophage

A
  1. Phage injects DNA into bacterial cell.
  2. Circularization of viral DNA.
  3. Phage DNA is replicated; proteins are synthesized. The bacterial DNA is broken down.
  4. Phage clones are assembled; the cell breaks open, and the mature phages are released.
173
Q

lysogenic pathway of bacteriophage

A
  1. Phage injects DNA into bacterial cell.
  2. Circularization of viral DNA.
  3. Recombination takes place between a specific site in the phage DNA and the bacterial DNA.
  4. Phage DNA is replicated with bacterial DNA, and transmitted to bacterial offspring.
  5. When conditions are met (e.g. more cells needing infection), phage DNA is replicated; proteins are synthesized. The bacterial DNA is broken down.
  6. Phage clones are assembled; the cell breaks open, and the mature phages are released.
174
Q

life cycle of non-enveloped virus (e.g. poliovirus)

A
  1. The virus is absorbed; endocytosis occurs.
  2. The capsid breaks down.
  3. Viral genomes are replicated.
  4. New viruses are assembled within the cell via viral mRNA, viral proteins, and viral glycoproteins.
  5. New viruses are released.
175
Q

life cycle of enveloped virus (e.g. HIV, Zikavirus)

A
  1. Glycoproteins bind to receptors on the cell membrane.
  2. The virus fuses with the membrane; endocytosis occurs.
  3. Viral contents are released into the host cytoplasm.
176
Q

SARS-CoV-2 (COVID-19 virus)

A
  • (+)ssRNA virus
  • the spike, envelope, and membrane proteins are glycoproteins
  • one of many coronaviruses that infect humans
177
Q

life cycle of SARS-CoV-2

A
  1. Viruses enter the body.
  2. Spike proteins on the virus bind ACE2 on host cells.
  3. Viral RNA is released into the cytoplasm.
  4. Viral RNA is translated to make viral proteins.
  5. Viral RNA is replicated using an RNA-dependent RNA polymerase.
  6. New viruses are assembled.
  7. New viruses are released.
178
Q

how viruses spread

A

direct and indirect contact

179
Q

20% of all human cancers arises from…

A

viruses; cancer results due to a host’s response to the viral infection or the impact of viral genes on the host cell

180
Q

cancer

A

mutations ingenes that control growth and division

181
Q

oncogenesis

A
  • the development of cancer
  • can arise from inherited mutations, carcinogenes, and viruses
182
Q

kinase

A

enzyme that phosphorylates its targets

183
Q

oncogene

A

cancer-causing gene

184
Q

proto-oncogene

A

a normal gene important in promoting cell division, that could become cancerous if mutated

185
Q

tumour suppressor

A

a gene that encodes proteins that inhibit cell division

186
Q

a virus that can cause cervical cancer

A

human papilloma virus (HPV)

187
Q

three cell cycle checkpoints

A
  • DNA damage checkpoint (before entering S phase): Is DNA damaged?
  • DNA replication checkpoint (at the end of the G2 phase): Is all DNA replicated?
  • Spindle assembly checkpoint (before anaphase): Are all chromosomes attached to the spindle?
188
Q

p53 regulation at the DNA damage checkpoint

A
  • p53 is a protein found in the nucleus
  • DNA damage activates protein kinases that phosphorylate p53
  • phosphorylated p53 turns on genes that inhibit the cell cycle; giving the cell time to repair damaged DNA
189
Q

HPV’s effect on p53

A
  • HPV E6/7 proteins bind and inactivate p53
  • cells with damaged DNA continue to divide, leading to oncogenesis
190
Q

Multiple-Mutation Model for Cancer Development

A
  1. inactivation of first tumour suppressor gene
  2. benign cancer: activation of an oncogene
  3. malignant cancer: inactivation of second tumour suppressor gene
  4. metastatic cancer: inactivation of third tumor suppressor gene
191
Q

transmissable spongiform encephalopathies (TSEs)

A

incurable fatal brain diseases known as “prion diseases”

192
Q

examples of prion diseases

A
  • Kuru
  • classic Creutzfeldt–Jakob disease (CJD)
  • Scrapie
  • variant Creutzfeldt–Jakob disease (vCJD)
  • Bovine spongiform encephalopathy (BSE); “mad cow disease”
193
Q

how prions work

A
  • normal prion proteins are formed of α helices (PRPC), whereas mutant prion proteins are formed of β sheets (PRPSC)
  • PRPSC forms a heterodimer with PRPC, and converts it into PRPSC; forming a homodimer
  • PRPSC homodimers stack up, forming useless amyloids
  • neurons try to get rid of said amyloids, but are incapable; leading to neurodegradation
194
Q

iatrogenic prion diseases (iCJD)

A

prion diseases are transmissable by blood (i.e. organ donations or blood transfusions)

195
Q

the protein that encodes PRPC

A

the PRNP gene

196
Q

prion proteins and copper

A

prion proteins bind copper ions; playing a role in copper metabolism and redox within the brain

197
Q

three genetic prion diseases

A
  • familial Creutzfeldt-Jakob disease (fCJD)
  • fatal familial insomnia (FFI)
  • Gerstmann-Sträussler-Scheinker syndrome (GSS)
198
Q

types of prion disease acquisition

A
  • sporadic: spontaneous conversion (e.g. sCJD)
  • acquired: acquired conversion (e.g. Kuru)
  • inherited: germline mutation, spontaneous conversion more likely (e.g. fCJD)
  • sporadic: somatic mutation, spontaneous conversion more likely
199
Q

Most prion diseases are…

A

sporadic

BIO A01 (1 decks)

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