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Biology 2 > Unit 3 > Flashcards

Unit 3 Flashcards

Energy and Metabolism (ch 8,9,10)

1
Q

Can you describe the structure of a nucleotide?

A

1 phosphate group
1 sugar (a pentose)
1nitrogenous base
“nucleoside” = nitrogenous base + sugar

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2
Q

How do ribonucleotides and deoxyribonucleotides differ?

A

deoxy = missing an O
= DNA a 2’ carbon attached to 2 H

RNA has a 2’ carbon attached to a OH and a H groups

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3
Q

Can you describe the structure of a polynucleotide?Mention phosphodiester bond and sugar-
phosphate backbone.

A

chain of many phosphate-sugar-phosphate-sugar

dehydration synthesis rxn occurs:
phosphate group + sugar of another nucleotide
= phosphodiester bond

2 phosphate groups must be released to provide energy to make the phosphodiester bond

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4
Q

Can you describe how a polynucleotide has a 5’ to 3’ orientation?

A

one side ending with a phosphate group
= 5’ end

one side ending with the -OH group on the sugar groups
= 3’ end

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5
Q

Can you describe complementary base pairing in nucleic acids? Mention the type of bond involved
and how many bonds are between each base pair.

A

RNA can associate with itself in complementary base pairing

the 2 strands of DNA can associate by complementary base pairing
-> Hydrogen bonds between the nitrogenous bases
-> Cytosine + Guanine = 3 H-B
-> Adenine + Thymine = 2 H-B

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6
Q

Complementary base pairing in DNA occurs between what types of nitrogenous bases? (structure)

A

between a pyrimidine and a purine

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7
Q

Can you describe the levels of structure in RNA (up to quaternary structure)?

A
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8
Q

Can you list the characteristics of DNA that allows it to act as genetic material? Describe the types
of information that is stored in DNA.

A
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9
Q

Can you discuss the role of complementary base pairing in the functions of DNA. Which bases are
purines? Pyrimidines?

A

pyrimidine = 1 ring (cytosine, thymine, uracil)
purines = 2 rings (adenine, guanine)

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10
Q

Can you describe some of the many functions of RNA? Compare coding vs. non-coding RNAs. Explain
why RNA is capable of producing many functional classes (similar to proteins)

A
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11
Q

What is Chargaff’s Rule?

A

% of A is equal to the % of T
% of G is equal to the % of C

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12
Q

How did Watson, Crick and Franklin’s discovery of the double-stranded nature of DNA explain Chargaff’s Rule ?

A

DNA has a helical shape
the double helix has an uniform diameter
= shows that purines must be paired with pyrimidines
= shows that one strand can be used as template

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13
Q

Can you describe the components of Watson and Crick’s model of DNA’s secondary structure?

A

they discovered:
- the helical shape of DNA
- the width of the helix
- the spacing between nitrogenous bases

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14
Q

Explain the Hershey and Chase experiment

A

was the hereditary material DNA or protein?

  1. bacteriophage injects one batch with radioactive sulfur and a second batch with radioactive phosphate
  2. each batch is mixed with bacteria cells in a blender
  3. the phage DNA enters the bacteria cell
  4. the mixture is centrifuged
  5. the bacterial cells is heavier = sink in the bottom
  6. the bacteriophage (“virus”) floats

results
1st batch: radioactive substance (pink) is floating
2nd batch: radioactive substance (blue)is sinking
= blue entered the bacteria cells and pink stayed outside
= DNA entered the bacteria cells and proteins stayed outside
= DNA is hereditary and not proteins

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15
Q

Why were radioactive sulfur and radioactive phosphate good tags?

A

good tags because phosphate is only found in dna and sulfur is only found in protein

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16
Q

Explain the manipulations in the Meselson-Stahl experiment

A
  1. bacteria from a medium with N15 were cultured
  2. dna was synthesized from N15
  3. bacteria was transferred to a medium with N14
  4. dna was centrifuged after 1 dna replication
  5. bacteria sample was collected
  6. dna was centrifuged after a 2nd dna replication
  7. bacteria sample was collected
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17
Q

Explain the observations in the Meselson-Stahl experiment

A

after 1 replication
half of the dna molecule is heavy and half is light

after 2nd replication
half is light and half is heavy or it is all light

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18
Q

Explain the conclusion in the Meselson-Stahl experiment (which theory of dna replication)

A

3 theories of dna replication
1. conservative = dna gets copied and make a new dna
2. dispersive = dna gets cut at various part and each cut would get copied and then reattach to make a new dna
3. semi-conservative = dna strands separate and each serve as a template to copy a second strand and producing 2 dna molecules

conclusion
= semi conservative dna replication

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19
Q

To form the phosphodiester bonds in DNA polymerization, where does the energy come
from?

A

the energy required for the formation of phosphodiester bonds is provided by the dephospho rylation of nucleoside triphosphate.
= removing 2 phosphate groups from the nucleoside

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20
Q

Can you describe the function of a DNA polymerase? Include the specific rules that it follows: can it
initiate polymerization? In what direction does it synthesize a new DNA strand?

A

DNA polymerase cannot initiate synthesis of a polynucleotide strand

it can only add nucleotide to the 3’ end of an existing polynucleotide strand

so primase comes in 1st, adds the short chain of RNA, then DNA polymerase comes in

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21
Q

Can you define a replication origin?

A

specific sequence of nucleotides that tell te enzymes to start replication

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22
Q

Can you define a replication bubble?

A

proteins recognize the sequence of the replication origin and attach to the DNA.
once attached, it separates the two strands and creates a replication bubble

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23
Q

Can you define a replication forks?

A

there is a replication fork at each end of the replication bubble
= a Y shaped region where replication occurs

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24
Q

Can you define a bidirectional replication?

A

replication occurs in both direction from the origin

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25
Q

Can you sketch a replication fork?
o Label the leading strand template and indicate its orientation (using 5’ and 3’ as markers).
o Label the lagging strand template and indicate its orientation.
o Use arrows (one for continuous synthesis and multiple for discontinuous synthesis) to
indicate the direction of leading and lagging strand synthesis.
o Indicate the orientation of the newly synthesized DNA.

A
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26
Q

Can you describe the machinery (enzymes and proteins) and process for each of the following:
1. Opening the double helix at the replication fork. (Helicase, SSBP, Topisomerase, Primase +
RNA nucleotides)
2. 3. Synthesis of the leading strand (DNA Pol III + DNA nucleotides)
Synthesis of the lagging strand (synthesis of Okazaki fragments, Primase, DNA Pol III, RNase
H, DNA Pol I, DNA ligase)

A
  1. unzip the double-stranded DNA & keeping it open
    -> helicase
    =unzip
    -> SSBP
    = keep them from reannealing = zipping back
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27
Q

Describe the fourth step of DNA polymerization

A
  1. synthesis of the new complementary DNA strand
    -> DNA polymerase III
    = adds complimentary DNA nucleotides to the free 3’ end of the strand
    -> Sliding clamp
    = makes sure DNA pol III stays in contact with the template strand during polymerization. it is right next to the DNA pol III.

DNA pol II can only add nucleotides to an open 3’ end
= needs the help of the leading strand and lagging strand

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28
Q

What is a lagging strand?

A

DNA pol III synthesizes the leading strand, then works along the other template strand
= forms a new DNA strand called lagging strand

-> replicates itself 1 section (“Okazaki fragments”) at the time
-> in the opposite direction from the movement of the replication fork

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29
Q

What is a leading strand?

A

DNA pol III synthesizes a complementary strand in the 5’ -> 3’ direction
= in the same direction of the replication fork
this makes a new DNA strand called the “leading strand”

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30
Q

What is a primer ?

A

the primase forms a primer, a short chain of NA that is added to the parental DNA strand.
it uses the parental DNA as a template

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31
Q

Complementary DNA strands can only be
elongated in the ___ → ___ direction.

A

Complementary DNA strands can only be
elongated in the 5’ → 3’ direction.

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32
Q

how many RNA primer(s) are required for each leading strand? for each lagging strand?

A

leading strand = one primer
lagging strand = one primer for each Okazaki fragments

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33
Q

Describe the second step of DNA polymerization

A
  1. release the tension
    -> topoisomerase
    =relieve strain by uncoiling the strand on the left of the replication fork
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34
Q

Describe the third step of DNA polymerization

A
  1. start synthesizing the new strand
    -> primase
    = forms a “primer”
    -> DNA polymerase
    = catalyzes the polymerization of DNA nucleotides
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35
Q

Describe the fifth step of DNA polymerization

A
  1. remove & replace RNA primers w/ DNA nucleotides
    -> Rnase H
    = recognizes RNA-DNA hybrid segments
    = degrades the RNA primer by hydrolysis of the phosphodiester bonds
    -> DNA polymerase I
    = adds DNA nucleotides to free 3’ ends of leading/lagging strands
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36
Q

Describe the sixth step of DNA polymerization

A
  1. glue fragments of lagging strands together
    -> DNA ligase
    = attach fragments of DNA on the new strands
    = join 3’ end of one to the 5’ of another fragment
    = forms a continuous polynucleotide strand
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37
Q

Can you define the replisome (replication factory) and briefly discuss how this factory increases the
efficiency of DNA replication?

A
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38
Q

Can you compare other differences between prokaryotic and eukaryotic replication?

A

prokaryotes
= 1 origin of replication
= circular genome
= uses only DNA pol III and I
= longer Okazaki fragments
= no telomeres

eukaryotes
= linear genome
= more than 1 origin of replication
= much more base pairs in its DNA = takes longer
= uses over 11 different DNA pol
= shorter Okazaki fragments
= has telomeres

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39
Q

Why would eukaryotic chromosomes need telomeres? What are telomeres? What do they prevent
in linear chromosomes?

A

telomeres
= short repeated DNA sequence at both ends of a linear DNA strand
= it contains no genes
= get shorter with each replication event
-> so eukaryotes can’t live forever, bc the telomeres would disappear at some point

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40
Q

What do telomeres prevent in linear chromosomes?

A
  • prevent activation of DNA damage signalling
  • protects against the organism’s genes shortening
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41
Q

What is telomerase? How is this enzyme implicated in the difference between replication in somatic
cells versus germ line cells?

A

an enzyme that extends the length of telomeres
it is found in
germ cells
cells in embryos/fetuses
tumor cells

it is active all the time in germ cells, whereas other cells don’t have telomerase.

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42
Q

Telomeres acts as a protection against cancer, how?

A

shortening of telomeres protect against cancer because it limits the number of division that somatic cells can undergo

bc cancer cells = unlimited cell division

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43
Q

Can you list the reasons why polymerization of DNA by DNA polymerase limits mistakes? Why this is
important?

A
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44
Q

Can you describe the mechanism of proofreading by DNA polymerase?

A

DNA pol:
- proofreads each nucleotide against its template
- replaces wrong nucleotide by the right one

this is possible bc DNA pol has exonuclease abilities
= it can cleave off nucleotides

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45
Q

Can you describe some of the many types of damage that DNA sustains?

A

reactive/harmful chemicals
radioactivity
x-rays
uv light

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46
Q

Describe the damage of UV light to DNA

A

= it links two adjacent pyrimidines and forms thymine dimer)
= it distorts the DNA molecule
= it can cause the disease xeroderma pigmentosum

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47
Q

what is xeroderma pigmentosum

A

-> inherited disease that causes hypersensitivity to sunlight
->mutations caused by UV light
-> mutations lead to defect in the excision repair mechanism, which is supposed to repair the damage of UV light
= damages of UV light are left unresolved
-> defect in the excision repair mechanism
-> mutation of the skin

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48
Q

Can you describe how DNA damage such as a mismatch base pair created by mistake during DNA
replication or an external agent can lead to a base pair substitution mutation after cell division?

A
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49
Q

Can you describe DNA excision repair? Mention general steps, and types of enzymes required in
each step.

A
  1. mismatched base pairs are detected
  2. nuclease
    = makes 2 cuts on the damaged strand & releases the damaged section
  3. DNA polymerase
    = places the correct nucleotides
  4. DNA ligase
    = seals everything together
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50
Q

What is DNA methylation? What are some of its functions?

A

put a tag on the parental strand by adding a methyl group
= it allows for fast repair

bc mistakes in DNA tend to happen when you are making a new parental strand has already gone trough spell check etc so it should be mistake free

functions:
1. so we can know which strand has the right sequence and which one is mistaken:
- > parental DNA is methylated & daughter DNA isn’t
2. methyl group helps protecting the DNA by getting in the way of the binding site of the enzyme that wants to cut the DNA

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51
Q

What causes DNA dimerization? What is an example of dimerization?

A

UV light exposure
thymine dimer

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52
Q

What is it important for DNA in prokaryotes and eukaryotes to be properly packaged?

A

to prevent bad enzymes from digesting the DNA and prevent the DNA from breaking

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53
Q

Can you describe the general structure of histones and their function in DNA packaging?

A

histones proteins =
= proteins responsible for the first level of DNA packing in chromatin
= content a lot of +ve charged amino acids
= help pack DNA in small clusters

54
Q

Can you define chromatin?

A

a complex of DNA combined with a large amount of proteins

55
Q

Describe a nucleosome?

A

basic unit of DNA packaging
in the form of unfolded chromatin

1 nucleosome = 8 histones

56
Q

Can you describe the changes DNA undergoes as it is packaged and moved around during its cell
cycle? When is DNA at its most condensed? What diameters are achieved?

A
57
Q

Indicate the levels of DNA packaging (diameter)

A
  1. relaxed DNA in double helix form
    = 2nm
    = (don’t see in microscope & susceptible to breaking)
  2. 8 histones + DNA = 1 nucleosome
    = 10 nm (hard to detect in microscope)
    = nucleosome isn’t too coiled bc it is going into S phase and replication (DNA must be accessible)
  3. after synthesis, during interphase
    = 30nm
  4. when entering mitosis
    = chromatin will form loops and form thick fibres
    = 300nm at the beginning of prophase
  5. final form is right as they hit metaphase
    = 700nm
58
Q

order the chromatin phases of mitosis from less condensed to most condensed:

A

interphase > prophase > metaphase

59
Q

Why higher levels of DNA packaging are achieved in cells?

A

tightly coiled
= difficult for bad enzymes to digest DNA in the bacteria
= prevents unintentional DNA breaking

60
Q

How is DNA spatially organized in the nucleus?

A

each chromosome has an address to where it should attached on the nuclear envelope

more loosely packed chromatin in regions more easily accessible for transcription

61
Q

Can you compare heterochromatin and euchromatin in the nucleus of a eukaryotic cell in
interphase? Describe the link with these forms of DNA and gene expression.

A

heterochromatin
= regions of highly condensed chromatin
= DNA inaccessible for transcription
= some regions contain genes that are only made as a child = less used in transcription = coiled

euchromatin
= regions of loosely packed chromatin
= regions accessible for transcription

62
Q

Can you describe Beadle & Tatum’s neospora experiment ?

A

experiment:
X-rays on Neurospora (fungi) cells to mutate DNA

Manipulations:
1. expose fungi to X-ray
2. wait for the spores to develop in complete medium
3. transfer the mutated spores to minimal medium
4. see if fungus grow in minimal medium
5. if fungus no longer grows = DNA mutation has altered the production of arginine

Pathway of arginine:
->precursor
-> enzyme A
-> ornithine
-> enzyme B
-> citrulline
-> enzyme C
-> arginine

63
Q

What are the results for the first mutant in the Beadle & Tatum’s neospora experiment?

A

Observations:
MM + mutant = no growth
MM + ornithine = growth ( = enzyme B works)
MM + citrulline = growth ( = enzyme C works)
MM + arginine = growth ( = arginine works)

= this shows X-ray mutation I altered the enzyme A

64
Q

What are the results for the second mutant in the Beadle & Tatum’s neospora experiment?

A

Observations:
MM + mutant = no growth
MM + ornithine = no growth
MM + citrulline = growth ( = enzyme C works)
MM + arginine = growth ( = arginine works)

= this shows X-ray mutation II altered the enzyme B

65
Q

What are the results for the third mutant in the Beadle & Tatum’s neospora experiment?

A

Observations:
MM + mutant = no growth
MM + ornithine = no growth
MM + citrulline = no growth
MM + arginine = growth ( = arginine works)

= this shows X-ray mutation III altered the enzyme C

66
Q

In the Beadle & Tatum’s neospora experiment, what is the final conclusion?

A

observation:
-> construction of proteins are dependent on DNA
-> 1 gene tells your cells to make ONE enzyme
= DNA control the making of enzymes

67
Q

In the Beadle & Tatum’s neospora experiment, what do these terms mean?

arginine
minimal medium
complete medium
wild type fungus

A

minimal medium
= bare minimum nutrients to keep your fungus alive

complete medium
= rich nutrients

arginine
= amino acids that fungi makes

wild type fungus
= not exposed to X-ray = doesn’t depend on medium to survive

68
Q

Why are there changes to the original “one gene one enzyme” model?

A

problematic with “1 gene 1 enzyme” model:

  • not all genes encode for enzymes
  • many genes encode proteins that aren’t enzymes
  • many proteins are formed from 2+ polypeptides
    and each polypeptide = its own gene
69
Q

What is the name of the new model after 1gene 1 enzyme and why is it also inaccurate?

A

“1 gene, 1 polypeptide” model

-> also accurate model bc:
- many genes can code for a set of polypeptides via alternative splicing
- some genes code for RNA molecules

70
Q

What is a transcription unit? Is it the same as a gene?

A

the stretch of DNA that is transcribed into RNA molecule

= found downstream from the promoter

71
Q

How RNA polymerases are in prokaryotes?

A

only one type of RNA pol

72
Q

How RNA polymerases are in Eukaryotes?

A

three known variants of RNA pol

RNA pol I
-> transcribes rRNA
RNA pol II
-> transcribes mRNA
RNA pol III
-> transcribes small RNA (tRNA and more)

73
Q

In what direction are nucleotide strands always synthesized?

A

5’ -> 3’ direction

74
Q

What does upstream, downstream, transcription start site mean?

A

downstream
= direction of transcription

upstream
= opposite of the direction of transcription
= before the start site of transcription

transcription start site
= where RNA coding starts

75
Q

If a location on a gene is negative,
what does this mean? What does +1 mean on a gene?

A
76
Q

What is the terminator sequence and is it downstream or upstream?

A

in prokaryotes
an RNA sequence that signals the end of transcription
downstream (after the site of transcription)

77
Q

What is the promoter and is it downstream or upstream?

A

specific sequence at which RNA pol will attach
upstream (before the start site)

78
Q

What is the template strand in a gene? Non-template (aka coding) strand in a gene?

A

template strand is the one that is used as a template during transcription

the other stand is the non-template strand

one strand can be a template for some genes and a non-template strand for other genes (and vice versa)

79
Q

Can you briefly describe the process of transcription in prokaryotes and eukaryotes ?

A

initiation
-> RNA polymerase binds to DNA via the promoter
-> RNA polymerase separates the double strands and adds a complementary RNA nucleotide to the 1st base in the coding region of the template strand

elongation
-> RNA pol moves along the DNA and unwinds it (10-20 nucleotides at a time)
-> RNA pol adds RNA nucleotides to the empty 3’ end
-> new RNA strand peels away
-> DNA double helix re-forms itself

termination
-> primary transcript and RNA polymerase is released

80
Q

what is a polyribosome? Why is it useful?

A

multiple RNA pol that work together simultaneously to transcribe ONE single gene

it increases the amount of mRNA made from one gene so it helps make the protein in large amounts

81
Q

what is the difference between initiation in prokaryotes vs eukaryotes?

A

prokaryotes
-> sigma subunit of RNA pol binds to the promoter

eukaryotes
-> histones get acetylated = DNA is loose
-> transcription initiation complex binds to the promoter (TATA box)

82
Q

what is the difference between elongation in prokaryotes vs eukaryotes?

A

eukaryotes
-> pre-mRNA must be modified into mRNA within the nucleus before it is used for translation
-> mRNA must leave the nucleus into the cytoplasm, where ribosomes are found

prokaryotes
-> transcription and translation happens at the same location

83
Q

what is the difference between termination in prokaryotes vs eukaryotes?

A

prokaryotes
-> RNA pol reaches a termination sequence
-> RNA pol stops transcription
-> RNA pol & the new RNA strand detach from the gene
-> the new RNA = mRNA = ready for translation

eukaryotes
-> RNA pol transcribes a polyadenylation signal
-> the polyadenylation signal is attached to the pre-mRNA
-> 10-35 nucleotides lated, the pre-mRNA is cut and released & goes into modification
-> RNA pol continues to transcribe the rest of the nucleotides on the DNA and then leaves

84
Q

what is a polyadenylation signal?

A

a repetition of AAUAAA
it signals the RNA pol to detach the pre-mRNA

85
Q

what is the rate of mRNA synthesis in eukaryotes?

A

50 nucleotides per second

86
Q

what does it mean to be acetylated?

A

histones are acetylated to make the DNA more loose
= add acetyl groups to the histones tails

87
Q

what is a transcription initiation complex ? Why is it important?

A

in eukaryotes
= RNA pol + transcription factors
-> transcription factors bind to the promoter first
& then invite RNA pol in

without transcription factors, the whole complex is stuck = no transcription

88
Q

what is a TATA box?

A

a type of promoter in eukaryotes

89
Q

describe what happens in eukaryotic post-transcriptional modifications?

A
  • exons and introns are transcribed into the pre-mRNA strand
  • a 5’ cap and a 3’ poly-A tail are added
    = both ends of the pre-mRNA are modified
90
Q

 Can you describe the RNA polymerization reaction and the role of an RNA polymerase in the
process? Aside from synthesizing different types of polynucleotides, how else is RNA polymerase
different from DNA polymerase?

A

RNA pol is the enzyme that transcripts DNA into RNA

it opens the 2 strands of DNA apart
uses 1 strand as a template
and doesn’t use the other (“non-template strand”)

91
Q

 Can you explain whether or not an RNA polymerase requires a primer and the direction of RNA
synthesis?

A
92
Q

Can you detail how promoters and control elements encode instructions for transcription? Mention
the role of sequence identity and spacing of important sequences.

A
93
Q

What is the difference between the 1st RNA transcript in eukaryotes vs prokaryotes?

A

eukaryotes
pre-mRNA containing exons and introns

prokaryotes
mature RNA

94
Q

Can you describe the 5’ cap and 3’ tail processing events of an mRNA.

A

both tails are altered during transcription, 1st the 5’ end then later on the 3’ end

the 5’ cap
= modified guanine nucleotide that is synthesized first

the 3’ Poly-A tail
= polyadenynation signal
= synthesized once the AAUAAA is transcribed

95
Q

how are the 5’ cap and 3’ tail of an mRNA helpful?

A

both components help to:
- facilitate export of mRNA into cytoplasm
- protect mRNA from being eaten by enzymes
- help ribosomes attach to the 5’ end of the mRNA

96
Q

Can you describe mRNA splicing using the terms introns and exons?

A

once your mRNA is made, you have different regions;

introns
= noncoding regions on protein-coding genes

exons
= coding regions on protein-coding genes

97
Q

What is the general structure of
the spliceosome and the role it plays in splicing?

A

a circular molecule made of proteins and snRNA (small RNAs)

-> cuts the exons (good part/coding region) out of the pre-mRNA
-> removes the introns
-> keeps the 5’ and 3’ UTRS
-> splice (=glue together) the cut out exons

= left with one intron + 1 exon (now a mRNA)

98
Q

What are 5’ and 3’ untranslated regions (UTRs) of an mRNA?

A

UTRs
= nucleotides that will not be translated into polypeptides

even though exons are usually expressed,
5’ UTR and 3’ UTR are part of exons that will not be expressed

99
Q

where are 5’ and 3’ untranslated regions (UTRs) of an mRNA found?

A

= 5’ UTR is found right after the 5’ cap (between 5’ cap and coding segment)
= 3’ UTR is found just before the 3’ Poly-A tail (between poly-A tail and the coding segment)

100
Q

Can you describe the process of alternative splicing in eukaryotes and its role?

A

let’s say youre left with the following exons:
A, B, C, D
when splicing, the spliceosome can make:
ABC protein or ABD protein
= 1 gene can make multiple polypeptide

101
Q

what is the role of the cut-off introns by spliceosome?

A

some introns contain sequences that regulate gene activity

102
Q

what is a codon?

A

each sequence of 3 nitrogenous bases in a mRNA strand is a codon that codes for a specific aa’s

same 3 nitrogenous bases but in different order
= make different amino acids

103
Q

Can you describe the genetic code and the characteristics of the genetic code discussed in class?

A

genetic code
= genes from one organism can enter another organism and have an effect (jellyfish in pigs)

104
Q

describe the general path of transcription and translation for eukaryotes

A

start with DNA
1. template strand is copied during transcription
= makes mRNA (same sequence as non-template strand, except for Thymine->Uracil)
2. pre-mRNA -> mature mRNA
3. mature mRNA exit nucleus and goes to cytoplasm
4. a polypeptide is made from the mRNA during translation
= nucleic acids become amino acids

105
Q

where does transcription and translation occur?

A

transcription
= nucleus (eukaryotes) and cytoplasm (prokaryotes)

translation
= cytoplasm for both

106
Q

what is the reading frame in translation?

A

translation process reads one codon at a time
= 1 extra nitrogenous base changes the whole translation bc each codon will be décalé

107
Q

what is the codon for start and stop?

A

start codon
AUG

stop codon
UAA
UAG
UGA

108
Q

Describe the process of tRNA charging

A
  1. tRNA assembly
    -> aminoacyl-tRNA synthetase
    = the enzyme matches tRNA to its specific amino acid
  2. it forms a “charged tRNA”
    = a tRNA with an amino acid on it

-> the charged tRNA can now do its job

109
Q

What is the job of a tRNA?

A

here’s is many aa’s found in the cytoplasm
-> tRNA transfer aa’s from the cytoplasm to a growing polypeptide in a ribosome

110
Q

explain the wobble rule

A

anticodon GAG
should only bind to mRNA codon CUC
but it can also bind to mRNA codon CUU

= more freedom on the 3rd base of a codon

111
Q

Can you describe how transcription and translation can be used to amplify gene expression and why
that is important in cells?

A
112
Q

Can you describe the function of the ribosome.

A
  1. host the mRNA and tRNA and allows them to come close together = facilitate the coupling
  2. allows the addition of aa’s to create a polypeptide
113
Q

Can you describe the structure of the ribosome.

A

ribosomes are 1 small subunit and 1 large subunit, each made of rRNAs

the 2 subunits (each made in the nucleolus) only assemble when they get attached to mRNA (in the cytoplasm)

114
Q

what are the 4 different binding sites on a ribosome ?

A

small subunit
= 1 binding site for mRNA

large subunit
= 3 binding sites for tRNA
= A site, P site, E site
A: arrival = aminoacyl-tRNA binding site
P: park = peptidyl-tRNA binding site
E: exit = contains an exit tunnel

115
Q

how are bacterial infections treated using the different properties of ribosomes ?

A

ribosomes in prokaryotes are smaller than eukaryotes
= drugs that affect prokaryote’s ribosome but not eukaryote’s are used to fight bacterial infections

ie: streptomycin or tetracycline

116
Q

what is an rRNA

A

the most prevalent form of RNA in the cell
2/3 of the mass of a ribosome

= a catalyst of the peptide bond formation

117
Q

Why does the wobble base pairing occur only in the third nucleotide of the codon (first nucleotide of
the anticodon)?

A

Because there is redundancy in the genetic code: the first two nucleotides are
conserved but the third can vary.

118
Q

Can you describe the process of translation: initiation, elongation, and termination.

A

initiation
-> formation of the translation initiation complex

translation
-> codon recognition
-> formation a peptide bond
-> translocation

termination
-> a stop codon reaches the A site
-> the translation complex dissociate

119
Q

Explain the translation initation complex formation

A
  1. small ribosomal subunit binds to 5’ cap of mRNA
  2. subunit slides downstream until AUG codon
  3. initiator tRNA (tRNA with the start anti-codon) comes in from P SITE
  4. large ribosomal subunit attaches

these 4 steps need:
initiation factors (specific proteins)
energy provided by hydrolysis of GTP (not ATP)

120
Q

Explain codon recognition in translation

A

anticodon of a aminoacyl tRNA base
+
mRNA codon
= pair together in the A site

121
Q

Explain formation of a peptide bond in translation elongation

A

new amino acid at A site
+
carboxyl end of the growing polypeptide at the P site
= form a peptide bond

-> the growing polypeptide that was on the P site goes on the tRNA at the A site

122
Q

explain the translocation in translation elongation

A

after the peptide bond, the now free initiator tRNA exits the ribosome through the E site

the second tRNA with the growing polypeptide is moved from the A site to the P site with the energy from hydrolysis of GTP

= process repeats in the 5’ to 3’ direction until stop codon is met

123
Q

explain termination in translation

A
  1. stop codon on mRNA reaches the A site
  2. a release factor (protein shaped like a tRNA) enters the A site and binds to the stop codon
  3. release factor forces the addition of water molecule to the polypeptide instead of the amino acid
  4. the bond between polypeptide-tRNA is broken
  5. polypeptide chain is released in the P site
124
Q

where does most mutation occur?

A

in protein synthesis
bc translation/transcription doesn’t have “proof-reading” check ups and thus can make mistakes

125
Q

what is the difference between a polypeptide and a protein?

A

protein
= composed of many different polypeptides

polypeptide
= chain of aa’s that all come from one mRNA chain

126
Q

Which type(s) of errors would cause the least change to the amino acid sequence of the peptide?
Where in a codon would these silent mutations occur? Why?

A

substitution error, which are point mutations
occur mostly in the third base of codon
bc they are more flexible
bc of the wobble rule

127
Q

Can you describe one type of signal used to alert a transport system to bring a protein to the correct
destination?

A
128
Q

 Can you explain what causes point mutations? What are point mutations?

A

mistakes made in 1 or a few nucleotides when DNA is copied (mitosis or translation or transcription)

causes:
inherited (if mutation in cells that produce gametes)
acquired
-> UV or X rays
-> radioactivity
-> chemicals
-> high temperature

129
Q

What are insertion errors?

A

add extra nucleotide
= one extra thymine shifts everything
= frameshift mutation

130
Q

Which type(s) of errors would cause the greatest changes to the aa sequence of the peptide?

A

deletion and insertion error

131
Q

What are substitution errors?

A

= one thymine is substituted by a cytosine
= missense mutation

132
Q

What are deletion errors?

A

remove one nucleotide
= one thymine missing
= frameshift mutation

Biology 2 (5 decks)

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