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MCAT > Bio 1 > Flashcards

Bio 1 Flashcards

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1
Q

Nucleic Acid

A

Macromolecule composed of nucleotide monomers.

DNA and RNA (mRNA, tRNA, rRNA, snRNA, etc.).

Structure: linear strand of nucleotides joined by phosphodiester bonds.

May be single or double stranded.

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2
Q

Nucleotide

A

Nitrogenous base + sugar + 1-3 phosphates.

Nucleic Acid “backbone”: sugar and phosphate group of each nucleotide linked by phosphodiester bonds.

Glycosidic bond between sugar and the base; Hydrogen bonds between the bases if double stranded.

DNA and RNA differ in the 2’ carbon of the sugar; RNA (ribose) has an OH; DNA (deoxyribose) has H.

Base linked to the 1’C of sugar, phosphate linked to 5’C.

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3
Q

Nitrogenous Bases

A

Purines: Adenine/Guanine (double ring).

Pyrimidines: Cytosine, Uracil, Thymine (single ring).

U and T differ in a methyl group.

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4
Q

Base Pairing

A

A always pairs with T (with U in RNA -> 2H bonds).

C always pairs with G
-> 3H bonds (stronger base pair)

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5
Q

DNA Replication: Overview

A

Overall: one DNA molecule replicated -> 2 identical copies .

  • Occurs during the S phase (synthesis phase) of the cell cycle.
  • Cell division requires DNA replication to occur.
  • Semi-Conservative nature
  • The synthesis of the new “daughter strand” occurs on top of the “parent strand” through the addition of free floating nucleotides.

DNA replication requires a template (the parent DNA strand), as well as a primer to jumpstart the synthesis (RNA primer).

DNA is built in the 5’ -> 3’ direction of both daughter strands.

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6
Q

Semi-Conservative nature of DNA replication

A
  • When the mechanism of DNA replication was first discovered, there were 3 different methods proposed; semi-conservative was found to be correct.
  • The strands of the original DNA molecule separate and serve as templates for the synthesis of new, complimentary strand.
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7
Q

Enzymes involved in DNA Replication

A

DNA Helicase

Topoisomerase

DNA Gyrase
Single Strand Binding (SSB) Proteins

Primase

DNA Polymerase

Ligase

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8
Q

Step 1 of DNA Replication

A

Beginning at a specific region of the DNA (the ORI), helicase binds to the DNA and begins to unwind it by breaking H-bonds between bases -> forms a replication bubble with replication forks on either end.
-ORI found by other helper proteins.

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9
Q

Step 2 of DNA Replication

A

Topoisomerase relaxes supercoils that occur upstream of the replication bubble due to to the unwinding of the strands.
-Cuts DNA and unwinds the excess coils.

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10
Q

Step 3 of DNA Replication

A

SSBPs stabilize the newly separated parent strands, making sure they don’t reanneal.

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11
Q

Step 4 of DNA Replication

A

Primase lays down a few RNA bases that are complimentary to the parent strand and serve as a primer, from which DNA polymerase can build off of.

  • DNA Pol can only extend, can’t initiate
  • These RNA primers must later be removed and replaced with DNA.
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12
Q

Step 5 of DNA Replication

A

DNA Polymerase elongates from the primer, adding nucleotides one by one and using the parent strand as a template.

  • Free floating dNTPs are added (triphosphate) and the release of two phosphate groups from the molecule provides the energy for this reaction.
  • 3’ hydroxyl group on the last nucleotide of the daughter strand performs nucleophillic attack onto phosphate (at 5’ end) of the incoming nucleotide.
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13
Q

Step 6 of DNA Replication

A

At each replication fork, there is a leading strand and a lagging strand of the daughter molecules, due to the requirement that the new strands are built in 5’ -> 3’ direction of elongation.

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14
Q

Step 7 of DNA Replication

A

Leading strand is synthesized in the same direction as the extending replication fork and is a single continuous strand.

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15
Q

Step 8 of DNA Replication

A

Lagging strand is not continuous and made up of multiple Okazaki fragments that are soon after joined together by DNA ligase.

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16
Q

Step 9 of DNA Replication

A

Synthesis is bidirectional because it extends in both directions from the replication bubble.

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17
Q

Step 10 of DNA Replication

A

RNA primers are eventually replaced with DNA using DNA Polymerase

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18
Q

Eukaryotes

A
  • Process occurs in Nucleus
  • Many ORI per DNA molecule (linear DNA) -> multiple replication bubbles at once; ultimately the bubbles meet each other and the newly formed DNA molecules separate.
  • Many simultaneous replication bubbles enables fast replication
  • 5 DNA polymerases
  • Only eukaryotes have telomeres.
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19
Q

Prokaryotes

A

-The process occurs in the Cytosol
-One ORI per DNA molecule (circular DNA) -> theta replication
-3 DNA polymerases
DNA Pol III: main DNA Pol that extends the daughter strands.
DNA Pol I: slower than Pol III; exonuclease activity enables it to remove RNA primer and replace with DNA; also plays a role in DNA error repair

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20
Q

Telomeres

A

At the very end of each eukaryotic DNA molecule, on the newly synthesized lagging strand, there is an RNA primer that can’t be replaced once removed.

As a result, chromosomes shorten at each round of replication.

To prevent this shortening from affecting coding DNA regions, non-coding repeats called telomeres are added to the ends of DNA.

  • Telomeres are a form of protection
  • Telomeres shorten at each cell division

If telomere is too short the cell will stop dividing and functioning properly (senescence = biological aging)

Length of telomere associated with age of cell -> biological clock.

21
Q

Telomerase

A

an enzyme that catalyzes the lengthening of telomeres.

  • Adds to the ends of telomere a specific repeated base sequence.
  • Uses its built-in RNA strand as a template to add this DNA
  • RNA-dependent DNA Pol (makes DNA but must use complimentary RNA as the template) -> reverse transcriptase.
  • Telomerase is found in germ line, stem cells, and often in cancerous cells.
22
Q

Point Mutations (Substitution)

A

characterized by their effect on the transcribed mRNA/translated polypeptide.

23
Q

Silent mutation

A

same AA will be translated despite a base pair error.

24
Q

Missense mutation

A

base pair change results in a change in the AA that is translated.

25
Q

Conservative mutation

A

new AA has similar biochemimcal properties to the original one.
-Impact of this type of mutation depends on the specific change in the AA (D-> E unlikely to have a huge effect; D-> G more likely to have an effect).

26
Q

Nonsense mutation

A

base pair changes cause the DNA and transcribed mRNA to encode a stop signal so that transcription and translation prematurely.

27
Q

Insertions and Deletions

A

insertions occur when one or more additional base pairs are inserted and deletions occur when one or more base pairs are deleted.

  • Insertions and deletions may result in a frameshift, meaning that the reading frame of the gene is changed so that all of downstream region of the gene will also be affected.
  • frameshift occurs when insertion/deletion is not a multiple of 3 base pairs.
28
Q

Forms of DNA damage

A

Other forms of DNA damage occur due to some endogenous agent (reactive metabolites, free radicals, ROS, etc.) or due to exogenous trigger (UV radiation, X-Rays, chemical exposure, etc.)

-A mutagen is any agent that causes damage to and changes in DNA.

  • Hydrolysis of DNA
  • Chromosomal translocations
  • UV radiation -> Pyrimidine dimers
  • Cross-linking of bases
  • Chemical intercalation: a chemical (usually aromatic ring) inserts itself between the bases of DNA
29
Q

Transposon/Transposable Element (TE)

A

Regions of DNA that can move around in the genome and often cause structural changes and mutations in DNA.

-Found in both prokaryotes and eukaryotes; make up over 40% of human DNA.

-Part of the TE encodes
for enzymes that copy and paste the DNA segment into a different place in the genome (cut & paste) -> transposase.

  • May cause insertions, inversions, deletions, duplications.
  • Can result in the disabling of a gene, and are implicated in many diseases.
30
Q

Mechanisms of DNA Repair

A

DNA polymerase has proofreading and editing capabilities so that errors detected during replication can be immediately fixed (nuclease activity enables it to remove the incorrect base, like a backspace button, and then it adds the correct one).

If the mutation is not initially detected, then DNA mismatch repair (MMR) can detect a mismatch in the base pairs, figure out which strand is the new daughter strand, and correct it.

After that, there are many other mechanisms that also fix different types mutations. If the mutation cannot be fixed, the cell often undergoes apoptosis.

31
Q

Mismatch Repair Pathway

A
  • DNA polymerase errors may result in a base mismatch (A with C, G with T, etc.)
  • Via MMR, the daughter strand is recognized and the mismatched base of that strand is removed then replaced.
  • Bacteria -> new strand recognized by lack of methylation.
32
Q

Nucloetide and Base Excision Repair

A
  • Remove bulky DNA legions that are caused by UV radiation, chemicals, and other mutagens -> prevent future error in the next DNA replication.
  • Small region of DNA surrounding the error is removed, DNA polymerase replaces the region, and DNA ligase joins the fragments.
33
Q

Homologous End Joining

A
  • Fix double strand breaks and removals of DNA regions.
  • Must be done after DNA replication because requires a sister chromatid (another copy of that DNA region).
  • Homologous DNA serves as a template for removed region to be synthesized -> requires DNA Pol and Ligase.
34
Q

Non-Homologous End Joining

A
  • Fix double strand breaks and removals of regions of DNA when homologous DNA is not available.
  • Cleaved ends of DNA are ligated together ->mutagenic.
35
Q

Eukaryotic Chromosomes

A

Composed of double stranded DNA molecules and associated proteins that are folded and bundled into a rod-like shape (unduplicated) or an x-like shape (duplicated).

-Following DNA replication and during metaphase of mitosis, the X shaped chromosome is visible. It is composed of 2 identical sister chromatids linked by a centromere.

36
Q

Human chromosomes

A

Telomeric DNA caps the ends of the chromosomes.

When centromere is slightly off-center one arm of each chromatid will be longer than the other arm.
-Shorter arm: p arm; longer arm: q arm.

Structure:
-Nucleosome: region of DNA wrapped around a histone octamer (8 histone proteins) -> histones have a + charge to attract -DNA.

37
Q

Chromatin and Centromere

A

-Chromatin: DNA + Histone proteins -> “Beads on a string”.

  • Chromatin bundles up and condenses into long rods.
  • Centromere (binding proteins and specific DNA sequences) links two DNA molecules (sister chromatids).

-Chromatin is classified as hetereocrhomatin and euchromatin, indicating structural properties and transcriptional activity.

38
Q

Heterochromatin

A

chromatin is densely packed and not accessible to enzymes of transcription -> transcriptionally “silent”

39
Q

Euchromatin

A

Chromatin is loosely packed, making it accessible to transcriptional enzymes -> transcriptionally active.

40
Q

Chromosome abnormalities

A

May or may not be deleterious; often fatal and many associated with disease.

  • Large-scale structural changes: deletion, duplication, inversion, insertion, translocation, etc.
  • Aneuploidy: organism has an abnormal number of chromosomes.
  • Polysomy: organism has one or more additional copies of a chromosome.
41
Q

Repetitive DNA

A

A large proportion of eukaryotic and prokaryotic DNA is comprised of highly repetitive sequences (2/3 in humans).

Non-coding and not translated.

Many different types: tandem repeats (satellite and microsatellite DNA), transposons, etc.

Highly variable between individuals.

42
Q

Single Copy DNA

A

Most translated genes

Highly conservative (low mutation rate).

43
Q

DNA Helicase

A

Unwinds the parent DNA strands

44
Q

Topoisomerase

A

Relaxes DNA supercoils that accumulate due to the unwinding

45
Q

DNA Gyrase

A

Type of topoisomerase

46
Q

Single Strand Binding (SSB) Proteins

A

Stabilize the single parent strands of DNA once unwound.

47
Q

Primase

A

Lays down the RNA primer (a type of RNA polymerase)

48
Q

DNA Polymerase

A

Builds the daughter strand of the DNA: proofreads and corrects errors; replaces the RNA primer.

49
Q

Ligase

A

Links the Okazaki fragments of DNA daughter strand

MCAT (6 decks)

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