Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Malika Biochem MCAT > Chapter 6 > Flashcards

Chapter 6 Flashcards

1
Q

Difference between RNA & DNA

A

-DNA is double stranded while RNA is single stranded
-DNA contains thymine, RNA contains uracil
-DNA doesn’t have an OH group on the C-2’ of its sugar, RNA does

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What makes up a nucleoside?

A

A Pentose (5 carbon sugar) and a nitrogenous base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What makes up a nucleotide?

A

pentose, nitrogenous base, phosphate group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

To what C does the phosphate group attach to?

A

5’ C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

To what C does the nitrogenous base attach to?

A

1’ C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Is breaking off a phosphate group exothermic or endothermic?

A

Breaking off a phosphate group releases energy (exothermic). Usually in biological reactions, breaking a bond would require energy, but since there is so much negative repulsion between phosphate groups, the compound becomes more stable when losing a phosphate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

A nitrogenous base can be divided into two categories. What are those categories?

A

A nitrogenous base can either be a purine or a pyrimidine. A purine is made of two rings, while a pyrimidine is only made up of one ring.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Name all of the purines.

A

Adenine and guanine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Name all the pyrimidines.

A

Cytosine, thymine, and uracil (found in RNA only).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the structural characteristics of nitrogenous bases?

A

They are aromatic compounds, which are very stable because they have delocalized electrons that travel through the entire compound.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What makes up the sugar phosphate backbone?

A

It is made of alternating sugar and phosphate groups, which is determines the directionality of DNA. It is read from 5’ to 3’. The 5’ end has a phosphate group while the 3’ end has a free sugar with a free OH group on C-3’.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How is the sugar phosphate backbone connected?

A

It is connected through phosphodiester covalent bonds. This bond occurs when a phosphate group links the 3’ C of one sugar to the 5’ C of the next sugar. Specifically the O on the 3’C sugar links to the central P in the phosphate group of the subsequent nucleotide.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What did Chargaff’s rule tell us?

A

They tell us that in double stranded DNA, the total amount of purines = the total amount of pyrimidines. The amount of adenine = the amount of thymine. The amount of guanine = the amount of cytosine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What did Watson and Crick discover about DNA?

A

They discovered that DNA is double stranded and wraps around each other in a right, handed helix that resembles a twisted ladder. They said that the two strands are anti-parallel (opposite polarity). The outside of the helix consists of a sugar phosphate backbone, which carries no information, while the inside has nitrogenous bases which carries the genetic code. They also laid out the specific base pairing rules.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What were the base pairing rules that Watson and crick discovered?

A

A pairs with T - there are two H bonds between the bases
G pairs with C - There are 3 H bonds between the bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What type of bond forms between base pairs?

A

A hydrogen bond, which is a weak non-covalent bond. This is an example of intermolecular forces.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How is eukaryotic DNA packaged?

A

Eukaryotic DNA is packaged in nucleosomes. A nucleosome is made of a segment of DNA wound around eight histone proteins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What histone proteins make up the histone core?

A

2 of each ( H2A, H2B, H3 and H4)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the role of the H1 histone protein?

A

The H1 histone protein does not make up the core like the other histone proteins. Instead, it seals off the DNA as it enters and leaves the nucleosome making it less susceptible to be cut.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is heterochromatin?

A

Heterochromatin is dark, remains highly compacted, has many repetitive, sequences, and most often is transcriptionally silent (no gene expression).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is euchromatin?

A

Euchromatin is light under the microscope, more spread out and contains genetically active DNA. 90% of our genome is made of euchromatin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Where is constitutive heterochromatin mostly found in the human body?

A

It is found in telomeres and centromeres of chromosomes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are telomeres made of?

A

They are made of guanine rich, repetitive double stranded DNA sequences.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are the functions of telomeres?

A

They serve to protect the ends of our DNA from degradation and provide chromosome stability however, as we age telomeres shorten as DNA replicates. Telomeres are present in germline cells, and some stem cells, but they are not present in somatic body cells.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are centromeres made of?

A

They are made of double standard constitutive heterochromatin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What are centromeres and what function do they serve?

A

They are the middle region of a chromosome to which the microtubules attach. They are responsible for aiding in the binding of the kinetochore during mitosis and meiosis.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the difference between single copy vs. repetitive DNA?

A

Single copy DNA are sequences that don’t repeat and hold the organisms genetic information, present in euchromatin, have a low mutation rate, found in exons

Repetitive DNA are sequences that repeat, which are found near centromere’s and telomeres, they don’t contain genes, and have a high mutation rate, they are found in introns

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the leading strand?

A

It is the DNA strand that is synthesized continuously away from the origin, towards the replication fork.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the lagging strand?

A

It is synthesized in Okazaki fragments towards the origin, away from the replication fork.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the function of DNA ligase?

A

After RNA primer removal, it seals the nick by catalyzing the formation of a phosphodiester bond to join Okazaki fragments.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

In DNA prokaryotic replication what is the function of DNA A protein?

A

At the start of initiation, DNA A binds to the 9-mer sequence region, inducing stress or super coiling upon the DNA, and forcing the unwinding/denaturation of the 13-mer region to form an open complex. 13-mer region is AT-rich.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is the function of DNA B (helicase)?

A

DNA B is carried to the 13-mer region to use energy to break H bonds and separate the double stranded helix.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is the function of DNA C?

A

The only function that DNA C serves is to carry helicase to the 13-mer region.

34
Q

What are the functions of single-stranded binding proteins? (SSBs)

A

After helicase unzips the double helix, SSBs bind to the two separated strands to prevent the DNA from reannealing.

35
Q

What is the function of topoisomerase?

A

Ahead of the replication fork, topoisomerase alleviates the supercoiling of the DNA by nicking one or both strands and resealing the cuts right away.

36
Q

What phase of the cell cycle does proofreading occur?

A

S phase

37
Q

At what phase of the cell cycle does nucleotide and base excision repair occur?

A

G1 and G2 phases.

38
Q

What are oncogenes?

A

They are mutated genes that cause cancer, typically only one copy of the allele is sufficient to promote cancer. Oncogenes are dominant.

39
Q

Proto-oncogenes

A

This is the name for oncogenes before they are mutated.

40
Q

What are tumor suppressor genes?

A

They are genes that inhibit the cell cycle and growth. Their main function is to stop tumor progression so mutations in both copies of the allele would be needed for a complete loss of function, and to cause cancer.

41
Q

Is p53 an oncogene or tumor suppressor gene?

A

It is a tumor suppressor gene. It is the most commonly mutated gene in cancer cells.

42
Q

What is the function of primase?

A

It synthesizes a short strand of RNA, that acts as a primer for DNA polymerase III.

43
Q

What is the function of DNA polymerase III?

A

It is a multi-protein holoenzyme complex, which begins synthesis of the daughter DNA strand in the 5’ to 3’ direction. Note that it reads the template strand in a 3’ to 5’ direction.

44
Q

What is the function of a primosome?

A

The main function is to initiate synthesis of a DNA strand. It delivers primase and accessory proteins to the origin of replication.

45
Q

What is the function of DNA polymerase I in prokaryotic DNA replication?

A

It has 5’ to 3’ exonuclease and polymerase activity. It removes the RNA primer, and then fills the gap by adding DNA nucleotides to the 3’ end preceding the primer.

46
Q

Eukaryotic chromosomes are _______ with _________ origins/s of replication.

A

Linear, many

47
Q

Prokaryotic chromosomes are _______ with _________ origins/s of replication.

A

Circular, one

48
Q

How does eukaryotic and prokaryotic DNA replication differ, in terms of which protein synthesizes the RNA primer?

A

In eukaryotic DNA replication, DNA polymerase alpha synthesizes the RNA primer.
In prokaryotic DNA replication, primase synthesizes the RNA primer .

49
Q

How does eukaryotic and prokaryotic DNA replication differ in terms of removal of the RNA primer?

A

In eukaryotic DNA replication the RNA primer is removed by RNAase H.
In prokaryotic DNA replication the RNA primer is removed by DNA polymerase I.

50
Q

How does eukaryotic and prokaryotic DNA replication differ in terms of the protein which synthesizes the DNA strands?

A

In eukaryotic, DNA replication, DNA polymerases Alpha, Delta, and Epsilon synthesize the DNA strands.
In prokaryotic DNA replication, DNA polymerase III synthesizes the DNA strands .

51
Q

In eukaryotic DNA replication, after the RNA primer is removed, what protein adds the DNA nucleotides in the gaps?

A

DNA polymerase Delta adds the DNA nucleotides to the gaps where the RNA primer was removed.

52
Q

What does the semi-conservative model of DNA replication say?

A

After one round of DNA replication, each double strand contains one side that is the parental strand and the other side that is the daughter strand.
After two rounds of DNA replication, there are four double strands. Two of the double strands contain only daughter genetic material. The two other strands contain half parental strand and half daughter strand genetic material.

53
Q

AAMC FL1 #57 HAVE TO APPLY Semiconservative Theory of DNA

A

Based on semiconservative method of DNA replication, after 2 rounds of division some bacteria will only contain 14N daughter DNA (genome mass 5.4 fg) and some others will contain half 14N daughter DNA and half 15N parental DNA (take AVERAGE mass: 5.45 fg).

54
Q

What causes nucleotide excision repair to occur?

A

It can occur if DNA is exposed to high UV radiation, causing adjacent thymine bases to dimerize creating a kink in the sequence.

55
Q

What causes base excision repair to occur?

A

This type of repair occurs if a base such as cytosine is converted to uracil due to radiation exposure.

56
Q

Name the steps of nucleotide excision repair.

A

First excision endonuclease recognizes the bulb in the sequence, and makes nicks in the phosphodiester backbone on both sides of the bulb of the damaged strand.
The damaged region is removed and DNA polymerase synthesizes new nucleotides to fill in the gap, using the undamaged strand as a template.
Lastly, DNA ligase seals the nick in the strand.

57
Q

Name the steps of base excision repair.

A

A glycosylated enzyme recognizes the mutated base and excises it without breaking the phosphodiester backbone.
This leaves an abasic site or AP site, which is recognized by AP endonuclease, which removes the rest of the affected backbone.
Then DNA polymerase fills in the gap by synthesizing, the DNA nucleotides using the undamaged strand .
Lastly, DNA ligase seals the strand by catalyzing a phosphodiester bond.

58
Q

How does gene therapy work?

A

It utilizes modified virus vectors that insert their own genetic material into human DNA, thus exposing the individual to the desired copy of the gene that will help cure the target disease. Basically, the modified virus is used as a mode of delivery of the target gene.

59
Q

What is a knockout gene?

A

It is a gene which has been intentionally deleted in an organism often to find out the function of that specific gene.

60
Q

What is DNA hybridization used for?

A

It is a method used to compare the genomics similarities between two separate DNA fragments.

61
Q

Name the steps of DNA hybridization.

A

You denature both double stranded DNA samples, and then mix a single DNA strand from one sample with another single DNA strand from the second sample to produce a hybrid. The stronger the hybrid double-stranded DNA is, the more complementary base pairing occurred, which means that the two sample sequences were more similar to each other than different.

62
Q

What is southern blot used for?

A

It is used to detect the presence, and quantity of a desired DNA sequence in a sample.

63
Q

How does southern blotting work?

A

First, you cut the DNA sample with restriction enzymes, and then the fragments are separated by a gel electrophoresis. The separated fragments are transferred to a filter membrane, retaining the separation. Then radial labeled DNA probes with the desired complementary sequence, or added to the filter, which promotes binding to the target sequence of the DNA strand.

64
Q

What is needed for a polymerase chain reaction?

A

In the test tube, you need your target DNA strand, two short single stranded primers that are complementary to the 3’ ends of the template & coding strand, deoxyribonucleotides, and Taq DNA polymerase.

65
Q

What are DNA libraries and the two main types of DNA libraries?

A

DNA libraries are large collections of known DNA sequences, which consist of either genomic DNA or cDNA.

66
Q

What are genomic libraries?

A

They are large collections which contain the entire genome of an organism, including both the coding and non-coding regions of the genome. They are constructed by restriction enzyme endonuclease, and DNA ligase via cloning.

67
Q

What are cDNA libraries?

A

They are large collections, which contain only the coding regions of the organism’s genome. They are constructed by the enzyme reverse transcriptase, which reverse transcribes the mRNA into cDNA. cDNA libraries are used to sequence specific genes, produce recombinant proteins, or produce transgenic animals.

68
Q

What is the function of restriction enzymes?

A

They are proteins from bacteria that cut DNA at specific sequences that are usually 4 to 8 base pairs long. The sequences are called a palindrome (they read the same no matter the direction that you read them).

69
Q

What are the two ways that restriction enzymes cut?

A

They cut either in the middle leaving blunt ends or off the center, leaving overhangs called sticky ends. These sticky ends can either be 5’ or 3’.

70
Q

What is a plasmid?

A

A plasmid is a small and circular extra chromosomal piece of DNA naturally found in bacteria.

71
Q

How can we make large quantities of a protein or drug?

A

We can insert the recombinant gene into a plasmid downstream of an inducible promoter that is able to produce large quantities of the protein only when we want the gene expressed. This plasmid often contains antibiotic resistance, so that when large quantities of the plasmid are produced in bacterial colonies and an antibiotic is introduced, the vectors that don’t contain this antibiotic resistance can be killed off.

72
Q

How do you actually insert your target gene into the plasmid?

A

You cut the foreign DNA which is your target gene with a restriction enzyme, and you use the same restriction enzyme to cut the plasmid. This allows the DNA fragment to directly fit into the plasmid. Next you introduce DNA ligase which seals the nicks in the sugar phosphate backbone.

73
Q

Gene transfer technique using a fertilized ova

A

Target gene/DNA is micro injected into an egg cell/ova which is then implanted into a surrogate which produces all offspring with the target gene. (Homozygous transgenic offspring)

74
Q

Gene transfer technique using embryonic stem cells

A

Transgenic, embryonic stem cells are created by micro injecting your target gene into the embryonic stem cells. These transgenic stem cells are then microinjected into a developing blastocyte. This blastocyst is injected into a surrogate who is able to produce chimera offspring which have germs lines derived from two cell lineages (one from transgenic cells & other from host blastocyst). Phenotypically, this shows on mice having patchy coats of two colors.

75
Q

Which nucleotides are more likely to be found at the origin of replication?

A

Adenine paired with thymine

76
Q

In prokaryotes, the 13mer region is where the DNA helix starts to unwind prior to replication. Which base pairs are more likely to be found in this region?

A

Adenine paired with thymine

77
Q

What is Z-DNA?

A

It is a type of DNA that forms a left-handed double helix. This is the opposite of B-DNA which makes up the human genome.

78
Q

True or false:
In DNA replication, daughter strands contain the same ratio of total purines to total pyrimidines as the parent template strand.

A

True, daughter strands contain the same ratio of bases as the parent strand with the exception of a few nucleotides due to DNA polymerase not being able to synthesize all the way to the end of the strand. This cause shortening of telomeres, but doesn’t harm the actual gene coding regions.

79
Q

What is the role of the sliding clamp in DNA replication?

A

Sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand.

80
Q

How does northern blotting work?

A
  1. Run through a gel electrophoresis
  2. Transferred to a membrane where the RNA retains separation
  3. Hybridization with a labeled complementary RNA probe
81
Q

Steps of a western blot

A
  1. Extract proteins and put run them through a gel electrophoresis
  2. Take them off the gel with the separation still intact and transfer them to a protein binding membrane such as nitrocellulose.
  3. Once proteins have transferred(stuck) to the nitrocellulose membrane, you wash it with PBS.
  4. Then add a blocking buffer solution whose purpose is to bind all the antibodies on the surface of the proteins non specifically. Wash again with PBS.
  5. Now, add the primary antibody for your protein target which will compete with the blocking buffer and bind directly to specific protein antigens only.
  6. Lastly, add secondary antibodies which are fluorescently labeled. This allows multiple secondary antibodies to bind to the primary antibody and cause signal amplification producing a brighter spot.

Malika Biochem MCAT (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions