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Biochemistry Flashcards

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1
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleoside- a 5 carbon sugar (pentose) bonded to a nitrogenous base

Nucleotide- A nucleoside + one or more phosphate groups attached to the 5th carbon of the pentose

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2
Q

What are the building blocks of DNA?

A

Nucleotides

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3
Q

What is the difference between the 2nd carbon on the pentose sugar on DNA and RNA?

A

RNA- has an -OH group

DNA- has an -H group because it is deoxyribose

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4
Q

On what carbon due RNA and DNA differ?

A

2 carbon of the pentose sugar ribose

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5
Q

How are Nucleic Acids and Nucleotides related?

A

Nucleic Acids (DNA and RNA) are long chains of nucleotides

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6
Q

In what direction is DNA always read?

A

5’ to 3’

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7
Q

Between what two carbon atoms of nucleotides does a phosphodiester bond form?

A

The 3’ of the top nucleotide and the 5’ of the bottom nucleotide

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8
Q

Why are DNA and RNA given an overall negative charge?

A

Because the phosphate groups are negative

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9
Q

If the nitrogenous base on a DNA molecule has two rings what are the possible nucleotides that make it up? What group of nitrogenous bases is this?

A

Adenine and Guanine

Both are in the Purine Group

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10
Q

If a nitrogenous base on an RNA molecule has one ring what are the possible nucleotides that make it up? What group of nitrogenous bases it this?

A

Uracil and Cysteine

Both are in the Pyrimidine Group

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11
Q

In DNA, what other nucleotide does Adenine bond with and how many hydrogen bonds does it make with it?

A

It bonds with Thymine and makes 2 Hydrogen Bonds

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12
Q

In DNA, what other nucleotide does Guanine bond with and how many hydrogen bonds does it make with it?

A

It bonds with Cysteine and makes 3 Hydrogen Bonds

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13
Q

Is the A w/ T or G w/ C base pairing stronger?

A

G with C because it uses one more H-bond

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14
Q

What must occur for DNA to be opened up for transcription and replication?

A

The Hydrogen bonds between the nucleotides must be broken

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15
Q

What does the process of reannealing DNA entail?

A

Two denatured strands of complementary DNA can be reannealed by slowly removing the denaturing condition such as heat. This brings the two strands back together

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16
Q

What are the proteins that DNA is folded around to form chromatin?

A

Histones

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17
Q

What are the various stages of DNA folding and consolidation?

A
  1. DNA double helix
  2. Nucleosomes (beads on a string)
  3. Supercoiling of nucleosomes
  4. heterochromatin
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18
Q

What is the difference between euchromatin and heterochromatin?

A

Euchromatin- unwound and loose chromatin

Heterochromatin- tightly bound chromatin

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19
Q

Do centromeres consist of euchromatin or heterochromatin?

A

Heterochromatin because they are tightly condensed

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20
Q

How does bacterial DNA replication differ from humans?

A

Bacteria have a large circle of DNA that is replicated starting at one origin of replicaton

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21
Q

What protein goes ahead of helicase and starts to unwind the DNA helix to prevent torsional strain?

A

DNA Topoisomerase

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22
Q

What protein is responsible for breaking the H-bonds between nucleotides to separate the 2 strands of DNA for replication?

A

Helicase

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23
Q

What proteins are responsible for synthesizing the new daughter strand of DNA by reading the parent strand?

A

DNA polymerases

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24
Q

What direction do DNA polymerases read? What direction do they synthesize daughter strands in?

A

They read from 3’ to 5’ direction

They then synthesize new DNA in the 5’ to 3’ direction

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25
Q

Why can only one of the parents strands of replicating DNA be effectively worked on by DNA polymerases?

A

Because the polymerase makes new DNA from 5’ to 3’ end and thus only one strand matches this pattern (the leading strand)

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26
Q

Why are Okazaki fragments created in the lagging strand?

A

Because the lagging strand cannot be read in a forward direction by the DNA polymerases and thus it works in a circular short segments

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27
Q

Which nucleic acid, RNA or DNA, can be synthesized without a primer? How does this effect replication?

A

RNA; this is why an RNA primer is added to DNA by primase to initiate replication

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28
Q

What proteins are responsible for the joining of Okazaki fragments on the lagging strand?

A

Ligases

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29
Q

What do oncogenes usually code for?

A

Cell-Cycle related proteins

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30
Q

What do antioncogenes usually code for?

A

Cell-Cycle inhibiting proteins (ex. p53 and retinoblastoma)

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31
Q

During S-phase, how does the cell regulate the errors associated with DNA replication?

A

The replicating DNA passes through part of the DNA polymerase to undergo proofreading

This is done by checking the stability of the H-bonds associated with the new DNA

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32
Q

During the G1 and G2 phase what are the two methods of repairing damaged DNA?

A
  1. Nucleotide Excision Repair- where proteins find errors in DNA and then endonuclease nicks the phosphodiester bond so that the nucleotide is removed and replaced correctly
  2. Base Excision Repair- the effected base is found and removed and then this indicates to an endonuclease that the nucleotide is removed and replaced correctly
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33
Q

What is a common way of creating many copies of a strand of DNA? Why is it useful?

A

Polymerase Chain Reaction (PCR)

It allows for DNA to be tested for genetic markers

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34
Q

Why do DNA primers used for PCR have high amount of Guanine and Cysteine nucleotides?

A

So that they are more stable

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35
Q

What two molecules can bind to histone proteins and what are there effects on the accessibility of DNA to transcription? What is the mnemonic to remember this?

A

Acetylation- occurs when acetyl groups bind to histone proteins and INCREASE accessibility

Methylation- occurs when methyl groups bind to histone proteins and DECREASE accessibility

Acetylation makes DNA Accessible

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36
Q

During transcription, what strand of the original DNA is identical to the new hnRNA except for the Uracil for Thymine exchange?

A

The Coding Strand

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37
Q

During Transcription, what strand of the original DNA is complementary and antiparallel to the new hnRNA?

A

The Template Strand

38
Q

In what direction is new hnRNA transcribed?

A

From the 5’ to the 3’ end

39
Q

What are the 4 types of RNA in the cells?

A
  1. mRNA- carries genetic information from DNA to ribosome
  2. tRNA- translates the mRNA information into an amino acid
  3. rRNA- function as enzymes made of RNA (ribozymes) and help the ribosome function
  4. snRNA- used in post-transcriptional modification of DNA by excising introns and exons
40
Q

What is the difference between monocistronic and polycistronic mRNA? In what cell types do these separate RNA types exist?

A

Monocistronic- mRNA codes information for only one protein product; exists in Eukaryotes

Polycistronic- mRNA codes information for many proteins; exists in Prokaryotes

41
Q

What does it mean for a tRNA to become activated?

A

It bonds with a specific amino acid

42
Q

What is the name for the 3 letter codes of nucleotides that relate to a specific amino acid?

A

Codon

43
Q

What are the 3 stop codons?

A

UAA
UAG
UGA

44
Q

What is the start codon?

A

AUG

45
Q

What is the first amino acid in every protein?

A

Methionine

46
Q

What is the third (and often variable) base in a codon referred as?

A

Wobble Position

47
Q

What two enzymes, used in replication and transcription, are important for the unwinding and breaking apart of the DNA double helix?

A

Topoisomerase- unwinding

Helicase- breaking apart

48
Q

What are two names for the strand of DNA that is complementary and antiparallel to the new hnRNA strand?

A

Template or Antisense Strand

49
Q

What is the protein that is responsible for transcribing DNA into hnRNA?

A

RNA Polymerase II

50
Q

What are the specialized DNA regions to which RNA Polymerase II can bind to and initiate transcription?

A

Promoter Regions (ex. TATA box)

51
Q

In what direction does RNA Polymerase II read the DNA antisense strand?

A

From 3’ to 5’ direction so that it can create hnRNA in the 5’ to 3’ direction

52
Q

What is the difference between hnRNA and mRNA?

A

hnRNA is what is left immediately following transcription from DNA and has not undergone post-transcriptional modification

53
Q

What are the 3 main events that occur during post-transcriptional processing?

A
  1. Splicing of Introns from Exons
  2. Addition of the 5’ GTP-cap
  3. Addition of the 3’ Poly-A tail
54
Q

What is the way to remember that introns are removed from hnRNA and that exons are kept in mRNA?

A

Exons are Expressed (thus they have to be left in the mRNA)

55
Q

What type of RNA is used in the processing of splicing introns?

A

snRNA that are a component of spliceosomes

56
Q

Why is a GTP-cap given to the 5’ end of hnRNA in post-transcriptional modication?

A

This cap protects the 5’ end from degradation in the cytoplasm as well as serves as a target for ribosome binding

57
Q

Why is a Poly-A tail given to the 3’ end of the hnRNA during post-transcriptional modication?

A

It serves as a protecting fuse for the hnRNA in the cytoplasm

58
Q

Is the Poly-A tail of post-transcriptional modification added to the 5’ or 3’ end of hnRNA? What is the mnemonic for remembering this?

A

3 rats with poly-A tails

59
Q

Where does the process of translation take place?

A

Ribosomes

60
Q

What are the 3 steps of translation?

A
  1. Initiation
  2. Elongation
  3. Termination
61
Q

What occurs in the process of initiation during translation?

A

The small ribosomal subunit binds to the 5’ untranslated region and the initiator tRNA binds to the start codon in mRNA

62
Q

In what section of the Ribosome do new tRNA molecules enter and bind to the mRNA?

A

the A site

63
Q

In what section of the Ribosome do the amino acids get added to a growing polypeptide chain?

A

the P site

64
Q

In what section of the Ribosome do the deactivated tRNA molecules exit?

A

the E site

65
Q

Proteins that are created to be secreted outside the cell contain signal sequences that direct the ribosome to move to what organelle?

A

The Rough ER

66
Q

What processes allow a translated polypeptide chain to become a functioning protein?

A

Post-Translational modification

67
Q

What are some examples of post-translational modification?

A
  1. Protein Super-folding (aided by chaperones)
  2. Cleavage events (ex. prohormones)
  3. Subunits coming together to form quaternary structure (ex. Hb)
68
Q

What is the name for a group of genes, in prokaryotes, that are transcribed as a group?

A

Operon

69
Q

What is the difference between an inducible and repressible system in operons?

A

Inducible- a protein binds to the regularly bound repressor on the operator site, this increases transcription (ex. lac operon)

Repressible- without a corepressor bound to it, a repressor cannot bind to the operator site, this increases transcription (ex. trp operon)

70
Q

What is the difference between the lac and trp operons?

A

Lac- inducible operon

Trp- repressible operon

71
Q

What are some of the methods that Eukaryotes control gene expression?

A
  1. Alternative Splicing
  2. Transcription Factors
  3. Enhancers
  4. Gene Duplication
  5. Histone Acetylation
  6. Histone Methylation
72
Q

What is the role of transcription factors?

A

They are used in eukaryotes as a method of controlling gene expression by binding to specific regions of DNA and attracting proteins used in transcription

73
Q

What is the role of Enhancers?

A

They are used in eukaryotes as a method of controlling gene expression by being activated by signaling molecules (cAMP, cortisol) and serve as a group of transcription factors

74
Q

What is the role of gene duplication in controlling gene expression in eukaryotes?

A

Cells will create multiple copies of the same gene on the same chromosome to control how often it is transcribed

75
Q

What would be the effect of histone deacetylation?

A

Decreasing gene expression

76
Q

How does gel electrophoresis work?

A

A polyacrylamide gel is set up with a cathode (-) on one side and an anode (+) on the other

Proteins that are negatively charged will migrate toward the anode (+) thus separating them out by charge

77
Q

What are the three main types of gel electrophoresis?

A
  1. Polyacrylamide Gel Electrophoresis (PAGE)
  2. SDS-PAGE
  3. Isoelectric Focusing
78
Q

What is the limitation of a regular Polyacrylamide Gel Electrophoresis?

A

Proteins that are very massive but are heavily charged may migrate the same as a smaller but more charged molecule

Thus PAGE is best at analyzing proteins that are known to have similar sizes

79
Q

How does SDS-PAGE differ from regular gel electrophoresis?

A

The Protein being analyzed is treated with SDS which disrupts all non-covalent interactions and binds to the protein with an equal mass to charge ratio

This allows SDS-PAGE to separate out proteins based on molecular mass alone

80
Q

What is the process of Isoelectric Focusing?

A

A gel electrophoresis is set up with an acidic gel near the anode and a basic gel near the cathode

As the electric current is sent through the gel, proteins with a basic charge (+) will migrate toward the cathode and stop moving when they reach a gel pH that is equal to the proteins PI

81
Q

When is chromatography favored over gel electrophoresis?

A

When large amounts of protein are being separated

82
Q

Assuming the a group of proteins or DNA have similar net charges, what type of protein or DNA fragment would travel the farthest in a PAGE setup?

A

A small protein or DNA fragment

83
Q

What are the different blotting techniques and what do they measure respectively?

A

Southern Blot- DNA
Northern Blot- RNA
O O
Western Blot- Protein

Mnemonic = SNOW DROP

84
Q

Assuming a group of proteins have a similar size, what type of protein would travel the farthest in a PAGE setup?

A

The protein with the most negative net charge`

85
Q

Is net charge a consideration for measuring results of a PAGE experiment done on DNA or RNA?

A

No; because DNA and RNA molecules of any length have proportional net charges

86
Q

What is the difference between a regular SDS-PAGE and a reducing SDS-PAGE?

A

the reducing SDS-PAGE adds a chemical that breaks the cysteine-cysteine salt bridges left behind from the SDS treatment

87
Q

What is a native-PAGE?

A

Running a PAGE setup with the natural protein (regular and untreated)

88
Q

What is the general process of a Northern or Southern Blot?

A

RNA is separated using a PAGE setup and then added to nitrocellulose and UV light to immobilize it. Then a reporter (marker) RNA fragment is added to label a specific part of the RNA you are analyzing

89
Q

How is a Western Blot different from a Norther and Southern Blot?

A

A Western Blot analyzes proteins and thus cannot use RNA probes to mark a specific segment

Instead a Western Blot uses a Primary (for protein) and Secondary (for reporter) Antibody

90
Q

What is an Enzyme-Linked Immunosorbent Assay (ELISA) used to find?

A

If a specific antibody (protein) binds to a specific antigen or determine the concentration of an antigen in a sample

91
Q

What does the Sanger method find?

A

Find the sequence of a particular DNA strand

MCAT (8 decks)

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