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First Aid: Biochemistry > Principles: Molecular Biochemistry 2 > Flashcards

Principles: Molecular Biochemistry 2 Flashcards

1
Q

What are some principles about the genetic code (4).

A
  1. Unambiguous - each codon specifies only 1 amino acid
  2. Degenerate/redundant: Most amino acids are coded by multiple codons. Exceptions: Met (AUG) and tryptophan (UGG)
  3. Commaless, nonoverlapping: Read from a fixed starting point as a continuous sequence of bases. Exception: Some viruses.
  4. Universal: Genetic code conserved throughout evolution. Exception in humans: Mitochondria.
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2
Q

What word describes how DNA strands are conserved during DNA replication?

A

Semiconservative (one complete new strand pairs with one complete “old” strand used as a template)

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3
Q

What is an origin of replication?

A

Particular consensus sequence of base pairs in genome where DNA replication begins.

May be single (prokaryotes) or multiple (eukaryotes)

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4
Q

What is a replication fork?

A

Y-shaped region along DNA template where leading and lagging strands are synthesized.

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5
Q

What is helicase?

A

Unwinds DNA template at replication fork

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6
Q

What are single-stranded binding proteins?

A

Prevent strands from reannealing

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7
Q

What are DNA topoisomerases?

A

Create a single or double-stranded break in the helix to add or remove supercoils.

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8
Q

What class of antibiotic inhibits DNA topoisomerases?

A

Fluoroquinolones - inhibit DNA gyrase (prokaryotic topoisomerase II)

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9
Q

What does DNA polymerase III do?

A

Prokaryotic only.

Elongates leading strand by adding deoxynucleotides to the 3’ end. Elongates lagging strand until it reaches primer of proceding fragment. 3’-5’ exonuclease activity “proofreads” each added nucleotide.

DNA pol III has 5’->3’ synthesis and proofreads with 3’->5’ exonuclease.

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10
Q

What does DNA polymerase I do?

A

Prokaryotic only.

Degrades RNA primer and replaces it with DNA.

Has same functions as DNA polymerase III but also excises RNA primer with 5’->3’ exonuclease.

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11
Q

What is the function of DNA ligase?

A

Catalyzes formation of phosphodiester bond within a strand of double-stranded DNA (i.e., joint Okazaki fragments).

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12
Q

What is the function of telomerase?

A

A RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication.

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13
Q

What is a silent mutation?

A

Silent << missense < nonsense < frameshift

Silent mutation: A nucleotide substitution that codes for the same (synonymous) amino acid. Usually base change in the 3rd position of the codon (wobble base)

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14
Q

What is a missence mutation?

A

Missence mutation is a nucleotide substitition resulting in a changed amino acid (called conservative if new amino acid is similar in chemical structure

Example: Sickle cell disease

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15
Q

What is a nonsense mutation?

A

Nucleotide substitution resulting in early stop codon.

“Stop the nonsense!”

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16
Q

What is a frameshift mutation?

A

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream.

Usually results in a truncated, nonfunctional protein.

Example: Duchenne muscular dystrophy

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17
Q

What are transition and transversion mutations?

A

For silent, missence, and nonsense mutations…

Transition: Change from purine to purine (A to G) or a pyrimidine to a pyrimidine.

Transversion: Change from a purine to a pyrimidine or vice-versa (A to T)

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18
Q

What are the categories of single stranded DNA repair?

A

Nucleotide excision

Base excision

Mismatch repair

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19
Q

What is nucleotide excision repair?

In what disease is it defective?

A

A single-stranded DNA repair mechanism.

Specific endonucleases release the ologonucleotide-containing damaged bases; DNA polymerase and ligase fill and reseal the gap, respectively. Repairs bulky helix-distorting lesions.

Defective in xeroderma pigmentosum, which prevents repair of pyrimidine dimers because of ultraviolet light exposure.

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20
Q

What is the mechanism of base excision repair?

What DNA damage does it fix?

A

Single-stranded repair.

Base-specific glycosylase recognizes altered base and creates AP site (apurinic/apyrimidinic). One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-beta fills the gap and DNA ligase seals it.

Important in repair of spontaneous/toxic deamination.

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21
Q

What is the mechanism of mismatch repair?

In what disease is it defective?

A

Single-stranded DNA repair.

Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed.

Defective in hereditary nonpolyposis colorectal cancer (HNPCC)

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22
Q

What is the major double-stranded DNA repair mechanism in humans?

In what disease is it defective?

A

Nonhomologous end joining.

Brings together 2 ends of DNA fragments to repair double-stranded breaks.

No requirement for homology.

Mutated in ataxia telangiectasia.

23
Q

In what direction are RNA and DNA synthesized?

In what direction is mRNA read?

In what direction are proteins synthesized?

A

DNA and RNA synthesized from 5’->3’. The 5’ end of the incoming nucleotide bears the triphosphate (energy source for bond).

mRNA is read from 5’->3’.

Protein synthesis is N-terminus to C-terminus.

24
Q

What are the mRNA start codons?

What does it code for in eukaryotes and prokaryotes?

A

AUG inAUGurates protein synthesis

In Eukaryotes, codes for methionine, which may be removed before translation is complete.

In prokaryotes, codes for formylmethionine (f-met).

Rarely, start codon is GUG.

25
Q

What are the mRNA stop codons?

A

UGA = U Go Away

UAA = U Are Away

UAG = U Are Gone

26
Q

What is a gene promoter?

What is it composed of?

What happens if it is mutated?

A

Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus.

Composed of AT-rich upstream sequence with TATA and CAAT boxes.

Promoter mutations dramatically reduce gene transcription.

27
Q

What is a gene enhancer?

Where is it located?

A

Stretch of DNA expression that alters gene expression by binding transcription factors.

Can be located close to, far from, or even within (in an intron) the gene whose expression it regulates.

28
Q

What is a gene silencer?

Where is it located?

A

Silencer - site where negative regulators (repressors) bind.

Can be located close to, far from, or even within (in an intron) the gene whose expression it regulates.

29
Q

How do RNA polymerases differ between eukaryotes and prokaryotes?

A

Eukaryotes have three RNA polymerases (RNA pol I, II, and III) with separate functions.

Prokaryotes have one RNA polymerase (multisubunit complex) that makes all three types of RNA.

30
Q

What types of RNA do RNA polymerase I, II, and III make, respectively?

A

RNAP I: rRNA (most numerous RNA, rampant).

RNAP II: mRNA (largest RNA, massive)

RNAP III: tRNA (smallest RNA, tiny).

The three are numbered as their products are used in protein synthesis.

31
Q

Can the RNA polymerases proofread?

Where does RNAP II open DNA for transcription?

A

No.

RNAP II opens DNA at the promoter site.

The RNA polymerases can initiate chains.

32
Q

What toxin can inhibit RNA polymerase II, and what is the clinical effect?

A

α-amanitin, found in Amanita phalloides (death cap mushrooms) inhibits RNAP II.

Causes severe hepatotoxicity if ingested

33
Q

What is the initial transcript made by RNAP II called?

What modifications occur in the nucleus?

A

Heterogeneous nuclear RNA (hnRNA)

  1. Capping of 5’ end (addition of 7-methylguanosine cap)
  2. Polyadenation of 3’ end (200ish A’s)
  3. Splicing out of introns

Once all three finished, called mRNA.

34
Q

Where is mRNA stored in the cytoplasm?

A

Quality control at cytoplasmic P-bodies. Contain exonucleases, decapping enzymes, and microRNAs. Can be stored for future translation.

35
Q

What are some features about the Poly-A polymerase?

A

Does not require a template.

AAUAAA = Polyadenylation signal.

36
Q

How does splicing work?

A
  1. Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome.
  2. Lariat-shaped (looped) intermediate is generated
  3. Lariat is released to precisely remove intron and join 2 exons.
37
Q

What are antibodies to spliceosomal snRNPs called, and what disease are they specific for?

A

Anti-smith antibodies.

Specific for SLE

38
Q

What disease are anti-U1 RNP antibodies associated with?

A

Mixed connective tissue disease

39
Q

Introns versus exons?

A

Introns are intervening sequences and stay in the nucleus.

Exons exit and are expressed.

40
Q

How big is tRNA? What is its three-dimensional structure?

What part of the tRNA carries amino acids?

A

75-90 nucleotides, 2° structure. Cloverleaf form.

Anticodon end is opposite 3’ aminoacyl end.

All tRNAs have CCA at 3’ end along with a high percentage of chemically modified bases. The amino acid is covalently bound to the 3’ end of the tRNA.

CCA = Can Carry Amino acids.

41
Q

What does the T-arm of tRNA contain?

What is its function?

A

Contains TΨC (thymine, pseudouridine, cytosine) sequence necessary for tRNA-ribosome binding.

42
Q

What does the D-arm of tRNA contain, and what is its function?

A

Dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase

43
Q

What does the acceptor stem of tRNA contain?

A

3’ CCA is the amino acid acceptor site.

44
Q

What occurs during the process of tRNA charging?

A

Aminoacyl-tRNA synthetase (1 per amino acid; “matchmaker”; uses ATP) scrutinizes amino acid before and after it binds to tRNA.

If incorrect, bbond is hydrolyzed.

The amino acid-tRNA bond has energy for formation of a peptide bond.

A mischarged tRNA reads usual codon but inserts wrong amino acid.

Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection.

45
Q

What are the ribosomal subunits for eukaryotes?

A

40s + 60s = 80s.

Eukaryotes = Even.

46
Q

What are the ribosomal subunits for prokaryotes?

A

30s + 50s -> 70s

Prokaryotes = Odd.

47
Q

What NTP is required for tRNA charging and translocation?

A

ATP - tRNA Activation (charging)

GTP - tRNA Gripping and Going places (translocation)

48
Q

What occurs during protein synthesis initiation?

A

Initiated by GTP hydrolysis; initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60s subunit assemble with the complex.

49
Q

What occurs during the elongation phase of protein synthesis?

A
  1. Aminoacyl-tRNA binds to A site (except for initiator methionine)
  2. rRNA (“ribozyme”) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
  3. Ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P site (translocation)
50
Q

What occurs during the termination phase of protein synthesis?

A

Stop codon recognized by release factor, completed polypeptide is released from ribosome.

51
Q

What are the ribosomal tRNA binding sites?

A

Think of “going APE”

A site = incoming Aminoacyl-tRNA

P site = accomodates growing Peptide

E site = holds Empty tRNA as it Exits.

52
Q

What is the posttranslational trimming?

A

Removal of N- or C-terminal propeptides from zymogen to generate mature protein (e.g., trypsinogen to trypsin).

53
Q

What are some posttranslational covalent alterations?

A

Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination.

54
Q

What are chaperone proteins?

A

Intracellular protein involved in facilitating and/or maintaining protein folding.

In yeast some are heat shock proteins (hsp60) that are expressed at high temperatures to prevent protein denaturing/misfolding.

First Aid: Biochemistry (7 decks)

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