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Kaplan: Biochemistry Part I > Chapter 4: The Genetic Code, Mutations, and Translation > Flashcards

Chapter 4: The Genetic Code, Mutations, and Translation Flashcards

1
Q

How many codons are there total?

A

64 codons

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2
Q

How many codons code for amino acids?

A

61 codons

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3
Q

What are the three stop codons?

A

UAA (u are away, umbrella apple apple)
UGA (u go away, umbrella gold apple)
UAG ( u are gone, umbrella, apple gold)

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4
Q

What is the start codon and what does it code for?

A

AUG methionine (Met) in eukaryotes
fMet) formyl group in prokaryotes

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5
Q

What is a mutation?

A

any permanent, heritable change in the DNA base sequence of an organism

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6
Q

What is a transition?

A

a point mutation that replaces a purine-pyrimidine base pair with a different purine-pyrimidine base pair

i.e A-T base pair becomes a G-C base pair

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7
Q

What is a transversion?

A

a point mutation that replaces a purine-pyrimidine base pair with a pyrimidine purine base pair

i.e A-T base pair becomes a T-A or a C-G base pair

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8
Q

What is a trinucleotide repeat expansion? What is a common feature of these types of abnormalities?

A

expansions in coding regions cause protein product to be longer than normal and unstable

disease often show anticipation in pedigree

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9
Q

What is an example of a large segment deletion?

A

a-thalassemia is a well-known genetic disease in which unequal crossover has deleted one or more a-globin genes from chromsome 16

another example is cri -du-chat

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10
Q

What are some effects on the cellular level of mutations of splice sites?

A
  1. deletion of nucleotides from the adjacent exon
  2. leave nucleotides of the intron in the processed mRNA
  3. Use the next normal upstream or downstream splice site, deleting an exon from the processed mRNA
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11
Q

List examples of conditions that are caused by mutations in splice sites?

A

B-thalassemia, Gaucher disease, and Tay-Sachs

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12
Q

What is anticipation?

A

Disease in which the severity for the disease increases while the age of onset decreases with successive generations

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13
Q

Name some translation repeat disorders? Another name for translation repeat disorders?

A

Some polyglutamine disorders would be:

Huntington disease: (CAG)n
Spinobulbar muscular atrophy (CAG)n

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14
Q

What are some untranslated repeat disorders?

A

Fragile X syndrome (CGG)n
Myotonic dystrophy (CTG) n
Friedreich’s ataxia (GAA) n

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15
Q

What are some signs of Huntington disease?

A

mood disturbance, impaired memory, and hyperreflexia are often the first signs, followed by abnormal gait, chorea (loss of motor control), dystonia, dementia, and dysphagia

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16
Q

Before an amino acid can be transferred to the 3’ end of the tRNA what enzyme must work on the amino acid?

A

aminoacyl tRNA synthetase must transfer the activated amino acid to the 3’ end of the correct tRNA and two high- energy bonds from ATP are required.

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17
Q

In prokaryotes, how does initiation of translation occur?

A

The small ribosomal subunit binds to the mRNA. In prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgarno sequence in the 5’ untranslated region of the mRNA.

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18
Q

In eukaryotes, how does initiation of translation occur?

A

the small subunit binds to the 5’ cap structure and slides down the message to the first AUG

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19
Q

Describe the P site of the ribosome.

A

Peptidyl site is the site on the ribsome where fMet-tRNAi initially binds.

P site becomes binding site for growing peptide chain

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20
Q

Describe A site of the ribosome. Also what is another name for this site?

A

aminoacyl site (A site) binds each new incoming tRNA molecule carrying an activated amino acid

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21
Q

Each cycle for elongation for protein translation uses how many energy bonds?

A

4 high-energy bonds (2 from ATP used in amino acid activation to charge the tRNA, and 2 from GTP)

22
Q

What is the direction the ribosome moves during elongation?

A

5’ to 3’ direction

23
Q

What occurs in the translocation step of protein translation?

A

the ribosome moves exactly 3 nucleotides (one codon) along the message. This moves the growing peptidyl-tRNA into the P site and aligns the next codon to be translated with the empty A site

24
Q

In eukaryotic cells, what is used in translocation and inactivated through ADP-ribosylation by Pseudomonas and Diphtheria toxin? (Give abbreviation and full name)

A

eEF-2 (elongation factor - 2)

25
Q

Name some inhibitors of eukaryotic translation?

A

cycloheximide and diphtheria and pseudomonas toxin

26
Q

Why do babies get gray baby syndrome from use of chloramphenicol?

A

babies do not have sufficient UDP-glucoronyl transferase activity needed to allow excretion of this drug

27
Q

What are some symptoms of gray-baby syndrome?

A

blue lips, nail beds, and skin (cyanosis)

death

low bp

28
Q

What are the 2 main secondary conformational arrangements of proteins?

A

alpha helix and beta pleated sheets

29
Q

What are the alpha helix and beta pleated sheets reinforced by?

A

hydrogen bonds

30
Q

What are some bonds that tertiary structures are stabilized by in a protein?

A

weak bonds (hydrogen, hydrophobic, and ionic)
strong (covalent disulfide bonds)

31
Q

There are certain proteins that are translated on ribosomes associated with the RER (rough endoplasmic reticulum)? Name the types of proteins?

A

secreted proteins
proteins inserted into the cell membrane
lysosomal proteins

32
Q

What are the type of proteins translated on free cytoplasmic ribosomes?

A

cytoplasmic proteins
mitochondrial proteins (encoded in nuclear genes)

33
Q

What are chaperones?

A

a class of specialized proteins essential for protein folding and an essential step in the final synthesis of proteins

34
Q

What is ubiquitin?

A

a type of protein that covalently links them to defective proteins and marks them for destruction by directing them to proteasomes for destruction.

35
Q

The majority of cases of cystic fibrosis have what genetic basis?

A

result from the deletion of phenylalanine at position 508 (F508), which interferes with proper protein folding and posttranslational processing of oligosaccharide side chains

The abnormal chloride channel protein is degraded by the cytosolic proteasome complex rather than being translocated to the cell membrane

36
Q

What is the signal sequence used to ensure translation occurs on the RER?

A

N-terminal hydrophobic signal sequence

37
Q

What is important protein responsible for directing an enzyme to a lysosome?

A

phosphorylation of mannose residues

38
Q

What is N-glycosylation?

A

refers to the addition of sugar chains to the nitrogen of asparagine residues

39
Q

Initiation of N-glycosylation of a protein is co-translational or posttranslational modification?

A

co-translational modification

40
Q

N-glycosylation requires the participation of what special lipid?

A

lipid called dolichol phosphate

41
Q

What is O-glycosylation?

A

refers to the addition of sugar chains to the hydroxyl group of either serine or threonine residues of the protein

42
Q

What is an example of a protein that is soley N-glycosylated?

A

transferin

43
Q

What are examples of proteins that are soley O-glycosylated?

A

heparin

44
Q

What are examples of proteins that are both N and O glycosylated?

A

LDL receptor

45
Q

What is the genetic basis of A, B, O blood groups? (related to translation modification)

A

significant structure and sequence of the oligosaccharide chains on proteins and lipids (glycolipids)

46
Q

What is a-1 antitrypsin?

A

a protein synthesized primarily in the liver and secreted in the bloodstream.

It protects cells by serving as an inhibitor of protease released during a normal inflammatory response

47
Q

Genetic basis for a1-antitrypsin deficiency?

A

mutation that causes the a1-antitrypsin protein to misfold and aggregate in the endoplasmic reticulum, where it damages cells, eventually leading to cirrhosis

48
Q

Explain lysosomal phosphorylation of mannose residues in the Golgi.

A

When lysosomal enzymes arrive in Golgi apparatus, specific mannose residues located in their N-linked oligosaccharide chains are phosphorylated by N-acetylglucosamine-1 phosphotransferase, forming a critical mannose-6-phosphate in the oligosaccharide chain

Phosphorylation step is critical because it removes them from the secretion pathway and directs them to lysosomes

49
Q

What is the function of lysosomes?

A

organelles whose major function is to digest materials that the cell has ingested by endocytosis

50
Q

What is the purpose of the enzymes that function in the lysosome?

A

collectively, digest carbohydrates (glycosylases), lipids (lipases), and proteins (proteases)

51
Q

What occurs when lysosomal enzymes are missing?

A

the undigested substrate accumulates in the cell, often leading to serious consequences.

52
Q

What are some major symptoms of I-Cell disease? Diagnosis?

A
  • coarse facial features, gingival hyperplasia, macroglossia
  • craniofacial abnormalities, joint immobility, clubfoot, claw-hand, scoliosis
  • psychomotor retardation, growth retardation
  • cardiorespiratory failure, death in first decade
  • bone fracture and deformities
  • mitral valve defect
  • secretion of active lysosomal enzymes into blood and ECF

Kaplan: Biochemistry Part I (27 decks)

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