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Biochemistry > Test 2 > Flashcards

Test 2 Flashcards

1
Q

Histone contain the amino acids ____ ?

A

Lys and Arginine (basic residues so they can interact with the negatively charged DNA)

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2
Q

The DNA located near centromeres and telomeres is called ____ and is said to be ___ condensed (very or not very?). This DNA is also mainly ___ (Active or inactive?)

A

heterochromatin, very, inactive

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3
Q

___ is the name for the condensed DNA that is rich in gene concentration and often under active transcription?

A

Euchromatin

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4
Q

The basic unit of chromosome packing is ___.

So histones are composed of ___ subunits, and when ___ of those histone proteins come together, DNA wraps around it and this is called a ____

A

Nucleosomes (not histones, even though they help in the packaging process)

4, 8, nucleosome

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5
Q

DNA replication is ___-conservative and ___-directional

A

Semi, Bi

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6
Q

In DNA replication, DNA polymerase requires a ___ and a free ___ ‘ group to begin

A

primer, 3’ OH

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7
Q

How does DNA helicase unwind the DNA? (what powers it?)

A

They hydrolysis of ATP -> ADP

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8
Q

What protein helps stabilize unwound DNA, keeps hairpins from forming, and keeps the DNA bases exposed?

A

SSB (Single stranded DNA binding proteins)

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9
Q

What keeps DNA polymerase on the DNA when moving?

A

PCNA (sliding clamps which also use the help of a clamp loader). They also change affinity depending on the base pair

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10
Q

Name the DNA polymerase used in DNA replication

1) Synthesis DNA in Oazaki fragments and also fills in the gap with DNA after FEN1 removes the primer
2) Main one used for synthesis of the leading strand
3) Synthesizes first step of DNA from 5’->3’ from the primer complex.

A

1) Delta
2) Epsilon
3) Alpha (RNA primer is 7-10 nucleotides long, and alpha extends the sequence to about 25 nucleotides)

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11
Q

Telomerase uses a ___ template strand to elongate the parental strand in the __ ‘ to ___ ‘ direction.

A

RNA, 5’->3’ (Then and RNA primer is layed down on the new elongated DNA strand, and DNA polymerase synthesizes new DNA in the 5’->3’ direction to fill in the gap)

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12
Q

Spontaneous DNA damage can occur by depurination (loss of purine obviously) or deamination. What is deamination, and what are the three changes that are possible?

A 
Deamination is the hydrolysis of an amino group (amino to double bond O) 
Adenine -> hypoxanthine 
Cytosine -> Uracil 
Guanine -> xanthine
(its all alphabetical)
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13
Q

UV radiation results in what kind of damage?

A

Pyrimidine dimers (T-T or C-T)

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14
Q

Depurination results in a ___ mutation, and deamination results in a ___

A

frame shift, base pair substitution

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15
Q

Nitrogen mustard and Cisplatin are examples of ___ agents
DMS and MMS (Methyl methanesulfonate) are examples of ___ agents
Ethidium bromide is an example of a ___ agent
What kind of radiation causes all of these examples?

A

Cross-linking
Alkylating (Causes bases to become methylated)
Intercalating (Inserts between stacked bases of the DNA)
Ionizing radiation

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16
Q

Although C -> U deamination is more common, methylated cytosine (5-methyl cytosine) is one of the most problematic deaminations. 5-methyl C -> ___?

A

Thymine (So now thymine is mismatched with G, since originally it was C-G and now its T-G once C was converted to T)

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17
Q

Types of damage repaired are listed below. Name the repair mechanism, how they work, and some of the enzymes involved

1) Pyrimidine dimers (can be repaired two different ways)
2) Deamination (a single base mismatch) or depurination (before a frameshift occurs aka base is just missing) - non distorting alterations
3) RNA polymerase during transcription is stalled (TFIIH mutation)
4) Ionizing radiation that causes double stranded breaks or interstrand cross linking (Name major name and two subcategories)
5) When a wrong nucleotide is accidentally inserted into the newly synthesized daughter strand (this is pretty much the same idea as a single base mismatch, but instead of a deamination creating the single base mismatch, this is simply from an error in DNA polymerase proofreading)

A

1) a) Direct repair (aka enzymatic repair) - simply breaks pyrimidine dimer bonds - DNA photolyase
b) Nucleotide excision repair - locates a shape change in backbone and cleaves backbone on both sides to create a large gap - NEr protein complex and DNA poly epsilon
2) Base excision repair (Cuts out backbone where base was mutated or missing and gap is repaired) - DNA glycolase (recognizes altered base)
3) Transcription coupled repair
4) Recombination repair (aka double strand break repair)
a) nonhomologous end joining (NHEJ) - Several bases from both ends removed and then DNA is joined (Results in loss of some nucleotides)
b) Homologous recombination - Genetic info from undamaged duplex is used to repair the damaged duplex (Way to confusing to explain details)
5) Mismatch excision repair (MER) - Instead of just cutting out the mismatched base, it cuts out a larger segment of the backbone - DNA polymerase delta fills in the gap - does distort

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18
Q

How does Cockaynes syndrom result? And what type of repair mechanism can fix it?

A

Stalled RNA polymerase dyring transcription and Transcription coupled repair (TCR)

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19
Q

___ has an OH on both 2’ and 3’

A

Ribose

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20
Q

Name the type of RNA

1) Carry amino acids to ribosomes for incorporation into the growing polypeptide chain
2) Direct carrier of genetic information from genes to ribosomes for protein synthesis
3) A structural and catalytic component of ribosomes
4) Direct the splicing of pre-mRNA to for mRNA
5) Regulate eukaryotic gene expression by degrading select mRNA (perfect base pairing so the mRNA is destroyed and thats it)
6) Regulate gene expression by blocking translation of selective mRNA (imperfect base pairing causes mRNA to be either stored or degraded)

A

1) tRNA
2) mRNA
3) rRNA
4) snRNA (small nuclear)
5) siRNA (small interfering) - pretty much can be used to knock out a gene of interest
6) miRNA (micro)

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21
Q

Name the RNA polymerase

1) Converts pre-mRNA to mRNA and found in the nucleoplasm
2) Synthesizes larger rRNA to 3 smaller rRNA fragments and is found in the nucleolus
3) Synthesis of tRNA, and a very small fragment of rRNA (smaller than the three fragments produced from the above example) ^

A

1) 2
2) 1
3) 3

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22
Q

Transcription factor ___, which contains the TATA binding protein (TBP), binds to the TATA box.
Transcription factor ___ unwinds the DNA double helix and exposed the DNA template strand

A

TFIID

TFIIH (A mutation in this transcription factor must be repaired by transcription coupled repair (TCR)

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23
Q

A 7-methylguanosine cap is added to the __ ‘ end, and a Poly A tail is at the __ ‘ end

A

5’ and 3’(once poly A tail is reached by RNA poly 2, it stops transcription) The poly A tail stands for polyadenylation

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24
Q

Formation of a RNA ___ provides the driving force to allow RNA polymerase 2 to begin synthesis

A

dinucleotide (hydrolysis of pyrophosphate aka 2 phosphate groups forms a RNA-dinucleotide)

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25
Q

What doe HATs and HDACs do?

A

They acetylate and deacetylate histones to allow and disallow DNA to be accessible for transcription (aka they remove the positive charge that aids in the binding to DNA)
(HAT- Histone acetyl-transferases)
(HDAC - Histone deacetylases)

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26
Q

What enzyme relieves superhelical tension during transcription?

A

RNA-gyrase (not telomerase that is used for DNA replication)

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27
Q

In termination, a __ structure followed by a poly __ tail destabilizes the interactions between RNA and RNA polymerase

A

hairpin, U

28
Q

___ are proteins that bind to specific DNA sequences and therefore control the rate of transcription of genetic information from DNA to mRNA. These proteins also all contain one or more ___ that serve as the domain for binding to DNA

A

Transcription factors, DNA-binding domains

29
Q

Homeodomain proteins, Zinc fingers, leucine zippers, and basic-helix-loop-helix are all examples of ___

A

DNA-binding domains/transcription factors

30
Q

___ is caused by expansion of CGG repeats, which makes it susceptible to ___ of cytosines, which causes the FMR1 gene and promoter to become silent.

A

Fragile x mental retardation, methylation

31
Q

Name the type of mutation:

1) Does not change the amino acid
2) Changes the amino acid
3) Changes into a stop codon
4) One or more nucleotides are deleted or added

A

1) Silent
2) Missense
3) Nonsense
4) Frameshift

32
Q

What are the three stop codons

A

UAA, UAG, UGA

33
Q

tRNA molecules match amino acids to ___ in mRNA

A

codons

34
Q

The tRNA contains a set of three nucleotides _ _ and _ and this is attached to the __ ‘ end of the tRNA which binds the amino acid that matches the corresponding codon (found on the mRNA)

A

CCA and 3’

35
Q

What enzyme catalyzes the transfer of an AMP residue onto the carboxyl residue of the amino acid, and also it catalyzes the transfer of the amino acid from the ___ onto tRNA

A

Aminoacyl-tRNA synthetase, aminoacyl-AMP

36
Q

The start codon for translation is ___

A

AUG

37
Q

Name the site on the ribosome complex

1) mRNA codon is exposed and set to receive all aminoacyl-tRNAs (except the initiating f-MET)
2) Empty tRNA occupies before leaving
3) aminoacyl-tRNA is attached to the growing polypeptide chain

A

1) A site
2) E site
3) P site

38
Q

In eukaryotes, the large __ S ribosomal complex has __ proteins and __ rRNAs. The small __ S complex has ___ proteins and ___ rRNAs. The small and large together make a ___ S ribosome

A

60, 49, 3
40, 33, 1
80

39
Q

The initiator tRNA contains the amino acid __ (for prokaryotes) and __ (for eukaryotes) and also bound GTP. This initiator first binds to the ___ subunit ribosome in the __ site.

A

fMet-tRNA (N-formylmethionyl tRNA for prokaryotes), Met-tRNA (methionyl tRNA in eukaryotes), small, P

40
Q

Loading of aminoacyl-tRNA is accomplished by the hydrolysis of ___ and the release of an elongation factor called ___

A

GTP, EF-TU (This elongation factor is important in proofreading because it makes sure that the correct amino acid is bound to its correct-tRNA)

41
Q

Which enzyme catalyzes the formation of a peptide bond between the amino acids in the A and P sites?

A

peptidyl transferase

42
Q

___ is very important for translational proofreading. It does its job by making sure that the amino acid- tRNA match is correct

A

EF- TU (elongation factor TU)

43
Q

Stop codons are recognized by ___ and cleave the ester bond between the C terminus of the polypeptide and the tRNA

A

release factors

44
Q

___ facilitate the binding of the small ribosomal subunit to the initiator tRNA and base pairing between the anticodon and codon

A

Initiation factors

45
Q

___ inhibits protein synthesis by binding in the ribosomal A-site as a mimic of tyrosyl-tRNA. Translation is then terminated because there is no free __ group available for further elongation

A

Puromycin, Carboxyl (because remember, the polypeptide grows from N -> C so there needs to be a free C terminal to add another N).

46
Q

Name 3 reasons why mitochondria protein synthesis is so similar to prokaryote synthesis?

A

fMet, no 7-methyl guanosine cap, affected by chloramphenicol (an antibiotic that inhibits elongation by inhibiting peptidyl transferase)

47
Q

Linker DNA has the ___ histone, that connects the nucleosomes into a 10nm fiber

A

H1

48
Q

There are two types of protein sorting pathways. Which one sorts proteins to the mitochondria and nucleus? What about the ER, lysosome, and cell membrane?

A

Cytoplasmic pathway (also proteins to the cytoplasm, but I didn’t want to mention it in the question since it would give the answer away. Also, cytoplasmic pathway proteins have no translocation signals), secretory pathway

49
Q

Name the sequence/signal associated with each protein

1) Mitochondria
2) Nucleus
3) Cytoplasm
4) ER
5) Lysosome
6) Plasma membrane

A

1) N-terminal hydrophobic alpha helix sequence
2) Lots or Lysine and Arginine sequences
3) No signal
4) C terminal (KDEL) signal
5) Mannose-6-Phosphate
6) TPR-rich domain (tryptophan)

50
Q

___ proteins protect the linear structure, which allows the protein to make its way through the two membranes TOM and TIM

A

Chaperone (HSP70 aka heat shock protein)

51
Q

An ER-signal peptide is recognized by a __ which causes the ribosomal complex to bind to the ER and synthesize the protein into the lumen

A

SRP (Signal recognition particle)

52
Q

What is the role of chaperone proteins and folding?

A

Large proteins can not fold themselves (although small ones can) therefore they need chaperones to help fold them into their tertiary structure. (Chaperonins are barrel shape and fold the proteins in an ATP manner)

53
Q

O linked glycosylation attaches to what?

N linked to what?

A

Hydroxyl group of Ser or Thr

Amino group of Asn (asparagine)

54
Q

What inhibits the initial step in the formation of the core oligosaccharide attached to the phosphorylated form of dolichol?

A

Tunicamycin

55
Q

What example did we cover that is autosomal recessive and can have distinct genotype, but the same phenotypes

A

Cystic fibrosis (Different genotypes such as different classes of CF, but all of them lead to CF aka One gene is affected, but that gene can be mutated in more than one way).

56
Q

What is an example where there can be the same genotype, but different phenotypes

A

PKU (Everyone has a dysfunction of phenylalanine hydroxylase, however depending on other factors depends on how bad the disease actually is shown. For example, if you cut out phenylalanine from the diet, you can be fine compared to someone who doesn’t cut it out can lose an IQ point or two each day aka same genotype, different phenotype)

57
Q

The first diagnoses person in a pedigree is called the ___

A

Proband (males) or propositus (females)

58
Q

___ : Even distribution of those affected (Male vs female)
___ : Uneven distribution of those affected (Male vs female)
___ : Appears in every generation (vertical)
___ : Skips generations and normally not seen in earlier generations
___ : Unaffected individuals do not transfer the trait
___ : Affected individuals who mate with normal individuals tend to have normal children

A 
Autosomal
Sex linked
Dominant
Recessive
Dominant
Recessive
59
Q

What is the usual Reaccurance risk in dominant and recessive autosomal inheritance?

A

50 %

25 %

60
Q

Does this occur in dominant or recessive autosomal inheritance?
Consanguinity?
Father to son transmission

A

Recessive

Dominant

61
Q

___ is a single disorder cause by mutations in genes at different chromosomal loci (PKU is a good example since you can have either mutation with phenyalanine or THB)

A

Locus heterogeneity

62
Q

___ refers to the degree of severity of the disease phenotype where as ___ is genes have more than one effect on phenotypic traits.

A 
Variable expression (Like in neurofibromatosis)
Pleiotropy (One example of this is Marfan syndrome. Also cystic fibrosis, where sweat glands, lungs, and the pancreas is affected).
63
Q

Two alleles of a gene pair in a heterozygote that are both fully expressed is called ___

A

Co-dominance

64
Q

First cousin mating pedigrees have a double line between two people rather than a single line. The word for two people who are related that have a child is called ___

A

Consanguineous

65
Q

Traits in which variation is thought to be caused by the combined effects of multiple genes is called ___. When environmental factors cause variation, the traits are said to be ___

A

Polygenic, multifactorial

66
Q

For multifactorial diseases that are either present or absent, it is thought that a ___ must be crossed before the disease can be expressed. Also, which gender has a higher one?

A

Threshold of liability. Females (so males are more likely to get the disease because they need less risk genes to get it)

67
Q

Children of women with pyloric stenosis are __ likely to be born with the condition, especially the __ sex. Children of affected males are __ likely to be born with pyloric stenosis, especially the __ sex.

A

More, male (This is because they have a higher liability threshold, so they must be exposed to more disease causing factors in order to develop the disease, which means they have a greater risk of passing the many conditions on to their offspring)

Less, female (Since the affected males have less risk factors since they have a lower threshold)

Biochemistry (4 decks)

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