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MCB > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

We eat food to give us energy, but how does the energy from food get to ATP?

A

Cellular Respiration

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2
Q

Cellular respiration is the breakdown of ______ to ______

A

CO2 to H2O

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3
Q

What are the 3 pathways of cellular respiration?

A
  1. glycolysis
  2. pyruvate oxidation and krebs cycle
  3. oxidative phosphorylation
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4
Q

Glycolysis starts with ______ and ends with _____

A

glucose ; 2 pyruvate

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5
Q

Is glycolysis endergonic or exergonic?

A

endergonic until the production of the first 3 carbon molecules

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6
Q

Where does glycolysis take place?

A

Cytoplasm

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7
Q

Problems at the end of glycolysis

A
  1. molecules are still not at their lowest energy state
  2. some energy is held in NADH
  3. NAD+ is being used and not replaced
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8
Q

If oxygen is present cells undergo

A

aerobic respiration

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9
Q

If oxygen is absent but an alternative electron accepter is there, cells undergo

A

anaerobic respiration

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10
Q

Is oxygen is absent and no alternative electron acceptor is there, cells undergo

A

fermentation

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11
Q

Mitochondria matrix organization

A
  • krebs enzymes
  • DNA and ribosomes
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12
Q

Mitochondria inner membrane organization

A
  • principal site of ATP generation
  • > 70% protein (no porins)
  • impenetrable to ions and small molecules except by transporters
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13
Q

Mitochondria outer membrane organization

A
  • typical protein %
  • porins
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14
Q

Mitochondria intermembrane space organization

A

composition of ions and small molecules is the same as the cytoplasm

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15
Q

Glycolysis net gain

A

2 ATP

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16
Q

anaerobic respiration yields

A

lactic acid

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17
Q

krebs cycle yields

A

6 NADH, 2 FADH2, 2 ATP

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18
Q

ETC yields

A

36 ATP

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19
Q

Pyruvate oxidation occurs in the

A

mitochondria

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20
Q

Problems at the end of krebs cycle

A
  1. still haven’t replaced NAD+; more NADH is made
  2. now you have FADH2 that needs to be re-oxidized
  3. still haven’t transferred energy carried by cofactors to ATP
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21
Q

Why does the kreb’s cycle require oxygen if the Kreb’s cycle itself doesn’t?

A

It is coupled to the ETC which DOES require oxygen

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22
Q

ETC Results

A

regenerated cofactors and electrochemical gradient but no ATP

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23
Q

Allosteric regulators

A

change conformation of active site
- positive regulator if it increases enzyme activity
- negative regulator if it decreases enzyme activity

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24
Q

Sometimes, the allosteric regulator is a product of a later reaction in that pathway. This is called

A

feedback inhibition

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25
Q

When the info in a nucleotide sequence of our genes is copied into an RNA intermediate this is called

A

Translation

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26
Q

When the nucleotide sequence information in the RNA is used to build proteins this is called

A

Transcription

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27
Q

Chargaff’s rules

A

dA = dT and dC-dG

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28
Q

rosalind franklin and maurice wilkins

A

x-ray diffraction suggested helix of 2 strands, with a uniform width that stacks bases, with sugar-phosphate on outside

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29
Q

james watson and francis crick

A

created a scale model that fit all the available data

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30
Q

order of events for DNA replication

A
  1. determine where to start
  2. separate the strands
  3. “prime the pump”
  4. synthesize SNA
  5. clean up
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31
Q

The “start signal” for DNA replication is the

A

Origin of replication (ori)

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32
Q

Ori

A

a specific sequence of bases in the DNA

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33
Q

DNA strands are separated by ______ and are kept single-stranded by ______________

A

helicase ; single-stranded DNA Binding protein

34
Q

DNA strand synthesis

A
  1. incoming dNTP is hybridized to parental template
  2. phosphodiester bond formed with 3’ end of chain
35
Q

True or false; DNA replication is bidrectional

A

True

36
Q

DNA synthesis occurs in the _______ direction and new strands are _________ to the template

A

5’ to 3’ ; antiparallel

37
Q

Okazaki fragments

A

small fragments of DNA

38
Q

Leading strand

A

When DNA synthesis starts at the ori and proceeds normally

39
Q

Lagging strand

A

When DNA synthesis starts away from the ori and works backwards

40
Q

Can DNA polymerases start a new strand from scratch?

A

NO! They need a free 3’ OH group group to add the incoming dNTPs to

41
Q

Primase

A

Creating primers that give DNA polymerase III a free 3’ OH group

42
Q

DNA polymerase I

A

removes RNA nucleotides and replaces them with DNA nucleotides

43
Q

DNA Ligase

A

seals the “holes” (where there are no covalent linkages) in the chain

44
Q

Nuclease

A

Enzyme that degrades a phosphodiester linkage

45
Q

Exonuclease

A

a nuclease that hydrolyzes nucleic acid from the end of a chain

46
Q

Endonuclease

A

a nuclease that hydrolyzes nucleic acid internally (ie not at one end of the other)

47
Q

Bacterial chromosomes are

A

supercoiled

48
Q

Topoisomerase

A

Nick DNA, wind or unwind, then reseal DNA

49
Q

Proteins that are part of chromatin

A

Histones

50
Q

Histones

A
  • small, basic proteins
  • highly conserved among species
51
Q

5 major types of histones

A

H1, H2A, H2B, H3, H4

52
Q

Do bacteria have histones?

A

Nope! But they do have histone-like proteins

53
Q

The core nucleosome

A
  • 2 each of histones H2A, H2B, H3, and H4
  • 146-147 base pairs
54
Q

Chromatosome structure

A

a nucleosome plus a single molecule of H1

55
Q

Interphase

A

life of the cell until division, not actively dividing

56
Q

Loosely condensed chromatin

A

Euchromatin

57
Q

Highly condensed chromatin

A

Heterochromatin

58
Q

Euchromatin

A
  • distributed throughout the nucleus
  • most in the form of 30nm fibres
59
Q

Heterochromatin

A

found at periphery of the nucleus and in pockets elsewhere in the nucleus

60
Q

DNA replication summary

A
  • semiconservative
  • initiates at ori
  • synthesis only happens in 5’ to 3’ direction
  • requires ssDNA template, free NTPs and dNTPs, and nucleic acid synthesizing enzymes
  • requires unwinding enzymes, stabilizing proteins, glue
  • DNA polymerase requires a free 3’ OH
  • RNA synthesizing enzymes require 3’ Oh for synthesis but can hybridize a nucleotide to a nucleic acid strand
61
Q

Carried out by DNA-dependent, RNA synthesizing enzyme called __________

A

RNA polymerase

62
Q

4 basic steps of transcription

A
  1. promoter recognition
  2. initiation
  3. elongation
  4. termination
63
Q

Promoters

A

starts signal for beginning of genes

64
Q

In promoter sequences, -10 and -35 sites are _______ and have ________ sequences

A

conserved ; consensus

65
Q

How does RNA polymerase know which strand to use as the Template strand

A

Either strand can be used as the template for a given gene; which strand is chosen depends on the location and orientation of the promoter sequence

66
Q

Why is different information encoded in each DNA strand?

A

DNA strands are complementary not identical

67
Q

Rho-Dependent Termination

A

binds to RNA and transcription complex, rho movies toward 3’ end, transcript dissociates from template strand, rho dissociates from RNAP

68
Q

mRNA

A

not functional by themselves, but instead carry the instructions for making specific proteins

69
Q

tRNA

A

small RNA molecules that carry amino acids to the ribosomes, where only the amino acid gets incorporated into the growing protein chain

69
Q

RNA polymerase III

A

transcribes tRNA genes and some rRNA

69
Q

rRNA

A

small RNA molecules form complexes with ribosomal proteins to make ribosomes

70
Q

RNA polymerase II

A

transcribes mRNA genes

70
Q

RNA polymerase I

A

transcribes rRNA genes

71
Q

True or false: Eukaryotic RNA polymerases have sigma factors and strongly associate with DNA

A

False; they have NO sigma factors and WEAKLY associate with DNA

72
Q

True or false: Bacterial RNA polymerase directly contacts DNA and binds to promoter sequence

A

True

73
Q

Transcription factors

A

accessory (regulatory) proteins

74
Q

What do transcription factors do?

A

They begin the formation of transcription initiation complex, which allows RNA polymerase to bind to the promoter sequence

75
Q

Noncoding DNA between genes

A

spacer DNA

76
Q

Non-coding DNA

A

DNA that does not code for proteins, rRNA, or tRNA

77
Q

Non-coding DNA within a gene

A

introns (aka intervening sequences)

78
Q

Coding regions within a gene

A

Exons (aka expressed sequences)

MCB (2 decks)

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