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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
When the info in a nucleotide sequence of our genes is copied into an RNA intermediate this is called
Translation
26
When the nucleotide sequence information in the RNA is used to build proteins this is called
Transcription
27
Chargaff's rules
dA = dT and dC-dG
28
rosalind franklin and maurice wilkins
x-ray diffraction suggested helix of 2 strands, with a uniform width that stacks bases, with sugar-phosphate on outside
29
james watson and francis crick
created a scale model that fit all the available data
30
order of events for DNA replication
1. determine where to start 2. separate the strands 3. "prime the pump" 4. synthesize SNA 5. clean up
31
The "start signal" for DNA replication is the
Origin of replication (ori)
32
Ori
a specific sequence of bases in the DNA
33
DNA strands are separated by ______ and are kept single-stranded by ______________
helicase ; single-stranded DNA Binding protein
34
DNA strand synthesis
1. incoming dNTP is hybridized to parental template 2. phosphodiester bond formed with 3' end of chain
35
True or false; DNA replication is bidrectional
True
36
DNA synthesis occurs in the _______ direction and new strands are _________ to the template
5' to 3' ; antiparallel
37
Okazaki fragments
small fragments of DNA
38
Leading strand
When DNA synthesis starts at the ori and proceeds normally
39
Lagging strand
When DNA synthesis starts away from the ori and works backwards
40
Can DNA polymerases start a new strand from scratch?
NO! They need a free 3' OH group group to add the incoming dNTPs to
41
Primase
Creating primers that give DNA polymerase III a free 3' OH group
42
DNA polymerase I
removes RNA nucleotides and replaces them with DNA nucleotides
43
DNA Ligase
seals the "holes" (where there are no covalent linkages) in the chain
44
Nuclease
Enzyme that degrades a phosphodiester linkage
45
Exonuclease
a nuclease that hydrolyzes nucleic acid from the end of a chain
46
Endonuclease
a nuclease that hydrolyzes nucleic acid internally (ie not at one end of the other)
47
Bacterial chromosomes are
supercoiled
48
Topoisomerase
Nick DNA, wind or unwind, then reseal DNA
49
Proteins that are part of chromatin
Histones
50
Histones
- small, basic proteins - highly conserved among species
51
5 major types of histones
H1, H2A, H2B, H3, H4
52
Do bacteria have histones?
Nope! But they do have histone-like proteins
53
The core nucleosome
- 2 each of histones H2A, H2B, H3, and H4 - 146-147 base pairs
54
Chromatosome structure
a nucleosome plus a single molecule of H1
55
Interphase
life of the cell until division, not actively dividing
56
Loosely condensed chromatin
Euchromatin
57
Highly condensed chromatin
Heterochromatin
58
Euchromatin
- distributed throughout the nucleus - most in the form of 30nm fibres
59
Heterochromatin
found at periphery of the nucleus and in pockets elsewhere in the nucleus
60
DNA replication summary
- 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
Carried out by DNA-dependent, RNA synthesizing enzyme called __________
RNA polymerase
62
4 basic steps of transcription
1. promoter recognition 2. initiation 3. elongation 4. termination
63
Promoters
starts signal for beginning of genes
64
In promoter sequences, -10 and -35 sites are _______ and have ________ sequences
conserved ; consensus
65
How does RNA polymerase know which strand to use as the Template strand
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
Why is different information encoded in each DNA strand?
DNA strands are complementary not identical
67
Rho-Dependent Termination
binds to RNA and transcription complex, rho movies toward 3' end, transcript dissociates from template strand, rho dissociates from RNAP
68
mRNA
not functional by themselves, but instead carry the instructions for making specific proteins
69
tRNA
small RNA molecules that carry amino acids to the ribosomes, where only the amino acid gets incorporated into the growing protein chain
69
RNA polymerase III
transcribes tRNA genes and some rRNA
69
rRNA
small RNA molecules form complexes with ribosomal proteins to make ribosomes
70
RNA polymerase II
transcribes mRNA genes
70
RNA polymerase I
transcribes rRNA genes
71
True or false: Eukaryotic RNA polymerases have sigma factors and strongly associate with DNA
False; they have NO sigma factors and WEAKLY associate with DNA
72
True or false: Bacterial RNA polymerase directly contacts DNA and binds to promoter sequence
True
73
Transcription factors
accessory (regulatory) proteins
74
What do transcription factors do?
They begin the formation of transcription initiation complex, which allows RNA polymerase to bind to the promoter sequence
75
Noncoding DNA between genes
spacer DNA
76
Non-coding DNA
DNA that does not code for proteins, rRNA, or tRNA
77
Non-coding DNA within a gene
introns (aka intervening sequences)
78
Coding regions within a gene
Exons (aka expressed sequences)

MCB (2 decks)

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