Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

M2M > Unit 1 > Flashcards

Unit 1 Flashcards

(88 cards)

Start Studying
1
Q

Name kinetic energy in living systems (4)

A

Radiant Energy Thermal Energy Mechanical Energy Electrical Energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Name potential energy in living systems (4)

A

(1) Chemical Bonds
(2) Concentration Gradients
(3) Electrical Fields
(4) Redox Pairs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

First law of Thermodynamics

A

Energy is neither created, nor destroyed. It can be converted but always conserved.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Second law of Thermodynamics

A

The entropy of the universe is always increasing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Gibb’s free energy equation (chemical)

A

ΔG = ΔH - TΔS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Gibb’s free energy equation (redox reaction)

A

ΔG = -nFΔE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Gibb’s free energy under non-standard conditions

A

ΔG = ΔG°’ + RT lnQ

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Transcription

A

DNA -> RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Translation

A

RNA -> Protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Building blocks of nucleic acids

A

Ribonucleotide 2’ deoxy-nucleotide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Universal energy currency of the cell

A

ATP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Nucleotide

A

Sugar-Base-Phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Nucleoside

A

Sugar-Base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Relative Solubility of nucleotide components

A

Nucleotide > Nucleoside > Pyrimidine > Purine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Nucleotide linkages

A

Phosphodiester bonds 5’ - 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Reverse Transcriptase inhibitors

A

(1) ddI (dideoxyinosine)
(2) AZT (azideothymidine)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Chargaff’s Rule

A

%G = %C

%A = %T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

B form DNA characteristics (6)

A

(1) Two strands in right-handed helix
(2) Anti-parallel arrangement
(3) Sugar-phosphate backbone is on outside of helix
(4) Bases are paired on the inside
(5) Geometry favors A-T and G-C pairs only
(6) Complementary of base pairing suggests a molecular mechanism for replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Stabilization of DNA (Increased Tm) (3)

A

(1) Increased salt concentration
(2) Increased chain length
(3) Increased GC content

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Major causes of Base-Change mutation (5)

A

(1) Deamination (A, C, G)
(2) Depurination/ Depyrimidination
(3) Oxidative damage (8-oxo-dG)
(4) UV induced covalent linkage (Thymidine dimers)
(5) Alkylating agents (O6-meG)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What recognizes the replication origin?

A

Origin binding proteins (Origin recognition complex)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What melts/unwinds DNA?

A

DNA helicase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What relaxes the torsional stress ahead of the replication fork?

A

Topoisomerase/gyrase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What protects unwound single-stranded DNA?

A

Single stranded binding proteins Replication Protein A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What synthesizes RNA primer?
Primase
26
What elongates DNA from the RNA primer?
DNA Pol III DNA Pol δ & DNA Pol ε
27
What removes RNA primer and replaces with DNA?
DNA Pol I DNA Pol α
28
What ligates DNA fragments?
DNA Ligase
29
What do origin binding proteins (origin recognition complexes) do?
Recognize origin of replication
30
What does DNA helicase do?
Unwinds DNA
31
What does topoisomerase/ gyrase do?
Relaxes torsional stress ahead of replication fork
32
What do single stranded binding proteins (replication protein A) do?
Protect unwound single-stranded DNA
33
What does primase do?
synthesizes RNA primers
34
What does DNA Pol III (DNA Pol δ & DNA Pol ε) do?
Elongates DNA from RNA primer
35
What does DNA Pol I (DNA Pol α) do?
Removes RNA primer and replaces with DNA
36
What does DNA ligase do?
Ligates DNA fragments
37
Characteristics of replication origins (3)
(1) Unique DNA segments with multiple short repeats (2) Recognized by multimeric origin-binding proteins (3) Rich in A-T base pairs
38
What contributes to the high processivity of DNA Pol III (DNA Pol δ)
β-subunit Proliferating Cell Nuclear Antigen
39
What do the β-subunit (Proliferating Cell Nuclear Antigen) do?
Contribute to the processivity of DNA Pol III (DNA Pol δ)
40
What elongates Telomeres (as a reverse transcriptase)?
Telomerase
41
What does Telomerase do?
Elongates telomeres using a reverse transcriptase function
42
Major causes of Structure-Change mutation (6)
(1) Insertion/Deletion of nucleotides (2) Bulky chemical adducts (3) Replication errors (4) Intra/inter-strand crosslinks (5) DNA Strand breaks (6) Stalled DNA replication forks
43
Types of DNA Repair (4)
(1) Direct Reversal (2) Excision (3) Tolerance/Bypass (4) Strand Break repair
44
Types of Direct Reversal (3)
(1) Single-stranded DNA Break by DNA LIGASE (2) UV-caused base damage by PHOTOLYASE (3) Base alkylation by O6-meG METHYLTRANSFERASE
45
Types of Excision Repair (3)
(1) Damage that doesn't distort DNA - BASE EXCISION REPAIR (2) Damage that distorts DNA - NUCLEOTIDE EXCISION REPAIR (3) Misincorporated nucleotides during DNA Replication - MISMATCH REPAIR
46
Types of Strand Break Repair (2)
(1) Single-strand break repair (SSBR) (2) Double-strand break repair (DSBR)
47
Types of Double-Strand Break Repair (2)
(1) Homologous Recombination (HR) (2) Nonhomologous End Joining (NHEJ)
48
Types of Excision Repair (3)
(1) Base Excision Repair (2) Nucleotide Excision Repair (3) Mismatch Repair
49
Base Excision Repair
Repairs base damages that do not distort DNA. Uses base specific glycosylases to remove damaged base
50
Nucleotide Excision Repair
Repairs base damages that distort DNA Removes oligonucleotide that contains damaged base
51
Mismatch Repair
Removes misincorporated nucleotides during DNA replication Distinguishes between template strand and new strand
52
Common Steps to Excision Repair Mechanisms
(1) Recognition of damaged/mismatched nucleotide (2) Cutting of phosphodiester backbone (endonuclease) (3) Removal of DNA fragment (nuclease) (4) Synthesis of missing nucleotides (DNA polymerase) (5) Sealing of nick in phosphodeister backbone (DNA ligase)
53
What does Endonuclease do?
Cuts phosphodiester backbone
54
What does Nuclease do?
Removes damaged DNA fragments
55
What does DNA polymerase do?
synthesizes nucleotides
56
What does DNA ligase do?
Ligates phosphodiester backbone nicks
57
Steps in Base Excision Repair
(1) Modified base recognized by specific DNA GLYCOSYLASE (2) AP site-specific endonuclease (APE1) cleaves sugar-phosphate backbone (3) Gap filled in by DNA Pol (4) Nick sealed by DNA ligase
58
Steps in Nucleotide Excision Repair
(1) Recognition and binding of damaged site by multi-protein complex (2) Local unwinding of DNA duplex by helicases (TFIIH) to form ~25base bubble (3) Incision of damaged strand by two endonucleases ~30base (4) Gap filled by DNA Pol 5. Nick sealed by DNA ligase
59
Two ways NER machinery recognizes damage
(1) Global Genome NER - recognizes damage anywhere in genome (2) Transcription-Coupled NER - recognizes damage within transcribed region
60
How does MMR recognize which strand to repair?
Lagging strand marked by transient 5' DNA ends of Okazaki fragments Leading strand marked by transient ribonucleotides processed into nicks?
61
When is DNA damage tolerance/ bypass employed?
When there is too much damage for normal repair machineries to handle
62
What do bypass DNA pol lack?
3'-5' exonuclease activity
63
Characteristics of Non-homologous end-joining
No homology needed Inaccurate, resulting in deletion/insertion
64
Characteristics of Homologous end-joining
Extended sequence homology needed Accurate
65
Three main classes of RNA
(1) Structural (rRNA, tRNA, snRNA, snoRNA) (2) Regulatory (miRNA, siRNA) (3) Information Containing (mRNA)
66
Why is RNA more easily hydrolized than DNA?
Due to nucleophilic attack by 2' OH on phosphodiester bond.
67
What is Puromycin?
A nucleotide analogue that mimics tRNA which terminates translation
68
What is the segment of DNA which gets transcribed into RNA?
Transcription Unit
69
What are two features of Transcription
(1) Unidirectional (2) Completely processive
70
What is the product of transcription called?
Primary Transcript
71
What is a Transcription Unit?
The segment of DNA which gets transcribed into RNA
72
What is a Primary Transcript?
The product of transcription
73
Which strand complements the RNA transcript?
DNA Template Strand
74
Which strand codes the RNA transcript?
DNA Non-Template Strand (Coding Strand)
75
What are the three steps of Transcription Initiation?
(1) Polymerase binds to promotor sequence in duplex DNA (2) Polymerase melts duplex DNA near transcription start site forming transcription bubble (3) Polymerase catalyzes phosphodiester linkage of two initial rNTPs.
76
What happens in RNA Transcription Elongation?
RNA Pol advances 3' - 5' down template strand, melting duplex DNA and adding rNTPs.
77
What happens at RNA Transcriptino Termination?
At transcription stop site, polymerase releases completed RNA and dissociates from DNA.
78
What are the functions of C-terminal domains in RNA Pol II?
Binding of proteins that regulate elongation and processing of RNA transcript.
79
What directs RNA Pol to the start of genes?
Promoters
80
What helps direct assembly of pre-initiation complexes at the promoter?
TATA-Box Binding Proteins
81
What does TFIIH do?
Functions in Transcription and DNA Repair
82
What are the three steps in RNA modification?
(1) Capping (2) Splicing (3) Polyadenylation
83
What caps RNA?
RNA Pol II
84
What are the steps for the 5' capping?
(1) Triphosphatase (2) Guanylyltransferase (3) Guanine 7 methyl transferase
85
How are introns recognized by spliceosomes
(1) 5': GU (2) 3': AG (3) Branchpoint: A
86
How does splicing proceed?
(1) Attack by the 2' OH of branch point A - Forms lariate intermediate (2) Attack by the 3' OH of exon 1
87
How can different proteins be encoded for by a single gene?
Alternative splicing
88
What are the steps in 3' polyadenylation?
(1) Cleavage (2) Polyadenylation (poly-A binding protein)

M2M (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions