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Psych/Soc > Biology Class 3 > Flashcards

Biology Class 3 Flashcards

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1
Q

Nucleoside vs nucleotide

A

nucleoside includes just the sugar and base, while nucleotide also includes the phosphates

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2
Q

Bond formed between two nucleotides

A

phosphodiester bond

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3
Q

Monomer of nucleic acids

A

Nucleotides/nucleosides

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4
Q

Important facts about nucleic acids

A
  1. 5’-3’ synthesis
  2. Antiparallel & complementary
  3. Phosphodiester bond
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5
Q

Pyrimidine vs Purine

A

Pyrimidine: Cytosine, thymine, uracil
- 6 C ring
Purine: Adenine & Guanine
- 6 C & 5 C ring

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6
Q

Bases in DNA vs RNA

A

DNA: Adenine, guanine, cytosine, thymine

RNA: Adenine, guanine, cytosine, uracil

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7
Q

How many H bonds hold a AT bond vs GC bond

A

2, 3 respectively

U pairs with A

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8
Q

Genome

A

All the DNA in an organism

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9
Q

Genome: Prokaryotes vs Eukaryotes

A

Prokaryote: one singular circular DNA genome
Eukaryote: 23 pairs of linear chromosomes (46 chromosomes)

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10
Q

How is the Prokaryote genome protected?

A
  1. Methylation - methylates chromosome to protect from own RE
  2. Supercoiling - Gyrase helps with supercoiling and helps compact the chromosome
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11
Q

How do Eukaryotes form chromosomes?

A
  1. DNA is wrapped around 8 histone molecules & forms a nucleosome
  2. Condenses to form chromatin
  3. Further condenses to form chromosome
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12
Q

Euchromatin vs Heterochromatin

A

Euchromatin
- unwound, active, light staining

Heterochromatin
- wound, inactive, dark staining

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13
Q

Centrosome

A

Region of the chromosome

  • attaches spindle fibers
  • connects sister chromatids after replications
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14
Q

Telomeres

A
  1. End of chromosomes
  2. Short sequence repeats
  3. Allows ends of chromosomes to loop around & bp with itself and allows it to stabilize the chromosome
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15
Q

Central Dogma

A

DNA (transcription) –> RNA (translation) –> Protein

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16
Q

What are the stop and start codons

A

Start: AUG (Met)
Stop: UAG,UAA,UGA

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17
Q

Human Genome

A
  1. 46 chromosomes
  2. ~21,000 genes
  3. 3 billion nucleotidesLarge intergenic regions (regions that don’t code for proteins)
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18
Q

Different types of point mutations

A

Missence- codon for aa becomes new codon for new aa (effect: change aa)

Nonsense: codon for aa becomes STOP codon (effect: shortened protein)

Silent: Codon for aa becomes new codon for same aa (effect: no effect)

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19
Q

Sources of Mutations

A

Polymerase Errors
Endogenous damage (a. ROS b. Physical Damage)
Exogenous Damage (a. radiation b. chemicals)
Transposons

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20
Q

Polymerase Errors

A
  1. Point mutations
  2. Small repeats
  3. Insertions/deletions (small, frameshift)
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21
Q

Endogenous Damage

A
  1. Oxidized DNA
  2. Cross-linked bases
    3, Double or single stranded breaks
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22
Q

Exogenous Damage

A
  1. UV radiation (pyrimidine dimers T-T or T-C)
    - > usually repaired by direct reversal by white light
  2. X-Rays = double stranded breaks & translocations
  3. Chemicals = can lead to physical damage or to intercalation (insertion of molecules into bases of DNA)
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23
Q

Transposons

A
  1. Insertions/deletions (large)
  2. Inversions
  3. Duplications
24
Q

Transposon Structure

A

Inverted repeats on both sides with transposae in center

25
Q

Transposase

A

enzyme that cuts out transposon to relocate it somewhere else

26
Q

Types of Transposons

A
  1. IS Element: composed of regular transposon structure
  2. Complex transposon: composed of transposae with some other genes flanked with inverted repeats
  3. Composite transposon: composed of 2 transposae with central region in middle
27
Q

How do transposons contribute to genomic variation?

A
  1. Transposase gene codes for the “cut & paste” transposae enzyme
  2. Transposae cuts transposon out & pastes it somewhere else
28
Q

Effect of ONE transposon vs TWO

A

If one transposon is inserted in:
Intergenic region, then likely no problems
Coding region, then could disrupt the gene & cause less proteins to be formed

If two transposons are inserted in:
Same direction - DNA loops around and causes both to pair up & delete some coding area (therefore loss of genetic info)

Opposite direction - DNA loops around and pair with each other BUT coding area is flipped (therefore less problematic, gene inversion, chromosome rearrangement)

29
Q

Inversions

A

Piece of DNA is flipped

30
Q

Amplifications

A

Region of gene is duplication therefore the amount of mRNA increases = increases proteins therefore disrupts homeostasis

31
Q

Translocations

A

Due to faulty DNA repair (non-homologous end joining) or abnormal recombination between non-homologous chromosomes. Can cause gene fusion

32
Q

DNA Repair

A

Direct Reversal: Use white light to reverse damage

Mismatch Repair Pathway: DNA polymerase & endonucleases do this; repairs DNA polymerases mistakes that happen DURING DNA replication; uses methylated strand as template to fix mismatch

Base/Nucleotide Excision Repair: removes & replaces bad nucleotide DURING DNA replication

Homology - directed Repair: intact DNA helps fix DS break that happen AFTER replication; use sister chromatid as template to repair broken strand & does it through homologous crossing over

Non-homologous end-joining: patch the ends & ligase the DNA bc intact is better than broken; used for DS breaks too; no sister chromatids because happens BEFORE replication or in cells where replication doesn’t happen; can be mutagenic

33
Q

4 Rules & requirements to carry out replication

A
  1. Semiconservative (one strand is old, one strand is new)
  2. 5’ - 3’
  3. Requires a primer
  4. Requires a template
34
Q

Helicase

A

Unwinds DNA

35
Q

Topoisomerase

A

Cuts DNA, relaxes supercoiling

36
Q

Primase

A

Synthesizes the RNA primer

37
Q

DNA polymerase

A

Replicates DNA, proofreads, removes primer

38
Q

Ligase

A

Links okazaki fragments

39
Q

DNA Replication

A
  1. At origin of replication, Helicase binds and so does Topoisomerase
  2. RNA primer makes DNA in 5’-3’ direction while reading in 3’-5’
  3. DNA polymerase binds to primer & what makes DNA and elongates
  4. Removes RNA primer and replaces with DNA
  5. Ligase hooks okazaki fragments together
40
Q

Prokaryotic DNA Replication vs Eukaryotic DNA replciation

A
  • Only 1 origin of replication
  • 5 DNA polymerases
  • goes through Theta replication
  • Multiple origins
  • Replication bubbles
  • several DNA polymerases composed of complex multisubunit enzymes
41
Q

DNA polymerases in prokaryotes

A

DNA Polymerase I:

  • low processivity
  • slow 5’-3’ polymerase AND 3’-5’ exonuclease
  • also a 5’-3’ exonuclease to remove primer
  • adds nucleotides at RNA primer
  • DNA excision repair

DNA Polymerase II:

  • 5’-3’ polymyerase AND 3’-5’ exonuclease
  • back up for DNA polymerase III
  • DNA repair

DNA Polymerase III:

  • high processivity
  • fast 5’-3’ polymerase AND 3’-5’ exonuclease
  • adds nucleotides at ~400 bp downstream of ORI
  • main replicating enzyme
  • no known fx in DNA repair

DNA Polymerase IV:

  • error prone 5’-3’ polymerase activity
  • DNA repair

DNA Polymerase V:

  • error prone 5’-3’ polymerase activity
  • DNA repair
42
Q

Telomerase

A

Elongates telomeres on parent strand of DNA

  1. Includes its own RNA template
  2. Reverse transcriptase activity (DNA from RNA)
43
Q

DNA vs RNA

A

DNA

  • double stranded
  • double helix
  • thymine
  • one type of DNA
  • Deoxyribose

RNA

  • single stranded
  • Lots of different 3D shapes
  • uracil
  • multiple types of RNA
  • ribose
44
Q

3 primary types of RNA

A

ribosomal RNA
messenger RNA
transfer RNA

Others:
heterogenous nuclear RNA (hnRNA)
micro RNA (miRNA)
small interfering RNA (siRNA)

45
Q

How does transcription work?

A
  • RNA polymerase binds at promoter and downstream at start site is where mRNA is made
  • RNA polymerase continues until it reaches stop site
  • RNA polymerase falls off at this point & mRNA leaves
  • DNA binding proteins bind to operator region (repressor - prevents more mRNA, enhancer - more mRNA)
46
Q

Transcription regulation

A
  1. Promoter
    Strong - lots of RNA
    Weak - less amount of RNA
  2. DNA binding proteins
    Repressors
    Enhancers
47
Q

Prokaryote vs Eukaryote transcription

A

Prokaryotes

  1. Transcription and translation happens at same time
  2. Polycistronic
  3. No mRNA processing
  4. 1 RNA polymerase

Eukaryotes

  1. Transcription happens in nucleus & translation happens in cytoplasm
  2. Monocystronic
  3. mRNA processing: 5’ g cap, 3’ a tail, splicing
  4. 3 RNA polymerases (rRNA, mRNA, tRNA)
48
Q

xtRNA^y translates to..

A 
x = type of a.a. that's attached
y = type of tRNA
49
Q

How many ATPs to load a.a. onto tRNA

A

2 ATP

50
Q

What enzymes attaches amino acids to tRNA?

A

aminoacyl tRNA synthetase

51
Q

Wobble Hypothesis

A

First two anticodon pairs bind normally (Watson-Crick pairing), third anticodon is more flexible

5' Base in anticodon (tRNA) --> 3' Base in mRNA
G --> C or U
C --> G
U --> A or G 
A --> U 
I -->A,U or C
  • Sometimes adenine can be converted to inosine for more flexibility
52
Q

What happens in ribosomes?

A

Protein synthesis

53
Q

Prokaryotic vs Eukaryotic ribosomes

A

Prokaryotic
Large subunit - 50 s
Small subunit - 30 s
Total - 70 s

Eukaryotic
Large subunit - 60 s
Small subunit - 40 s
Total - 80 s

54
Q

What does svedberg mean?

A

Svedberg tells you how fast it sediments (bigger the # = faster it sediments

  • Not addidtive because other factors affect sedimentation rates
55
Q

Translation process

A
  1. mRNA (first codon) is present in the P site while the first tRNA is present in the A site
  2. tRNA will translocate to A site and initiate translation
  3. tRNA #2 will bind to codon at empty A site with a.a. attached
  4. tRNA #2 and #1 a.a will bond and tRNA #1 now exits and tRNA will have 2 amino acids
  5. Continue the process until termination codon is detected in A site
56
Q

How to determine how many ATP is required for x amino acids?

A

of amino acids x 4 = # of ATP needed

1 ATP for initiation
1 ATP for termination
2 ATP per tRNA loading
1 ATP for A site binding (1 less than original a.a)
1 ATP for translocation (1 less than original a.a)

57
Q

Post translational Modification

A
  1. Protein folding
    - aided by chaperonins
  2. Covalent modification
    - phosphorylation, glycosylation, disulfide bridges, etc
  3. Processing (most enzymes are made in non-active stage)
    - cleavage to activate protein (eg. zymogens)
    Pepsinogen (zymogen) —> pepsin (active protein)

Psych/Soc (24 decks)

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