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MC Biochem 1 > Chpt 4 > Flashcards

Chpt 4 Flashcards

1
Q

Central Dogma of Molecular Biology

-What part is replication, Transcription, and Translation?

A

DNA->RNA->Protein

Replication= DNA to DNA or DNA directed DNA synthesis
Transcription=DNA to RNA or DNA directed RNA synthesis
—>Processing of mRNA capping, polyadenylation, splicing
Translation=RNA to Protein or RNA directed protein synthesis

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2
Q

Where does replication, transcriptions and translation take place? (In a eukaryotic cell)

A

Eukaryotic cell has a nucleus
Nucleus:
-replication
-transcription

Cytoplasm:
-Translation

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3
Q

Functions of Nucleic Acids (3)

A

Building blocks of DNA and RNA

  • DNA=Genetic Material
  • RNA=Adaptor molecule between DNA and protein

Transport chemical energy within the cell
-ATP

Signal Molecules
-Cyclic AMP

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4
Q

Nucleic Acids

A

-linear, non branched polymer of nucleotides

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5
Q

What are the classes of nucleic acids?

A

1) RNA=ribonucleic acid

2) DNA= 2’ deoxyribonucleic acid

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6
Q

What does. a nucleotide contain?

A
  • Pentose sugar
  • Nitrogenouse base
  • Phosphate (one or more)
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7
Q

What are the nucleotides? and the two classes of nucleotides?

A

Pyrimidines:
Thymine (T)
Cytosine (C)
Uracil (U)

Purines:
Adenine (A)
Guanine (G)

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8
Q

Thymine

A

Pyrimidine Base
5-methyl-2,4-dioxypyrimidine
DNA only

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9
Q

Cytosine

A

Pyrimidine Base
4-amino-2-oxypyrimidine
DNA and RNA

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10
Q

Uracil

A

Pyrimidine Base
2,4-dioxypyrimidine
RNA only

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11
Q

Adenine

A

Purine
6-aminopurine
DNA and RNA

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12
Q

Guanine

A

Purine
2-amino-6-oxypurine
DNA and RNA

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13
Q

Sugar Phosphate Backbone

A

Nucleotides connected by 3’ to 5’ phosphodiester bond

Imparts uniform negative charge to DNA/RNA

  • negative charge repels nucleophilic species (ex hydroxyl) thus the phosphodiester bond resists hydrolytic attack
  • Seperation by agarose gel electrophoresis

Creates 3’ and 5’ end (directionality)
-nucleotide sequences are written 5’ to 3’: L to R

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14
Q

How are bases attached to sugars?

A

Beta Glycosidic linkage

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15
Q

Nucleotide vs Nucleoside

A

Nucleoside:
sugar + nitrogenous base

Nucleotide
sugar + nitrogenous base + phosphate

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16
Q

What data did Watson and Crick use to determine the structure of DNA

A
  • xray diffraction photograph of DNA crystals
  • Chargraff’s rule
  • Bond Angles from reference books
  • Built models
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17
Q

Chargraff’s rule

A

Edwin Chargraff determined the composition of DNA from many organisms

  • [A]=[T]
  • [G]=[C]

rules:

  • the four nucleotides are not present in equal amounts
  • relative ratios of the four bases are not random, and vary from one species to another
  • A=T and G=C
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18
Q

X-ray diffraction photograph of DNA crystals

A

Maurice Wilkins and Rosalind Franklins
-two chains that wind in a regular helical structure

DNA is a HELIX- 3.4 A spacing

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19
Q

MP of DNA factors on?

A

nucleotide content determines melting point of DNA (# of h bonds)
G to C = 3 bonds
A to T= 2 bond

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20
Q

Who received the Nobel Prize in Physiology or Medicine in 1962?

A

Francis Crick
James Watson
Maurice Wilkins

DNA!

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21
Q

What holds DNA together?

A

Hydrogen bonding between base pairs

Hydrophobic interactions (Van Der Waals) due to base stacking

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22
Q

B form of Double Helix

A

Normal Form-Watson and Crick Form

Diameter of Helix- 20 A
10.4 Base pairs per turn
1 Base pair is 3.4 A

Characteristics:
Complementary base pairing
Major Groove
Minor Groove
Antiparallel
Hydrogen bonding between complementary BP
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23
Q

A form of Double Helix

A
  • dehydrated B form

- nucleotide tilted 20 degrees relative to helical axis

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24
Q

Z form of Double Helix

A

Zig Zag Form
stretches of alternating purine and pyrimidine
-base pairs flip 180 degrees
-left handed helix

25
what is DNA organized into?
Gene
26
Gene
- discrete functional unit of DNA - when expressed (transcribed), yields a functional product->rRNA, tRNA, snRNA, and mRNA is translated into a polypeptide sequence (protein) - open reading frame->long stretch of nucleotides that can encode polypeptide due to absence of stop codons
27
Karyotype
- Photograph of chromosomes from a single organism - Arranged by size (Largest #1 to smallest #22) - Homo sapiens- 46 chromosomes, 23 pairs
28
What are the parts of a chromosome
- Centromere - Kinetochore - Telomere
29
Centromere
Site that connects sister chromatids
30
Kinetochore
attachment site of spindle to chromosome
31
Telomere
nucleotide repeat at the end of linear chromosome - TTAGGG x 1000 - synthesized by telomerase
32
Properties of DNA
- Melt/Anneal/ Reanneal - Hypochromic effects - Supercoiled/Relaxed
33
Double Stranded DNA and Heat
Double stranded DNA can reversibly melt - Heating DNA breaks hydrogen bonds between base pairs (acid or base also works) - At melting Temperature half of the helical structure is lost - Single stranded DNA absorbs light more efficiently than double stranded
34
Hypochromic Effect
or Hypochromism - DNA can melt than reanneal - If sequences are similar they will reanneal or hybridize
35
In what organisms are DNA circular and what organisms are there DNA linear?
Prokaryotic, mitochondrial, and chloroplast genomes are circular -circular molecules may exist in topological isomers (relaxed and supercoiled) Eukaryotic genomes are linear
36
Single Stranded Nucleic Acids (DNA or RNA) can form complex structures
Stem loops - are produced by H-bonding between complementary regions in DNA and RNA - H-bonding stabilizes more complex structures - mismatches are observed - often observed in ribosomal RNA molecules
37
Testing the Semiconservative Replication Hypothesis
-Grew E. coli in 15NH4Cl until DNA was completely labeled -transferred E. coli to 14NH4Cl containing media -Followed labeling pattern of DNA through several generations using density gradient equilibrium sedimentation By 4 Generations you get Density 14, Hybrid and Density 15 gene
38
DNA replication: DNA polymerase
- adds deoxyribonucleotide units to an existing DNA molecule in a template directed fashion in the 5' to 3' direction - Requires: Four dNTPs- (dATP, dGTP, dCTP, dTTP) - Divalent Cation (Mg2+) - Template DNA - Primer provides 3' OH
39
DNA polymerase Rxn mechanism
Nucleophilic attack by the 3' OH on the alpha phosphate group of dNTP -PPi (pyrophophosphate) is hydrolyzed to Pi + Pi (orthophosphate)
40
Types of RNA
- ribosomal RNA (rRNA)- part of the ribosome - transfer RNA (tRNA) - messenger RNA (mRNA)- sequence translated into protein sequence - small nuclear RNA (snRNA)- involved in splicing (spliceosome) - micro RNA (miRNA)- small RNA complementary of mRNA that inhibits translation of mRNA - small interfering RNA (siRNA)- small RNA that binds to mRNA causing destruction of mRNA
41
Transcription: RNA polymerase
-adds ribonucleoside triphosphate units to an existing DNA molecule in a template directed fashion in the 5' to 3' direction requires: - four NTPs (A, U, G, C) - Divalent Cation (Mg2+) - Template DNA - no primer needed - lacks endo and eco nuclease activity
42
What are the RNA polymerase's for Eukaryotic and prokaryotic cells
Prokaryotic polymerase (1)- RNA polymerase Eukaryotic polymerase (4) - RNA poly I - RNA poly II - mRNA - RNA poly III
43
RNA transcribing
Genes may or may not be transcribed depending on the needs of particular cell type - gene is a functional region of DNA - expressed genes are TURNED ON - unexpressed genes are TURNED OFF
44
RNA polymerase Rxn Mechanism
Nucleophilic attack by the 3' OH on the alpha phosphate group of NTP (ribonucleoside triphosphates) -PPi (pyrophophosphate) is hydrolyzed to Pi + Pi (orthophosphate)
45
mRNA relationship to Template Strand and coding strand of DNA
mRNA is complementary to template strand | mRNA is identical (except for U to T changes) to the coding strand
46
Prokaryotic Promotor Site
Pribnow box (also called TATA box) - 5' TATAAT 3' centered -9/-10 - designated by the 5' to 3' sequence on the NONtemplate strand--> 8 to 10 nucleotides left (5' or upstream) of transcriptonal start site (designated +1-there is no 0 nucleotide) -35 sequence 5' TTGACA 3'
47
Eukaryotic Promotor
Class II genes -those synthesized by RNA poly II (pre mRNA and snRNA) Parts - TATA or Hogness box - GC box (GGGCGG) - CAAT box
48
Transcriptional Termination
Rho dependent -involves protein called RHO Rho independent - involves stem loop structure in mRNA - stem loop is followed by UUUs
49
prokaryotic and eukaryotic mRNA
prokaryotic mRNA are polycistronic -may encode two or more proteins eukaryotic mRNA are monocistronic -encode only one protein
50
eukaryotic mRNA post transcriptionally modified
Capping -attachment of 7-methylguansine using 5' to 5' triphosphate linkage Polyadenylation -attachment of 40 to several hundred adenine nucleotides to 3' end of mRNA Splicing -removal of introns
51
Amino Acids and tRNA
Amino acids are attached to 3' end of tRNA | -Aminoacyl-tRNA synthetase--> attach amino acid to tRNA
52
Stages of Translation
Initiation -assemble and align ribosome, mRNA, and tRNA^fmet Elongation -template directed synthesis of proteins Termination - termination factors halt protein synthesis - ribosome, mRNA, and new protein dissociate
53
Orientation of Translation
- Ribosomes move 5' to 3' along mRNA | - protein is synthesized N to C
54
Genetic Code
Specific Unambiguous - specific codon always codes for SAME amino acid - three nucleotides (codon)=one amino acid Universal - conserved from species to species - main exception=mitochondria Redundant (also called degenerate) -amino acid may have more than one codon Nonoverlapping and comma less (no punctuation) - read from fixed starting point (AUG) - lacks punctuation between codons
55
Translation Start Site
AUG encodes Met (n-terminal amino acid) - Prokaryotes use a Shine-Dalgarno sequence to align a ribosome on the mRNA upstream (5') of AUG - eukaryotes use the 5' cap to align the ribosome on the mRNA
56
Eukaryotic mRNA contain Exons and Introns
Exons-coding region | Introns- (intervening regions) nocoding regions
57
How were Introns discovered?
introns were discovered by hybridizing mRNA to genomic DNA
58
Splicing
removal of introns - spliceosome- specific proteins and small nuclear RNA - most introns start with GU and end with AG

MC Biochem 1 (30 decks)

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