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MOL. BIO LEC > MOL. BIO LEC 2 > Flashcards

MOL. BIO LEC 2 Flashcards

1
Q

● Structural components that forms the outer edge of the DNA double helix composed of alternating sugar and phosphate groups
● Arranged at specific distances from one another in the double helix
● 2 regions formed in the helix by the backbones: major groove & minor groove

A

SUGAR - PHOSPHATE GROUP

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2
Q

● Often found in nature
● Base modifications have significant effects on phenotype
● Some result from DNA damage, naturally modified for specific functions or to affect gene expression
● Used by bacteria & viruses as a primitive immune system

A

Modified nucleotides

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3
Q

● Macromolecule made of nucleotides bound together by the phosphate & hydroxyl groups on their sugars

A

NUCLEIC ACID

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4
Q

DNA is oriented in ___________

A

5’ to 3’ direction

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5
Q

It is the process by which DNA makes a copy of itself during cell division

A

DNA REPLICATION

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6
Q
  • every double helix in the new generation of an organism consists of 1 COMPLETE “OLD” strand and 1 COMPLETE “NEW” strand wrapped around each other
  • Key to maintaining the sequence of the nucleotides in DNA through new generations
A

SEMI-CONSERVATIVE

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7
Q

Demonstrated the mechanism of semiconservative replication using the technique of equilibrium density centrifugation on a cesium gradient

A

MATTHEW MESELSON & FRANKLIN STAHL

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8
Q

POLYMERASE
- 1st purified enzyme shown to catalyze DNA replication in prokaryotes
- Followed by DNA polymerase II & |||

A

DNA POLYMERASE I (POL I)

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9
Q

POLYMERASE
- Main polymerizing enzyme during bacterial replication
- Functions as a multi-subunit HOLOENZYME

A

DNA POLYMERASE III (POL III)

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10
Q
  • Addition of labeled nucleotides at nicks (single-strand breaks) in DNA
  • Often used in vitro as a method to introduce labeled nucleotides into DNA molecules, which will be used for DNA detection in hybridization analyses
A

NICK TRANSLATION

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11
Q
  • Type of DNA polymerase that can synthesize polynucleotide chains WITHOUT A TEMPLATE
    • How?
      ▪ By adding nucleotide to the end of a DNA strand in the absence of H-base pairing with a template
  • Used in the laboratory to generate 3’-end labeled DNA species
A

Terminal transferase

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12
Q

POLYMERASE CHARACTERISTIC:

A

⮚ Processivity (staying with the template longer to make longer products)
⮚ Fidelity (faithful copying of the template)
⮚ Substrate specificity (affinity for altered nucleotides)

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13
Q

It is the process by which cellular DNA is maintained

A

DNA MATABOLISM

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14
Q
  • Endonucleases that RECOGNIZE SPECIFIC BASE SEQUENCE AND BREAK OR RESTRICT THE DNA POLYMER at the sugar-phosphate backbone
  • Originally isolated from bacteria, as part of a primitive immune system Named for the organism from which they were isolated:
  • BamHI (from Bacillus amyloliquefaciens H)
  • HindIII (from Haemophilus influenzae Rd)
  • Smal (from Serratia marcescens Sbb)
A

RESTRICTION ENZYMES

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15
Q

TYPES OF RESTRICTION ENZYMES
- NUCLEASE & METHYLASE activity in a single enzyme
- Bind to host-specific DNA sites of 4-6 bp separated by 6-8 bp & containing methylated adenines
Example: Ecok from E. coli K 12, recognizes the ff site:

A

TYPE I RESTRICTION ENZYMES

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16
Q

TYPES OF RESTRICTION ENZYMES
- Used most frequently in the laboratory
- DO NOT have inherent methylation activity
- Bind as simple dimers to symmetrical 4-8 bp DNA recognition sites (palindromic)
- Cleave DNA directly at the binding site, producing fragments of predictable size

A

TYPE II RESTRICTION ENZYMES

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17
Q

TYPES OF RESTRICTION ENZYMES
- Resemble Type I enzymes in their ability to both methylate & restrict (cut) DNA
- Have multiple subunits, including helicase (unwinding) activity
- Recognition sites are asymmetrical & the cleavage of the substrate DNA occurs 24-26 bp from the site to the 3’ side
Example: Pstill from Providencia stuartii, recognizes the ff site & cuts DNA 25-26 bp 3’ to the recognition site

A

TYPE III RESTRICTION ENZYMES

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18
Q

TYPES OF RESTRICTION ENZYMES
- Similar subunit structures & enzyme requirements
- CUTTING & METHYLTRANSFERASE functions
Example: BseMII from Bacillus sterothermophilus, with target sequence:

A

TYPE IV RESTRICTION ENYMES

19
Q

CUTS 1 strand of DNA 10 bp ff the recognition sequence.

A

RESTRICTION ENDONUCLEASE FUNCTION

20
Q

ADDING METHYL GROUPS methyl groups to both of the adenine residues in the target sequence

A

METHYLATION FUNCTION

21
Q
  • Catalyzes the formation of a phosphodiester bond between
    adjacent 3’-hydroxyl & 5’-phosphoryl nucleotide ends
    (SEALS)
  • Discovered in 5 different laboratories in 1967
A

DNA LIGASE

22
Q

o Degrade DNA from free 3’-hydroxyl or 5’- phosphate ends
o Used under controlled conditions, to
manipulate DNA in vitro
o Different substrate requirements & will therefore degrade specific types of DNA ends

A

EXONUCLEASES

23
Q

degrades single-stranded DNA (ssDNA) from the 3’-hydroxyl end into mononucleotides

A

EXONUCLEASE I FROM E.coli

24
Q

removes 5’ mononucleotides from the 3’ end of double-stranded DNA (dsDNA) in the presence of Mg2+ & Mn2+

A

EXONUCLEASE III FROM E. coli

25
Q

digests ssDNA from either the 5’-phosphate or 3’-hydroxyl end

A

EXONUCLEASE IV FROM E.coli

26
Q

TYPES OF HELICASE
- interconvert topological isomers or relax super twisted DNA ((eukaryotes)

A

TOPOISOMERASE

27
Q

TYPES OF HELICASE
- (type II topoisomerase): untangles DNA through double-strand breaks & separate linked rings of DNA (prokaryotes)

A

GYRASES

28
Q

Catalyze the ADDITION OF METHYL GROUPS to nitrogen bases, usually adenines & cytosines in DNA strands

A

METHYLTRANSFERASE

29
Q
  • It is the mixture & assembly of new genetic combinations
  • Occurs through the molecular process of crossing-over or physical exchange between molecules
A

RECOMBINATION

30
Q

The one that holds a new combination of DNA sequences is called the _______

A

RECOMBINANT MOLECULE or ORGANISM

31
Q

Each generation of sexually reproducing organisms is a NEW COMBINATION of the parental genomes → generates genetic diversity

A

MENDEL’S LAW

32
Q

MENDEL’S LAW 3 WAYS OF Recombination in Sexually Reproducing Organisms

A

CROSSING - OVER
RANDOMLY ASSORTED
FERTILIZATION

  1. Beginning of meiosis: duplicated chromosomes line up & recombine by crossing over or breakage & reunion of the 4 DNA duplexes
  2. Recombined duplexes are randomly assorted into gametes
  3. Gamete will merge with the gamete from the other parent carrying its own set of recombined chromosomes
33
Q
  • Controlled mixing of genes
  • Single genes can be altered, replaced, deleted, or moved into new genomes
  • Implications:
    1. Laboratory
    2. Treatment & prevention of disease (gene therapy)
A

RECOMBINANT DNA TECHNOLOGY

34
Q

RECOMBINATION IN ASEXUAL REPRODUCTION 3 WAYS:

A

CONJUGATION
TRANSDUCTION
TRANSFORMATION

35
Q
  • Transfer of genetic information by PHYSICAL ASSOCIATION OF CELLS
  • 2 types (or sexes) of participating bacteria: F+ and F-
  • Conjugating cells must be in physical contact with each other for successful transfer of the F+ phenotype
A

CONJUGATION

36
Q
  • Extrachromosomal circle of dsDNA or plasmid carrying the
    genes coding for construction of the mating bridge
  • After mating: both bacteria are F+
A

F FACTOR

37
Q

o Strains with chromosomally embedded F factors
o Used in first mapping studies

A

High-frequency recombination (Hfr) bacteria

38
Q
  • Transfer of genetic information from 1 cell to another through a VIRAL INTERMEDIATE
  • 1960s, studied by Francois Jacob & Elie Wollman
  • Viral intermediate: BACTERIOPHAGE (bacterial viruses)
A

TRANSDUCTION

39
Q
  • Transfer of genetic information among cells WITHOUT PHYSICAL ASSOCIATION, such that a new phenotype is produced in the recipient cells
  • A bacterium takes up a piece of DNA floating in its environment (often DNA that has been shed by other bacteria)
A

TRANSFORMATION

40
Q

These are small, usually circular dsDNAs, often carrying genetic information, that replicates INDEPENDENTLY or in SYNCHRONY with host cell replication

  • Most are 2,000-100,000 bp (2-100 kilobase pairs) in size
  • Can carry limited amount of genetic information
  • DNA duplex is compacted, or supercoiled & can be relaxed by nicking or by local unwinding of the double helix
A

PLASMIDS

41
Q

PLASMID CLASSIFICATIONS:
- Include F factor & some of the R plasmids
- CARRY GENES for their own transfer & propagation & self-transmissible
- Occur in small numbers (1 or 2 copies per chromosome equivalent)

A

LARGE PLASMIDS

42
Q

PLASMID CLASSIFICATIONS:
- More numerous in the cell (20 copies per chromosomal equivalent)
- DO NOT CARRY GENES directing their maintenance
- Rely on high numbers for distribution into daughter cells at cell division or uptake by host cells in transformation

A

SMALL PLASMIDS

43
Q

PLASMID CLASSIFICATIONS:
- Class of plasmids carrying resistance to BACTERIOCINS (toxic proteins manufactured by bacteria)

A

COLLICINOGENIC

MOL. BIO LEC (14 decks)

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