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Flashcards in Lecture 4 Deck (44):
1

Genome

The entire genetic complement of an
organism; includes its genes and nucleotide sequences

2

Chromosome

usually ds, closed circular DNA

3

Base Pairs of nucleic acids

G-C DNA and RNA
A-T DNA
A-U RNA

4

Explain DNA Replication

Polymerization process that requires monomers and energy

5

What does it mean to be SEMICONSERVATIVE in terms of DNA replication?

New molecule is composed of one original and one daughter strand

6

What proteins are required for replication complex?

Helicases
SSDNA binding protein
primate
DNA polymerase

7

Explain initial processes in DNA Replication

Enzyme called TOPOISOMERASE is located at the position of the blue circle during DNA replication

8

What is the function of enzyme called TOPOISOMERASE?

It removes the helical stress that would accumulate for the unwinding of the two DNA strands

9

Define GYRASE

type of TOPOISOMERASE, target for the quinoline antibiotics

10

How does the DNA Replication Start ?

DNA polymerase adds 5' nucleotides to free 3' hydroxyl groups
All chains grow only in 5' to 3' direction

11

Why does the new strand of DNa need to be synthesized differently?

Because two parental strands of DNA are antiparallel

12

How is Leading strand synthesized ?

Continuously

13

How is Lagging strand synthesized ?

Discontinously

14

What is the replicative DNA polymerase in E. coli?

DNA polymerase III
two enzymes are needed one for each strand

15

What is RNA primase?

Special form of RNA polymerase
Begins chains for synthesis of both the leading and the lagging strands

16

What does the Lagging strand consists of ?

Okazaki fragments
100-1000 base long

17

What is the function of DNA Polymerase I ?

Repair enzyme, causes Okazaki fragment to lose their RNA beginning nucleotides

18

How is RNA primary made?

it is made by PRIMASE a special form of RNA Polymerase

19

Define OKAZAKI FRAGMETNS

RNA primer and covalently attached deoxyribonucleotides

20

What is the function of repair enzyme?

A repair enzyme removes RNA primer from okazaki fragments and fills the space with DNA
process called NICK TRANSLATION

21

What is the function of DNA ligase?

it seals the sugar-phosphate backbone

22

What is the error for Polymerization?

1 mistake for every 10^4

23

Wat is the advantage of proof reading?

it reduces the error to 1 mistake for 10^7

24

What is the function of RESTRICTION MODIFICATION SYSTEM?

The restriction modification system (RM system) is found in bacteria and other prokaryotic organisms, and provides a defense against foreign DNA, such as that borne by bacteriophages.

25

Define TRANSCRIPTION

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase.

26

Difference between RNA and DNA Polymerase

RNA polymerase does not require 3'-Oh primer to Begin Transcription

does not require helicase

it is SLOWER than DNA polymerase

lacks Proofreading

more errors in RNA

27

How is Transcription controlled in Bacteria?

only 75% of the genes are expressed at all times

other only used when cells need them

28

What are different kinds of Operons?

Inducible- must be activated by inducers
---Lactose
Repressible- transcribe continually until deactivated by repressors
---Tryptophan

29

The difference between Bacteria and Eukaryotes translation initiation?

In bacteria the 16S rRNA of small ribosomal subunit pairs with the Shine- Dalgarno sequences

30

Define Formylated MEt

first amino acid bounded to a specific initiator TRNA
all bacterial proteins begin with f-Met at their amino terminus

31

Define Shine-Dalgarno sequence

The Shine-Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon.

32

When does the Termination occurs?

when a stop codon occupies the A site and a protein release factor RF causes peptide transferase to release the growing polypeptide chain from the tRNA in the P site

33

What is a Riboswitch?`

a regulatory segment of a RNA that binds a small molecule resulting in a change in production of the proteins encoded by the mRNA

34

where are riboswitches locate?

in the 5' UTR of mRNA

35

How are riboswitches build?

Aptamer-- binds the small regulatory molecule
The expression platform- regulates gene expression by changing its structure in response to changes in the aptamer

36

Why Bacterial Riboswitches are important?

Provide some support for the RNA
They can function as a target for antibiotics

37

Define Mutation

change in the nucleotide base sequence of a genome

38

Types of mutation

Point mutation
Silent--- one codon changes to another-same amino acid
Missense--chagne codon for another amino acid
Nonsense-- change codon to stop codon

39

Define Virulent (Lytic) Phage

Phage that always causes death of their bacteria host via lysis of the bacteria cell

40

Nonlytic Filamentous Phage

Phage that are released from their bacterial host by "budding" from the living bacterial cell

41

Vertical Gene Transfer

Organisms replicate their genomes and provide copies to descendants

42

Horizontal Gene Transfer

DNA from outside of the cell contributes part of genome to recipient cell
3 forms:
Transformation-- naked DNA from solution
Transduction-- bacterial DNA in a virus
Conjugation--- sharing of DNA between two bacteria

43

Define Transposons

Segments of DNA that move from one location to another i the same or different molecules

44

Define CRISPR

A widespread system that provides acquired resistance against phages in bacteria and archaea