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Microbiology > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

Which statement regarding prokaryotic chromosomes is incorrect?
• There are two copies of the chromosome so that cells are diploid.
• There is a single copy of the chromosome so that cells are haploid.
• Prokaryotic chromosomes are located in the nucleoid.
• Prokaryotic chromosomes are now known to be circular or linear.

A

There are two copies of the chromosome so that the cells are diploid

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2
Q

Genetics

A
  • the study of genes, how they carry information, how information is expressed, and how genes e replicated
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3
Q

Chromosomes

A
  • structures containing DNA that physically carry hereditary information; the chromosomes contain genes
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4
Q

Genes

A
  • segments of DNA that encode functional products, usually proteins
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5
Q

genome

A
  • all the genetic information in a cell
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6
Q

Genotype
Phenotype

A

Genotype - a set of genes in the genome
Phenotype - physical features and functional traits of the organism

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7
Q

The structure and replication of genomes
- prokaryotic chromosomes

A
  • main portion of DNA, along with associated proteins and RNA
  • prokaryotic cells are haploid (single chromosome copy)
  • typical chromosome is a circular molecule of DNA in the nucleaid
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8
Q

The structure and replication of genomes
- the structure of prokaryotic genomes

A
  • plasmids
    • small molecules of DNA, among with associated proteins and RNA
    • not essential for normal metabolism, growth, or reproduction
    • can confer survival advantages
    • many types of plasmids:
      - fertility factors
      - resistance factors
      - bacteriocin factors
      - virulence plasmids
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9
Q

The structure and replication of genomes
- DNA replication

A
  • key to replication is the complementary structure of the two strands
  • replication is semi conservative
    • new DNA composed of one final and one daughter strand
  • anabolic polymerization processes require monomers and energy
    • triphosphate deoxyribonucelotides serve both functions
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10
Q

The structure and replication of genomes
- DNA replication -> initial processes in bacterial NDA replication

A
  • bacterial DNA replication begins at the origin
  • DNA polymerase replicated DNA only 5’ to 3’
  • because strands are anti parallel, new strands are synthesized differently
    • leading strand synthesized continuously
    • lagging strand synthesized discontinuously
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11
Q

The structure and replication of genomes
- DNA replication -> other characteristics of bacterial DNA replication

A
  • bidirectional (think of a phone cord and all of the circles it creates/how wound up it would be)
  • gyrases and topiocomerases remove supercoils in DNA
  • DNA is methylated (telling a gene to be quiet. Ex: giving/surrounding it by a bunch of cups continuing to say you be quiet as you add them. “You be quiet or you have activity”)
    • control of genetic expression
    • initiation of DNA replication
    • protection against viral infection
    • repair the DNA
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12
Q

The structure and replication of genomes
- DNA replication -> replication of eukaryotic DNA

A
  • similar to bacterial replication (bacterial have leading and lagging strands, may have more DNA polymerase that is more specialized, and have longer Okazaki fragments)
  • some differences:
    • uses four DNA polymerases
    • thousands of replication origins
    • shorter Okazaki fragments
    • plant and animal cells methylate only cytosine bases
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13
Q

What determines the genotype of a cell?
It’s proteins
It’s RNA
It’s DNA
It’s ribozymes

A
  • It’s DNA
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14
Q

Four types of RNA

A
  • RNA primer molecules
    • used for DNA polymerase during DNA replication
  • messenger RNA
    • carry genetic information from chromosome to ribosome
  • ribosomal RNA
    • combine with ribosomal polypeptides to form ribosomes
  • transfer RNA
    • deliver the correct sequence of amino acids to ribosomes based on the sequence of nucleotides in mRNA
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15
Q

Transcription

A

Promoter region - DNA sequences located upstream of transcriptional start site
Sigma factor - specificity to promoter region, the region interacts with RNA polymerase
RNA polymerase - workhorse of the transcription-> does all of the work
Transcriptional start site - the position in the gene where transcription starts
Termination - the sequence where transcription stops

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16
Q

Transcription in the eukaryotes

A
  • in eukaryotes, transcription occurs in the nucleus, whereas translation occurs in the cytosol or RER
  • exons are regions of DNA that code for proteins
  • introns are regions of DNA that do not code for proteins
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17
Q

Prokaryotic vs. eukaryotic transcription

A

Prokaryotic - located in the cytoplasm, have one polymerase, have pretty simple mRNA, are Rho in/ dependent termination
Eukaryotic - located in the nucleus, have many polymerases, have complex (processing) mRNA, and the termination sequence if polyU

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18
Q

Translation: protein synthesis
- players in translation

A

Messenger RNA (MRNA, start)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Ribosomes (work horse)
Polypeptides (outcome)

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19
Q

What types of RNA are ——— used in translation: protein synthesis?

A

Messenger RNA -> Cary genetic information from the chromosome to ribosomes
Ribosomal RNA -> combine with ribosomal polypeptides to form ribosomes
Transfer RNA -> deliver correct sequences of amino acids to ribosomes based on the sequence of nucleotides in mRNA

20
Q

Original DNA -> first replication -> second replication

A

Original DNA is the original form it comes in
- first replication is when the original strand is combined with a new strand
- second replication is when the first replication pair is joined by another separate pair of DNA

21
Q

What does the DNA polymerase 111 do in DNA replication? What do stabilizing proteins do?

A

The DNA polymerase 111 does the work in the end for the DNA replication
The stabilizing proteins keep the replication pieces separate but keep them together to continue with the replication process

22
Q

what repairs the junctions in DNA replication

A

Ligase (German for glue)

23
Q

What does the RNA primer, the Okazaki fragments, DNA polymerase 1 and DNA polymerase 3 do in DNA replication

A
  • RNA primer -> helps us to know where to start replication
  • Okazaki help us associate with leading or lagging lines (specifically lagging)
  • DNA polymerase 1 - helps repair by removing the RNA primer
    DNA Polymerase 3 - makes the long chains or lines
24
Q

What is essentially the outcome from DNA to protein?

A

mRNA

25
Q

How do you switch from 5’ to 3’ and 3’ to 5’ in dsDNA and mRNA

A

dsDNA
5’ to 3’: ATGAGCCATATTCAACGGGAAA
3’ to 5’: TACTCGGTATAAGTTGCCCTTT

mRNA:
5’ to 3’: AUGAGCCAUAUUCAACGGGAAA
3’ to 5’: UACUCGGUAUAAGUUGCCCUUU

26
Q

What is the way to switch between 5’ to 3’ and 3’ to 5’

A

Switch them all
In DNA: A goes to T and T goes to A, C goes to G and G goes to C
In RNA: A goes to U and U goes to A, C goes to G and G goes to C

27
Q

Difference between non-template and template strands in transcription of Kan^R cassette

A

Non - template strand = coding strand (the original strand)
Template strand = non-coding strand (the copied strand)

28
Q

define the following
metabolomics
metagenomics
genomics
proteomics

A

metabolomics - the study of the complete complement of small chemicals present in a cell at any given time
metagenomics - study of all genomes in a particular ecological niche
genomics - the systematic study of an organisms genes and their functions
proteomics - the study of an organisms complement of proteins and functions mediated by the proteins

29
Q

define the following:
semiconservative replication
somal complex
intron
exon

A
  • “half” helps explain how the replication process maintains accuracy and fidelity during successive cycles
  • an assembly line for mass production of proteins
  • the segments on split genes of eukaryotes that do not code for polypeptides. They can have regulatory functions
  • a stretch of eukaryotic DNA coding for a corresponding portion of mRNA that is translated into polypeptides.
30
Q

Sigma factor
RNA polymerase
Promoter region
Transcriptional start site
Termination

A

Sigma factor - specificity to promoter region, interacts with RNA polymerase
RNA polymerase - workhorse of transcription: does the work
Promoter region: DNA sequences located upstream of transcriptional start site
Transcriptional start site - position in gene where transcription starts
Termination - the position in the gene or sequence where transcription stops.

31
Q

Steps of transcription

A
  • initiation
  • elongation
  • termination
32
Q

How can we stop elongation

A

Rho dependent - makes a Hexamire of protein (like a donut) until the shape finds where the end should be and stops it
Rho independent - making the RNA and you come into a long region where Gs and Cs start to recognize each other and create a hairpin (bonds at the bottom of the hairpin are weak and don’t want to respond so they fall off). It can then stall transcription

33
Q

What is the input of transcript?
What is the output of transcript?

A

Input - a string of ATCG characters representing the DNA sequence
Output - the RNA sequence of the DNA sequence

34
Q

how do you start transcription?
How do you stop transcription?

A

Start - when an enzyme called RNA polymerase attaches to the template DNA strand and begins to catalyze production of complementary RNA
Stop - the recognition of the point where no further bases should be added. The sequence of DNA that is required for termination is called the terminator which at this point disassociated from the DNA

35
Q

Type of RNA used in protein synthesis of translation

A

Messenger RNA - carry genetic information from the chromosomes to ribosomes
Ribosomal RNA - combine with ribosomal polypeptides to form ribosomes
Transfer RNA - deliver the correct sequence of amino acids to ribosomes based on the sequence of nucleotides in mRNA

36
Q

Prokaryotic ribosomes in translation of protein synthesis

A

A: accommodates rRNA delivering an amino acid
P: holds a tRNA and growing peptide
E: discharged tRNAs exit ribosomes from this site

37
Q

30s subunit of prokaryotic ribosome

A
  • can hold 3 codons worth of mRNA at once
38
Q

A region on the DNA strand that carries the information needed for the synthesis of a specific protein is called what?

A

A gene

39
Q

In prokaryotes what can transcription and translation do with each other

A

In prokaryotes translation can occur simultaneously with transcription

40
Q

Translation: protein synthesis

A
  • the mRNA starts the initiation of synthesis. The tRNA prepares for elongation of synthesis, then the polypeptides are forming into chains to then create the outcome of the termination to be polypeptides
41
Q

Why can’t translation occur simultaneously with transcription in eukaryotes

A

The mRNA must be processed and moved which can’t because of the nucleus.
- has to leave the nucleus before it can continue so they can not occur simultaneously. You have to process the RNA then leave the nucleus and it can only go to one ribosome at once

42
Q

TRNA

A
  • transfers the correct amino acid to a ribosome during polypeptide synthesis
  • TRNA is a mail man (the head is amino acids, the foot is the anticodon, under the body is the codon which is located in the mRNA
  • when charging tRNA it requires energy to transfer and is an enzyme between the stages of tRNA and aminoacyl-tRNA
43
Q

Transfer of tRNA through translation

A

A: arriving
P: growing
E: exiting
- from amino acids 4-6 it is inside (4 is when it is added)
- from amino acids 1-3 it is exiting
- amino acid 7 is when it enters inside

44
Q

What can elongation of translation do

A

Repeat over and over again continuously

45
Q

Transcription verses translation: prokaryotic

A

Transcription: the enzyme is RNA polymerase, the template is one strand of DNA, the fidelity mechanism (where it starts) is promoter, the termination sequence is the terminator, the product is the ssRNA, the direction of synthesis is 5’to3’
Translation: the enzyme is ribosomes, the template is mRNA, the fidelity mechanism (where it starts) is the AUG complex/start, the termination is stop codons: UAA,UAG, and UGA
The product is polypeptides, the direction of synthesis is N terminus to C terminus (N terminus meaning it has H3N and c terminus meaning it has a carbonyl group)

Microbiology (23 decks)

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