Microbiology Genomics and Meta-omics Techniques

Question 1

What are the primary areas of microbial biochemistry?

Answer 1

• Structure/function
• Bioenergetic
• Information

Question 2

Why are proteins and RNA a significant portion of the cell?

Answer 2

Because numerous metabolic reactions happen in the cell

Question 3

What does DNA store?

Answer 3

• Information for synthesis of proteins for chemical reactions in a cell

Question 4

What does RNA stand for?

Answer 4

Ribonuclei acid

Question 5

What are proteins responsible for?

Answer 5

Proteins responsible for building cellular components for maintaining the proper functioning of the cell

Question 6

What’s inside the double helix?

Answer 6

Organic bases

Question 6

What is the shape of DNA?

Answer 6

Double helix Covalent bonds

Question 7

What the examples of base pairs?

Answer 7

• G-C
• T-A

Question 8

What’s the process from gene to enzyme?

Answer 8

DNA -> mRNA -> Protein/enzyme

Question 9

What is a gene?

Answer 9

A gene is a segment of DNA that encodes the synthesis of a
gene product, either RNA or protein/enzyme

Question 10

What happens in transcription?

Answer 10

Gene-encoding DNA segment is copied into messenger RNA (mRNA)

Question 11

What happens in translation?

Answer 11

mRNA is decoded by ribosomes to produce protein/enzyme
- three nucleotides on mRNA and read by tRNA

Question 12

What are ribosomes?

Answer 12

• A complex RNA-protein macromolecule, found in all living cells, that serves as the site of biological protein synthesis
• Read the mRNA and synthesize protein

Question 13

What does mRNA stand for?

Answer 13

Message RNA

Question 14

What are features of mRNA?

Answer 14

Unstable and short lived

Question 15

What is transfer RNA?

Answer 15

• Combined with an amino acid and incorporated it into a growing protein chain

Question 16

What is ribosomal RNA?

Answer 16

• Found in combination with proteins in ribosomes

Question 17

What is mRNA?

Answer 17

• Single stranded copy of a small part of the DNA
• Carries instructions from DNA to make protein

Question 18

What is the range for genome size of bacteria and archaea?

Answer 18

130 kbp to > 14 Mbp

Question 19

What are Meta-omics techniques?

Answer 19

The collection, classification, storage, and analysis of
biochemical and biological information using computers (called bioinformatics) especially as applied to molecular genetics and genomics

Question 20

What are some meta-comic techniques?

Answer 20

1. 16S rRNA gene sequencing (microbe’s identity)
2. Metagenomics (gene present)
3. Metatranscriptomics (gene transcription activity/metabolic pathway activity)
4. Proteomics (enzyme activity, 3D protein structure
   prediction)

Question 21

What is used in sequencing platforms?

Answer 21

• Short- read sequencer

Question 22

What is the criteria for the gene target for Phylogeny Taxonomy?

Answer 22

• The gene target should be present in all bacteria
  and archaea
• Adequate genetic variation within gene target to
  distinguish between different species of bacteria and archaea

Question 23

What is the 16S rRNA gene?

Answer 23

Encodes for an RNA product called 16S rRNA

Question 24

What does 16s rRNA form?

Answer 24

16S rRNA forms part of the prokaryotic ribosome (Conserved in parts – highly variable in other parts)

Question 25

How does the sequencing analysis happen?

Answer 25

DNA extraction -> 16S rRNA gene sequencing -> 16S rRNA gene sequence data -> bioinformatics analysis

Question 26

What's an example where 16S rRNA Sequencing Analysis took place?

Answer 26

Anaerobic Fluidized-bed Membrane Bioreactor (AFMBR)

Question 27

What is involved in Metagenomics?

Answer 27

- Investigate community of microorganisms present without the necessity of obtaining pure cultures - Predicts metabolic potentials - High resolution identification of microbes and correlation of genomes with functions of interest

Question 28

What the sequencing of metagenomics?

Answer 28

1. DNA extraction 2. Archaeal/Bacterial genomes present in a sample 3. Genomes cut into small fragments 4. Sequencing of random pool of fragments 5. Alignments of DNA sequences with a comp 6. Bioinformatics analysis

Question 29

What is Geobacter?

Answer 29

Geobacter species are anaerobic respiration bacterial species which have capabilities that make them useful in bioremediation.

Question 30

What are Metatranscriptomics used for?

Answer 30

- Analyse mRNA acquired from environmental samples, in order to study the gene expression of microbes - Determines activity (metabolic pathway)