©SIRJOEL EXAM SOLUTIONS
10/3/2024 9:54 PM
Brock Biology of Microorganisms - Chapter
9 Exam Study Guide.
Genome - answer✔entire complement of genetic information (including genes, regulatory
sequences, and noncoding DNA)
genomics - answer✔discipline of mapping, sequencing, analyzing, and comparing genomes
sequencing - answer✔determining the precise order of nucleotides in a DNA or RNA molecule
genome annotation - answer✔converting raw sequence data into a list of genes present in the
genome ("bottleneck")
bioinformatics - answer✔storing and analyzing sequences and structures
dideoxy method - answer✔-method of sequencing DNA invented by Fred Sanger
-copy original ssDNA
-small amounts of dideoxyribonucleotides (ddNTPs) used with dNTPs
-originally used radioactivity, but now use fluorescent labels
dideoxyribonucleotides (ddNTPs) - answer✔chain terminators that prevent further elongation of
DNA chain
pyrosequencing - answer✔-"next-generation sequencing"
-uses luciferase (bioluminescent enzyme) to detect incorporation of dNTPs
Functional ORF - answer✔ORF that actually encodes a protein; can be identified by a computer
codon bias - answer✔some codons used more frequently than others
how to find and identify ORFs - answer✔1) locate start and stop codons and Shine-
Dalgarno/ribosome-binding sequences
, ©SIRJOEL EXAM SOLUTIONS
10/3/2024 9:54 PM
2) look for similarity to ORFs in other genomes
hypothetical proteins - answer✔-uncharacterized ORFs; proteins that likely exist but whose
function is currently unknown (due to lack of aa sequence homology with knowns)
-assigned to family or general function
noncoding RNA - answer✔-RNA that is not translated (like tRNA, rRNA, noncoding regulatory
RNAs)
-lack start codons and have multiple stop codons
comparative genomics - answer✔uses databases to probe genomes for correlation between
genome size and ORF content
small genomes - answer✔-these genomes belong to parasitic or endosymbiotic prokaryotes
-this size means these symbionts are totally dependent on host for nutrients, but provide host
with essential aa and nutrients it can't synthesize
-Ex. Mycoplasma (Bacteria) and Nanoarchaeum equitans (Archaea) are the most extreme of
these
-probably needs at least 250-300 genes to be viable
-tend to encode more translational processes
large genomes - answer✔-some bacterial genomes are as "***" as some eukaryotic microbes
-can even have more genes than eukaryotes due to lack of introns
-Ex. Sorangium cellulosum (Bacteria)
-Archaeal extremes are typically smaller than Bacteria extremes in this manner
-tend to encode more transcriptional regulation and signal transduction processes
metabolic genes - answer✔typically the most abundant class of genes
Archaeal genomes - answer✔-these genomes tend to devote higher % of genomes to energy and
coenzyme production
-have fewer genes for carbohydrate metabolism and membrane functions
-subject to change as more types of this genome are able to be studied
mitochondria and chloroplast genomes - answer✔-encode necessary machinery for protein
synthesis
10/3/2024 9:54 PM
Brock Biology of Microorganisms - Chapter
9 Exam Study Guide.
Genome - answer✔entire complement of genetic information (including genes, regulatory
sequences, and noncoding DNA)
genomics - answer✔discipline of mapping, sequencing, analyzing, and comparing genomes
sequencing - answer✔determining the precise order of nucleotides in a DNA or RNA molecule
genome annotation - answer✔converting raw sequence data into a list of genes present in the
genome ("bottleneck")
bioinformatics - answer✔storing and analyzing sequences and structures
dideoxy method - answer✔-method of sequencing DNA invented by Fred Sanger
-copy original ssDNA
-small amounts of dideoxyribonucleotides (ddNTPs) used with dNTPs
-originally used radioactivity, but now use fluorescent labels
dideoxyribonucleotides (ddNTPs) - answer✔chain terminators that prevent further elongation of
DNA chain
pyrosequencing - answer✔-"next-generation sequencing"
-uses luciferase (bioluminescent enzyme) to detect incorporation of dNTPs
Functional ORF - answer✔ORF that actually encodes a protein; can be identified by a computer
codon bias - answer✔some codons used more frequently than others
how to find and identify ORFs - answer✔1) locate start and stop codons and Shine-
Dalgarno/ribosome-binding sequences
, ©SIRJOEL EXAM SOLUTIONS
10/3/2024 9:54 PM
2) look for similarity to ORFs in other genomes
hypothetical proteins - answer✔-uncharacterized ORFs; proteins that likely exist but whose
function is currently unknown (due to lack of aa sequence homology with knowns)
-assigned to family or general function
noncoding RNA - answer✔-RNA that is not translated (like tRNA, rRNA, noncoding regulatory
RNAs)
-lack start codons and have multiple stop codons
comparative genomics - answer✔uses databases to probe genomes for correlation between
genome size and ORF content
small genomes - answer✔-these genomes belong to parasitic or endosymbiotic prokaryotes
-this size means these symbionts are totally dependent on host for nutrients, but provide host
with essential aa and nutrients it can't synthesize
-Ex. Mycoplasma (Bacteria) and Nanoarchaeum equitans (Archaea) are the most extreme of
these
-probably needs at least 250-300 genes to be viable
-tend to encode more translational processes
large genomes - answer✔-some bacterial genomes are as "***" as some eukaryotic microbes
-can even have more genes than eukaryotes due to lack of introns
-Ex. Sorangium cellulosum (Bacteria)
-Archaeal extremes are typically smaller than Bacteria extremes in this manner
-tend to encode more transcriptional regulation and signal transduction processes
metabolic genes - answer✔typically the most abundant class of genes
Archaeal genomes - answer✔-these genomes tend to devote higher % of genomes to energy and
coenzyme production
-have fewer genes for carbohydrate metabolism and membrane functions
-subject to change as more types of this genome are able to be studied
mitochondria and chloroplast genomes - answer✔-encode necessary machinery for protein
synthesis
