Chapter 12: Genomes Flashcards
Human Genome Project
small # of genes
2003 completion
=next-generation DNA sequencing
miniaturization techniques DNA replication PCR
- cut up DNA
- denature DNA by heat breaking hydrogen bonds
- fragment attached at each e nd to short adapter sequences
- Amplified by PCR to make so many copies
- DNA poly adds nucleotides
- DNA added one nucleotide at a time
- FLUORESCE
4.remove tag and repeat synthesis
colors show things
Power of next generation DNA sequencing
fully automated and miniaturized
millions of different fragments are sequenced at the same time. This is called massively parallel
An expensive way to sequence large genomes. at the time od writing a complete genome could be sequenced in a few days
overlappingggggg
bioinformatics
Analyze DNA sequences using complex mathematics and computer programs
Functional genomics
biologists use sequence information to identify the functions of various parts of genomes
including
open reading frames, amino acid sequences of proteins, regulatory sequences, RNA genes, other noncoding sequences
open-reading frames
coding regions of genes
can be recognized by start and stop codon for coding and consensus sequences for introns
functional genomics
amino acid sequences of proteins
can be deduced from the DNA sequences of open reading frames by applying the genetic code
functional genomics
regulatory sequences
promoters and terminators for transcription
functional genomics
RNA genes
rRNA, tRNA, small nuclear RNA, and microRNA
functional genomics
Other noncoding sequences (functional genomics)
fucntional genomics
classified in various categories including centromeric and teolmerix regions, TRANSPOSONS, and repetitive
Comparative gentics
the comparison of a newly sequenced genome of parts thereof can be compared to other organisms
genetic determinism
person’s phenotype is determined solely by his or her genotype
Proteomics
seeks to identify and characterize all expressed proteins
Proteome
sum total of the proteins produced by an organism
more complex than the genome
How do people analyze proteins and the proteome?
using electrical charge and size with gel electrophoresis to separate proteins and isolate them
mass spectrometry uses electromagnets to identify molecules by masses of their atoms
determine structures of molecules
Metablomics
aims to describe the metabolome of a tissue or organism under particular environmental conditions
metabolome
quantitative description of all of the metabolites in a cell or organism
primary metabolites
involved in normal processes such as intermediates in pathways like glycolysis
also hormones and other signaling molecules
secondary metabolites
often unique to particular organisms or groups of organisms often involved in special responses to the environment
ex. antibiotics made by microbes and chemicals made by plants that are used in defense
Features of of bacterial and archaeal genomes
relatively small single circular chromosome
compact most is protein coding with only short sequences
genes usually do not contain introns except rRNA and tRNA
addition to the main chromosome, often have plasmids
transposons
segements of DNA that can move form place to place in the genome and can move from one piece of DNA to another
Metagenomics
analyzing genes without isolating the intact organism
use pCR to amplify sequences in enviornmental samples to determine whether specific microbes were there
True or False: Eukaryotic genomes are larger than those of prokaryotes
true
more genes
which is like very not surprising
True or false: Eukaryotic genomes have more regulatory sequences
true
more complex
True or false: a lot of eukaryotic DNA is noncoding
true
ransom seuqences don’t code for RNA
Yeast
single-celled eukaryotes
can live as haploid or diploid
lots of genes for targeting protein sinto organelles
nematode
only needs 10% if genes
drosophila
complex
arabidopsis
plant
flowering ]simpler
small
orthologs
genes with very similar sequences
gene families
closely related genes
came from duplkicated then mutated genes
pseudogenes
nonfunctional
result from loss of function mutations
Highly repetitive sequences
short seqeunces that are repeated thousands of time in tandem
not transcribed
short tandem repeats
1-5 bp can be repeated up to 100 times at a particular location
scattered about the genome
moderately repetitive sequences
repeated 10-1000 times in the rukaryotic genome
unclue genes which produce tRNA and rRNA
generally transposons
Retrotransposons
make RNA copies of themselves, which are then copied back into DNA before inserted into DNA class I transposons
LTR retrotransposons
long terminal repeats of DNA sequences at each end
about 8% of human genome
a type of Retrotransposons
Non-LTR retrotransposons
a type of Retrotransposon
do not have LTR sequences at the ends
makde up of SINEs and LINEs
SINEs
short interspersed elements are up to 500 bp long and are transcribed but not translated
a type of non-LTR retrotransposon
LINEs
Long interspersed elements
up to 7000 bp long and some are transcribed and translated into proteins
a type of non-LTR retrotransposon
DNA transposons
do not use RNA intermediaries
excised from location and inserted in a new place without replication
single nucleotide polymorphisms (SNPs)
DNA sequence variations that involve single nucleotides
used to create genetic maps of organisms
haplotype
a piece of chromsome with a set of linked SNPs `
DNA microarray
a grid of microscopic spots of oligonucleotides arrayed on a solid surface
depend on hypbridization to identify SNPs
has DNA and RNA complementary to oligonuleotides
pharmacogenomics
the study of how an individual’s genome affects his or her response to drugs or other agents
goal is to personalize drug treatment
Proteomics
proteins in families
lots of proteins just have reshuffled domains
disease
metabolomics
some progress needs to be related to physiology
DNA fingerprinting
a group og yrchniques used to identify particular individuals by their DNA the most common involves STR analysis
