51 terms

bio 2 unit 3 ch 12

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how many strands need to be sequenced for dna
just one; the other is complementary
key to interpreting DNA sequences
do several separate experiments simultaneously on a chromosome, first breaking the DNA into overlapping fragments
next generation DNA sequencing
cheap fast way for genome; use miniaturization techniques; uses DNA replication and polymerase chain reaction
one approach to next generation
1. Large molecule of DNA cut into small fragments either by physically breaking or enzymes that hydrolyze the phosphodiester bonds b/w nucleotides at intervals in DNA backbone
2. DNA denatured by heat, breaking hydrogen bonds that held strands together; single strands act as template for new complementary DNA
3. Ends of fragments attached to adapter sequences which are attached to solid support (microbead/flat surface)
4. DNA fragments amplified by PCR to get lots of copies; copies allow for detection of added nucleotides during the sequencing steps
ready for sequencing
1. Fragments are heated & denatured; primer, DNA polymerase, & 4 nucleotides added; universal primer that is complementary to an adapter is used
2. Replication process is set up so DNA is added one nucleotide at a time; unincorporated nucleotides are removed
3. Fluorescence of nucleotide is detected with a camera; color allows for detection of what nucleotide
4. Fluorescent tag removed and synthesis cycle repeated
power behind new generation method
1. Fully automated and miniaturized
2. Massively parallel sequencing (millions of fragments sequenced at once)
3. Cheap
reads
fragments
bioinformatics
analyzes DNA sequences using complex math and computer programs
functional genomics
biologists use sequence info to identify the functions of various parts of the genomes; assigns functions to the products of a gene
parts of functional genomics
-open reading frames : coding regions of genes; recognized by start/stop codons for translation & intron consensus sequences
-amino acid sequences: deduced from DNA sequences of open reading frames by applying genetic code
-regulatory sequences: promoters and terminators for transcription
-RNA genes
-other noncoding sequences
comparative genomics
comparison of newly sequence genome with sequences from other organisms; can provide further info about functions of sequences & used to trace evolutionary relationships
genetic determinism
a person's phenotype is determined only by genotype
proteome
sum total of proteins produced by an organism & more complex than its genome
2 methods to analyze proteome and proteins
1. Separated by gel electrophoresis
2. Electromagnets
genomics seeks
describe genome and its expression
proteomics seeks
identify and characterize all of the expressed proteins
metabolome
quantitative description of all metabolites in cell or organism
primary metabolites
normal processes; includes hormones & other signaling molecules
secondary metabolites
unique to particular organisms; involved in special responses to the environment
features of bacterial/archael genomes
-small
-compact
-no introns
-carry plasmids (small circle DNA molecules) that can be transferred b/w cells
transposons
segments of DNA that can move from place to place in the genome and can move from piece to piece in the same cell; can produce significant phenotypic effects by inactivating genes
metagenomics
analyzing genes without isolating the intact organism
-possible to do DNA sequencing with samples from almost any environment; can be cloned or amplified
comparison b/w prokaryotes and eukaryotes
some genes are present in all organisms
how can a minimal genome be identified
transposon mutagenesis can be used to inactivate genes one by one & the organism can be tested for survival
differences b/w eukaryotic and prokaryotic genomes
-eukaryotic genomes are larger & have more protein coding genes
-eukaryotic genomes have more regulatory sequences & proteins
-much of eukaryotic DNA is noncoding
orthologs
genes with very similar sequences
half of eukaryotic protein coding genes exist as
one copy in the haploid genome (2 alleles in somatic)
gene families
different copies of genes have undergone separate mutations, giving rise to groups of closely related genes
-as long as one member encodes a functional protein the others can mutate to change the proteins they encode
pseudogenes
results from mutations that cause a loss of function rather than an enhanced or new function; DNA may be same but just lack a promoter or a recognition site
highly repetitive sequences
short sequences that are repeated thousands of times in tandem; not transcribed; associated with heterochromatin
moderately repetitive sequences
genes that are transcribed to produce tRNAs and rRNAs; most are transposons
two types of transposons in eukaryotes
-retrotransposons: make RNA copies of themselves which are copied back into DNA before insertion at new locations
-DNA transposons: don't use RNA intermediates; excised from original location and inserted in a new one without being replicated
two types of retrotransposons
-LTR: long terminal repeats of DNA sequence at each end
-Non-LTR
2 types of non LTR
-SINEs: transcribed not translated
-LINEs: some are transcribed and translated into proteins
. Two-dimensional gel electrophoresis separates proteins based on _______ and _______.
size & charge
Different functional units of a protein are called
domains
haploytle maps
used to identify genes involved in disease
what are haplotype maps based on
single nucleotide polymorphisms (SNPs)
SNPs
DNA sequence variations that involve single nucleotides; arise at point mutations
what do biologists use SNPs for
create genetic maps, classify organisms/species, identify individual organisms carrying specific alleles
a set of snps that are all close together..
inherited as a unit
haploytpe
a piece of chromosome with a set of linked snps
DNA microarray
grid of microscopic spots of oligonucleotides; probed with mixture of DNA & RNA; if mixture has complementary sequence to olignecleotide the sequence will hybridize; colored fluorescent dyes are used to hybridize the spot
pharmacogenomics
how an individual's genome affects his or her response to drugs
dna fingerprinting
detect people by DNA; common technique is STR
method of generating new proteins.
reshuffling of protein domains
Which of the following statements about pseudogenes is true?

A. There often is little selective pressure to get rid of pseudogenes.
B. The sequences of a pseudogene and its functional counterpart must be very different.
C. In some gene families, pseudogenes outnumber functional genes.
D. Both a and b
E. Both a and c
E
Which of the following statements about eukaryotic genomes is false?

A. They tend to be larger than prokaryotic genomes.
B. They tend to have more regulatory sequences than prokaryotic genomes have.
C. The percentage of the genome devoted to coding sequence is higher than in prokaryotic genomes.
D. They usually have more repetitive DNA than prokaryotic genomes have.
E. All of the above are true; none is false.
C
Which of the following statements about yeasts is false?

A. They are always haploid.
B. Most have a few thousand genes.
C. They have linear chromosomes.
D. They have many organelles.
E. All of the above are true; none is false.
A
In next-generation DNA sequencing technology, the fluorescent dye
labels the 4 nucleotides
Which of the following statements about the human proteome is false?

A. It is the sum total of all proteins produced by an organism.
B. It is more complex than the genome.
C. It includes the small molecules found in a cell.
D. Its study often involves the use of two-dimensional gel electrophoresis.
E. All of the above are true; none is false.
C