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Cell biology III > quiz 4 information > Flashcards

quiz 4 information Flashcards

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1
Q

Genome

A
  • organisms complete set of DNA, including chromosomal and mitochondrial
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2
Q

Genomics

A
  • study of the genomes of organisms,
  • determining entire dna sequence of organisms/ genetic mapping
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3
Q

DNA sequencing

A
  • ## determining precise order of nucleotides within a DNA molecule
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4
Q

Methods of DNA sequencing

A
  • sanger chain-termination
  • high-throughput methods (next generation)
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5
Q

high-throughput methods

A
  • next generation sequencing
  • main difference between this and sanger sequencing is volume
  • massively parallel, sequencing millions of fragments simultaneously per run
  • real time sequencing, does not require lengthy electrophoresis
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6
Q

dNTP vs ddNTP

A
  • dNTP = deoxygenated at 2’ and have hydroxyl at 3’ carbon

-ddNTP = have hydrogen instead of hydroxyl at 2’ and 3’ carbons…. prevents from forming phosphodiester at 3’

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7
Q

What is sanger-chain termination

A
  • in vitro DNA replication reactions
  • includes DNA to be sequenced, a DNA primer, a DNA polymerase, normal dNTPs (high concentration), and modified ddNTPs (smaller amount)… many identical DNA fragments are used in each reaction, generated by cloning
  • produces a large number of partial replication products, each terminated by incorporation of a ddNTP at a different site in the sequence
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8
Q

what are the four standard nucleotides added to danger sequencing reactions?
What are the four options that could be added of the modified?

A
  • normal: dATP, dGTP, dCTP, dTTP
  • modified: ddATP, ddGTP, ddCTP, ddTTP
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9
Q

DNA sequence reactions with ddNTP

A
  • incorporation of dCTP allows chain to continue growing
  • incorporation of ddCTP terminates chain elongation
  • partial replication products terminate each cytosine of the chain due to the incorporation of ddCTP… different DNA fragment lengths are generated by ddCTP incorporation into C reaction micture products
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10
Q

what to do following sanger sequence reaction

A
  • contents of each reaction are electrophoresed, separated by length
  • can identify consecutive nucleotides by gel lane in which successively longer DNA fragments are locatedf
  • can then determine complementary strand
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11
Q

bioinformatics

A
  • application of computational methods to the storage and analysis of biological data
  • study of large sets of biodata
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12
Q

computational biology

A
  • emphasizes development of theoretical methods, computational simulations and mathematical modeling
  • use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships
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13
Q

Big Data

A
  • large data sets that cannot be processed by traditional approaches
  • data mining
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14
Q

data mining

A
  • analysis of the large data sets for useful information
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15
Q

Primer walking

A
  • potentially useful for a large DNA fragment, but not efficient for genome projects
  • primer allows ends of clone to be sequenced from both sides
  • new primers are designed based on newly obtained sequence
  • procedure is reiterated until sequence from both ends overlap
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16
Q

shotgun sequencing

A
  • genomes must be broken into small fragments and the pieces sequences in parallel…. shotgun seuqnecing everything… doing it all at the same time then piecing it together at the end
  • clone by clone sequencing
  • whole genome shotgun sequencing
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17
Q

clone by clone sequencing

A
  • chromosomes broken into overlapping fragments that are arranged in linear order to produce a map
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18
Q

whole genome shotgun sequencing

A
  • DNA of entire genome is fragmented and pieces chosen at random and sequenced
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19
Q

Human genome project outcomes

A
  • number of protein encoding genes did not correlate with complexity as expected
  • prevelance of the use of other mechanisms that increase complexity and variation without increasing number of coding genes
  • recognition of complex regulatory network
  • junk dna serve a purpose
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20
Q

metagenomics

A
  • study of genetic material recovered directly from environmental samples
  • with sequencing and computational techniques, one can go into environment, pick up sample, and put in test tube.. isolate DNA and sequence… and determine whats there…
  • discovered many species that had never been cultured
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21
Q

Sargasso Sea metagenomics project

A
  • environmental genomic shotgun sequence was performed on DNA isolated from microorganisms found in sargasso sea
    found:
  • 1800 different genomes
  • one million new protein coding genes
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22
Q

Microbiomes

A
  • entire habitat including microorganisms, their genomes, and the surrounding environmental conditions
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23
Q

microbiota

A

microorganisms in particular environment

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24
Q

metagenome in terms of microbiome

A
  • combined genomes and genes of the microorganisms in a particular environment
25
Q

We have a genome sequence… now what to do with it

A

Annotate to describe genes…

26
Q

annotation

A
  • attaching biological functions to DNA sequences, based on experimental evidence or computational analysis
27
Q

genome annotation

A
  • identification of important components in genomic DNA: location of genes and functional sequences
28
Q

gene annotation

A
  • defines biochemical, cellular and biological function of each product
29
Q

experimental approaches to genome anotation

A
  • compare cDNA to genomic sequence to identify sequences of a genome that undergo transcription leading to production of mRNA molecules.
  • large amounts of cDNA are available, allowing for partial/complete assembly of gene transcripts
  • comparing these allows accurate annotation of gene exons/introns
  • expressed sequence tags (ESTs): mRNA fragment sequences are derived through single sequencing reactions performed on randomly selected clones from cDNA libraries
30
Q

computational approaches to genome annotation

A
  • gene (reading frame) identification
  • non coding genes (for ncRNA)
31
Q

Gene families

A
  • groups of genes that are functionally and/or evolutionarily related. members of a family will have high sequence similarity
32
Q

protein families

A
  • groups of proteins that are evolutionary related, have related functions and similarities in their sequence and structure
33
Q

domains

A
  • many proteins are modular… distinct domans that are joined together… particular protein domain may be found in numerous genes
  • some genes may be very similar being they share functional domains
34
Q

domains

A
  • regions of a protein that have a specific function and can usually function independently of the rest of the protein
35
Q

motif

A
  • similar 3d structure conserved among different proteins that serve a similar function
    ex: helix-turn-helix motif
36
Q

what is the different between domains and motif?

A

motif:
- arrangement of secondary structures of protein molecule
- not stable
- no functional role

domain:
- 3D dimensional fundamental and functional unit of protein
- stable by itself
- functional unit of the protein

37
Q

examples of gene families

A
  • receptor tyrosine kinases
  • MAP kinase
  • G-proteins
  • SOX gene family (TFs)
  • immunoglobulin superfamily
  • ABC transporters
  • ion channels
38
Q

examples of protein domains

A
  • SH2
  • immunoglobulin
  • fibronectin type 3
  • kringle
  • Ca2+ binding
  • protease domain
  • UBA (ubiquitin- associated domain)
39
Q

genome annotation of human chromosome 21

A

-

40
Q

Why do bacteria have fewer genes but higher gene density (protein encoding genes) than eukaryotes?

A
  • lack of introns
  • compact gene regulatory sequences
  • lower complexity of protein structure
41
Q

does gene number determine organisms complexity?

A

no, complexity is in the network

42
Q

evolutionary genomics

A
  • comparative study of genomes…
  • provides clarity to the three of life (phylogenetic tree)
  • genes encoding rRNAs provide universal sequence for comparision
43
Q

Carl Woese

A
  • categorized three domains: eukaryote, archaea and bacteria
  • originator of RNA world hypothesis
  • work on horizontal gene transfer as a primary evolutionary process
44
Q

transcriptomics

A
  • study of gene expression (transcription) from a genomic perspective
45
Q

transcriptome

A
  • set of transcripts present in a cell or organism
    (identity and quantity of RNA in a biological sample at a given moment)
46
Q

What methods are used to determine transcriptome?

A
  • 1: DNA microarrays: old way…
    … widely used in data mining
  • 2: high throughput sequencing (RNA-Seq)
  • RNA-seq is dominant method
  • data mining
47
Q
A
48
Q

microarrays

A
  • array of spots on a microscope slide, oligonucleotides are fixed to the spots, spots represent different genes… enough spots on slide to represent all genes in entire genome
  • isolate RNA from sample, label RNA with a fluorescent label, mix the two together…
  • bathing slide with cDNA, cDNA anneal to complementary spot, binds quantitatively
  • more cDNA binding = higher quantity of transcript
  • measure transcript levels by brightness of spots
49
Q

method for interpreting microarray

A
  • raw data is converted to expression in one cell type relative to another
  • heat map
50
Q

RNA-seq

A
  • uses next generation methods
  • simultaneously sequence thousands of cDNAs in sa sample at one time
  • computer take all sequences and assign them to one gene or another
  • faster, cheaper
51
Q

Use of data mining

A
  • data is sent to a data base and used for other investigators to harvest the information
  • there are different databases and algorithms, wont always give you the same information.. can compare the information from each database
52
Q

proteomics:

A
  • study of all the proteins expressed in a cell
  • looking for proteins involved in a specific biological activity
53
Q

techniques used for proteomics:

A
  • 2D gel electrophoresis
  • mass spectrometry
  • affinity chromatography
  • two hybrid system
54
Q

2D gel electrophoresis

A
  • electrophores samples in 2 dimensions
  • 2 parameters:
    size (SDS page) , and charge (by isoelectric focusing)

apple pH gradient, migrate proteins and they find their charge and stay there… lay across SDS PAGE gel

55
Q

affinity chromatography

A
  • co-IP on a column to identify putative interacting partners
  • to isolate interacting partners and mass spectrometry to identify purified proteins
56
Q

interactome

A
  • whole set of molecular interactions in a particular cell
  • wiring diagram
57
Q

g

A

g

58
Q

Omics refers to…

A

collective techniques used to explore actions of various types of molecules that make up the cells of an organism

Cell biology III (18 decks)

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