Week 1 Flashcards by Sara Richmond

_______ a subsystem understanding of biology

systems biology

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systems biology focuses on the ingrain of __________

the parts

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systems biology was first described by

Leroy hood

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Explain how systems biology can help us understand a complex disease such as coronary artery disease

This is because disease often have connected pathogenesis to other diseases. Thus to better understand a disease we must understand the way it relates to other diseases.

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Compare reductive and systems science

Reductive: disease driven, aimed for a normal range, studies individual components in terms of time and space

Systems: individualized, multidimensional, synergistic, emphasis on interrelationship and independent treatment plans

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Systems biology is an extension of _______________

molecular biology

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systems biology is quantitative and focuses on _____________ rather than its parts

the dynamics of a system

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systems biology is ______________

ex: genomics, transcriptomics, proteomics

technology driven

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___________ is the study of genomes of organisms. The field include intensive efforts to determine the entire DNA sequence of organisms using high-output DNA sequencing machines and fine scale genetic mapping efforts

Genomics

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_______ the study of the total set of transcripts given to an organism or to the specific subset of transcripts present in a particular cell type

transcriptomics

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___________ is the set of all mRNA molecules or “transcripts” produced in one or a population of cells

transcriptome

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unlike the genome (which is roughly fixed for a given cell line) the transcriptome can _______________

vary with environmental conditions

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Because the transcriptome includes all mRNA transcripts in the cell, the transciptome reflects the genes that are being _______________

actively expressed at any given time

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proteomics is __________

the large scale study of proteins, particularly their structure.

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Because the proteome _______________and distinct requirements or stresses that a cell or organism undergoes.

will vary with time

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While on organisms genome is more or less constant the proteome ________

differs from cell to cell and time to time

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A ________ is a segment that in DNA Encodes for polypeptides.

Gene

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a gene is considered the functional unit of a genome as it is what ________________

encodes for polypeptides

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not all of human genes are useful act a given time because there is non coding regions that can be turned off at a given time. This is because _______________

gene expression is not ubiquitous

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A ______________ is a union of inheritance, a genetic determinant for phenotypes

gene

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On average a gene is _____________

7-`10 exons spanning 10-16 kb of DNA.

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___________ “fundamental” They are universal genes that carry out general metabolism of the cell

House keeping genes

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___________ information flow, DNA (gene) -> RNA -> Protein

gene expression.

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Explain. the central dogma of molecular biology

DNA (in the form of a gene) is transcribed and RNA processed into

mRNA which is translated into

Protein

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__________ the sequence typically right upstream or right next to where a gene is about to be transcribed (transcription start site)

promotor region

_____________ refers to DNA in the genome coding for protein coding

coding

_____________ refers to the part of DNA which does not code for proteins

non coding

The 5' and 3' end of flanking DNA contains promotor regains that are

not involved in coding

____________ the first codon of mRNA translated by a ribosome. The start codon always codes for methionine in eukaryotes

start codon:

Why can nucleic acids only be synthesized in the 5' to 3' direction:

this occurs because the 3' hydroxyl group can attack a 5' phosphate group forming the phophodiester bond and elongating DNA

How is DNA double stranded

each strand had a 5' and a 3' end and the 5' end of one strand is paired with the 3' end of another in the antiparallel orientation

Transcription is _______ and is mediated by _________

DNA -> RNA | RNA polymerase

__________ strand of DNA double helix used to make RNA

template strand

________ strand of DNA that is complementary to the template strand

coding strand

____________ the enzyme that synthesizes RNA from the DNA template

RNA polymerase

Which DNA strand has an identical sequence to the RNA strand

the coding strand and the RNA sequence have almost identical sequences

________ has opposite/ complementary codons to the produced mRNA

template strand

Steps of Transcription

1. Transcription factors promote transcription 2. RNA polymerase binds 3. Opening of the DNA double helix 4. Polymerase moves along template strand 5. Assembles ribonucleotides into strand of RNA 6. RNA is synthesized base d on base pairing rule 7. RNA strand grows in 5'-> 3' direction 8. When transcription is complete, the transcript is released from the polymerase and shortly thereafter the polymerase is released from the DNA

Which direction does the polymerase go relative to the template strand or the coding sequence?

Opposite to the coding strand

_______ are a type of cis regulatory sequences.

transcription factors

transcription factors bind to _________

specific DNA sequences | *binding sites are first determined empirically

Most transcription factors can bind to a range of similar sequences. We can represent these in either of two ways, as a __________________

consensus sequence or as a position weight matrix

transcription factors binding motif is important for bio informative ______________

so that we can predict binding sites

________ Is depicted on frequency matrix and sequence logos

the frequency of specific base binding sites

_________ is a concrete and compact way to represent the combined DNA sequence

consensus sequence

In a consensus sequence: A single base is shown if it occurs in more than half the sites and more than twice as often as the second most frequent base. Otherwise

a double degenerate symbol (G/C=S) is used if two bases occur more than 75% of the sites or a triple degenerate when one bases doesn't occur at all

For a frequency or weight matrix we...

divide each number by the total number of the sequence. This gives us the position weight sequence

In a sequence logo, ______________ of each stack indicates the sequence conservation at that position

the overall height

The height of symbols within the stack reflects the relative frequency of the ______________________________

corresponding amino or nucleic acids at that position

RNA Processing

1. synthesis of the cap. A modified guanine (G) which is attached to the 5' end of the pre-mRNA 2. splicing: removal of introns in the pre-mRNA and ligation of the remaining exons 3. solacing carried out by spiceosomes 4. synthesis of the poly A tail

_________ is the process by which introns are removed to generate a mature RNA molecule

splicing

Splicing in humans, many genes contain multiple introns and ______________

usually all introns need to be removed before the mRNA can be translated to produce a proteins

However, multiple introns may be __________ in different circumstances for example in different tissues

spliced differently

The many ways in which introns may be spliced illustrates how we have __________

one gene and many proteins

____________ acts as a diversity generator

alternative splicing

3's acceptor is

the acceptor

5's donor is

called the 5' splice cit because to is located on the 5' end

The most critical signals:

- first and second nucleotides (GT) int the intronic part of the 5'ss - first and second nucleotides (AG) into the intronic part of the 3'ss

-splice cites are termed relative to their __________

introns

Doner is called the 5' splice cite because it is located on the 5' end of the downstream intron

5'ss (donor)

what are the five major types of spicing

- skipped exon - alternative 5' splice sites - alternative 3' splice sites - mutally exclusive exons - introns retention

______________ is the most common form of alternative splicing in mammals

exon skipping

___________ is most common in plants

intron retention

more than 90% of the human genome is ________

alternatively spliced

__________ is a form of RNA splicing used to cause cells to skip over faulty or misaligned sections of genetic code leading to a truncated but still functional protein despite the genetic mutation

casette skipped exon

_______ are the critical elements at the 5' end of intron and are extremely diverse as thousands of different sequences act as bone fide.

5' splice sites

__________ indicates that exactly one out to two exons for one group out of two exons groups is retained while the other one is spliced out

mutually exclusive exons

_____________ occurs when the intron region is retained rather than spliced

intron retention

_______ are made of amino acids

proteins

amino acids are represented by _________

codons

protein synthesis:

The process to build proteins

_______________ set 3 nucleotides that specifies a particular amino acid

codon

_________ the series of nucleotides read in set of 3 (codon). Only 1 reading Fram is used to generate a protein

reading frame

What are the 3 stop codons

UAA, UGA, UAG,

What is the start codon

AUG

The remained of the code (with the exception of the start and stop codons is _________ meaning that some amino acids are specific buy more than one codon

degenerate

Translation: | _______ is an RNA/ protein hybrid

ribosome

Ribosomes bind to the translation initiation sequence on the mRNA, then move down the RNA in a ___________________

5' to 3' direction, creating a new polypeptide

Transfer RNA is the adapter between__________

3 bases of the codon and the corresponding amino acid

_________ are translated into protein products

not all transcribe RNA

Non coding RNA can function as RNA molecules in ____________

various steps of gene expression

__________ are a family of non coding RNA encoded individually and act to inhibit translation or cause mRNA degradation

microRNA

MicroRNAs are

cleaved out of a bigger complex

MicroRNA function: they bind to the _____________ of the mRNA

3' UTR

What are some other functions of micro RNAs

- Inhibition of translation - mRNA destabilization - degradation of target RNA (plants)

Micro RNAs are involved in almost all ___________

biological processes and numerous diseases

micro RNA binds to the _______

3' UTR

the most critical region for the binding of the micro RNA is

the seed region

What are some facts about human micro RNAS

- 100 microRNAS are identified in mammals - each micro RNA can regulate hundreds of targets - over 60% of human protein coding genes are targeted by one or more microRNAS