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Genomics > Previous > Flashcards

Previous Flashcards

1
Q

What is Genomics?

A

Genomics is the branch of molecular biology focused on the structure, function, evolution, and mapping of genomes.

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2
Q

What is a Genome?

A

A genome refers to all the genetic information of an organism, including its DNA sequences.

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3
Q

Characteristics of the Genome

A

The genome contains genes that code for proteins, essential for various cellular functions and traits.

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4
Q

Gene Expression and Its Regulation

A

Gene expression is controlled by regulatory elements such as promoters, enhancers, and silencers.

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5
Q

Organization and Regulation of a Typical Eukaryotic Gene

A

A typical eukaryotic gene is organized with a promoter region, regulatory elements, coding sequences, untranslated regions, splice sites, and an open reading frame.

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6
Q

Loss and Gain of Function

A

Gene Inactivation (Loss of Function) includes techniques like RNA Interference (RNAi) and CRISPR-Cas9.

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7
Q

What is RNA Interference (RNAi)?

A

RNAi involves using small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) to silence specific genes.

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8
Q

What is CRISPR-Cas9?

A

CRISPR-Cas9 is a powerful genome-editing tool that can create targeted mutations in genes.

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9
Q

Gene Overexpression (Gain of Function)

A

Transgenic Models and Inducible Expression Systems help assess the effects of increased gene expression.

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10
Q

What is Next Generation Sequencing (NGS)?

A

NGS technologies allow for high-throughput sequencing of DNA and RNA.

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11
Q

General Workflow of NGS (Illumina)

A

The typical workflow includes sample preparation, library preparation, amplification, sequencing, and data analysis.

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12
Q

Gene Sequencing Applications

A

Applications include genome sequencing, mutation screening, studying gene regulation, transcriptome sequencing, and noninvasive cancer detection.

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13
Q

Techniques for Studying Genomes

A

Techniques include whole genome sequencing (WGS), RNA sequencing (RNA-seq), CRISPR-Cas9 gene editing, and microarray analysis.

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14
Q

What is the basic structure of a gene?

A

A gene is a segment of DNA that contains the necessary information to produce a functional product.

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15
Q

What is the coding sequence in a gene?

A

The coding sequence is the part of the gene that contains the actual information for building proteins.

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16
Q

What are exons?

A

Exons are sequences within a gene that remain in the final mRNA after splicing.

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17
Q

What are regulatory elements in a gene?

A

Regulatory elements are sequences that control the expression of the gene.

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18
Q

What is a promoter?

A

A promoter is a region where RNA polymerase binds to initiate transcription.

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19
Q

What are enhancers and silencers?

A

Enhancers increase transcription levels, while silencers decrease transcription levels.

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20
Q

What is the transcription start site (TSS)?

A

The transcription start site is the location on DNA where RNA polymerase begins synthesizing RNA.

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21
Q

What are introns?

A

Introns are non-coding regions that are transcribed into pre-mRNA but are removed during RNA processing.

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22
Q

What is the 5’ UTR (Untranslated Region)?

A

The 5’ UTR is located upstream of the coding sequence and is involved in regulating translation.

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23
Q

What is the 3’ UTR (Untranslated Region)?

A

The 3’ UTR is located downstream of the coding sequence and plays a role in regulating gene expression.

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24
Q

What is a termination sequence?

A

A termination sequence signals the end of transcription.

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25
Q

What is the Human Genome Project (HGP)?

A

The Human Genome Project is an international research initiative aimed at mapping and sequencing the entire human genome.

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26
Q

When was the Human Genome Project initiated?

A

The HGP was initiated in 1990.

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27
Q

What significant milestone occurred in June 2000?

A

A working draft of the entire human genome was completed in June 2000.

28
Q

When were analyses of the working draft published?

A

Analyses of the working draft were published in February 2001.

29
Q

When was the sequencing of the human genome completed?

A

The sequencing was completed in April 2003.

30
Q

Who were the key leaders of the HGP?

A

Craig Venter and Francis Collins.

31
Q

What were the main goals of the Human Genome Project?

A

To determine the sequences of approximately 3 billion base pairs in human DNA and to identify around 30,000 genes.

32
Q

How does genome sequencing help in gene discovery?

A

It helps identify new genes and find gene regulatory sequences.

33
Q

What bioinformatics challenges did the HGP address?

A

The project produced a completed human genome draft and insights into GC content variation.

34
Q

What is genome assembly?

A

Genome assembly involves piecing together sequence fragments into chromosomes.

35
Q

What is GC content variation?

A

GC content variation refers to differences in GC-rich regions across the genome.

36
Q

What are CpG islands?

A

CpG islands are GC-rich regions where CG dinucleotides exceed 70%.

37
Q

What is notable about human gene structure compared to other organisms?

A

Human exons are generally shorter than those in worms and flies.

38
Q

How many chromosomes are in the human genome?

A

The human genome consists of 23 pairs of chromosomes.

39
Q

What characteristics remain unknown after the HGP?

A

Many functional implications of identified genes remain unclear.

40
Q

What is GC content?

A

GC content refers to the percentage of guanine (G) and cytosine (C) bases in a given DNA sequence.

41
Q

Why is GC content significant?

A

GC content can influence gene density and the overall functionality of genomic regions.

42
Q

What is GC bias?

A

GC bias occurs when sequencing data shows an uneven representation of reads from regions with varying GC content.

43
Q

How does GC bias affect RNA-Seq data?

A

GC bias can significantly impact differential expression analysis in RNA-Seq experiments.

44
Q

What are the implications of GC bias in genome assembly?

A

Strong GC bias can lower assembly completeness and increase fragmentation.

45
Q

What are CpG islands?

A

CpG islands are regions of DNA that have a high frequency of CpG dinucleotides.

46
Q

Where are CpG islands commonly found?

A

CpG islands are frequently located in the promoter regions of genes.

47
Q

What role do CpG islands play in gene regulation?

A

CpG islands help regulate gene expression by making DNA more accessible to transcription factors.

48
Q

How does methylation affect CpG islands?

A

Methylation of CpG islands can lead to gene silencing.

49
Q

What is the relationship between CpG islands and cancer?

A

Hypermethylation of CpG islands can contribute to the inactivation of tumor suppressor genes.

50
Q

How many CpG islands are estimated to exist in the human genome?

A

There are approximately 28,890 CpG islands in the human genome.

51
Q

What are the structural components of a gene?

A

Structural components include promoter, enhancer/silencer, exons, introns, UTRs, and splice sites.

52
Q

What is annotation in genomics?

A

Annotation is the process of assigning identities and functions to sequences within the genome.

53
Q

What are SNPs?

A

Single Nucleotide Polymorphisms (SNPs) are a type of genetic variation where a single nucleotide differs between individuals.

54
Q

How do SNPs contribute to genetic diversity?

A

SNPs can affect how genes function and influence disease susceptibility.

55
Q

What is a mutation?

A

A mutation is a change in the DNA sequence that can affect one or more nucleotides.

56
Q

How do SNPs differ from mutations?

A

SNPs are a specific type of mutation that occurs at a single nucleotide position.

57
Q

What are some applications of studying SNPs and mutations?

A

Applications include identifying genetic markers for diseases and developing personalized medicine approaches.

58
Q

What is the HapMap Project?

A

The HapMap Project is an international effort to develop a haplotype map of the human genome.

59
Q

What is a haplotype?

A

A haplotype is a group of alleles at multiple loci that are transmitted together on the same chromosome.

60
Q

Why are haplotypes important in genetics?

A

Haplotypes help identify associations between genetic variations and phenotypes.

61
Q

What are tag SNPs?

A

Tag SNPs are representative SNPs used to represent other nearby SNPs in a haplotype block.

62
Q

How does the HapMap Project aid in disease association studies?

A

The HapMap provides a resource for researchers to find genes associated with health and disease.

63
Q

What was achieved in Phase I of the HapMap Project?

A

Phase I identified over 1 million accurate SNP genotypes from 269 individuals.

64
Q

What advancements were made in Phase II of the HapMap Project?

A

Phase II added over 2.1 million additional SNPs.

65
Q

What role do phenotypes play in relation to haplotypes?

A

Phenotypes reflect observable traits influenced by genetic variations.

66
Q

What is meant by ‘multiple haplotypes’?

A

Multiple haplotypes refer to different combinations of alleles at multiple loci.

Genomics (10 decks)

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