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Biochemistry > Organization Of Human Genome > Flashcards

Organization Of Human Genome Flashcards

1
Q

Histones

A

. Small basic proteins
. Create higher order structures
. Provide compaction of chromosomes
. Match DNA in mass

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2
Q

Amino acids that make up histones and why?

A

. Rich in basic AA like Arg and Lys

. The positively charged AA help histones bind to negatively charged sugar phosphate of DNA

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3
Q

Nucleosomes

A

. Core w/ 8 histones proteins ( 2 molecules of histone H2A, H2B, H3, ad H4)
. DNA wound around it
. Packed into higher order structures by coiling and looping

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4
Q

T/F efficient replication of chromosomes requires presence of specialized DNA sequences

A

T

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5
Q

Chromosomes

A

. Non covalent complex of 1 long linear duplex DNA w/ histones
. Easy to observe in high compact state in cell division

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6
Q

Cells most commonly used for chromosome analysis

A

. Blood lymphocytes

. Skin fibroblasts, amniotic fluid cells, chorionic villus cells, or spontaneously dividing tumor cells can also be used

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7
Q

Telomere

A

. Type of sequence element needed at end of linear chromosomes
. Protects chromosomes from degradation

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8
Q

Centromere

A

. Sequence element that attaches any DNA molecules that contains it to mitotic spindle during cell division
. Region of chromosome that separates 2 arms of chromosome

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9
Q

Genes

A

Basic unit of inheritance
. Contained in chromosomes
. Minimal linear sequence of genomic nucleic acids that encode proteins and structural RNA
. Encode primary sequence of final gene product, protein, or stable RNA
. Regulatory sequences are signals at star and end of gene

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10
Q

Genome

A

Total genetic info stored in chromosomes of organism

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11
Q

Haploid genome

A

. Consists of 3.0X10^9 base pairs of DNA

. Subdivided into 23 chromosomes

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12
Q

T/F there are more transcripts created than proteins produced

A

T

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13
Q

No coding RNAs

A 
. New class of genes 
. No proteins created from these genes
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14
Q

RNA important in regulating gene expression

A 
. MicroRNA
. SnRNA
. Long non coding RNA 
. tRNA
. rRNA
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15
Q

ENCODE project purpose

A

. Understand all functional elements of human genome

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16
Q

Sequence classes of DNA

A

. Unique/non-repetitive

. Repetitive

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17
Q

Single copy DNA/genes

A

. Part of unique/non-repetitive DNA
. Encode info for specific protein products
. 21,000 genes below to this
. Categories: maintain genome, signal transduction, biochemical functions of cell, other

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18
Q

Types of repetitive DNA

A

. Satellite DNA (highly repetitive)

. Dispersed repetitive DNA (moderately repetitive)

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19
Q

Satellite DNA

A 
. Clustered
. Repeated many times in tandem 
. Not transcribed usually 
. Present in 1-10 million copies per haploid genome 
. Associated w/ centromere and telomeres
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20
Q

Alpha satellite

A

. 171 bp sequence that extends several million base pairs or more in length

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21
Q

Mini satellite DNA

A

. 20-70 bp in length

. Total length a few thousand base pairs

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22
Q

Micro satellite DNA

A

. Repeat units only 2,3,4 bp in length

. Total length of a few hundreds

23
Q

What are micro and mini satellites useful for?

A

Genetic mapping

. Have hypervariability in individuals

24
Q

Short tandem repeats (STRs)

A

. Contain repeat units 2-6 bp in length
. Can be amplified w/ polymerase chain reaction (PCR)
. Big in forensic research

25
Q

Trinucleotide repeats

A

. Expansion in number fo trinucleotide repeats causes several human diseases

26
Q

Kennedy’s disease repeat sequence, normal number, disease number, and location of mutation

A

. CAG
. Normal: 11-33
. Disease: 40-62
. Located on protein

27
Q

Huntington’s disease repeat sequence, normal number, disease number, and location of mutation

A

. CAG
. Normal: 11-34
. Disease: 42-100
. Located on protein

28
Q

Fragile X disease repeats sequence, normal number, disease number, and location of mutation

A

. CGG
. Normal: 6-54
. Disease: 250-4000
. Located on 5’ untranslated

29
Q

Myotonic dystrophy disease repeat sequence location, normal number, disease number, and location of mutation

A

. CTG
. Normal: 5-30
. Disease: over 50
. Located on 5’ untranslated

30
Q

Dispersed repetitive DNA

A

. Not clustered, interspersed w/ unique sequences
. Present at less than 10^6 copies per haploid genome
. Transcribed into RNA
. Grouped according to size

31
Q

LINES DNA type

A

. Long interspersed elements
. 7,000 bp long
. About 20-50,000 copies

32
Q

SINES DNA type

A

. Short interspersed elements
. 90-500 bp in length
. About 100,000 copies

33
Q

T/F genes are Collinear w/ RNA transcripts and proteins

34
Q

Epigenetics

A

. Biology of dynamic interactions btw genes and their products that bring phenotype into being
. As effect on developmental plasticity

35
Q

Structural changes present in genome during development and differentiation

A

. Tissue specific alterations in chromatin structure

. Methylation of specific cytosines in genome

36
Q

Alterations to histones

A 
. Acetylation 
. Methylation
. Phosphorylation 
. Ubitquitylation
. Physiologically reversible 
. Prepare chromatin for DNA replication and transcription
37
Q

Is transcriptionally active chromatin more or less condensed?

A

Less condensed

38
Q

When chromatin is in compacted state, there is or is not RNA transcription and why?

A

There is no transcription

. DNA is packaged too tightly so it is inaccessible to proteins that complete RNA transcription

39
Q

What histone alterations are known for controlling chromatin structure?

A

Acetylation

Deacetylation

40
Q

Acetylation of histones

A

. Modification of Lys residues
. Weakens DNA-histone interactions
. Makes DNA more accessible for transcription
. Catalyzed by histone acetyl transferases (HAT)
. Association w/ transcriptional activation

41
Q

Histone deacetylation

A

. Catalyzed by histone deacetylase (HDAC)

. Associated w/ silencing

42
Q

T/F all tissues have the same chromatin structure

A

F, different tissues have different structures dependent on functions carried out by that tissue

43
Q

Histone code

A

. For histone methylation
. Assoc. w/ transcriptional activation of repression
. Trimethylation of histone H3 at Lys4 activates
. Trimethylation of histone H3 ar Lys 27 respresses

44
Q

What 2 things work in concert to affect gene expression?

A

. DNA methylation

. Histone alterations

45
Q

Major site of DNA methylation

A

. Cytosine base in DNA

. Most common 5’ cytosine in dinucleotide 5’-CpG-3’

46
Q

Methylation

A

. S-adenosyl-methionine is methyl donor

. DNA methyl transferases (DNMT) catalyze moving methyl group to cytosine ring

47
Q

CpG islands

A

. Distribution of CpG residues in DNA where methylation occurs is asymmetric
. Clusters of CpG in small stretches
. ASOS. W/ sites where transcription of DNA into RNA begins (promoter regions)

48
Q

CpG methylation can ____ transcription and how?

A

. Inhibit transcription
. Blocks interactions btw DNA and transcription factors
. Get demethylated as they are activated. During cell differentiation

49
Q

Pathway of methylation to inactive gene at CpG

A

. DNA methyltransferases mehtylated
. Methyl-CpG binding protein (MeCP2) binds to area
. HDAC and HMT form complex w/ MeCP2 that is bound to promoter
. Causes inactivation of gene

50
Q

Genomic imprinting

A

. Individual are methylated differently in maternal and paternal chromosomes at CpG nucleotides
. Makes it so only one copy of same gene is active

51
Q

Prader-Willi syndrome (PWS) mutation

A

. Loss of expression of genes in paternally derived chromosome 15 region 2 via methylation

52
Q

Angelman Syndrome mutation

A

. Loss of expression of genes in maternally derived chromosome 15 region 1

53
Q

What environmental factor early in life can modify epigenome and affect development of age-related diseases?

Biochemistry (64 decks)

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