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H2 Biology > COPEG > Flashcards

COPEG Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What is coding DNA?

A

DNA sequences which code for amino acids in proteins and functional RNA

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2
Q

What is Non-coding DNA?

A

DNA sequences which do not code for amino acids in proteins or functional RNA

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3
Q

What are the 3 types of non-coding DNA?

A

Control elements, repetitive DNA and introns

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4
Q

What are the 2 main regulatory regions?

A

Promoter and distal control elements

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5
Q

How does the half-life of RNA affect gene expression?

A

mRNAs with longer half-lives are translated into many more protein molecules

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6
Q

What is the stability of mRNA affected by?

A

It is affected by the presence of a longer 3’ poly(A) tail

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7
Q

What are introns?

A

They are non-coding DNA sequences part of a gene which are transcribed into RNA but excised before translation

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8
Q

What are the 2 types of repetitive DNA?

A

Centromeres and telemores

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9
Q

What is meant by heterochromatic regions?

A

Tightly coiled structure which is not actively transcribed

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10
Q

What are distal control elements?

A

Specific nucleotide sequences of DNA within the gene which regulates the rate of transcription via binding of regulatory proteins

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11
Q

What do distal control elements consist of?

A

Enhancers and silencers which are bound by activators and repressors respectively

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12
Q

Where are distal control elements located?

A

Upstream or downstream of the transcriptional unit, distant from the promoter

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13
Q

What is the promoter?

A

Specific nucleotide sequences of DNA which is the binding site for RNA polymerase and general transcription factors to initiate transcription

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14
Q

Are all exons translated?

A

No because some of these exons will be found within the untranslated regions

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15
Q

What is the function of the terminator sequence?

A

Involved in terminating transcription by causing RNA polymerase to dissociate from the DNA template

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16
Q

Where is the 5’ UTR found?

A

The 5’ UTR is found between the 5’ modified guanosine cap of mRNA and the start codon

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17
Q

Where is the 3’ UTR found?

A

The 3’ UTR is found after the stop codon

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18
Q

What is the function of the 5’ UTR?

A

It serves as a binding site for ribosomes and regulatory proteins which control the rate of translation

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19
Q

What is the function of the 3’ UTR?

A

It contains sequences which are binding sites for specific proteins that regulate the polyadenylation of mRNA which in turn controls the rate of translation

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20
Q

What are the structural features of the centromere?

A

Centromeres consist of repetitive DNA sequences which are made up of tandem repeats.
Centromeres are also found as densely packed heterochromatin in the cell.

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21
Q

What are the 4 functions of centromeres?

A

Centromeres are the adhesion point for sister chromatids in a nucleus.
Centromeres are the site of assembly of the kinetochore complex which binds to the microtubules of spindle fibres.
Centromeres organise the chromatin within the nucleus during interphase.
Centromeres is essential for the equal segregation of sister chromatids in mitosis, chromatids in meiosis II
and segregation of homologous chromosomes in meiosis I to opposite poles, and hence to each daughter nuclei.

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22
Q

What are the structural features of telomeres?

A

Telomeres are made up of short repeated sequences arranged in tandem repeats.
Telomeres are found on the ends of linear DNA of the eukaryotic chromosome.

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23
Q

How are telomeres formed?

A

Telomeres are synthesised by the binding of telomerase to the 3’ overhang of DNA which catalyses the formation of phosphodiester bonds which form multiple DNA repeats at the 3’ end of the telomere.

DNA polymerase can then extend the 5’ end of the other DNA strand

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24
Q

Where can telomerase be found?

A

Telomerase can be found in stem cells, unicellular eukaryotes, germ-line cells and cancer cells

25
Q

Describe the structure of telomerase

A

It is a ribonucleoprotein.

The RNA component acts as a template to guide the insertion of multiple repeats of TTAGGG by complementary base pairing to extend the 3’ end of the telomere.
The protein component acts a reverse transcriptase to synthesise new DNA at the 3’ end of the telomere

26
Q

What are the 4 functions of telomeres?

A

Telomeres protect the genes found at the end of linear chromosomes from being eroded.
Telomeres prevent chromosomal end to end fusions.
Telomeres protect the ends of chromosomes from inappropriate enzymatic degradation.
Telomeres act as a signal for cells to undergo replicative senescence.

27
Q

What are the 3 basic functions of packaging genetic material in the cell?

A

Packaging allows all genetic material to be contained within the nucleus of the cell.
Packaging allows gene expression to be regulated.
Packaging protects DNA from breakage or damage especially during cell division.

28
Q

Describe the first level of condensation of DNA

A

It involves the formation of nucleosomes as part of a chromatin fibre.
DNA is wound around histone octamers, giving the chromatin a “beads-on-a-string” structure.
Each nucleosome is separated from each other by a region of naked DNA known as linker DNA.

29
Q

What makes up the octamer of histone proteins?

A

Two of each histone proteins H2A, H2B, H3 and H4

30
Q

Describe the second level of condensation of DNA

A

DNA is further coiled into a 30-nm chromatin fibre which gives a solenoid structure.
The chromatin fibre is formed due to the nucleosome-to-nucleosome linkages formed by histone tails and the binding of H1 histone proteins to linker DNA.

31
Q

What are the 2 types of chromatin visible in a cell in interphase under the microscope?

A

Heterochromatin which is densely packed and not actively transcribed. (Chromatin existing as 30-nm chromatin fibre or a higher level of condensation)
Euchromatin which is less densely packed and actively transcribed. (DNA more loosely coiled)

32
Q

Describe the third level of condensation.

A

Non-histone proteins known as scaffold proteins further condense the 30-nm chromatin fibre to form looped domains.
In the chromosomes, the looped domains coil and fold, further condensing the chromosome into metaphase chromosomes

33
Q

What are the 2 important properties of the cell that is contributed by the control of gene expression?

A

Cells respond to the internal and external environment by turning genes on and off.
Cells of a multicellular organism become highly specialised with specific structures and functions because they have different genes of a same genome being expressed.

34
Q

What are the 5 stages where gene expression can be regulated in eukaryotes?

A
  1. Chromatin level
  2. Transcriptional level
  3. Post-transcriptional level
  4. Translational level
  5. Post-translational level
35
Q

What are the 2 ways chromatin packing can be regulated?

A

Histone modification and DNA modification

36
Q

What are the modifications which cause histones to be less tightly bound to the DNA and suggest why this happens?

A

Acetylation of histones, catalysed by histone acetyltransferase.
This neutralises the positively-charged R groups of lysine residues on histone tails.
This reduces the affinity of histone octamers for DNA.
Chromatin becomes less condensed.
Promoter becomes more accessible to RNA polymerase and transcription factors.

37
Q

What are the modifications which cause DNA to become more condensed?

A

DNA methylation, Histone methylation and Histone deacetylation

38
Q

What enzyme catalyses the deacetylation of histones?

A

Histone deacetylases (HDACs)

39
Q

Describe the process of histone methylation.

A

Histones are methylated by histone methyltransferase.
Methylated histones recruit other proteins which keep chromatin tightly packed.
RNA polymerase and transcription factors have less accessibility to genes in methylated regions.
Genes are transcriptionally inactive

40
Q

Describe the process of DNA methylation

A

DNA is covalently modified by the addition of a methyl group to cytosine nucleotides of CpG dinucleotides by DNA methyltransferase after DNA replication.
CpG islands are found at high frequencies within the promoter regions of many genes.
Methylation changes the 3D conformation of DNA which prevents the binding of transcription factors to the promoter.
Methylated DNA also attracts other proteins which recruits histone deacetylase that removes acetyl groups from histones, and restoring the positive charge of lysine residues and the affinity of histone tails for DNA.
DNA thus becomes more compact.

41
Q

What are the 2 differences in transcriptional regulation between prokaryotes and eukaryotes?

A
  1. Eukaryotic genes have individual promoters and associated control elements whereas prokaryotic genes of related functions are organised into operons which are controlled by one promoter and transcribed into a single mRNA molecule.
  2. Repressors play a more prominent roles in prokaryotic regulation whereas activators are more commonly involved in eukaryotic regulation in transcription
42
Q

What is the TATA box?

A

It is the binding site of a general transcription factor, TFIID, and is located within the promoter.

43
Q

What are the 4 ways repressor proteins operate?

A

Repressors compete with activators for the binding to the same regulatory DNA sequences.
Repressors block the assembly of the transcription initiation complex.
Repressors recruit histone deacetylase to the promoter which promotes chromatin condensation.
Repressors recruit histone methyltransferase which methylates histones such that bound proteins maintain genes in transcriptionally inactive form

44
Q

How is simultaneous transcription of related genes promoted?

A

The same specific combination of control elements are associated with each specific gene.

45
Q

Why does post-transcriptional modification not occur in prokaryotes?

A

Transcription and translation occur simultaneously

46
Q

What occurs during modification of RNA?

A

5’ Capping
RNA splicing
3’ Polyadenylation

47
Q

How can a cell carry out alternative splicing?

A

Using different splice sites, different combination of exons are linked together in mRNA to form different mature mRNA molecules from one pre-mRNA molecule.
This gives rise to more than one polypeptide being coded for by a single gene

48
Q

What are the 3 functions of Poly(A) binding proteins?

A

They facilitate the initiation of translation.
They slow down the degradation of the 3’ end of mRNA by exonucleases.
They promote the export of mRNA from the nucleus

49
Q

How do mature mRNA exit from the nucleus?

A

Proteins bound to the 5’ cap and the 3’ poly(A) tail help to direct the mature mRNA to the nuclear pores where it exits the nucleus into the cytoplasm

50
Q

How are mRNAs broken down?

A

Enzymes known as deadenylase shortens the Poly(A) tail of the mRNA, triggering enzymes which remove the 5’ modified guanosine cap.
Once cap is removed, exonucleases rapidly degrade the mRNA

51
Q

How is the translation of all mRNA regulated?

A

Initiation of translation must occur which involves translation initiation factors
These initiation factors can be activated or inactivated, depending on the conditions of the cell whether to carry out translation for all mRNA.

52
Q

What is the role of translation initiation factors?

A

The initiation factors is responsible for the binding of the small ribosomal subunit to the mRNA and the recruitment of aminoacyl-tRNA to the ribosome

53
Q

What are the 2 ways in which translation of specific mRNA is regulated?

A

The binding of the translation repressor proteins to the 5’ UTR region of mRNA which blocks the initiation of translation by preventing the small ribosomal subunit from binding to the ribosomal binding site at the 5’ UTR region.
The initiation of translation is dependent on a longer poly(A) tail of mRNA

54
Q

What are the 3 ways in which gene expression is regulated in the post-translational level?

A

Cleavage, chemical modification of proteins and protein degradation

55
Q

How does cleavage regulate gene expression?

A

Cleavage cuts longer inactive polypeptides into shorter active products

56
Q

How does the chemical modification of proteins regulate gene expression?

A

Chemical modification involves the addition of specific groups which in turn affect the function of the protein

57
Q

How does protein degradation affect gene expression?

A

Protein degradation acts as a control mechanism which involves the selective breakdown of protein. This in turn adjusts the type and amount of protein needed in response to changes in environment.

58
Q

How can proteins be marked for destruction?

A

Enzymes in the cytoplasm attach ubiquitin to the protein marked for destruction. ATP is expended.
Ubiquitainated protein is recognised by proteasomes.
Proteasome degrades the ubiquitinated protein into short peptides. ATP is expended. Proteasomes and ubiquitin are released and recycled

H2 Biology (3 decks)

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