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+ BIOL 112 > FINAL Unit 2 > Flashcards

FINAL Unit 2 Flashcards

1
Q

Compare chromosomal structure in bacterial vs.eukaryotic cells.

  • chromosome
  • cell
  • DNA
A

bacteria:

  • chromosome: circular
  • cell: haploid
  • DNA: double-stranded

eukaryotic:

  • chromosome: linear
  • cell: diploid
  • DNA: double-stranded
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2
Q

Describe bacterial cell packaging in DNA.

A

packaged as a nucleoid composed of many loops

  • DNA helix is underwound: topoisomerase II breaks helix, rotates ends to unwind helix, and seals the break
  • underwinding creates strain on DNA, which is relieved by formation of supercoils (DNA molecule coils on itself) to form the nucleoid
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3
Q

What do supercoils do?

A
  • allow base pairs to form
  • form the nucleoid
  • DNA is negatively supercoiled, loops are bound together by proteins
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4
Q

Describe eukaryotic cell packaging in DNA.

A

each DNA molecules forms a single chromosome —> chromosome condensation

  • in chromosome, DNA is packaged with proteins to form DNA-protein complex called chromatin
  • when the cell divides, chromatin further wounds into chromosome
  • DNA is wound around histones and wound into chromatin
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5
Q

What is a chromatid?

A

one long piece of DNA double helix wrapped up

there are 2 chromatids in 1 chromosome

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6
Q

What are histones?

A
  • proteins that form the core of a nucleosome
  • evolutionarily conserved
  • interact only with double-stranded DNA
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7
Q

What is a gene?

A

sequence of bases in a region pf DNA that can code for a protein (via mRNA) or RNA (tRNA or rRNA)

aka transcriptional unit

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8
Q

What is a genome?

A

all genetic material, usually DNA, transmitted from parent to offspring

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9
Q

What is a genotype?

A

genetic make-up of a cell/organism

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10
Q

What is a phenotype?

A

observable characteristics of an organism

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11
Q

Discuss the diversity in genome sizes among organisms.

A
  • genome size is measured in base pairs
  • prokaryotes tend to have smaller genomes
  • genome sizes are highly variable among species
  • only a portion of human genomes code for proteins (~20,000)
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12
Q

Is genome size a good predictor of organismal complexity?

A

in eukaryotes, there is little correlation between number of genes and genome size

genome size is unrelated to metabolic, developmental, behavioural complexity of organism

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13
Q

Describe DNA macromolecular assembly.

A

monomer: nucleotides with 4 possible bases
polymer: linear nucleic acid
functional structure: double-stranded DNA helix

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14
Q

What is the directionality of nucleotides?

A

3’ and 5’ based on numbering of ribose sugar

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15
Q

What is a nucleotide?

A

nucleoside + phosphate group

important carrier of chemical energy (ie. ATP)

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16
Q

What is a nucleoside?

A

ribose or deoxyribose sugar + base

adenosine, guanosine, uridine, cytidine, thymidine

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17
Q

What are the 3 structures of DNA?

A

primary: sequence
secondary: double helix
tertiary: chromatin

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18
Q

What stabilizes the DNA double helix?

A

non-covalent interactions

  • H bonds between bases
  • base stacking in the same strand: occurs because nonpolar, flat surfaces of the bases tend to group together away from water molecules therefore they stack as tight as possible, and supports H bonds between bases
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19
Q

What is Chargoff’s rule of DNA base pairing?

A 
AT = 2 H bonds
GC = 3 H bonds

purine-pyrimidine: just enough space, same distance between bases on two strands
purine-purine: not enough space
pyrimidine-pyrimidine: too much space

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20
Q

Describe the DNA double helix.

A
  • base pairs cluster inside helix: are energetically favoured due to increased entropy of water
  • sugar-phosphate backbone is hydrophilic
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21
Q

What is mRNA?

A

transcribed from DNA then translated into polypeptide chain during protein synthesis

UNSTABLE

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22
Q

What is tRNA?

A

folds to form secondary structures, carries amino acids for translation

STABLE

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23
Q

What is rRNA?

A

complexes with proteins to make a ribosome

STABLE

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24
Q

What protects RNA from degradation?

A

tRNA and rRNA functions

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25
Q

What is RNases?

A

enzyme that degrades RNA, they are present everywhere

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26
Q

What is a promoter?

A

DNA sequence where regulatory proteins called transcription factors bind to recruit RNA POL to start transcription of one strand (controls gene expression)

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27
Q

What is a terminator?

A

sequence that tells RNA POL where to stop binding

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28
Q

In which direction are genes read?

A

from promoter to terminator

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29
Q

What are transcription factors?

A

DNA binding proteins

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30
Q

What do DNA binding proteins do?

A
  • can bind in either major or minor grooves of DNA
  • recognize specific sequences of base pairs
  • bind by H bonds and other non-covalent interactions (ie. amino acid side chains/R groups interact with bases)
31
Q

What does how strongly DNA binding proteins bind determine?

A

how long it will stay on DNA strand and whether transcription will proceed

32
Q

Why does the promoter control gene expression?

A

because different promoters have different sequences but still can be recognized by transcription factors

33
Q

What is a consensus sequence?

A

calculated order of most frequent nucleotides (bases) found at each position in a sequence

conserved DNA sequences, model for DNA binding site

34
Q

What is a strong promoter?

A

closer to consensus sequence

will bind transcription factors (and RNA POL) more tightly/strongly and more often

35
Q

What is a weak promoter?

A

further to consensus sequence

will bind transcription factors (and RNA POL) more less tightly (weakly) and more often

36
Q

What interactions are weak vs. strong interactions?

A

non-covalent interactions between R groups on proteins or bases on DNA

37
Q

What is the biological information flow from DNA to proteins in cells.

A

information in cell is from DNA to RNA (transcription) to protein (translation)

38
Q

What is replication?

A

two strands of parental double helix unwind and separate into single strands that serve as template for synthesis of daughter strands

39
Q

What is transcription?

A

genetic info in molecule of DNA is used as template for RNA synthesis

40
Q

What is translation?

A

RNA is used as a code for sequence of amino acids in a protein

41
Q

Where does T&T occur in prokaryotes?

A

transcription: cytoplasm
translation: cytoplasm

42
Q

Where does T&T occur in eukaryotes?

A

transcription: nucleus
translation: cytoplasm

43
Q

What does the separation of T&T in eukaryotes allow?

A

additional levels of gene regulation

44
Q

What is the template strand?

A

3’ to 5’ strand

45
Q

What is the non-template strand?

A

opposite to template strand and antiparallel (5’ to 3’)

sometimes called coding strand because it resembles the mRNA that encodes protein

46
Q

What are the common features of transcription units in bacteria and eukaryotes?

A
  • all genes have promoter and terminator sequences

- in genes encoding mRNA, coding sequence specifies amino acids of the protein

47
Q

What are the different features of transcription units in bacteria and eukaryotes?

A

transcription and translation occur at the same time in the cytoplasm

48
Q

Describe the process of transcription.

A
  1. initiation
  2. elongation
  3. termination
49
Q

Describe elongation in the process of transcription.

A
  • transcription starts at position called +1 site/transcription start site (where RNA POL transcribes the first base/nucleotide, then reads template) downstream of promoter
  • RNA POL transcribes DNA and polymerizes RNA: separates strands of DNA and catalyzes addition of new bases
  • incoming ribonucleotides are accepted if they correctly base pair with template
  • 3’ OH of growing strand attacks high energy phosphate bond of incoming ribonucleotide, providing the energy to drive the reaction
50
Q

Describe termination in the process of transcription.

A
  • transcription stops after RNA POL passes through the terminator, releasing the mRNA transcript
  • part of termination sequence is copied into 3’ UTR of region of RNA and makes a hairpin loop that helps stop transcription
51
Q

Summary of transcription initiation in bacteria.

A
  1. initiation of transcription occurs at promoter sequence
  2. sigma factor protein binds to promoter (-10 and -35 boxes)
  3. this helps recruit RNA POL to bind and promote start of transcription
  4. RNA POL bound to DNA is oriented such that catalytic site (catalyzes phosphodiester bond) is about 10 bases away from -10 box
  5. first base that serves as template to transcribe into RNA is called +1 site
52
Q

Summary of transcription initiation in eukaryotes.

A
  1. initiation of transcription occurs at promoter sequence with TATA box
  2. general transcription complex are proteins (factors) that assemble at protein (ie. TBP)
  3. these help RNA POL to bind and promote transcription (basal transcription complex)
  4. regulatory transcription factors (ie. activators, repressors) bind to DNA sequences and regulate transcription
  5. first base that serves as template to transcribe into RNA is called transcription start site
53
Q

Describe transcriptional control of DNA packaging in bacterial cells.

A

promoters are unpackaged and accessible to RNA POL, therefore the default state is always on

54
Q

Describe transcriptional control of DNA packaging in eukaryotic cells.

A

DNA is packaged tightly and must be unpackaged (decondensed) for RNA POL to access DNA and start transcription

eukaryotic DNA is packaged into chromatin:

  • condensed chromatin = transcription OFF
  • decondensed chromatin = transcription ON
55
Q

What is RNA processing?

A

process between transcription and translation, that only occurs in eukaryotes: DNA transcribed a PRIMARY TRANSCRIPT (pre-mRNA) and now needs to be processed into mRNA

5’ cap, polyadenylation, RNA splicing

56
Q

What is a 5’ cap?

A

special nucleotide attached to 5’ end of primary transcript in an unusual linkage of a bridge composed of three phosphates

57
Q

Why is 5’ cap essential for translation?

A

because in eukaryotes, ribosome recognizes an mRNA by its 5’ cap, therefore without the cap, ribosome would not attach to mRNA and translation would not occur

58
Q

What is polyadenylation?

A

addition of poly(A) tail to the 3’ end

59
Q

Why is polyA tail essential for translation?

A

important in export of mRNA into cytoplasm for translation

60
Q

What do 5’ cap and polyA tail both do?

A

help stabilize RNA transcript until it is translated in the cytoplasm and protect the two ends of the transcript

61
Q

What is RNA splicing?

A

intron removal catalyzed by a complex of RNA and protein called spliceosome

exon: region of protein-coding sequence
intron: interspersed non-coding regions

62
Q

Describe the process of RNA splicing.

A
  1. spliceosome brings a site within the intron close to 5’ splice site and attacks
  2. cleaved 5’ splice site attacks 3’ splice site
  3. cleaved end of intron connects back on itself, forming a loop and tail called a lariat
  4. lariat quickly breaks down into individual nucleotides
  5. spliced exons are adjacent in processed RNA
63
Q

How can introns/exons be predicted?

A

by comparing genomic DNA to observed mRNA because the RNA transcription is short-lived

64
Q

What is alternative splicing?

A

primary transcript from same gene can be spliced in different ways to yield different mRNAs and therefore different proteins

65
Q

What are the RNAs involved in translation and what are their functions?

A

charged tRNA: carries an amino acid
rRNA: combines with proteins to form small and large ribosomal subunits
mRNA: from transcription of gene, used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain

66
Q

What are the features if the genetic code?

A
  1. universal: same genetic doe applies to most organisms (64 codons, 3 codons for ‘stop’, 61 for amino acids)
  2. redundant: more than one codon codes for an amino acid, results almost exclusively from third codon position
  3. non-overlapping: ribosome ensures the nucleotide sequence of mRNA is read in successive, non-overlapping groups of three nucleotides called codons
67
Q

What are the mRNA features important for translation?

A

final, mature RNA transcription needs to have:

  • sequence where ribosome will bind: bacteria - Shine-Dalgaro sequence or RBS, and eukaryotes - RBS is the 5’ cap
  • start codon: first amino acid synthesized
  • stop codon: stops translation, does not code for amino acid
68
Q

What is an open reading frame?

A

sequence of bases from and including start codon to stop codon

  • mRNA codons are read starting at AUG, not first base of mRNA (transcription start site/+1 site)
  • usually only one reading frame encodes for a functional protein
69
Q

What is the function of amino acyl tRNA synthetase enzymes?

A

they connect specific amino acids to specific tRNA molecules

  • directly responsible for actually translating codon sequence in nucleic acid to a specific amino acid in polypeptide chain
  • each amino acyl tRNA synthetase binds to one uncharged tRNA and its amino acid
  • specific enzyme for each amino acid
  • enzyme attaches amino acid to 3’ end of tRNA
70
Q

What is the function of tRNA in translation.

A

tRNA is sequence of RNA bases that form a secondary structure (ie. hairpin loop)

  • bind to codons on mRNA
  • deliver amino acids
  • interact with mRNA by non-covalent interactions (ie. H bonds)
  • have an anti-codon sequence complementary to codon on mRNA
71
Q

What is the wobble effect?

A

last base (3’ end) can vary in a codon

  • 61 possible codons; without wobble, a cell would need 61 tRNAs
  • most species can have ~45 tRNAs and the tRNAs can have modified bases in their 5’ position to permit binding to more than one nucleotide
  • non-standard base pairing at 3rd base of codon allows a single tRNA to bind to multiple codons
  • structure of ribosome also permits “wobble”
72
Q

Describe the process of initiation in translation.

A
  • initiation factors recruit small ribosomal subunit and tRNAmet and scan the mRNA for an AUG codon
  • initiation complex then moves along mRNA until it encounters the first AUG
  • large ribosomal subunit joins, initiation factors are released, tRNA complementary to next codon binds to A site
  • a reaction transfer the met to the amino acid on tRNA in A site, forming a peptide bond

bacteria: RBS (Shine-Dalgaro sequence) is in 5’ UTR upstream of start codon
eukaryotes: ribosome binds to 5’ cap and scans 5’ UTR for start codon

73
Q

Describe the process of elongation in translation.

A
  • ribosome moves down one codon, which puts the tRNA carrying the polypeptide into the P site and the now uncharged tRNA into the E site where it’s ejected
  • new tRNA complementary to next codon binds to A site
  • polypeptide transfers to the amino acid on the tRNA in the A site
  • polypeptide is elongated by repeating these steps until it reaches stop codon

ribosome movement along mRNA and formation of peptide bonds require energy, which is obtained with the help of elongation factors that are bound to GTP molecules and break their high-energy bonds to provide energy for elongation

74
Q

Describe the process of termination in translation.

A
  • when ribosome encounters stop codon, termination occurs because stop codons don’t have corresponding tRNA molecules
  • release factor protein binds to A site and causes the bond connecting polypeptide to tRNA to break, creating carboxyl terminus of polypeptide and completing the chain
  • polypeptide is released and the small and large ribosomal subunits dissociate from mRNA and each other

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