FINAL Unit 2

Question 1

Compare chromosomal structure in bacterial vs.eukaryotic cells.

• chromosome
• cell
• DNA

Answer 1

bacteria:

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

eukaryotic:

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

Question 2

Describe bacterial cell packaging in DNA.

Answer 2

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

Question 3

What do supercoils do?

Answer 3

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

Question 4

Describe eukaryotic cell packaging in DNA.

Answer 4

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

Question 5

What is a chromatid?

Answer 5

one long piece of DNA double helix wrapped up

there are 2 chromatids in 1 chromosome

Question 6

What are histones?

Answer 6

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

Question 7

What is a gene?

Answer 7

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

aka transcriptional unit

Question 8

What is a genome?

Answer 8

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

Question 9

What is a genotype?

Answer 9

genetic make-up of a cell/organism

Question 10

What is a phenotype?

Answer 10

observable characteristics of an organism

Question 11

Discuss the diversity in genome sizes among organisms.

Answer 11

• 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)

Question 12

Is genome size a good predictor of organismal complexity?

Answer 12

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

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

Question 13

Describe DNA macromolecular assembly.

Answer 13

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

Question 14

What is the directionality of nucleotides?

Answer 14

3’ and 5’ based on numbering of ribose sugar

Question 15

What is a nucleotide?

Answer 15

nucleoside + phosphate group

important carrier of chemical energy (ie. ATP)

Question 16

What is a nucleoside?

Answer 16

ribose or deoxyribose sugar + base

adenosine, guanosine, uridine, cytidine, thymidine

Question 17

What are the 3 structures of DNA?

Answer 17

primary: sequence
secondary: double helix
tertiary: chromatin

Question 18

What stabilizes the DNA double helix?

Answer 18

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

Question 19

What is Chargoff’s rule of DNA base pairing?

Answer 19

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

Question 20

Describe the DNA double helix.

Answer 20

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

Question 21

What is mRNA?

Answer 21

transcribed from DNA then translated into polypeptide chain during protein synthesis

UNSTABLE

Question 22

What is tRNA?

Answer 22

folds to form secondary structures, carries amino acids for translation

STABLE

Question 23

What is rRNA?

Answer 23

complexes with proteins to make a ribosome

STABLE

Question 24

What protects RNA from degradation?

Answer 24

tRNA and rRNA functions

Question 25

What is RNases?

Answer 25

enzyme that degrades RNA, they are present everywhere

Question 26

What is a promoter?

Answer 26

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

Question 27

What is a terminator?

Answer 27

sequence that tells RNA POL where to stop binding

Question 28

In which direction are genes read?

Answer 28

from promoter to terminator

Question 29

What are transcription factors?

Answer 29

DNA binding proteins

Question 30

What do DNA binding proteins do?

Answer 30

- 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)

Question 31

What does how strongly DNA binding proteins bind determine?

Answer 31

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

Question 32

Why does the promoter control gene expression?

Answer 32

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

Question 33

What is a consensus sequence?

Answer 33

calculated order of most frequent nucleotides (bases) found at each position in a sequence conserved DNA sequences, model for DNA binding site

Question 34

What is a strong promoter?

Answer 34

closer to consensus sequence will bind transcription factors (and RNA POL) more tightly/strongly and more often

Question 35

What is a weak promoter?

Answer 35

further to consensus sequence will bind transcription factors (and RNA POL) more less tightly (weakly) and more often

Question 36

What interactions are weak vs. strong interactions?

Answer 36

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

Question 37

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

Answer 37

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

Question 38

What is replication?

Answer 38

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

Question 39

What is transcription?

Answer 39

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

Question 40

What is translation?

Answer 40

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

Question 41

Where does T&T occur in prokaryotes?

Answer 41

transcription: cytoplasm translation: cytoplasm

Question 42

Where does T&T occur in eukaryotes?

Answer 42

transcription: nucleus translation: cytoplasm

Question 43

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

Answer 43

additional levels of gene regulation

Question 44

What is the template strand?

Answer 44

3' to 5' strand

Question 45

What is the non-template strand?

Answer 45

opposite to template strand and antiparallel (5' to 3') sometimes called coding strand because it resembles the mRNA that encodes protein

Question 46

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

Answer 46

- all genes have promoter and terminator sequences | - in genes encoding mRNA, coding sequence specifies amino acids of the protein

Question 47

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

Answer 47

transcription and translation occur at the same time in the cytoplasm

Question 48

Describe the process of transcription.

Answer 48

1. initiation 2. elongation 3. termination

Question 49

Describe elongation in the process of transcription.

Answer 49

- 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

Question 50

Describe termination in the process of transcription.

Answer 50

- 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

Question 51

Summary of transcription initiation in bacteria.

Answer 51

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

Question 52

Summary of transcription initiation in eukaryotes.

Answer 52

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

Question 53

Describe transcriptional control of DNA packaging in bacterial cells.

Answer 53

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

Question 54

Describe transcriptional control of DNA packaging in eukaryotic cells.

Answer 54

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

Question 55

What is RNA processing?

Answer 55

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

Question 56

What is a 5' cap?

Answer 56

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

Question 57

Why is 5' cap essential for translation?

Answer 57

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

Question 58

What is polyadenylation?

Answer 58

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

Question 59

Why is polyA tail essential for translation?

Answer 59

important in export of mRNA into cytoplasm for translation

Question 60

What do 5' cap and polyA tail both do?

Answer 60

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

Question 61

What is RNA splicing?

Answer 61

intron removal catalyzed by a complex of RNA and protein called spliceosome exon: region of protein-coding sequence intron: interspersed non-coding regions

Question 62

Describe the process of RNA splicing.

Answer 62

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

Question 63

How can introns/exons be predicted?

Answer 63

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

Question 64

What is alternative splicing?

Answer 64

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

Question 65

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

Answer 65

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

Question 66

What are the features if the genetic code?

Answer 66

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

Question 67

What are the mRNA features important for translation?

Answer 67

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

Question 68

What is an open reading frame?

Answer 68

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

Question 69

What is the function of amino acyl tRNA synthetase enzymes?

Answer 69

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

Question 70

What is the function of tRNA in translation.

Answer 70

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

Question 71

What is the wobble effect?

Answer 71

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"

Question 72

Describe the process of initiation in translation.

Answer 72

- 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

Question 73

Describe the process of elongation in translation.

Answer 73

- 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

Question 74

Describe the process of termination in translation.

Answer 74

- 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