Exam 4 Concepts Lecture 23

Front 1

Are machinery involved in replicating and expressing archaea genomes more like bacteria or eukaryotes?

Back 1

Eukaryotes

Front 2

What does DNA polymerse catalyze?

Back 2

Synthesis of complementary strands of DNA

Front 3

Do bacteria have multiple or single chromosomes?

Back 3

Single

Front 4

Do humans have multiple or single chromosomes?

Back 4

Multiple

Front 5

Are eukaryotic chromosomes ring shaped or linear?

Back 5

Linear

Front 6

How are eukaryotic chromosomes wound?

Back 6

Around histone proteins

Front 7

How is DNA replication initiated in Eukaryotic cells?

Back 7

Multiple origins of replication (so replication starts at multiple sites, and eventually the chromosome will meet up) which are marked with an ORC. ORC will recruit other proteins to the origin to form the pre-replicative complex, then will recruit the DNA replication enzymes, and then the fun starts.

Front 8

What is ORC and what does ORC do?

Back 8

ORC is a complex of proteins which will recruit other proteins and form a pre-replicative complex. Then it will recruit the DNA replication enzymes and start replication.

Front 9

How many polymerases are responsible for DNA replication in Eukaryotes? What are they? What do they do?

Back 9

3 polymerases. Alpha, epsilon and Delta. Alpha will lay do the RNA/DNA hybrid starting point. Epsilon will synthesize the leading strand. Delta synthesizes the lagging strand.

Front 10

What are the problems we see with linear chromosomes?

Back 10

Their ends can be digested with DNases. The ends can fuse with other DNA molecules. Normal replication prevents the bits of missing DNA in the Okazaki fragments, so each round of replication shortens the DNA.

Front 11

How does the Eukaryotic DNA protect against linear DNA challenges?

Back 11

The cell must contain telomeres and telomerases.

Front 12

Where are telomeres located and what do they do?

Back 12

They are protein/DNA hybrids located by the G-tail at the ends of DNA, and they contain tandem repeats to protect against any DNA end problems.

Front 13

How does Telomerase work?

Back 13

It has an internal RNA template that partially matches the G-tail sequence, so it attaches on to it. It then begins at the 3’OH of the G tail to begin synthesis and the internal RNA sequence is used as a template for DNA synthesis.

Front 14

What is the G-Tail?

Back 14

DNA ends with the base G. This is the G tail. It partially binds to telomerase and is extended (multiple times) to make the tandem repeats called telomeres.

Front 15

How much do G tails lengthen?

Back 15

Enough for a DNA polymerase to fully fit on it so that the length of the chromosome is maintained.

Front 16

Are archaea chromosomes more similar to Eukaryotes or Bacteria?

Back 16

Bacteria in size and shape. However, there are histones located in archaea chromosomes, and the DNA replication is a hybrid between them.

Front 17

How many origins of replication do archaea have?

Back 17

Typically 1…. Although some can hand more.

Front 18

On a basic level, how does transcription occur in all organisms?

Back 18

RNA is synthesized by an RNA polymerase via DNA. RNA is produced in the 5’3’ direction. RNA is complementary to template DNA. Promoter is at the start of a gene, it has a binding site for the RNA poly, and it orients the poly.

Front 19

What is the Bacterial RNA polymerase?

Back 19

Holoenzyme that recognizes the genes on the DNA and synthesizes the mRNA.

Front 20

Overview of Eukaryotic transcription?

Back 20

Occurs in the nucleus. DNA to mRNA. mRNA is edited. mRNA is moved into the cytoplasm

Front 21

What are the 3 types of RNA polymerases in Eukaryotes? What do they do?

Back 21

1, 2, 3. 1: rRNA synth. 2: mRNA synth. 3: tRNA synth.

Front 22

How many bacterial core RNA polymerase subunits are in eukaryotic polymerases?

Back 22

5

Front 23

What elements define the core promoter in Eukaryotes?

Back 23

TATA box, BRE, Inr, DPE.

Front 24

How does RNA poly 2 recognize the promoter?

Back 24

1 or more elements that are in the core promoter will be recognized by RNA poly 2

Front 25

What differs between promoter structure in Archaea and Eukaryotic cells?

Back 25

No DPE in archaea

Front 26

Do Eukaryotes have sigma factors?

Back 26

No

Front 27

What do Eukaryotes have instead of sigma factors, and what do they do?

Back 27

Transcription factors. They bind to the DNA and line up the polymerase correctly.

Front 28

Does mRNA processing occur in all 3 domains in life?

Back 28

No. Only in Eukaryotes.

Front 29

How must pre-mRNA be modified?

Back 29

5’Cap of 7-methylguanosine is added, introns are removed and the excons are spliced together, poly-A tail is added

Front 30

What is the 5’Cap?

Back 30

It aids in recognition of mRNA by ribosomes.

Front 31

Why are introns removed?

Back 31

It allows a single gene to code for more than one final protein.

Front 32

Is intron/exon splicing found in archaea or bacteria?

Back 32

Nope

Front 33

What is the Poly-A tail?

Back 33

It protects the mRNA from degradation and signal it’s ready for transport to the cytoplasm

Front 34

How is transcription in Archaea similar to transcription in Eukaryotes?

Back 34

The RNA polymerases are similar, archaea also has promoters for binding the RNA polymerase, and in SOME archaea genes there are introns

Front 35

How is transcription in Arcahea similar to transcription in Bacteria?

Back 35

Transcription occurs in the cytoplasm, mRNA is polycistronic, and introns are rare and if they’re present they’re excised differently

Front 36

How does translation work in Eukaryotes?

Back 36

Initiation factors bind to the 5’ cap, PABPs bind to the 3’ poly-A tail, and the Cap/Tail protein complexes form a bridge activating the mRNA molecule. Initatior tRNA interacts with the 40S ribosomal subunit to make a 43S subunit, the 43 S binds to the activated mRNA, and the 43S unit scans until it finds the mRNA, and the 60S subunit is recruited to begin elongation steps.

Front 37

What are polysomes and how do they affect Eukaryotic translation?

Back 37

They are multiple ribosomes translating the same mRNA molecule.

Front 38

Are transcription and translation coupled in Bacteria? Eukaryotes? Archaea?

Back 38

Yes. No. Yes.

Front 39

How does Archaea translation differ from bacteria?

Back 39

There is no N-formylmethionine. The first codon is methionine. There are polycistronic transcripts. Each coding region is translated into separate proteins.

Front 40

What are the thee levels cellular regulation can take place in in All domains of life?

Back 40

Transcription, translation, posttranslation

Front 41

How is transcription regulated?

Back 41

Activators binding to Upstream activating sequences and enhancers, and repressors binding to Repressor binding sites and silencers. Also (in eukaryotes) histone acetylation

Front 42

What is histone acetylation?

Back 42

When the DNA in eykaryotes is wound around the histones, the proteins can be covalently modded by addition/removal of acetyl, methyl or phosphoryl groups.

Front 43

How is gene expression regulated in Eukaryotes?

Back 43

Antisense RNA , Riboswtiches, sRNA molecules that regulate through alternative splicing modulation. miRNA and siRNA

Front 44

How do siRNA’s work to regulate gene expression?

Back 44

It forms a complex with proteins, it prevents translation initiation and elongation and can degrade mRNAs

Front 45

What are the 6 levels of gene regulation?

Back 45

Transcription initiation, splicing efficiency, mRNA trafficking, mRNA stability and degradation, translation rate, post translational modification.

Front 46

How is transcription regulated in Archaea?

Back 46

Some regulatory proteins bind to operators, others bind to TATA box in the promoter preventing binding of transcription factors. Some archaea use forms of transcription factors that differ from their eukaryotic counterparts. And for the archaea that have histones, they can be modded by the histones.