Lecture 7 - Exam 1

Question 1

In the lipid bilayer, how can molecules move?

Answer 1

Freely, rotating and moving laterally

Question 2

Who is associated with the fluid mosaic model?

Answer 2

Seymour Singer & Garth Nicolson

Question 3

How do gases, hydrophobic and small uncharged molecules diffuse through a phospholipid bilayer?

Answer 3

Freely

Question 4

How do larger molecules, like glucose and amino acids, and ions diffuse through the bilayer?

Answer 4

They don’t, the bilayer is impermeable to these.

Question 5

What do channel proteins do?

Answer 5

Form open pores through which molecules of the appropriate size (e.g. ions) can cross the membrane down their concentration or electrochemical gradient.

Question 6

What do carrier proteins do?

Answer 6

Selectively bind the small molecule to be transported and then undergo a conformational change to release the molecule on the other side of the membrane.

Question 7

Model of active transport:

Answer 7

Energy derived from the hydrolysis of ATP is used to transport H+ against the electrochemical gradient (from low to high H+ concentration).
Binding of H+ is accompanied by phosphorylation of the carrier protein, which induces a conformational change that drives H+ transport against the electrochemical gradient.
Release of H+ and hydrolysis of the bound phosphate group then restores the carrier to its original conformation.

Question 8

What are membrane rafts?

Answer 8

Dynamic regions of the plasma membrane enriched in cholesterol, sphingomyelin (not so kinky), glycolipids (sticky), GPI-anchored proteins and some membrane proteins (protein-protein interactions)
- Important for signaling
- Important as sites for entry and egress of viruses
- Markers for clathrin-mediated endocytosis are not present in rafts.

Question 9

How did we extend the studies on simple model organisms to eukaryotic cells? The main problem in the 1970s was how were we supposed to isolate individual genes so that we could study them?

Answer 9

We figures out recombinant DNA technologies.
Enzymes that cleave DNA at specific sequences.
It was identified in bacteria & many of these can cleave DNA at over 100 specific recognition sites.

Question 10

DNA has a net ____ charge.

Answer 10

Negative

Question 11

EcoRI digestion will cleave lambda DNA at how many sites?

Answer 11

5, yielding 6 DNA fragments. Then separated by electrophoresis… the DNA migrates toward the positive electrode, with smaller molecules flowing more rapidly through the gel.
6 cutters will cleave DNA with a statistical frequency of once per 4096 bps.

Question 12

Describe the generation of a recombinant DNA molecule.

Answer 12

A fragment of human DNA is inserted into a plasmid DNA vector.
The resulting recombinant molecule is then introduced into E. coli, where it replicated along with the bacteria to yield a population of bacteria carrying plasmids with the human DNA insert.

Question 13

Genomes of most eukaryotes are ______ and more ______ than prokaryotes.

Answer 13

larger ; complex

Question 14

The genome size of many eukaryotes does/or does not correlate to genomic complexity.

Answer 14

Does not

Question 15

The ___________ in eukaryotic genomes is not simply related to either genome size or genomic complexity.

Answer 15

number of genes

Question 16

The number of genes in eukaryotic genomes is not simply related to either genome size or genomic complexity. So, what’s up?

Answer 16

Genomes of most eukaryotic cells contain protein-coding sequences as well as large amounts of DNA that does not code for proteins. –> we call this noncoding DNA

Question 17

Does noncoding DNA play any roles in our cells?

Answer 17

Many noncoding sequences play critical roles in our cells.

Question 18

Most eukaryotic genes contain segments of _____________ interrupted by ___________.

Answer 18

coding sequences (exons) ; noncoding sequences (introns)

Question 19

Both exons and introns are transcribed to do what?

Answer 19

Yield a long primary RNA transcript.
The introns are then removed by splicing to form the mature mRNA.

Question 20

An electron micrograph of a between hexon mRNA and a portion of adenovirus DNA encoding hexon is associated with who?

Answer 20

Phillip Sharp and Richard Roberts

Question 21

How many exons does the gene encoding the adenovirus hexon consist of?

Answer 21

Four exons, interrupted by three introns

Question 22

A nested gene is contained where?

Answer 22

Within an intron of a larger host gene

Question 23

Transcription yields primary transcripts of _____?

Answer 23

both the host and nested genes, which are then spliced to yield host gene and nested gene mRNA.

Question 24

Transcriptional regulatory elements are commonly called…?

Answer 24

cis-regulatory elements

Question 25

All cells contain the same genes, but only a subset of genes is expressed in each cell. How?

Answer 25

Noncoding regulatory elements control transcription of mRNAs in each cell.
Regulatory elements that control transcription of a gene may be located up to hundreds of kilobases aways from the gene, immediately upstream of the gene, within noncoding exons or within introns.
Most regulatory elements within genes are in the introns or in the 5’ untranslated region encoded by the first exon.

Question 26

What is alternative splicing?

Answer 26

Allows the exons to be joined, in different combinations, resulting in the formation of three distinct mRNAs and proteins from the single primary transcript.

Question 27

____% of the human genome is transcribed. Much more than protein coding genes.

Answer 27

75

Question 28

1) Noncoding micro RNAs (miRNAs): miRNA genes are transcribed to do what?
2) Pre-miRNAs are sequentially cleaved by what, and yields what?
3) miRNAs will associate with what?
4) The miRNA then targets what, and leads to what?

Answer 28

1) Yield primary transcripts (pri-miRNAs) that contain hairpin structures.
2) Pre-miRNAs are sequentially cleaved by the nucleases Drosha and Dicer to yield double-stranded miRNAs of approx. 22 nucleotides.
3) Associates with the RISC complex in which the two strands of the miRNA are unwound.
4) The miRNA then targets RISC to the 3’ untranslated region of an mRNA, leading to repression of translation and mRNA degradation.

Question 29

Long noncoding RNAs (IncRNA): What are they?

Answer 29

IncRNAs are noncoding RNAs that are greater than 200 base pairs

Question 30

There are more than ______ IncRNAs in the human genomes. That’s more than the number of protein coding genes!!

Answer 30

50,000

Question 31

Importantly, the expression of IncRNAs is?

Answer 31

Mostly tissue specific. This suggests that many have specific functions depending on cell type.

Question 32

An inactive X chromosome is coated and inactivated by…?

Answer 32

the IncRNA Xist.

Question 33

What are simple sequence repeats?

Answer 33

Complex eukaryotic genomes contain highly repeated DNA sequences, which can be present in hundreds of thousands of copies per genome.

Question 34

What are the two important repetitive DNA sequences?
These are examples of what?

Answer 34

Short interspersed elements (SINES) and long interspersed elements (LINES). Examples of transposable elements.

Question 35

SINES and LINES are ___________.

Answer 35

Retrotransposons, meaning that their transposition is mediated by reverse transcription.

Question 36

What does SINES encode?

Answer 36

SINES encode reverse transcriptase and an integrase-like molecule.

Question 37

A 3rd class:
A 4th class:

Answer 37

retrovirus-like elements
DNA transposons

Question 38

What is the example of an insertion of a transposable element?

Answer 38

Gave moths elevated gene expression and darker pigmentation.

Question 39

What about repetitive sequences has played a major role in evolution?

Answer 39

Recombination between repetitive sequences in different locations of the genome can lead to gene rearrangements, which has played a major role.