Quiz 1 PPT Notes

Question 1

Why clone and make GFP-fusion proteins when antibodies localize the protein the cell?

May not …
May want to look at …, … cells

Answer 1

have antibodies;

dynamic; living

Question 2

Using antibodies gives us great data on … But, we need to make antibodies (takes …, ….)

Answer 2

localization;
time;
variable recognition

Question 3

what gives cells their shape? the cytoskeleton

• cellular “skeleton” that gives the cell structure and shape
• serves as tracks for … proteins
• participates in … and …
• drives …
• also has roles in …
• cytoskeletal proteins are …

Answer 3

motor;
mitosis; cytokinesis; 
cell migration; 
cell adhesion; 
highly conserved

Question 4

Three cytoskeletal systems/elements:
…
…
…

Answer 4

microtubules;
intermediate filaments;
actin filaments

Question 5

stages of first 75 hr of sea urchin embryo. notice many changes:
1. number of … –> …
2. change in … shape, change in … shape
3. … of cells
(all things that rely on the …)

Answer 5

cells; cell division;
embryo; cell;
movement;
cytoskeleton

Question 6

DNA nucleotide =

… + … (…) + …

Answer 6

phosphate group;
sugar; deoxyribose;
base

Question 7

DNA:

phosphate backbone = … joins …

Answer 7

5’ phosphate;

3’ OH

Question 8

DNA is: 
double stranded 
held together by H bonds 
... strands 
double helix 
all of these contribute to increased stability, which is exactly what we want for something that is responsible for genetic info

Answer 8

antiparallel

Question 9

how do we manipulate DNA?

• … it - …
• … it - …
• … it

Answer 9

amplify; PCR;
digest; restriction enzymes;
sequence it

Question 10

how do we manipulate DNA?

• … it - … into …
• … it - ….
• … it - ….

Answer 10

clone; ligate; vectors;
label; hybridization;
analyze; agarose gel electrophoresis

Question 11

nucleotide entry tells us different sequence features:

1. …
2. ….
3. … features
4. … sequence
5. … sequence

Answer 11

source; 
gene length; 
coding sequence; 
protein; 
mRNA

Question 12

Determine the … by finding the start and stop codons by eye or by using a translation tool

Answer 12

open reading frame (ORF)

Question 13

the absorbance for a molar concentration of a substance with a path length of / cm determined at a specific … Its value is obtained from the equation …

Answer 13

wavelength;

epsilon = A/cl

Question 14

beer lambert equation: …

Answer 14

A = epsilon * b *c

Question 15

beer lambert equation: 
A = epsilon * b * c 
A: ... 
epsilon: ... 
b: ... 
c: ...

Answer 15

absorbance;
molar absorption coefficient;
path length;
concentration

Question 16

In DNA, … can be deaminated and become uracil. There are enzymes that recognize the G-U mismatched base pairs, excise out the uracil, and replace with a …, thereby maintaining the accuracy of the genetic material

Answer 16

cytosine;

cytosine

Question 17

rRNA: … RNA, is made in the … of the …, and transported to the cytoplasm where they will form ribosomes

Answer 17

ribosomal;
nucleoli;
nucleus

Question 18

tRNA: … RNA, base pairs with the codon sequence on mRNA and brings in the appropriate amino acid during translation

snRNA: …, reside in the …, participate in …

Answer 18

transfer;

small nuclear RNAs; nucleus; splicing

Question 19

snoRNA: …, reside in … and participate in …

Answer 19

small nucleolar RNAs;
nucleoli;
editing rRNA

Question 20

… and … RNAs act at the level of … regulation, controlling the translation of the mRNA into protein

Answer 20

microRNA;
silencing;
posttranscriptional

Question 21

other species of small RNAs are involved in regulation of … and …

Answer 21

transcription;

translation

Question 22

how do we isolate RNA:

… cells –> inhibit … activity –> … –> recover intact RNA

Answer 22

lyse;
ribonuclease;
remove proteins

Question 23

what can be done with isolated RNA:

1. …. (aka …)
2. …
3. …
4. … and …
5. …
6. ….

Answer 23

northern analysis; northern blots; 
nuclease protection assay; 
in vitro translation; 
cDNA library construction; screening; 
RT-PCR; 
qRT-PCR

Question 24

Northern analysis is a method used to determine:
… of an mRNA
… of transcript
presence of …

Answer 24

abundance;
size;
alternative splicing

Question 25

cDNA library:

• a collection of all the … at that time in that tissue/cell
• isolated mRNA is reverse transcribed into cDNA
• the cDNA is digested with restriction enzymes and …
• the library can be amplified in … and screened for specific sequences

Answer 25

expressed gene sequences;
ligated into vectors;
bacteria;

Question 26

Going from RNA to DNA occurs in:
…
…
…

Answer 26

retroviruses;
retroposons;
telomeres

Question 27

Reverse transcriptase is a …

Answer 27

RNA-dependent DNA polymerase

Question 28

for reverse transcription we need: 
... 
... 
... 
....

Answer 28

RNA template;
primer;
reverse transcriptase;
nucleotides

Question 29

+RT is a …

Answer 29

positive control

Question 30

for - RT: since no RT in reaction, no … can be made. Therefore, any product in PCR is due to … contamination

For -RNA, since there’s no RNA in the reaction, nothing is there to provide a … Therefore, any product in PCR is due to one of the reaction components being contaminated

Answer 30

cDNA;
gDNA;
template

Question 31

forward primer has … and is the …

reverse primer for actin has … To form reverse primer … and …

Answer 31

ATG; direct sequence;

TTA; reverse; complement;

Question 32

Location of primer depends on …, aka what you want to …

Answer 32

what you want to do;

copy