Biochemistry Final Exam

Front 1

What is the central dogma of molecular biology?

Back 1

DNA stores information, which determines RNA sequence, which determines protein sequence/structure and properties.

DNA --> (transcription) RNA --> (translation) Protein

Front 2

What are the major bases for DNA and RNA

Back 2

DNA - adenine, cytosine, guanine, thymine

RNA - same, except: uracil instead of thymine

Front 3

What is the difference between a nucleoside and a nucleotide?

Back 3

Nucleoside - is a nucleobase glycosylated with either form of pentose sugar (ribose or deoxyribose)
- can form either a ribonucleoside or a deoxyribonucleoside

Nucleotide - is a nucleoside with a phosphate group attached at the 5' end
- any hydroxyl group on the sugar can be phosphorylated, but never the base

Front 4

A phosphodiester bond between two nucleotides goes from which terminus to which?

Back 4

3' --> 5'

therefore: A new nucleotide is always added to the 3' terminus, or in other words, the 3' hydroxyl position on the sugar

Front 5

What are the nucleoside name for the following?

- Adenine
-Cytosine
-Guanine
-Thymine
-Uracil

Back 5

-Adenosine
-Cystidine
-Guanidine
-Thymidine
(only DNA, thus interchanged with deoxythymidine)
-Uridine (only RNA)

(For those found in DNA add "deoxy" in front of word - ie: deoxyadenosine)

Front 6

The perpendicular bar represents what in the shorthand notations for RNA and/or DNA?

Back 6

It represents the sugar moiety..aka either ribose or deoxyribose

Front 7

When writing shorthand notations for RNA and/or DNA, what is found at the bottom of the perpendicular bar? At the top of the bar?

Back 7

-The 5' terminus is at the bottom of the perpendicular bar

- The base are shown through their initials at the top of the perpendicular bar

Front 8

Which terminus does the phosphate group add to on a nucleoside?

Back 8

The 5' terminus

Front 9

Which terminus does the base add to on a sugar?

Back 9

1' terminus of the sugar (could be ribose or deoxyribose)

Front 10

What's the difference between a ribose and deoxyribose? (be specific)

Back 10

Ribose is found in RNA
Deoxy is found in DNA

Main difference - ribose has a OH group at the 2' position of the sugar moeity

Deoxyribose does not have a OH group at the 2' position (hence it's De-oxy)

Front 11

What kind of bonds are between two bases in DNA?

Back 11

Hydrogen bonds

Front 12

How many bonds are between C and G? A and T? A and U?

Back 12

C and G = 3 H2 bonds (strong)
A and T - 2 H2 bonds (relatively weak)

A and U = You can't have one because RNA is single stranded


HAHAHAHHAHA!

Front 13

What region of the DNA is hydrophobic? Hydrophilic?

Back 13

The interior core of DNA is hydrophobic (where the bases are)

Sugar-phosphate backbone (exterior part) is hydrophilic

Front 14

What is the function of H2 bonds in DNA?

Back 14

According to his NOTES:
-they are the "glue" and "zipper" allowing for two DNA strands to stick together

According to Book:
H2 bonds are NOT the glue, instead they provide directionality for base stacking and indirectly give stability to double helix.

Front 15

What other interactions allow for double helix formation?

Back 15

Hydrophobic interactions between bases and van der waals forces (4-15 kcal/mol)

Note: these are stronger than H2 bonds (2-3 kcal/mol)

Front 16

True or False:

Anions are necessary for stabalizing the backbone of DNA

Back 16

False: Divalent cations are necessary like Mg+2

Front 17

What can lead to denaturation of DNA?

Back 17

- High temperature
-pH above 11.3 (alkaline denaturation)
-Low pH

Front 18

What four factors could indicate that DNA denaturation has occured?

Back 18

- Increase in buoyant density
-High UV absorption
-Less viscosity
-Change in ability to rotate polarized light

Front 19

There is __________ (increased/decreased) UV absorption in DNA when it is denatured

Back 19

increased!!


Why: Purines and pyramidines can absorb UV light, when denatured those are exposed

Front 20

There is __________ (increases/decreased) UV absorption in DNA when it is double helix

Back 20

Decreased!!

Why: Purines and pyramidines can absorb UV light, when in double helix they are not exposed,

Front 21

If you are in a lab, and your DNA solution absorbs light at 260 nm, what can you deduce about the structure of the DNA?

Back 21

It's denatured (bc it's absorbs UV light)

Front 22

True or False:
The higher the G-C content in DNA, the higher the Tm

Back 22

True!

Tm: stands for either melting temp or midpoint temp. DNA strands are NOT completely separated at this temperature.

Front 23

True or False:
Renaturation is the same as reannealing

Back 23

True

Front 24

True or False:
The first step during reannealing is fast

Back 24

False!!

It's slow, but after formation of "nucleation site," double helix rapidly forms

Front 25

What is a nucleation site?

Back 25

The formation of a 3-5 bp during renaturation

Front 26

What is hybridization?

Back 26

technique based on association of complimentary polynucleotide strands.

It's been developed for detection and quantitation of specific sequences of target nucleic acids

Front 27

True or False:
Southern Blot detects DNA with DNA probe

Back 27

True

Front 28

True or False:
Northern Blot detects DNA with DNA probe

Back 28

False

Detects RNA with RNA probe

Front 29

A-DNA can be found under ______ humidity (high/low) and __________ salt concentrations (high/low)

Back 29

Low
High

Front 30

B-DNA can be found under ______ humidity (high/low) and __________ salt concentrations (high/low)

Back 30

High
Low

That's us - B-DNA is native DNA, and our native is Florida (high humidity)

Front 31

What form of DNA is left - handed?

Back 31

Z-DNA

Front 32

Of the DNA sequence motifs, which ones are on the same strand?

Back 32

- Mirror repeats (palindromes)
- Direct repeats

Inverted repeats - are on separate strands

Front 33

What type of motif is found in a cruciform structure?

Back 33

An inverted repeat

Front 34

Slipped mispaired DNA (SMP-DNA) is formed as a result of which motif?

Back 34

Direct repeats

Front 35

Slipped mispaired DNA (SMP-DNA) can cause what type of problem?

Back 35

Frameshift mutations that result in either base addition or base deletion.

-deletions or duplication of DNA segements that can occur during DNA replication between direct repeats

Reference page in book - Pg 46

Front 36

What are examples of Hogsteen triple helixes?

Back 36

T A:T
C+ G:C

Front 37

True or False
The sugar-phosphate backbone is positively charged

Back 37

False!

It's negatively charged

Front 38

Slipped mispaired DNA is _____ (is/is not) found in vivo, while H-DNA _____ (is/is not) found in vivo

Back 38

-is not

is

Front 39

H-DNA is formed through _______ repeats, which form triple helixes ___________ (intramolecularly/extramolecularly)

Back 39

-mirror repeats
-intramolecular

Front 40

True or False:
Plasmids are considered extrachromosomal DNA in bacteria

Back 40

True

They are completely separate from chromosomal DNA; have their own replication cycle

Front 41

True or False:
The Endoplasmic reticulum has its own DNA

Back 41

False:
Mitochondria and chloroplasts are the only organelles that do

Front 42

Underwound circular DNA is ____________ charged and ________ handed

Back 42

negatively
right

Front 43

Overwound circular DNA is ___________ charged and ______ handed

Back 43

postively charged
left

Front 44

___________ (superhelical/supercoiled) is biologically active form of circular DNA, whereas, ________ (superhelical/supercoiled) is inactive form of DNA

Back 44

Superhelical
Supercoiled

Front 45

True or False:
Topoisomerase I relaxes DNA by breaking only one strand

Back 45

True

Front 46

True or False:
Topoisomerase II breaks only one strand

Back 46

False!

Breaks both strands of DNA

Front 47

In bacteria, _________ scaffold is found at the nucleiod core

Back 47

RNA-protein

Front 48

RNase unfold the chromosome in ________ (single/multiple), whereas, the DNase unfolds the chromosome in a ______ (single/multiple) step

Back 48

single
multiple

Front 49

True or False: In prokaryotic cells, histones interact with DNA to form a polynucleosome.

Back 49

Falseeee. Its eukaryotic.

Front 50

What is another name for the beads-on-a-string structure?

Back 50

Polynucleosome

Front 51

What makes up the histone octamer?

Back 51

- 2 molecules of H2A
- 2 molecules of H2B
- 2 molecules of H3
- 2 molecules of H4

That makes 8. Get it? Oct-amer

Front 52

True or False: Histones are in contact with the major groove of DNA.

Back 52

Falseee its minor!

Front 53

What is the function of linker DNA?

Back 53

It forms polynucleosomes by connecting each individual nucleosome

Front 54

What is a chromatosome?

Back 54

Linker DNA associated with histone H1 that locks the coiled DNA in place

Front 55

How many total base pairs are found on a chromatosome? How many pase pairs are found in nucleosome? How many base pairs are associated with linker DNA? And how many turns of DNA are found on a histone octamer?

Back 55

Chromatosome - 166
Nucleosome - 146
Linker DNA - 20 to 90
2 turns

Front 56

Nucleosome + Linker DNA + Histone H1 =

Back 56

A chromatosome

Front 57

Describe the process of the generation of negative supercoiling in eukaryotic DNA.

Back 57

- First the histone and the DNA bind together to form negative supercoil. As a result, a positive supercoil is also made. Topoisomerase comes and relaxes the positive supercoil leaving one net negative supercoil.

Front 58

What are some differences between prokaryotic and eukaryotic DNA?

Back 58

- Prokaryotic DNA has 4.6 x 106 bp of DNA and 4200 genes (a lot less than eukaryotic). Prokaryotic also has more densely organized genetic information meaning less 'junk DNA.' There are very few repeating sequences

- Eukarotyic DNA has as few as 30,000 genes but the majority of it is noncoding DNA or "junk DNA." Eukaryotic DNA has a lot of repeated sequences found in its DNA.

Front 59

What function might junk DNA have?

Back 59

Regulating gene expression

Front 60

Noncoding intervening nucleotide sequences are known as what?

Back 60

Introns!

Front 61

The nucleotide sequences that are expressed in the final mRNA are known as what?

Back 61

Exons!

Front 62

What is the process which removes introns from a mRNA transcript?

Back 62

Splicing!

Front 63

The intron sequences are __________ (translated/transcribed) but are removed during splicing.

Back 63

Transcribed!

Front 64

What are the pyrimidines for RNA?

Back 64

- Cytosine
- Uracil!

(You were thinking of saying thymine weren't you? Good thing you didn't!)

Front 65

What are the main differences between DNA and RNA?

Back 65

- RNA has ribose not 2'-deoxyribose as its main sugar component
- RNAs are generally single stranded whereas DNA is generally double stranded
- Hydrolysis of RNA is accelerated by its 2'-OH group making it less stable than DNA

(Also, this isn't a main difference but RNA doesn't have equal proportions of A & U, and C & G like DNA does)

Front 66

Describe the secondary structure of RNA.

Back 66

It involves intramoleuclar base pairing where base pairs are formed from complementary sequences in the same molecule

The double-helical stem-loop regions in RNA are often called "hairpins"

Front 67

What are the double-helical stem-loop regions found in secondary RNA called?

Back 67

Hairpins

Front 68

What are the two functions of tRNA?

Back 68

Activating amino acids
Recognizing Codons

Front 69

What the function of rRNA?

Back 69

Involved in protein synthesis apparatus

rRNA accounts for 80% of cellular RNA

Front 70

Which RNA carries the primary information for the primary structure of proteins?

Back 70

mRNA

Front 71

Catalytic RNAs are called _______

Back 71

ribozymes

Front 72

What are ribozymes

Back 72

-Enzymes whose RNA subunits carry out catalytic reactions.
-These are NOT proteins
-Five classes
(3 self splicing, ribonuclease P (RNase P) and rRNA)

Front 73

What is a hammerhead ribozyme?

Back 73

- Used to downregulate gene expression, if bound to DNA

- If bound to RNA, it could cleave it

Front 74

Name are the different types of RNAs?

Back 74

-tRNA
-mRNA
-rRNA
-Catalytic RNA (ribozymes)
-RNPs (RNA in ribonucleoproteins)
-RNA forming binding sites on other molecules

Front 75

What are the three R's of DNA?

Back 75

Replication
Recombination
Repair

Front 76

What do the three R's of DNA have in common?

Back 76

They all involve making and breaking phosphodiester bonds.

Front 77

What is the function of the primer in DNA replication?

Back 77

It provides a free 3' OH group to which nucleotides can be added.

A primer is basically a small sequence of DNA, from which you can start adding nucleotides.

Front 78

What are 4 requirements for DNA replication

Back 78

- Templates
- Primers
- Precursors
- Enzymes

Front 79

Codon sequences in mRNA specify what?

Back 79

- Single amino acid
-Starting point of translation
-termination of peptide chain

Front 80

What acts as the precursor for DNA replication?

Back 80

5'-deoxynuceloside triphosphates (5'-dNTPs)

Front 81

What is the function of the template in DNA replication?

Back 81

It provides sequence information

Front 82

How is a phosphodiester bond formed in DNA replication?

Back 82

- First an incoming nucleoside triphosphate forms correct hydrogen bonds with the base on the template
- Then the 3'OH from the primer attacks the triphosphate group on the dNTP, causing 2 phosphate groups to be kicked off.

The 2 phosphate groups are called a pyrophosphate

Front 83

The degenerate property of the genetic code states what?

Back 83

The degenerate property allows for 64 codons to code for 20 amino acids. Aka more than one codon sequence can code for an amino acid.

Front 84

What is the function of DNA polymerase?

Back 84

It catalyzes the function of nucleotides during chain elongation

Front 85

What does DNA polymerase require in order to properly do its function?

Back 85

- A template
- A primer
- 5'-dNTP

Front 86

Translation is centered on _________ (RNA/DNA)?

Back 86

RNA

Note:
mRNA - Transmits genetic code
tRNA - carries amino acids
rRNA - shapes ribosomes, catalyzes peptide formation

Front 87

How is proofreading by DNA polymerase carried out?

Back 87

- The DNA has exonucleolytic activity that removes mispaired nucleotides from the 3'end of the growing chain.

A primer that has a proper base-paired terminal is a bad substrate for exonuclease but a good substrate for the addition of a next molecule

In the same sense, a primer that has a mismatched terminal nucleotide is a bad substrate for adding a new nucleotide but a good substrate for exonuclease

Front 88

What are 2 ways DNA polymerase ensures accuracy in DNA replication?

Back 88

- By initially selecting the proper nucleotide to add
- By enzymatic proofreading

Front 89

Synthesis of a peptide chain is from ______________ (amino/carboxyl) terminus to ____________terminus (amino/carboxyl)

Back 89

From Amino to Carboxyl

Front 90

Review the table on Chapter 4 lecture slides Slide number 5.

Back 90

Its the DNA polymerase stuff

Front 91

Which enzyme/protein is needed to separate the DNA strands to create the replication fork?

Back 91

Helicase

Front 92

Postranslational and cotranslational modifications of proteins can affect what aspects of protein?

Back 92

-protein shape
-function
-localization in cell
-export from cell
-protein's lifetime

Front 93

The __________ strand can be elongated by simple sequential addition of new nucleotides

Back 93

Leading

Front 94

Which enzyme/protein keeps the 2 DNA strands apart in the replication fork?

Back 94

SSBs (single-stranded DNA-bindng proteins)

Front 95

True or False
The proteosome is involved in protein degradation

Back 95

True

Front 96

The __________ strand is elongated with the addition of okazaki fragments

Back 96

Lagging

Front 97

DNA synthesis is usually ___________ where the parental strands separate and each serves as template for the synthesis of a new strand.

Back 97

Semiconservative

Front 98

The _________ (leading/lagging) strand has its 3' end oriented towards the fork.

Back 98

Leading

Front 99

True or False:
Folding of a protein into its final conformation can only be done with help of protein chaperones

Back 99

False: Protein folding into final conformation can be spontaneous as well

Front 100

Describe the process of DNA replication starting after the formation of the replicating fork.

Back 100

1. The leading strand is elongated at its 3'end by repeated cycles of nucleotide addition
2. Using the template for the lagging strand, primase synthesizes an RNA primer
3. A DNA polymerase covalently extends the 3' end of the RNA primer, incorporating deoxyribonucleotides
4. As the growing Okazaki fragment approaches, the RNA primer on the older fragment is removed with RNase or Poly I
5. The gap is filled by a DNA polymerase that elongates the Okazaki fragments
6. When the gap has been filled, and only a nick remains, a DNA ligase seals the two fragments together

Front 101

The ___________ (leading/lagging) strand has its 5' end oriented towards the fork.

Back 101

Lagging

Front 102

True or False: In DNA replication, when using the topoisomerase mechanism, there is no net loss or creation of phosphodiester bonds and nicking and resealing can occur without high energy.

Back 102

True!

Front 103

Eukaryotic mRNA is _________ (monocistronic/ polycistronic)

Back 103

Monocistronic

Front 104

Which protein/enzyme seals the 'nicks' found on the lagging strand?

Back 104

DNA ligase

Front 105

Explain the process of replication in E.coli/prokaryotes.

Back 105

Pol III elongates the continuous strand and most of the lagging/discontinuous strand

Pol I removes RNA primers and fills the gap at the same time which is called nick translation

DNA helicase/primase complex moves along the template of the lagging strand and allows primase to create a primer evrey 1000-2000 base pairs

Front 106

Describe the process of DNA ligation.

Back 106

- ATP and ligase combine to make ligase-AMP and a pyrophosphate
- The ligase then binds to a nicked DNA duplex and the ligase transfers the AMP at the 5' end of the nick
- The 3'OH then attacks the phosphate and kicks of the rest of the ligase molecule, releasing AMP in the process
- The result is a resealed phosphodiester backbone

The cost of all of this is an ATP split into AMP + PPi

Front 107

Prokaryotic mRNA is _________ (monocistronic/ polycistronic)

Back 107

Polycistronic

Front 108

Explain the process of adding nucleotides to the lagging strand during DNA replication.

Back 108

- First RPA binds to the lagging strand to keep it open
- Then the pol alpha/primase complex comes to the strand and makes a primer of 10 base pairs
- Once 10 base pairs of primer have been made, the pol alpha of the pol alpha/primase complex beings to make an okazaki fragment that is about 15 to 30 base pairs long.
- Once it reaches 15 to 30 bp, it dissociates
- Then the real pol activty begins first with the binding of RFC and 3 molecules of PCNA to make a sliding clamp
- Pol delta binds to the sliding clamp and begins elongating the okazaki fragments
- As the replication complex reaches the next primer, the primer is degraded by RNase H and FEN 1
- Finally the gap is filled by the elongation of the okazaki fragments and the remaining nick is sealed with ligase

Front 109

Replication begins from specific sites called what?

Back 109

Origins of Replication (ori)

Front 110

What is the function of slide clamps in DNA replication?

Back 110

It makes DNA polymerase more processive by holding them in contact with the DNA chain, which increases the speed of synthesis and DNA polymerase's accuracy

Front 111

What are the main differences between Eukarytoic mRNA and Prokaryotic mRNA?

Back 111

Euks
-monocistronic (one peptide from one mRNA)
-5' cap (7-methylguanosine)
-5' untranslated region (UTR)
-3' UTR
-3' polyadenylate (poly A) tail
-Usually initiation signal is AUG (not always)

-Proks
-polycistronic (codes several polypeptides from one mRNA)
- No 5' cap
-No poly A tail

Front 112

Known origins of replication contain 2 main things. What are they?

Back 112

- Multiple, short repeated sequences that bind specific proteins
- AT-rich regions at which the initial separation of parental strands occur

(In bio we learned it was called a TATA box)

Front 113

True or False: the E.coli chromosome has single origin of replication, oriC, a region of approximately 245 base pairs.

Back 113

True!

Front 114

What are the names of the 3 people who won a noble price for discovering how chromosomes are protected by telomeres and the enzyme telomerase?

Back 114

- Elizabeth Blackburn
- Carol Greider
- Jack Szostak

Front 115

What is the step-by-step process by which the sliding clamp attaches to the DNA molecule?

Back 115

1. A clamp-loading protein binds to DNA
2. The clamp loader assembles the sliding clamp from its subunits (the circle around the DNA)
3. DNA polymerase associates with the assembled clamp and becomes processive

Front 116

Which two amino acids only have single codons to code for them?

Back 116

Methionine (AUG, also start codon)
Tryptophan (UGG)

Front 117

What are ori's called in yeasts?

Back 117

ARS (autonomously replicating sequences)

Front 118

What are the major steps for elongation of peptide chain?

Back 118

1. P site (donor site) has the Met-tRNA positioned in it.

2. Another aminoacyl-tRNA that has a EF1a attached to it, enters the A site (acceptor site); GTP hydrolysis resutls in conformational change = dissasociates EFa
3. The peptidyl transferase catalyzes the rxn between Met and the other A.acid in 80s ribosome
4. EF2 (translocase) shifts the mRNA and dipeptidyl-tRNA from A site to P site; deacylated tRNA moves from P site to E site (to exit)
5. Now, since A site is empty, a new aminoacyl-tRNA can bind, releasing the deacylated tRNA from E site

Front 119

True or False: The greater the distance, the more the chance of recombination.

Back 119

True!

Front 120

What is the exchange of genetic information known as?

Back 120

Recombination

Front 121

True or False: In humans specific sequences that serve as oris have been identified.

Back 121

Falseeeee! They have notttt

Front 122

What are the 2 types of recombination?

Back 122

- Homologous recombination (does not require enzymes)
- Nonhomologous recombination (does require enzymes)

Front 123

The genetic code is nearly universal in proks and euks, except in the _______ (hint: organelle) of the same organism.

Back 123

Mitochondria

Front 124

How does a replisome work?

Back 124

By binding two replicative polymerases together and looping the discontinuous strand so that it can pass through the complex, both strands can be made in one place. DNA feeds through the complex, rotating as it passes through; the large protein complexes do not have to rotate around the DNA.

Front 125

Which type of recombination occurs between identical or nearly identical sequences?

Back 125

Homologous recombination

Front 126

What 2 complexes bind at the ori?

Back 126

ORC (origin recognition complex) and MCM (minichromosome maintainence proteins)

Front 127

The probability that a recombination event will occur between any two points on a chromosome is roughly proportional to the _______ ________ between them.

Back 127

Physical distance

Front 128

Genetic code uses a _________ alaphabet of nucleotides, while codons in mRNA use ___________ words

Back 128

Four (ATCG, AUCG)
Three (AUG, UGG, etc)

Front 129

What are the key features of the Holiday Model of homologous recombination?

Back 129

- Homology
- Symmetry of both breaks and strand invasion
- Prescence of a four-stranded "Holiday Junction" as a key intermediate

Front 130

What is the problem of termination during replication in linear genomes?

Back 130

There is no room to synthesize another primer at the end of the strand so each new daughter strand that is synthesized could be shorter than the mother strand before it.

Front 131

What are the key features of the Meselson-Radding model?

Back 131

- The asymmetrical heteroduplex that results from the invasion by one strand from one of the two duplexes

Front 132

How is recombination in the double-strand break model of recombination initiated?

Back 132

By a double-strand break in one DNA molecule

Front 133

A UGA, UAG, UAA in a normal eukaryotic mRNA would signify ___________ (initiation/termination)

Back 133

Termination

Note: these are only stop codons that do not encode any amino acid, so technically these are "nonsense codons"

Front 134

How is the problem of termination during replication in linear genomes solved?

Back 134

Its solved using telomeres. Telomeres are found at the end of each strand in DNA and they are just excessive repeats of the TTAGGG sequence.

So basically because these are found at the end of the DNA, and have no meaning, when the daughter strand ends up being shorter than the mother strand, it doesn't matter because the only thing its missing are these telomeres.

Front 135

What are 3 different ways of having nonhomologous recombination?

Back 135

- Insite-specific recombination
- Transposition
- Nonhomologous End Joining (Recombination)

Front 136

What is the process where specific enzymes catalyze the integration of a sequence into particular sites in the DNA?

Back 136

In-site specific recombination

Front 137

What enzyme/protein maintains telomeres by catalyzing the addition of 6 nucleotide sequences to the 3'end of a DNA chain?

Back 137

Telomerase!

Front 138

What is the process of the movement of specific pieces of DNA in the genome called?

Back 138

Transposition

Front 139

What are the basic steps for nucleotide excision repair?

Back 139

1. Double excision removes the oligonucleotide
2. DNA polymerase fills the gap
3. DNA ligase seals the nick

Front 140

mRNA codons interact with the ___________ sequences on tRNA

Back 140

Anticodon

Front 141

How does transposition resemble site-specific recombination?

Back 141

They both are catalyzed by special enzymes

Front 142

What are the 2 key features of transposons that allow them to move nearly anywhere?

Back 142

- They encode transposase enzymes
- They have insertion sequences that are recognized by the transposase

Front 143

In mismatch repair, how is the parental strand identified and why is this important?

Back 143

The parental strand is methylated where as the daughter strand is not. And this is important because if you change the parental base, it would lead to a completely different sequence, whereas its the daughter base that you would want to change.

Front 144

How does mismatch repair work in Ecoli?

Back 144

1. MutS and MutL bind to the mismatch and ATP is hydrolyzed
2. MutH binds at a hemi-methylated site which could be either to the right or the left (doesn't matter)
3. DNA of the unmethlyated strand cut (nicked) at 2 points (where MutH is and where the mismatch is) and then thrown out (excised) and
4. The gap is filled by DNA polymerase
5. The nick is sealed by DNA ligase

Front 145

What happens in illegitimate recombination?

Back 145

- Genes are randomly introduced into mammalian cells and no homology is needed.

This sometimes can repair DNA strands that have broken apart or it can disrupt genes and cause mutations or dysregulation.

Front 146

True or False: The accuracy of DNA replication is 100%

Back 146

Falseeeeeeeee! Its not!

Front 147

Name the 3 types of point mutations.

Back 147

Silent (no amino acid change)
Missense (amino acid change)
Nonsense (premature termination)

Front 148

What are the major differences between silent, missense and nonsense mutations?

Back 148

Silent:
-involves a single base change at 3rd position in codon, because of degeneracy property, amino acid produced is the same

Missense- causes a single base pair change (not at 3d position) thus, incorporating a different amino acid in the protein

Non-sense: This is results when the single base pair change encodes for a stop codon, causing premature termination of protein synthesis (a "non-sense" protein is produced)

Front 149

Difference between point and frameshift mutations?

Back 149

point mutations are really just substitutions of single base pairs.

Framshifts are insertion or deletion of single base pairs, causing the entire reading frame to shift.

Front 150

What are "Read Through" mutations?

Back 150

There is a mutation of a stop codon with another amino acid that allows message to be "read" through.

Aka: incomplete stopping, (sorta of the opposite of non-sense)

Front 151

What are some major characteristics of tRNA?

Back 151

- 3' CCA sequence where amino acid is bound (aka: Acceptor stem)
-conserved secondary "cloverleaf" structure
-L-shaped 3-D structure
-Anti-codon sequence (complimentary and antiparallel mRNA codons attach)

Front 152

________ repair is used when one of the wrong bases is paired up with another.

Back 152

Mismatch

Front 153

True or False
Each tRNA has a unique polynucleotide sequence which interacts with rRNA and aminoacyl tRNA synthetase

Back 153

False:
It interacts with mRNA and aminoacyl tRNA synthetase

Front 154

Where does transcription take place?

Back 154

- In the nucleus
Or
- In the mitochondrial matrix

Front 155

True or False:
aminoacyl tRNA synthetase are specific for the 20 amino acids

Back 155

True - there are about 20 aminoacyl tRNA synthetase for the 20 amino acids.

Front 156

What is the process by which RNA chains are made from DNA templates?

Back 156

Transcription

Front 157

Which enzymes catalyze transcription?

Back 157

RNA polymerase

Front 158

What is the function of aminoacyl - tRNA synthetase

Back 158

- it selects both appropriate tRNA and its specific amino acid to be attached
- it's central for proper protein synthesis

Front 159

What are the three parts of the process of transcription?

Back 159

1. Initiation where RNA polymerase binds to the promoter
2. Elongation which is the actual synthesis of the RNA chain
3. Termination and release

Front 160

Why does the maintenance of genetic information require constant repair of DNA damage?

Back 160

Because DNA in cells is constantly being altered by cellular constituents and many environmental agents attack and modify DNA

Front 161

_________ polymerase does not require a primer.

Back 161

RNA!

Front 162

What are the two steps for activating an amino acid to be attached to a tRNA?

Back 162

1. Amino A + ATP + Energy-> [Amino Acid-AMP + E] + PPi

2. [Amino Acid-AMP + E] + tRNA --> Amino Acid-tRNA + AMP + E

Overall Rxn:

A.Acid + ATP + E --> A.Acid-tRNA + AMP + PPi

Front 163

What are DNA sequences that stimulate transcription but are located further away from the initiation site?

Back 163

Enhancers

Front 164

Oxidative damage can convert C to _____?

Back 164

U!

Front 165

Eukaryotic transcription takes place in which organelle(s)?

Back 165

Nucleus (genomic DNA)

But, also mitochondria and/or chloroplasts

Front 166

True or False: Enhancers can only stimulate transcription at the beginning of the gene.

Back 166

False! At the beginning, middle, or end.

Front 167

Codon sequences in mRNA specify what?

Back 167

- Single amino acid
-Starting point of translation
-termination of peptide chain

Front 168

The RNA polymerase initiates transcription at the __________ (primer/promoter)

Back 168

Promoter (begins polymerizing sequences)

Front 169

What does cis-acting as related to enhancers?

Back 169

An enhancers sequence must be on the same DNA molecule (chromosome) as is the transcribed gene

Front 170

The RNA polymerases are ___________ (large/small) subunits

Back 170

large (E.coli RNA Pol is made up of five subunits)

Front 171

What is an AP site?

Back 171

Its a site that is lacking a base

Front 172

E.Coli's RNA polymerase is made up of how many subunits?

Back 172

Five!

Note:
2 alpha
1 Beta
1 Beta prime (B')
1 Sigma factor

"Core enzyme" = 2 alpha, 1 beta, and 1 beta'

"Holoenzyme" - Core enzyme plus sigma factor

Front 173

How does an activator work?

Back 173

When an activator binds to an enhancer, it causes a structural change in the DNA template that allows the interaction of the activator with other factors or with RNA polymerase.

This interaction helps transcription by "recruiting" RNA polymerase to form an initiation complex

Front 174

True or False:
Usually one major sigma factor is used to for transcription, but sigma factors can be specific for certain genes

Back 174

True

Okie so sigma factors in nutshell:

Your core enzyme can start transcription, but it's not necessarily going to start at promoter sites..so once the sigma factor binds to the core enzyme, it forms the holoenzyme. This particular structure is now specific enough to bind at promoter sites, and initiate transcription specifically from the promoter.

Front 175

The degenerate property of the genetic code states what?

Back 175

The degenerate property allows for 64 codons to code for 20 amino acids. Aka more than one codon sequence can code for an amino acid.

Front 176

___________ drug is used to inhibit RNA polymerase activity in prokaryotes (treates TB).

Back 176

Rifampicin

It specifically binds to the beta subunit of the RNA pol.

Front 177

True or False: Promoters are located a short distance upstream from the transcription start sites.

Back 177

True!

Front 178

Another name for "sense" strand is _________

Back 178

coding strand

Front 179

What are 4 ways DNA can be damaged?

Back 179

- Oxidative deamination
- Creation of AP site
- Oxidation
- Ultraviolent light

Front 180

There are how many highly conserved sequences within the promoter for porakaryotes?

Back 180

2 highly conserved sequences

Note: one is located 10 bp upstream from transcription start site (-10bp) and the other iis at -35 (35 bp upstream from start site)

Front 181

What are the steps for transcription initiation in euks?

Back 181

Transcription in euks is very complex

1. Therefore, the promoter region on the chromatin must be made accessible to the RNA pol
2. Transcription factors, other than the RNA pol must bind to the promoter region for gene to be active
3. Enhancers bind to other protein factors (like activators) to stimulate transcription

Front 182

Which 2 short sequences in prokaryotic promotors are highly conserved?

Back 182

35 Region - TTGACA
10 Region - TATAAT

Front 183

The highly conserved sequences at the -10 region in the promoter sequence for proks is also called what?

Back 183

The Pribnow box (not in the notes..more of a fyi)

Front 184

In eukaryotes, a _________ (looser/tighter) chromatin conformation means active/higher transcription ability

Back 184

Looser

Note: Looser conformation of the chromatin (bc nucleosomes are not bound) means higher transcription activity, because the promoter and/or gene is more accessibile to transcription factors, RNA pol etc..

Front 185

Translation is centered on _________ (RNA/DNA)?

Back 185

RNA

Note:
mRNA - Transmits genetic code
tRNA - carries amino acids
rRNA - shapes ribosomes, catalyzes peptide formation

Front 186

In Euks, the enhanced accessibility to promoter sites(not the actual genes) by transcription factors, RNA pol etc is called __________

Back 186

DNase I (one) Hypersensitivity

Note: it's called this because during experiments they saw that promoter sites where not really wound up around nucleosomes, hence making them more accessible to transcription factors, but their associated genes were - and researchers were able to figure this out, because in the presence of DNase I, the promoter sequences would get degraded, while those genes with nucleosomes around them did not.

Front 187

The RNA transcript usually starts with a _________ (purine/pyrimidine) base

Back 187

purine (pppG or pppA)

Front 188

___________ (hint: type of RNA pol) is responsible for mRNA synthesis in nucleus (for euks)

Back 188

RNA pol II (two)

Front 189

True or False:
RNA synthesis occurs in the 5' to 3' direction using a DNA template

Back 189

True!

Front 190

Explain the start and synthesis of RNA transcription?

Back 190

Two step process

1. RNA polymerase holoenzymme binds WEAKLY to promoter DNA and forms a "closed complex"

2. Then, holoenzyme forms a more TIGHTLY bound "open complex"
(here you get the opening of double helix at the Pribnow box - which is an A-T rich region - hence easier to open vs G-C rich region)

Front 191

True or False: Excision repair can only repair a specific type of base damage.

Back 191

False! It can repair many different type of base damages.

Front 192

Explain the elongation process of RNA transcription?

Back 192

- MOST IMP: It's considered that once the sigma factor disassociates with core enzyme, the RNA pol enters elongation phase
- RNA pol can add nucleotides at about 40bp/sec
- Topoisomerase I and II are involved in controlling superhelicity double helix

Few notes:
- Elongation phase is considered to be a very stable interaction with DNA template - does not easily disengage, until specific signal are given to stop.

Front 193

The DNA template for RNA is ______________ (antisense/sense)

Back 193

Antisense

Front 194

What two ways do prokaryotes use to terminate transcription?

Back 194

- Rho independent
- Rho dependent

Rho is a protein, and in some cases transcription termination is dependent on this protein, or it's not

Front 195

Synthesis of a peptide chain is from ______________ (amino/carboxyl) terminus to ____________terminus (amino/carboxyl)

Back 195

From Amino to Carboxyl

Front 196

How does the transcription termination work through Rho-independent?

Back 196

-it does not require the Rho protein

-G-C rich palindrome is present before a sequence of 6-7 U resides in RNA chain
- The RNA chain forms a stem and loop structure (through G-C base pairing) ahead of polyU sequence and physically halts transcription

Front 197

In the DNA, which strand is considered the "sense" strand? Which is considered the "antisense" strand?

Back 197

5' --> 3' is sense strand (the template that is NOT used for transcription)

3'-->5' is the antisense strand (this strand IS used for transcription, the mRNA made is 5'--> 3')

Front 198

How does the Rho-dependent termination work?

Back 198

- it is dependent on Rho protein
- it's a hexameric protein
- has RNA-dependent ATPase activity

-Rho-dependent protein is seen to work over a termination region where there are regular intervals of C-rich regions
- Somehow, the Rho protein interacts with the RNA polymerase, once it's done transcribing and releases DNA template and RNA chain from RNA pol.

Front 199

What are the basic steps of excision repair?

Back 199

- Recognize damage
- Removing damage by excising part of one strand
- Resynthesizing to fill gap using the genetic information from other strand used
- Ligating to restore continuity of DNA

Front 200

True or False:
In proks, transcription of a DNA template can not be done simulataneously by different RNA polymerases

Back 200

False!

It can be done simultaneously by different RNA polymerases. ("christmas tree picture" slide 12 in notes)

Note: Translations starts at the same time too..which is completely different from eukartyotic mechanism

Front 201

Once the mRNA is made during transcription, the strand is the same as the _________ (sense/antisense) DNA strand.

Back 201

Sense strand (5'-->3')

Front 202

Postranslational and cotranslational modifications of proteins can affect what aspects of protein?

Back 202

-protein shape
-function
-localization in cell
-export from cell
-protein's lifetime

Front 203

Gene overlapping within mRNA is seen in _________ (proks/euks)

Back 203

proks

Front 204

What are the 2 types of excision repair?

Back 204

- Base excision repair
- Nucleotide excision repair

Front 205

Transcription does not require a ___________ (primer/promoter)

Back 205

Primer

Note: (DNA synthesis, done by DNA polymerase does require a primer)

Front 206

Which family of enzyme catalyzes the activation of amino acids to bind to tRNA?

Back 206

Aminoacyl-tRNA synthetases

Front 207

Processing of mRNA in Euks is __________ (cotranscriptional/post-transcriptional)

Back 207

Co-transcriptional

Note:
Euks - transcription and mRNA (I think it's only mRNA processing) processing is usually co-transcriptional

Proks - (in general) translation and transcription occur simultaneously

Front 208

What are the basic steps for base excision repair?

Back 208

1. Glycoyslase recognizes and removes the base while leaving the backbone intact
2. AP endonuclease cuts the backbone and AP lyase removes the sugar
3. DNA polymerase fills the gap
4. DNA ligase seals the nick

Front 209

Pre-mRNAs are _____________ (longer/shorter) than mature mRNAs

Back 209

Longer

Front 210

Aminoacyl-tRNA synthetases interact with which two parts of tRNA?

Back 210

Acceptor stem
Anticodon loop

Front 211

Non-coding sequences found in pre-mRNA, but not in the mature mRNA are called ___________, while those re-tained are called ___________

Back 211

Introns
Exons

Front 212

What structural feature on the tRNA helps the aminoacyl-tRNA synthease to bind specific amino acids to specific tRNAs?

Back 212

aminoacyl-tRNA synthetase recognizes the anticodon loop on tRNA to allow specific activation and binding of amino acids

Front 213

The net result of rRNA processing in both proks and euks is?

Back 213

The release of smaller rRNAs

Note:
Euks - release 3 pieces rRNAs
(28S, 5.8S, 18S)
Proks -release 2 pieces rRNAs
(23S and 16S)

Front 214

Amino acid bound to a tRNA is called _________________

Back 214

Amino-acyl tRNA

Note: Aminoacyl-tRNA synthetase is the enzyme which catalyzes the activation of amino acids

Front 215

The three steps involved in modifying tRNA are? Explain each.

Back 215

1. Cleavage
Involves cleaving extra nucleotides off from both 5' end and 3' end
- 5' cleaved with Ribonuclease P (RNase P) = endonuclease activity
- 3' end with exconuclease activity

2. Addition
Add on the 3' CCA sequence to tRNA with
tRNA-Nucleotidyltransferase

3.Base Modification
tRNAs are the most modified RNAs
-over 60 different modifications w/ over 100 enzymatic reactions
(ie: methylation)

NOTE: If Intron splicing occurs, it's after addition of CCA sequence, so after the 2nd step

Front 216

mRNA sequences are written, transcribed and translated from _____ terminus to ____ terminus

Amino acids are written and synthesized from _____ terminal to _____ terminal

Back 216

5' to 3' (written, transcribed and translated in this direction)

Amino to carboxyl (written and synthesized)

Front 217

Examples of RNA processing include?

Back 217

- Removal of extra nucleotides (ie intron splicing)
- Base modification
-Adding nucleotides
-Separating different RNA sequences through nucleases (ie: in rRNA)
-In Euks, transporting RNA out of nucleus

Front 218

Formation of Initiation complex:

1. GTP binds to _____ (which initiation factor) + tRNA-Met forming _______ complex

2. Ternary complex binds to ________ ribosomal subunit, which is bound by _____ (hint: initiation factor)

3. The mRNA, with help from ____ initiation factor, binds to the 40S subunit, forming the _________ complex

4. The ______ large subunit now binds forming the _________ complex

Back 218

1. eIF2a (eukaryotic Initiation factor 2); ternary complex

2. 40s (small subunit); eIF3

3. eIF-4a; pre-initiation complex

4. 60s; initiation complex (80s)

Front 219

In Euks, during mRNA synthesis, RNA polymerase ____ is recruited once bound transcription factors _______ (bind/un-bind) to each other

Back 219

RNA Pol II (two)
Bind

Aka - not only do transcription factors have to be bound to their specific sequences on the DNA, they must interact with one another to actually recruit RNA Pol II

Front 220

What is RNA processing?

Back 220

It's a method of modifying RNA sequences (once they've been transcribed)

It can either be done co-transcriptionally or post-transcriptionally

Front 221

Name a few common promoters for mRNA synthesis?

Back 221

-TATA box
- 25 bp upstream from transcription unit
- housekeeping genes are found within TATA box

-CAAT box
-not as highly conserved as TATA
- further upstream than TATA
-In highly differentiated tissues

NOTE: None of these sequences are found on the mRNA strand, these are found on DNA templates for mRNA synthesis!!

Front 222

What are the functions of each site?

A site
P site
E site

Back 222

A site - the acceptor site AKA aminoacyl site. In charge of selecting the next specified amino acid based on the mRNA codon here.

P site: AKA donor site or peptidyl transferase. Site where Met-tRNA first binds. P site "donates" the methionyl residue to alpha amino group of next incoming aminoacyl-tRNA .

E site - exit site from where the deacylated tRNA exits. It leaves once the A site is occupied with another aminoacyl-tRNA

Front 223

True or False:

In Euks, transcription factors with RNA Pol II can bind/recognize a variety of promoter sequences

Back 223

True!

Note: Prok RNA Pol can only recognize a single promoter sequence

Front 224

What makes transcription by RNA Pol III different from other eukaryotic RNA polymerases?

Back 224

RNA Pol III synthesizes 5S rRNA and tRNA.

Know this:
5S rRNA - TFIIIA (binds within gene)
tRNA - TFIIIC (binds within gene)

Note:
Some of the sequences where transcription factors need to bind (to recruit RNA Pol III) are found within the genes for 5S rRNA and tRNA, and not within the promoters, or upstream from promoters. The examples above show which transcription factor (TF) bind within the genes

Front 225

What are the characteristics of mRNA transcription through RNA Pol II

Back 225

In general:
- Euk transcription is complex, so there are a number of transcription factors which work together to give a finely tuned control
- Transcription is controlled by different transcription factors interacting with sequences (ie: activator binding to enhancer)
- Transcription factors can bind to one another and re-cruit RNA Pol II
- Once RNA Pol II can recruits other enzymes during elongation phase

Front 226

Enhancer-binding transcription factors are called _________

Back 226

Activators (these are proteins which bind to the enhancer sequence to stimulate transcription)

Note: These form loops and allow the enhancer sequence to interact with promoter sequence

Front 227

Which two releasing factors are involved in the termination process for translation?

Back 227

-RF1-GTP occupies the A site, once a stop codon is read on the mRNA.
-With the help of eRF3, the peptidyl transferase hydrolyses the peptide bond and releases the protein.

Front 228

Of the 3 types of rRNAs found in a transcriptional unit, which ones show up pre-dominantly on gel electrophoresis?

Back 228

28S and 18S

Front 229

During elongation of peptide chain peptidyl transferase makes ______ bonds.

During termination, peptidyl transferase _______ the ester bonds between protein and tRNA

Back 229

Peptide bonds

Hydrolyses

Front 230

what are some important characteristics of transcription by RNA Pol I

Back 230

- synthesizes rRNA
- Each transcriptional unit contains 28S, 5.8S and 18 S, and it's repeated on chromosome
- These units are separated by spacer regions/sequences, where promoters are found

Note: the entire transcriptioal unit is always transcribed, so that equimolar amounts of 28S, 5.8S and 18S are produced. This is called "Pre-RNA," which is then sliced into separate rRNAs

Front 231

Peptidyl transferase functions as a __________ (hint: hydrolysis) during termination of translation

Back 231

Hydrolase

Front 232

Each transcription unit in the rRNA contains sequences for which 3 types of rRNA?

Back 232

28S rRNA
5.8SrRNA
18S rRNA
It's transcribed in this order

Note: (if you're thinking 5S RNA- that was where RNA Pol III synthesizes it along with tRNA)

Front 233

The rate-limiting step for cell growth is dependent on transcription/synthesis of ___________ (rRNA/mRNA/tRNA)

Back 233

rRNA

rRNA produces ribosomes which eventually helps in protein production, which is needed for cell growth.

Aka: During cell growth, rRNA transcription is rapid, and visa-versa

Front 234

What 3 codons would need to present in the A site to being termination of translation?

Back 234

UGA, UAG, UAA

Front 235

Name the factors used for initiation, elongation and termination during translation (only name)

Back 235

Initiation: eIF2a, eIF3, eIF-4a, eIF2b

Elongation: EF1a, EF2

Termination: eRF1 and eRF 3

Front 236

True or False:
Translation is a process that requires very little energy

Back 236

False: Requires a lot of energy, a total of four high-energy bonds are broken per peptide formed

Front 237

How does puromycin interefere with protein synthesis?

Back 237

-Puromycin is an antibiotic, which stops translation by acting as a aminoacyl-tRNA analog (intereferes with peptidyl transferase rxn)
-competitve inhibitior of tRNA

Front 238

True or False:

Failure to properly fold a protein leads to rapid protein degradation and/or accumulation of misfolded proteins, causing serious diseases

Back 238

True :)

Front 239

True or False:

Proteins can independently and spontaneously fold into their correct 3D structure

Back 239

True - some can and some cannot..those that cannot need chaperone proteins to help in folding

Front 240

What are the major functions of chaperone proteins?

Back 240

- stabalize intermediates
-maintain unfolded state of proteins to help in passage through membranes
-unfold misfolded segments
-prevent incorrect intermediate formation
-prevent inappropriate interactions with other proteins

Front 241

Chaperones bind to ____________ (hydrophobic/hydrophilic) portions of unfolded proteins and folding intermediates

Back 241

Hydrophobic portions

Front 242

True or False
Proteins that are exported out of the cell are synthesized on free, unbound ribosomes in the cytosol.

Back 242

False! They are synthesized on membrane-bound ribosomes on rough ER

Front 243

Proteins destined for export, plasma membrane, lysosomes, endosomes, or Golgi are synthesized on _________ (membrane bound/unbound ribosomes)

Back 243

Membrane-bound ribosomes on rough ER

Front 244

A signal peptide for secretory proteins, which emerge from free ribosomes in the cytosol are _________ (hydrophobic/hydrophilic)

Back 244

hydrophobic

Front 245

The main characteristics of a signal peptide are?

Back 245

- positivitely charged N-terminus
- core of 8-12 hydrophobic amino acid
- polar C-terminus

Front 246

What temporarily halts elongation once a signal peptide is formed from the ribosome?

Back 246

Signal recognition particle (SRP)

Front 247

What is a signal recognition particle (SRP)? It's mechanism of halting signal peptide elongation?

Back 247

-SRP has 6 different proteins on it, with a small RNA molecule.

-When signal peptide binds to SRP's hydrophobic pocket, and when the signal peptide's postivively charged N-terminus binds to SRP-RNA, SRP halts elongation

Front 248

Difference between N-linked glycosylation and O-linked glycosylation

Back 248

N-linked begins in the ER and continues to occur in Golgi - thus it's co-translational - occurs while protein is synthesized and can thus affect folding)

O-linked glycosylation only takes place in Golgi, thus it is consiered a post-translational modification (occurs on fully folded proteins)

Front 249

True or False
In N-glycosylation, dolichol phosphate serves a receptor for N-acetylglucosamine (sugar)

Back 249

True!

Front 250

True or False:
During N-glycosylation, glycosylation initially occurs on the cytosolic side.

Back 250

True - the sugar chain grows on the cytosolic side of the ER lumen and then inverts and enters the ER lumen

Front 251

Once the (Man)5(GlcNAc)2- forms and inverts into the lumen, which sugars are added on?

Back 251

4 Mannose residues
3 Glucose residues

Sequentially added in that order.

Front 252

Steps for N-linked Glycosylation

Back 252

1. N-acteylglucosamine binds to Dolichol phosphate on cytosolic side
2. Glycosylation occurs, chain grows
3. Chain inverts into ER lumen
4. 4 Mannose + 3 Glucose residues are added
5. This oligosacchride is linked to asparagine's amide N - forming the "N-linked"

Front 253

How do proteins targeted for the mitochondria get there?

Back 253

-Mitochondrial proteins, "pre-proteins," are made on free, cytosolic ribosomes
- The pre-sequences on N-terminus mark pre-protein for mitochondira
-the pre-sequence is not any specific sequence; it's a postively charged amphiphilic -helix- this is recognized by mitochondria rececptor

AKA - more of a structural recognition rather than a sequence recognition

Front 254

How do proteins reach the nucleus?

Back 254

-Nuclear proteins are made in cytosol
- Nuclear proteins are targeted through localization signals (ie: two clusters of basic amino acids)
- These interact with carrier proteins like importin
- These help transport proteins through nuclear pores.

This transport is GTPas Ran dependent.

Front 255

True or False:
Amino acids can be modified after incorporated into proteins

Back 255

True!

Through post-translational modification.

Front 256

True or False:
Modifications made to amino acids after they are incorporated into proteins are irreversible

Back 256

FALSE!

modifications to amino acids in proteins can be both reversible or irreversible

Front 257

Give examples of post-translational modifications

Back 257

-Acetylation
-Methylation
-Phosphorylation (kinases and phosphatases; reversible)
-ADP-ribosylation
-Partial Proteolysis (for maturation of some proteins, ie: insulin)
-Gama-carboxyglutamate formation

Front 258

Protein maturation and/or post-translational modification involve which 4 major processes?

Back 258

-Folding
-Modification
-Secretion
-Targeting

Front 259

What is PCR?

Back 259

Polymerase chain reaction

Front 260

What is the purpose of PCR?

Back 260

It's used to amplify the amount of target DNA

Front 261

What are the steps for PCR?

Back 261

1. Heat the target DNA to 95 or 90 C to denature the protein
2. Reduce the temperature to 55 C to allow for the primers to bind to target sequence
3. Raise temperature to 77 C to allow for extension
4. Repeat cycle to continue amplifying

Front 262

What are different things do you need for PCR?

Back 262

Template
2 primers
dNTPs
Taq Polymerase
Pfu (?)

Front 263

What are 4 functions that intracellular signaling can cause?

Back 263

- Ion transport
- Metabolism
- Gene expression
- Cell movement

Front 264

What is another name for juxtacrine signaling?

Back 264

Contact-dependent

Front 265

In which type of signaling do cells communicate through gap junctions and there is direct contact of ions/metabolites between neighboring cells?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 265

E. Juxtacrine

Front 266

Which type of cell signaling involves the signal traveling a short or long distance through the bloodstream and it takes a long time?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 266

B. Endocrine

Front 267

In which type of cell signaling does the sender cell secrete the signaling molecule or "local mediator" into its immediate or local environment?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 267

A. Paracrine

Front 268

Which type of signaling is known as an extreme type of paracrine signaling?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 268

C. Synpatic

Front 269

What are the signaling molecules called in synaptic signaling and which types of cells are used in the process of signaling?

Back 269

- The signaling molecules are called neurotransmitters
- Neurons are used to transmit the signal

Front 270

Synaptic signaling has high concentration of __________ and in turn low affinity ___________.

Back 270

Neurotransmitters; receptors

Front 271

Which types of signaling (more than 1 answer) are generally more localized?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 271

A. Paracrine
C. Synpatic
D. Autocrine

Front 272

In which type of signaling is one cell type both the sender cell and the target cell?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 272

D. Autocrine

Front 273

Which type of signaling is often used by embryonic/neonatal organisms during tissue and organ development and by adult organisms as a part of immune and inflammatory responses?
A. Paracrine
B. Endocrine
C. Synaptic
D. Autocrine
E. Juxtacrine

Back 273

D. Autocrine

Front 274

What are the 2 major classes of receptors?

Back 274

- Cell-surface receptors
- Intracellular receptors

Front 275

____________ (hydrophilic/hydrophobic) secreted molecules such as _________ hormones and certain vitamins readily permeate through the plasma membrane of target cells.

Back 275

Hydrophobic secreted molecules
Steroid hormones

Front 276

Cell-surface receptors act as the recognition site for the vast majority of signaling molecules that are either too _________ (small/big) or too (hydrophilic/hydrophobic) to rapidly cross the target cell plasma membrane.

Back 276

Big
hydrophilic

Front 277

What is the term for any molecule that binds to a receptor protein?
A. Antagonist
B. Physiological agonist/antagonist
C. Pharmacological agonist/antagonist
D. Ligand
E. Agonist

Back 277

D. Ligand

Front 278

What is the term for a ligand that on binding activates signal transduction?
A. Antagonist
B. Physiological agonist/antagonist
C. Pharmacological agonist/antagonist
D. Ligand
E. Agonist

Back 278

E. Agonist

Front 279

What is the term for a ligand that prevents signal transduction when it binds to the receptor?
A. Antagonist
B. Physiological agonist/antagonist
C. Pharmacological agonist/antagonist
D. Ligand
E. Agonist

Back 279

A. Antagonist

Front 280

What is the term for any naturally occuring molecule (like a hormone or neurotransmiter) that acts as a receptor ligand?
A. Antagonist
B. Physiological agonist/antagonist
C. Pharmacological agonist/antagonist
D. Ligand
E. Agonist

Back 280

B. Physiological agonist/antagonist

Front 281

What is the term for a synthetic molecule that acts as receptor ligand?
A. Antagonist
B. Physiological agonist/antagonist
C. Pharmacological agonist/antagonist
D. Ligand
E. Agonist

Back 281

C. Pharmacological agonist/antagonist

Front 282

Why is it that drugs aimed at receptors can have dangerous side affects when used improperly?

Back 282

Because the same ligand can bind to different receptors and lead to distinct responses. So a receptor subtype may activate opposing signal transduction responses.

Front 283

What is the term for signaling proteins that are distal to but activated by the agonist-bound receptor?

Back 283

Effectors

Front 284

True or False: In some cases, the receptor protein itself can be the effector.

Back 284

True

Front 285

What are small intracellular molecules that transmit and amplify the initial signal from agonist-activated receptors?

Back 285

Second messengers

Front 286

What are 3 ways that you can terminate the signal transduction by cell-surface receptors?

Back 286

- Receptor inactivation
- Receptor internalization
- Receptor down-regulation

Front 287

True or False: Ligand-gated ion channels have very rapid signaling and are generally found on nerve-nerve synapses or muscle-nerve synapses.

Back 287

True!

Front 288

In ligand gated ion channels, the ligand binds to their receptors with ________ (high/low) affinity which permits rapid dissociation of the ligand-gated receptor complex upon reduction of the extracellular concentration.

Back 288

Low!

Front 289

Cation-selective receptors are gated by the __________ (excitatory/inhibitory) neurotransmitters and these cations cause ________ (depolarization/hyperpolarization).

Back 289

Excitatory
Depolarization

Front 290

Anion-selective receptors are gated by the __________ (excitatory/inhibitory) neurotransmitters and these anions cause ________ (depolarization/hyperpolarization).

Back 290

Inhibitory
Hyperpolarization

Front 291

Name the excitatory neurotransmitters that can activate the cation-selective receptors.

Back 291

- Acetylcholine
- Glutamate
- Serotonin
- ATP

Front 292

Name the inhibitory neurotransmitters that can activate the anion-selective receptors

Back 292

- GABA
- y-amino butyric acid
- Glycine

Front 293

In ligand-gated ion channels, the depolarization or hyperpolarization caused by the influx of ions may, in turn, activate which type of channels?

Back 293

Voltage-gated

Front 294

What is the term for the receptors which primarily regulate long-term cell functions by initiating intracellular signaling cascades that end in the activation/inhibition of gene expression?
A. Ligand-Gated Ion channel receptors
B. Voltage-Gated Ion channel receptors
C. G-protein coupled receptors
D. Enzyme-linked receptors
E. Cytokine Receptors

Back 294

D. Enzyme-linked receptors

Front 295

What does Ras activate?

Back 295

MAP kinase

Front 296

Which type of receptors are multimeric and have a intracellualr caboxy-terminus that can have protein-protein interaction?
A. Ligand-Gated Ion channel receptors
B. Voltage-Gated Ion channel receptors
C. G-protein coupled receptors
D. Enzyme-linked receptors
E. Cytokine Receptors

Back 296

E. Cytokine Receptors

Front 297

Having a diverse range of ligands and having seven transmembrane regions is characteristic of what type of receptors?
A. Ligand-Gated Ion channel receptors
B. Voltage-Gated Ion channel receptors
C. G-protein coupled receptors
D. Enzyme-linked receptors
E. Cytokine Receptors

Back 297

C. G-protein coupled receptors

Front 298

________ binds to enhancers, while _________ bind to silencers, both of which control the transcription of genes by affecting the promoter.

Back 298

Activators
Repressors

Note: both are proteins binding to either an enhancer sequence or a silencer sequence

Front 299

Which subunit of the G-protein is the largest?
A. alpha
B. beta
C. gamma
D. beta-gamma
E. None of the above

Back 299

A. alpha

Front 300

Which subunit of the G-protein is hydrophilic?
A. alpha
B. beta
C. gamma
D. beta-gamma
E. None of the above

Back 300

A. alpha

Front 301

Which subunit of the G-protein is hydrophobic?
A. alpha
B. beta
C. gamma
D. B & C
E. None of the above

Back 301

D. B & C

Front 302

Describe the step-by-step process of the G-protein cycle.

Back 302

- First an agonist binds to GPCR causing a conformational change in it
- Then the G-protein binds to the GPCR which causes the release of GDP from the alpha subunit and GTP to bind to it.
- The binding of GTP at the alpha subunit causes dissociation of the alpha subunit from the BY complex
- The alpha subunit then travels to the effector to change second messenger levels

Front 303

True or False: One agonist-occupied receptor may serially interact with 10-100 molecules of trimeric G protein which results in major signal amplification.

Back 303

True

Front 304

Which type of RNA is the most abundant in the cell?

Back 304

rRNA

Front 305

rRNA is synthesized by which RNA Polymerase?

Back 305

RNA Pol I (one)

Note:
RNA Pol II = mRNA synthesis
RNA Pol III = tRNA, 5S RNA and other viral RNAs

Note: These are all for Euks!
Proks only use one RNA polymerase for transcribing all their genes (remember: holoenzyme stuff)

Front 306

RNA Pol III synthesiszes which types of RNAs in Eukaryotes?

Back 306

tRNA, 5S RNA and other viral RNAs

Front 307

Eukaryotes have how many types of polymerases?
What are they?
What do type of RNA chains do they form?

Quiz: Would rifampin work on these RNA Pols?

Back 307

-Euks have 3 types of RNA Polymerases

-They are:
-RNA Pol I - rRNA
-RNA Pol II - mRNA
-RNA Pol III - tRNA, 5S RNA

Quiz answer - I dont know..but I would think NO, because rifampin is an antibiotic - it inhibits RNA Pol in bacteria, and we are talking about Euk RNA Polymerases.

Front 308

What is the primary mechanism for rapid GPCR desensitization?

Back 308

Phosphorylation of the cell-surface receptor which results in loss of function

Front 309

The use of cAMP as a second messenger is largely limited to which type of receptors?
A. Ligand-gated ion channel receptors
B. Voltage-gated ion channel receptors
C. G-protein coupled receptors
D. Enzyme-linked receptors
E. Cytokine receptors

Back 309

C. G-protein coupled receptors

Front 310

What does G-protein alpha (i) lead to?

Back 310

- Activation of ion channels
- Inhibition of cAMP
- Activation of phospholipases
- Activation of phosphodiesterases

Front 311

What does G-protein alpha (l2) lead to?

Back 311

-Activation of Rho GEFs

Front 312

What are the 2 types of guanylate cyclase?

Back 312

- Membrane-associated guanylate cyclase
- Soluble form of guanylate cyclase

Front 313

Which protein kinase does cGMP activate?

Back 313

Protein kinase G

Front 314

The binding of what to the heme group on soluble guanylate cyclase causes a conformational change that increases catalytic activity of the guanylate cyclase dimer?

Back 314

NO nitric oxide!

Front 315

Calmodulin needs ______ to undergo a conformational change and facilitate in interactions with kinases, phosphotases, signaling proteins, etc.

Back 315

Calcium!!!

Front 316

MAP kinase pathways can be regulated by G-protein coupled receptors and growth factor receptor kinases. What is this an example of?

Back 316

Cross-talk

Front 317

what are snRNPs?

Back 317

small nuclear ribonucleoproteins which immediately bind to mRNA once it's released from RNA Pol II

- has a dual job :
1. breaks intron at 5' end
2. joins the upstream and downstream exons together

Front 318

True or False:
Almost all introns begin with a GU sequence and end with a AG sequence

Back 318

True

GU - is the 5' donor junction
AG - 3' acceptor junction

Front 319

Which RNA recognizes the GU sequence on the intron? Which one recognizes the 3' end?

Back 319

U1 RNA recognizes the GU sequence (5' end)
U2 RNA recognizes the 3' end (does not bind to the AG sequence)

Front 320

Describe the splicing mechanism

Back 320

1. First the phosphodiester bond between GU and exon is broken (through snRNPs)
2. the 5' end of the intron attacks 2' OH of adenine within the intron - forming a lariat (branched RNA structure)
2. Then the 3'OH from the first exon attacks the 5' end of the second exon, kicking the intron off

Front 321

True or False
Presence of introns in Euks generates protein diversity

Back 321

True!

The concept of alternative pre-mRNA splicing, which allows for certain introns to be cleaved, while certain remain - generating protein diversity

Ex - tissue-specific tropomyosin is generated from one tropomyosin gene

Front 322

What is alternative splicing?

Back 322

The concept allows for certain introns to be cleaved, while certain introns to remain - generating protein diversity

Front 323

True or False:
DNA and RNA both have repair mechanisms

Back 323

False!
Only DNA does - b/c it stores important information, but RNA is usually never repaired if damaged - instead it's broken down into nucleotides and is re-used.

- RNAs can be removed from cytoplasm by ribonucleases (RNase)

Ex: half life of tRNA in liver = 5 days
Half life of mRNA = 30 hours

Front 324

True or False
RNA molecules are stable

Back 324

False:
Relatively unstable

half life of tRNA in liver = 5 days
Half life of mRNA = 30 hours