1
Q
What are the 3 main types of RNA?
A
- mRNA: the shuttle that transfers genetic information from DNA to the ribosome
- few % of total cellular RNA
- highly variable in length and composition - rRNA: a structural and catalytic component of the ribosome
- 85% cellular RNA
- low variability - tRNA: an adaptor that decodes genetic information
- 10% cellular RNA
- low variability
2
Q
Which part of the RNA structure is vulnerable to hydrolysis?
A
2’OH on the ribose sugar
3
Q
What is special about the single strand of RNA molecules?
A
can form an extensive variety of structures via intra-strand base pairing and folding
- bulges
- internal loops
- junctions
- hair pins
4
Q
How does a bulge form on a single RNA strand?
A
There is no complementary base on one side of the region which results in the nucleotide bulging out
5
Q
How does an internal loop form on a single RNA strand?
A
There isn’t complementary bases on both sides of the regions so technically both sides bulge out.
6
Q
What are pseudoknots?
A
base-pairing between non-contiguous regions
7
Q
What is non-conical base pairing in RNA?
A
non-watson crick base pairs can be found in all combinations in RNA and gives RNA an enhanced capacity for self-complementarity. RNA is able to do this because it is very flexible in structure since it is not confined to form a double helix like DNA.
8
Q
What is non-conical base pairing in RNA?
A
non-watson crick base pairs can be found in all combinations in RNA and gives RNA an enhanced capacity for self-complementarity. RNA is able to do this because it is very flexible in structure since it is not confined to form a double helix like DNA.
9
Q
When RNA forms a double helix, what form is it in? Describe this form.
A
A form
- the 2’OH in the backbone prevents RNA from adopting a B-form helix
- minor groove: wide and shallow making it more accessible
- major groove: narrow and deep
- unlike DNA, RNA double helical regions are not as well suited for sequence-specific interactions with proteins
10
Q
____ ____ can stabilize RNA structures.
A
Metal Cations
- divalent and monovalent metal ions bind to specific sites in RNA and help shield the negative charge of the back bone phosphates
- allows parts of the molecule to pack more tightly
11
Q
Give 3 reasons why RNA can fold up into complex tertiary structures?
A
- doesn’t have the constraint of forming long regular helices
- single strand regions of RNA have a lot of rotational freedom
- often involves unconventional base pairing
- base triples
- non watson-crick base pairs
- base-backbone interactions
***important for catalytic activity for ribozymes
12
Q
What is the name given to RNA enzyme catalysts?
A
Ribozymes
13
Q
What are ribozymes?
A
RNA enzyme catalysts
- in addition to proteins, RNAs can also be enzymes where they bind to a substrate and perform a chemical reaction, and release a product
- ability to form tertiary structures is important for catalytic activity; this allows the formation of binding sites
1. for substrates
2. small molecule cofactors
3. an active site for catalysis
14
Q
RNase P
A
an Endoribonuclease
- cleaves 5’ end of precursor tRNA to make mature tRNA
- composed of both RNA and protein
- RNA: catalyst
- protein: shields the negative charges on the RNAso that it can bind to its substrate tRNA which is also negatively charged
15
Q
RNase P
A
an Endoribonuclease
- cleaves 5’ end (leader segment) of precursor tRNA to make mature tRNA
- composed of both RNA and protein
- RNA: catalyst
- protein: shields the negative charges on the RNA (itself) so that it can bind to its substrate tRNA which is also negatively charged
16
Q
RNase P
A
an Endoribonuclease
- cleaves 5’ end (leader segment) of precursor tRNA to make mature tRNA
- composed of both RNA and protein
- RNA: catalyst (metal cations help here)
- protein: shields the negative charges on the RNA (itself) so that it can bind to its substrate tRNA which is also negatively charged
17
Q
What are restriction endonucleases?
A
they cleave DNA at specific sites
- useful to be able to work with smaller, workable fragment sizes
- recognize specific sequences in the DNA (4-8bps) and cut at defined positions
- they are palindromic which means they can read the sequence from both sides
18
Q
What are the 4 different kinds of restriction endonucleases?
A
Hpal (blunt ends)
EcoRl (sticky ends)
Hindlll (sticky ends)
Pstl (sticky ends)
19
Q
What are the 4 different kinds of restriction endonucleases?
A
Hpal (blunt ends)
EcoRl (sticky ends)
Hindlll (sticky ends)
Pstl (sticky ends)
20
Q
What is the difference between restriction endonucleases leaving behind blunt ends or sticky ends?
A
other sequences can only bind to sticky ends
21
Q
How do you calculate how often you might see s specific sequence in DNA?
A
a 4 nucleotide sequence
4^4
a 8 nucleotide sequence
4^8
a 6 nucleotide sequence
4^6
22
Q
What technique can be used to identify specific DNA molecules?
A
DNA hybridization where a labeled radioactive or fluorescent probe is mixed with a mixture of ssDNA fragments.
23
Q
What is a Southern blot?
A
- technique based on DNA hybridization
- detects specific DNA sequence in complex DNA samples as well as relative quantity
- DNA fragments are digested by a restriction enzyme and run out on agarose gel- probe is then seen
Exp:
- DNA is cleaved and electrophoresis is used to separate DNA
- DNA fragments are blotted onto nitrocellulose filter and are invisible. This filter is positively charged so negatively charged DNA is able to bind to it. Alkaline PH is needed in this fluid for single stranded conditions to be maintained.
24
Q
What is a Southern blot?
A
- technique based on DNA hybridization
- detects specific DNA sequence in complex DNA samples as well as relative quantity
- DNA fragments are digested by a restriction enzyme and run out on agarose gel- probe is then seen
Exp:
- DNA is cleaved and electrophoresis is used to separate DNA
- DNA fragments are blotted onto nitrocellulose filter and are invisible. This filter is positively charged so negatively charged DNA is able to bind to it. Alkaline PH is needed in this fluid for single stranded conditions to be maintained.
- Filter is placed in a heat sealed bag that contains a solution and the radioactive probe and it hybridizes with homologous DNA fragments.
- Filter is exposed to photographic film and the film is developed. X-ray
25
What is a Northern blot?
- used to detect mRNA in a complex population of RNAs that is extracted from cells
1. size
2. quantity (reflects gene expression for the gene that encodes that mRNA)
- similar procedure to southern blot
* *no need to cleave RNA extracted from cells since they are already small enough to work with
- mRNA is single stranded already
* **the probe can be RNA or DNA; it doesn't matter here as long as it is single stranded
26
Protein structure
- polymers made of aa
- composed of C H O N S
- 20 different aa
- 3D shape adopted by its sequence of aa
* protein structure is related to protein function
27
What are 6 different functions of proteins
- structure
- regulation
- movement
- catalysis
- transport
- signaling
28
What does the amino acid structure consist of?
- amino group
- carboxyl group
- R: side chain
- H
29
What does the amino acid structure consist of?
- amino group
- carboxyl group
- R: side chain
- H
30
Neutral Non-polar amino acids have what kind of side chains?
hydrophobic
| tend to cluster inside of proteins because they do not like to be in aqueous environments
31
Neutral polar amino acids have what kind of side chains?
hydrophilic
| can interact extensively with water and atoms in other side chains through H-bonds
32
Acidic amino acids
donate H readily in aqueous environments
Glu, Asp ASSS
33
Basic amino acids
acquire H readily in aqueous environments
His, Lys, Arg, BASIC
34
____ bonds link nucleotides.
| ____ bonds link aa.
- phosphodiester bonds link nucleotides
| - peptide bonds link amino acids
35
How is a peptide bond formed?
- between 2 amino acids
- the carboxyl group of one and the amino group of the other
- through a dehydration reaction where H20 is removed to form the bond
36
Peptide bond characteristics
- partial double bond character due to the lone pair on N that can be localized onto the carbonyl oxygen
- carbonyl and amide components are nearly coplanar
- peptide bond has very little rotational freedom
37
Polypeptide backbone characteristics
- has directionality
- uncharged except for the N and C terminus
- NH and CO in backbone are available for H-bonding
38
What are the 3 special amino acids?
1. glycine: smallest side group and has more rotational freedom than any other amino acid
2. proline; only cyclic amino acid; has less conformational freedom than many other amino acids
3. cysteine- forms disulfide bonds that are covalent
39
What are the 3 special amino acids?
1. glycine: smallest side group and has more rotational freedom than any other amino acid
2. proline; only cyclic amino acid; has less conformational freedom than many other amino acids
3. cysteine- forms disulfide bonds that are covalent
40
How are disulfide bonds formed?
1. free -SH in reducing environments are oxidized
2. disulfide bonds already formed in more oxidizing environments with as extracellular proteins and cell surface proteins are reduced
*disulfide bonds enhance the stability of a folded protein by adding these covalent cross-links
41
Primary structure of a protein
- linear sequence of aa
| - unique order that makes each protein different
42
Secondary structure of a protein
local folding
1. alpha helix
2. beta sheet
* both are stabilized by backbone H-bonds
43
Describe the alpha helix
```
1948
Pauling and Corey at CalTech
-R-handed
-3.6 residues per turn
-H-bonding between every 4th amino acid parallel to the axis of the helix. The backbone NH group donates a hydrogen bond to the backbone C=O group of the amino acid 4 residues earlier
```
44
Describe the alpha helix
```
1948
Pauling and Corey at CalTech
-R-handed
-3.6 residues per turn
-H-bonding between every 4th amino acid parallel to the axis of the helix. The backbone NH group donates a hydrogen bond to the backbone C=O group of the amino acid 4 residues earlier
```
45
Describe the beta sheet
- H-bonds between backbone atoms in different segments of the polypeptide chain
- R groups project alternately to either side of the backbone
- strand is pleated (folded)
46
Beta sheets can be parallel or anti-parallel. Which direction does the arrow point- from which terminus to which?
N-terminus to C-terminus
47
What is the difference between parallel and anti-parallel Beta sheets?
anti-parallel beta strands have longer linker regions in between
48
What is a stable polypeptide chain structure defined as?
A stable structure is one where all H-bond donors and acceptors are involved in H-bonds. Since there is one H-bond donor and one H-bond acceptor in every backbone residue that must be bonded, much of the polypeptide is found in the alpha helix or beta sheet conformation.
49
Tertiary structure of a protein
3D folded structure
- depends on interaction of aa side chains
- folding creates an inside region and an outside region
*lowest energy state is most often attained with hydrophobic amino acids buried and hydrophilic amino acids exposed***
50
What are 5 factors that promote protein folding and stability in the tertiary structure?
1. H-bonds
2. ionic bonds
3. disulfide bridges
4. van der waals forces
5. hydrophobic effect
51
What are 5 factors that promote protein folding and stability in the tertiary structure?
1. H-bonds
2. ionic bonds
3. disulfide bridges
4. van der waals forces
5. hydrophobic effect
52
What are the 3 principle classes of a fold?
1. all alpha helical (myoglobin)
2. all beta strands (immunoglobulin)
3. mixture (ras)
53
What are motifs? What are the 3 kinds?
regular combinations of secondary structures
- tertiary structures composed of a defined arrangement of alpha helices and or beta sheets
- often a signature for a specific function
1. helix loop helix
2. zinc finger motif: alpha and 2 beta strands linked by a Zn
3. coiled coil motif
54
What experiment proved that the amino acid sequence is sufficient to determine tertiary structure of a protein?
1960s
Anfinsen experiment
1. Took a native tertiary structure protein
2. Added:
- urea: denaturant
- b-mercaptoethanol: reducing agent
3. got a denatured, unfolded protein
* 4. when they removed denaturant and reducing agent together, the protein was able to go back to its native state
* 5. when they removed the reducing agent and then the denaturant, they noticed that the protein was scrambled and disulfide bonds were made in the wrong places
55
What experiment proved that the amino acid sequence is sufficient to determine tertiary structure of a protein?
1960s
Anfinsen experiment
1. Took a native tertiary structure protein
2. Added:
- urea: denaturant
- b-mercaptoethanol: reducing agent
3. got a denatured, unfolded protein
* 4. when they removed denaturant and reducing agent together, the protein was able to go back to its native state
* 5. when they removed the reducing agent and then the denaturant, they noticed that the protein was scrambled and disulfide bonds were made in the wrong places
56
What are the 4 types of protein folding that can occur?
1. spontaneous folding: most can fold to their native conformation spontaneously
2. chaperone assisted folding: chaperone proteins required for proper folding of some polypeptide chains
3. denature: loss of native folding and protein activity due to the break of weak or strong bonds, via chemical or physical agents
- urea
- heat
- pH
- detergents
- reducing agents
4. renature: regain native conformation and solubility in aqueous solution
57
Quaternary structure of a protein
- subunits in multimeric proteins
- subunits held together by
1. noncovalent bonds
2. also covalent disulfide bonds
- multimeric proteins can be made up of identical (homo) or unidentical (hetero) subunits
- homodimer
- homotrimer
- heterooligomer (heterotetramer)
LS3
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