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Bio 243 > Theme 2C > Flashcards

Theme 2C Flashcards

1
Q

Where are peptide bonds found, how are they formed

A

Between the amino and carboxyl group

Formed through dehydration reaction between amino and carboxyl

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2
Q

What is an amino acid?

A

They contain amino groups, carboxyl groups, R groups on a central carbon with a hydrogen

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3
Q

What is a polypeptide?

A

A linear chain of amino acids linked by peptide bonds does not include R groups

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4
Q

What are the classes of amino acids? What are the special functional amino acids

A

Nonpolar
Uncharged polar
Charged amino acids
Aromatic amino acid

Methionine
Proline
Cysteine

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5
Q

What is a nonpolar amino acids?

A

It’s R group usually has CH2 or CH3

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6
Q

What is an uncharged polar amino acid?

A

It’s R group usually has oxygen or OH

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7
Q

What is a charged amino acid?

A

It has r groups that contain acids or bases that can ionize

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8
Q

What is an aromatic amino acid?

A

R groups have a carbon ring with alternating single and double bonds

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9
Q

What is methionine

A

First amino acid in a polypeptide always

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10
Q

What is proline

A

Causes a kink in the polypeptide chains
This makes the 3-D structure because of the bend

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11
Q

What is cysteine

A

It is a disulfide bridge that contributes to the overall structure of polypeptides (s-s)

Only one that has sulphide bond

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12
Q

What is the primary amino acid sequence and why is it important

A

It determines the protein folding and 3-D structure, which is critical for the proper function of the protien, so is the primary protien structure

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13
Q

What is the secondary protein structure?

A

The structure depends on hydrogen bonding in the polypeptide backbone
Either comes as alpha helicis, which are ribbons or beta sheets, which are flat paper like

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14
Q

What is the tertiary proteins structure?

A

The 3-D structure of a single polypeptide formed by interactions between amino acid side chains, includes R groups

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15
Q

What is the quaternary structure of a protein?

A

Interactions between more than one polypeptide to form a multi subunit proteins.

Example is hemoglobin, which has two alpha helices, and two beta sheets.

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16
Q

How is protein folding disrupted?

A

Buy denaturation (heat, or chemicals) causes loss of function
Or mutations that change the amino acid sequence

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17
Q

How do chaperones help proteins?

A

Protect slow folding, or denatured proteins by preventing their aggregation (meaning sticking together and forming masses) (help proteins fold)

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18
Q

What are diseases associated with misfolded proteins?

A

Alzheimer’s (plagues of protein) Parkinson’s and creutzfeldt-Jakob

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19
Q

What are tRNAs

A

Adaptors between codons and amino acids
The molecule that is between the processes of going from mRNA to amino acid
Bridge between nucleotide and amino acid

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20
Q

What does the 2D and 3D shape of TRNA look like

A

Cloverleaf
L shape

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21
Q

Where did the amino acid attach to on the tRNA , what end!@?

A

tha acceptor stem which is at the 3’ end of the TRNA

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22
Q

What is the sequence of the acceptor stem (3’ end) in tRNA

A

5’-CCA-3’

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23
Q

Where and what is the anticodon in TRNA

A

The bottom loop
It has a three nucleotide sequence that recognizes the mRNA codon and base pairs with it

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24
Q

What direction is the anticodon pairing with the mRNA?

A

Antiparallel
If mRNA is 5-3
tRNA is 3-5

25
Q

What enzyme adds the amino acid to it corresponding acceptor stem of tRNA? What is this process called

A

Aminoacyl-tRNA synthase
Charging

26
Q

How many aminoacyl tRNA synthases are there

A

20 different ones for the 20 different amino acids that correspond to the correct anticodons

27
Q

What is the charging reaction of Aminoacyl-tRNA

A

Amino acid+tRNA+ATP——> aminoacyl-tRNA+AMP+PPi

28
Q

How many sense codons are one the codon table. What direction are they

A

61 sense codons that code for amino acids

Read in 5’ to 3’ direction

29
Q

What is the start codon?

A

AUG methionine

30
Q

what are the stop codons? what’s special about them

A

UAA UAG UGA
They don’t code for amino acids (tRNA doesn’t bind to them)

31
Q

What is the +1 reading frame, +2, +3?

A

Reading directly from the very first ribonucleotide
Reading from second
Reading from third

32
Q

Which reading frame is most likely to code for polypeptide

A

the one that translates the start codon.

33
Q

Why is there no +4 reading frame?

A

Cause then you’ll just start translating the same way as the +1 frame

34
Q

What is wobble, where does it not occur

A

When the base at the 5 prime end of anticodon can bind (form h bonds) to more than one other type of base at the three prime end of the codon.

There is no wobble at the two other nucleotide in the anticodon, their pairing is precise.

35
Q

What are the base pair combos with wobble?

A

Anticodon/codon

G/U or C
U/A or G
Inosine/A U C

36
Q

What are ribosomes made of?

A

Large subunit (50s)
Small subunit (30s)

37
Q

What is the large subunit

A

Made of 34 protiens and 5s and 23s ribosomal rna. Has the peptide l transferase centre that forms peptide bonds

38
Q

What is the small subunit

A

This is the part of ribosome where the codons of mRNA is being read and decoded.

39
Q

Where are each ribosome subunit in the cell?

A

In the cytoplasm, they exist separately and come together to start translation

40
Q

Ribosomal rna is ____

A

Non coding

41
Q

What is the p-site (peptidyl)

A

Bind to the trna that has the growing peptide chain

42
Q

What is the A-site (aminoacyl)

A

Bind to the tRNA that is carrying the next amino acid to be added to the p site

43
Q

What is the e- site (exit)

A

Binds the tRNA that gave away the previous amino acid

Ejects the tRNA

44
Q

What is the process of translation initiation in eukaryotes

A

The initiator tRNA (met) is brought to the p site of the small ribo subunit, need GTP (energy) to do so

The subunit then attaches to 5 prime cap of mRNA then scans along 5-3 direction until it reaches the first start codon

Complimentary base pairing occurs between the anti codon and the first start codon

After, the large ribo subunit and fuses to small subunit. Then waits for first tRNA in A site.

GTP is hydrolozed into GDP then translation begins

45
Q

Explain translation elongation process

A

The correct charged aminoacyl tRNA is loaded into the A SITE by elongation factor GTP.

The peptidyl transferase in psite makes peptide bond between the charged tRNA and the met. Now the initiator tRNA is not charged cause it has no AA

The ribosome then moves 3 ribonucleotide over so the the initiator tRNA is now in the e site (to eject) and the trna which peptidyl chain is in p site

The next charged tRNA comes in and repeats proccess.

46
Q

Describe the termination proccess

A

There are three stop codons at the end of the protien coding sequence

The stop codons are recognized by protiens called release factors

When ribosome reaches the stop codon, the release factor binds to the a site and make peptidyl transferase cleave off the polypeptide from the tRNA

The ribo subunits separate and detach from mRNA. Release fact and empty tRNA also separate

47
Q

What are some ways for post translation regulation,

A

Phosphorylation
Ubiquitination
Proteolysis

48
Q

What is phosphorylation

A

The adding of phosphate to proteins by the enzyme kinase.

This inhibits or activates the activity

Ex. CDK1 phosphorylates MAP (microtubule associated protein) to enhance spindle assembly.

49
Q

What is ubiquination

A

Adding ubiquitin molecules to proteins which targets the proteins for destruction by the proteasome

50
Q

What is proteolysis

A

The specific cleavage of a protein which induces activity

51
Q

What is epigenetics

A

The post-translational modification of histones that affect transcription

Changes the way the dna is wound on the histones

52
Q

What does histone acetyltransferase do

A

Adds actetyl groups (-) to the histone tails.

This loosens the dna bonding because the acetyl is negative and makes histones more negative. The dna is also negative so repulsion occurs and loosens dna

Increase gene transcription

53
Q

What is methylation

A

Histone tails get methyl groups that activate or repress transcription (represses some phenotypes) droning on the histone

54
Q

What happens if DNA is methylated at CpG islands?

A

Since CpG islands are close to promoters, the transcription can be repressed

55
Q

What is the chromatin remodeling complex

A

kicks out the nucleosomes from the promoter region thus increases transcription rate

Because histones are in the way of rna polymerase, make it easier for rna pol to get on the promoter and start transcription

Reaction requires atp

56
Q

What is translation regulation

A

The control of protien synthesis

(Rate of translation initiation or formation of the initiation complex)

57
Q

What is post translation regulation

A

This is after the polypeptide is made

Controlling the protien abundance and activity.

58
Q

What does the amount of protien depend on

A

Rate of its synthesis (translational)
And degradation (post translation)

59
Q

What does the activity of protein depend on

A

Post translation modifications (ex phospphorilaytion and cleavage)

Bio 243 (8 decks)

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