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Genetics > Translation > Flashcards

Translation Flashcards

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Biology 101 flashcards
1
Q

Translation

A

Takes the “message” from the mRNA and makes proteins

Converts the mRNA sequence into a sequence of amino acids using the genetic code (amino acid will get folded into a protein which will be the end result of our gene expression) we express genes to get proteins to do stuff in our bodies

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2
Q

Peptide bonds

A

a type of covalent bond that joins amino acids in polypeptide chains
formed between the amino and of one amino acid and the carboxyl end of the adjoining amino acid

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3
Q

polypeptide

A

a chain of amino acids joined by peptide bonds

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4
Q

Where does translation occur?

A

occurs in ribosomes(RNA protein structure), where mRNA nucleotides are “read” in groups of 3 (called codons), which specify the specific amino acid that will be added

TRNA will bring in the specific amino acid to the ribosomes and growing the polypeptide chain

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5
Q

codons

A

The nucleotide triplet of mRNA that encodes a single amino acid
part of the genetic code

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6
Q

Start codons

A

(5’-AUG-3’) initiate translation, which will go until a stop codon is read
Most commonly AUG, encoding methionine, the first codon translated in poly- peptide synthesis

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7
Q

stop codon

A

One of three codons that bind a release factor instead of base-pairing with tRNA to initiate a series of events that stops translation

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8
Q

genetic code

A

The universal set of correspon- dences of mRNA codons to amino acids. Used in translation to synthesize polypeptides.

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9
Q

i

A

each protein has a unique sequence of amino acids, may be composed of one or more polypeptide chains, and generally has its own characteristic three-dimensional structure.

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10
Q

How many amino acids are there what do they all contain?

A

20 different amino acids, all of which have:

Central α-carbon (alpha carbon)

Amino group (NH3 +)

Carboxyl group (COO- )

R-group (distinctive for each amino acid)

Abt 8 amino acids we have to get from food or different sources(metabloism)

Essential amino acids must be obtained through diet- cant be made by our bodies

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11
Q

What are the different properties of the R groups?

A

Basic: Arg, His, Lys

Acidic: Asp, Glu

Basic and acidic have a charge and issociate in water and accpet or donate hydrogens

Neutral nonpolar

Neutral polar

Neutral means neither acidic or basic but may or may not have a charge depending on polar or non polar group

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12
Q

Where are polypeptides assembled

A

are assembled in ribosomes (transcribed in the nucleolus in nucleus and exported out of nuclear envelope to cytoplasm and assembled into fully functioning ribosomes)

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13
Q

What direction does translation occur in?

A

Translation is in the 5’-to-3’ direction

Similar to RNA direction of transcription

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14
Q

Outline the basic process of translation

A

Ribosomes bind to the mRNA

Complementary base pairing between mRNA codon sequences and tRNA anticodon sequences

he start and stop codons define the regions of mRNA to be translated

Resulting polypeptides have an Nterminal (amino terminal) at the 5’ end and a C-terminal (carboxyl terminal) at the 3’ end

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15
Q

Is all of the mRNA translated

A

Two regions of mRNA are not translated

5’ untranslated region (5’ UTR):
- Helps with translation initiation

3’ untranslated region (3’ UTR):
Helps with transcription termination

These regions are Analogous to promoter and terminators

Regions that are not actively translated into a protein but help with initiation process and termination

We start with long DNA and then end with shorter molecule that is the polypeptide

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16
Q

5’ untranslated region (5’ UTR)

A

upstream of the Start codon at the 5’ end of the mRNA transcript

Helps with translation initiation

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17
Q

3’ untranslated region (3’ UTR):

A

downstream of the Stop codon at the 3’ end of the mRNA transcript

Helps with transcription termination

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18
Q

Primary structure

A

(this present mostly in active translation process)

Sequence of amino acids

Stabilized by peptide bonds

Order of amino acids critical to function of resulting protein

is a direct result of expression of our genetic code

DNA to RNA and RNA tells us how to make polypeptide

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19
Q

Secondary structure

A

Alpha helices (twisting coil) and beta-pleated sheets (130° bended parallel sheets)

Gives shape

Stabilized by hydrogen bonds within the polypeptide backbone (polar R-groups) and ionic interactions

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20
Q

Tertiary structure

A

3d shape of the protein

Results from polypeptide folding

Stabilized by hydrogen bonds, covalent bonds, ionic interactions, hydrophobic interactions, disulphide binds between R-groups

Direct result of interaction between R groups in our amino acids

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21
Q

Quaternary structure

A

(like hemoglobin protein)

Contains 2 or more polypeptides (multimers)

2 or more tertiary structures coming together

22
Q

alpha helix

A

is a twisted coil of amino acids stabilized by hydrogen bonds between partially charged R-groups;

23
Q

beta-pleated sheets

A

is a roughly 130-degree bend created when hydrogen bonding between amino acids induces a segment of a polypeptide to fold

24
Q

What are the 3 common functions of ribosomes?

A

Throughout Life’s diversity, ribosomes have 3 common functions: (doesn’t matter if prokaryote or eukaryote ribosomes have all these functions)

Bind mRNA and identify the Start codon for translation

Facilitate complementary base-pairing between mRNA codons and tRNA anticodons (complementary to specific codon)

Catalyze peptide bond formation

25
Q

What are the differences in ribosome structure between prokaryotes and eukaryotes?

A

Differences in ribosome structure between prokaryotes and eukaryotes are in the number of ribosomal subunits and sequence of rRNA molecules

Protein synthesis is conserved through all life (across all domains its similar)

Prokaryotes(70s) in general have smaller ribosomes than eukaryotes (80s)

26
Q

What do ribosomes across the 3 Domains share?

A

ribosomes across the 3 Domains share structural homology

Large ribosomal subunit

Small ribosomal subunit

Measured in Svedberg units (S) (are measured according to centrifuge rate)

27
Q

What does a higher S mean?

A

Higher (S) means larger molecules

refers to cumulative weigth

28
Q

i

A

he rRNA molecules within the ribosomal subunits are conserved sequences within the genome, and specific to the organism
We can use these sequences to ID organisms with metagenomics

29
Q

Describe Ribosome Structure:

A

The large and small ribosomal subunits contribute to translation

Peptidyl site (P site): holds the tRNA containing the nascent polypeptide

Aminoacyl site (A site): binds the new tRNA molecule

Exit site (E site): tRNAs leave the ribosome

The small subunit has a channel for the mRNA

The large subunit has a channel for the growing (nascent) polypeptide chain- what the polypeptide chain comes out of

30
Q

i

A

1st RNA comes in at A site gets bumped over to P site and next RNA comes in to A site there’s some bonding going the P site Trna moves to E site, former A site one moves to P site

As soon as the polypeptide starts coming out of ribosome it starts to get folded, the r groups are going to interact with cytoplasm and start forming beta pleated sheets or alpha helics

Protein folding happens at same time as translation is going on in Ribsome

31
Q

What are the 6 components for initiation ?

A

mRNA

Small ribosomal subunit

Large ribosomal subunit

Initiator tRNA

  • MET
  • First initial Trna is brough to p site

3 essential initiation factors

GTP

32
Q

Describe general the process of translation - Initiation

A

The small ribosomal subunit binds to the 5’-end of the mRNA and identifies the Start codon (AUG)

Initiator tRNA carries Methionine(MET) (the starting amino acid) to the start codon

The large ribosomal subunit joins the small subunit, forming an intact ribosome

Initiation factor proteins help control ribosome formation, the binding of the initiator tRNA

GTP (guanosine triphosphate) provides the energy

Translation can now proceed

  • Charged tRNAs
  • Uncharged tRNAs( as soon as TRNA deposits amino acid to growing polypeptide chain and leaves the e site) leave the ribosomal complex to get another amino acid

Floats around the cytoplasm and look for another amino acid

Lots of Trna recycling going on

33
Q

Charged tRNAs

A

(as soon as tRNA has amino acid attached) bring in specific amino acids

34
Q

Uncharged tRNAs

A

( as soon as TRNA deposits amino acid to growing polypeptide chain and leaves the e site) leave the ribosomal complex to get another amino acid

Floats around the cytoplasm and look for another amino acid

Lots of Trna recycling going on

35
Q

Describe first part of bacterial initiation

A

Small subunit is affiliated with IF3 (initiation factor protein)

  • Facilitates binding to mRNA and prevents the two subunits from binding together
  • Binds near the 5’ end of the mRNA and looks for AUG
  • Forms the preinitiation complex after the 16S rRNA (30S subunit) base -pairs with mRNA located upstream of the start codon in the 5’UTR

The preinitiation complex is going to form at very specific sequences in the bacteria- going to look for the shine sequence and that is where its going to help position the small subunit just upstream of start codon
Once initiation complex is ready we have initiation factor that is bound to the shine sequence

36
Q

Shine -Dalgarno

A

is purine rich consensus sequence

Helps to position the 30S subunit

37
Q

Describe first part of bacterial initiation

A

(one small subunit has found the shine sequence) Initiator tRNA binds to the start codon, which will become the P site

  • Amino acid on this tRNA = N-formylmethionine (fMET)- has additional nitrogen
  • Anticodon = 3’-UAC-5’

Initiation factor IF2 + GTP bind to P site to bind the Met

Initiation factor IF1 then binds to the 30S subunit, creating the 30s initiation complex which now also includes mRNA

Last step, the 50S subunit then joins the 30S subunit to form the intact ribosome

  • The IFs dissociate, leaving behind the 70S initiation complex
  • Ribosome with P(loaded with MET), A(ready to accept more TRNA), and E sites
38
Q

N-formylmethionine (fMET)-

A

A modi- fied methionine amino acid usually used as the amino acid that initiates bacterial translation. Carried by a specialized tRNA.

39
Q

30s initiation complex

A

in bacterial translation, the complex formed by a small ribosomal sub- unit, mRNA, and the tRNA carrying fMet.

40
Q

eukaryotic initiation factor (eIFs)

A

A group of eukaryotic proteins that associate with ribo- somal subunits and help initiate translation.

41
Q

Describe Eukaryotic Translation Initiation

A 
The 40S (small) ribosomal subunit complexes with eukaryotic initiation factor (eIFs) proteins eIF1, eIF1A, eIF3  
- Forms the preinitiation complex

The preinitiation complex then joins with initiator tRNA and eIF5

This complex then joins with mRNA, becoming the initiation complex

The initiation complex scans the mRNA 5’UTR looking for the start codon

  • 90% will go to the first 5’-AUG-3’ it finds (Called the authentic start codon )
  • 10% will go to the 2nd or 3rd AUG
  • This authentic start codon (the one it actually needs to translate) has the Kozak sequence

Once found, the 60S (large) subunit is recruited to the complex using GTP

eIFs dissociate, leaving the now 80S ribosome to begin translation

42
Q

Kozak sequence

A

named after Marilyn Kozak, 1978)

5’-ACCAUGG-3’

A specific consensus sequence of eukaryotic mRNA that contains the authentic start codon (AUG) sequence.

43
Q

What are some difference between eukaryotic and prokaryotic initiation?

A

Difference between eukaryotic and prokaryotic is number and type of initation factors that are involved

Also the Kozak is in eukaryotes and shine sequence is prokaryotes

Every result of gene expression is going to have a kozak sequence

44
Q

Describe the general process of elongation

A

Elongation factors (EFs) are added to the initiation complex

  • Assist in the recruitment of charged tRNAs to the A site
  • Formation of the peptide bond
  • Translocation of the ribosome in the 3’ direction along the mRNA

GTP provides the energy

45
Q

Describe differences in the elongation process across the different domains

A

Elongation factors may differ in the 3 domains, but the overall process is the same across prokaryotes and eukaryotes

  • Bacteria add 20 new amino acids per second to the nascent(being synthesized) polypeptide chain
  • Eukaryotes add 15 amino acids per second to the nascent polypeptide chain

Proteins are the ultimate products of gene expression

46
Q

Describe polypeptide elongation in bacteria

A
  1. Charged tRNA is bound by EF-Tu and GTP
  2. tRNA enters the A site
  3. Hydrolysis of GTP releases EF-TU-GDP from tRNA
  4. Peptidyl transferase catalyses the peptide bond between the amino acid in the P site and the newly added amino acid
  5. The tRNA in the P site moves to the E site and departs

Elongation factor EF-G uses GTP to translocate (move) the ribosome in the 3’ direction

Moves the A site tRNA now to the P site

  1. The next charged tRNA can now enter the newly empty A site

The amino acid will be specific to the codon present in the A site

47
Q

Polypeptide elongation in eukaryotes

A

Elongation follows the same overall steps as in bacterial elongation, only it uses different elongation factors

The process of polypeptide formation is universally conserved

48
Q

Describe termination

A

Elongation continues until a stop codon is reached
- UAG, UGA, UAA (memorize)

There are no tRNAs with anticodons complementary to the stop codons

  • Release factors (RFs) are used to bind a stop codon to the A site to initiate the termination event
  • The catalytic activity of the RF releases the polypeptide bound at the P site
  • Polypeptide release causes ejection of the RF from the P site and the ribosomal subunits separate
49
Q

Release factors (RFs)

A

Molecules that bind mRNA stop codons and contribute to translation termination.

50
Q

What are some differences in eukaryotic and prokaryotic termination?

A

Release factors vary slightly between bacteria and eukaryotes

Bacteria: RF1 and RF2 recognizes UAG/UAA and UAA/UGA respectively

Also has RF3 which recycles RF1

Eukaryotes: eRF1 recognizes all 3 stop codons

Also has eRF3 which recycles eRF1

51
Q

Explain how translation is a fast and efficient process

A

Each bacterial cell contains ~20,000 ribosomes, which is about ¼ of the cell’s mass

Eukaryotes also contain tens of thousands of ribosomes

Ribosomes can form rings or chains, forming polyribosomes
- Translate the same mRNA, each independently making their own polypeptide- helps amplify gene expression

In prokaryotes, absence of the nucleus allows for coupling of transcription and translation
- Uncoupled in eukaryotes

52
Q

Why does the genetic code have to be redundant ?

A

To avoid mutations

Genetics (12 decks)

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