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Biol 130 > Module 5: Protein Structure, Function & Synthesis > Flashcards

Module 5: Protein Structure, Function & Synthesis Flashcards

1
Q

Proteins are ___, ___, &___

A

ubiquitous, diverse and versatile

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2
Q

Many of the cellular activities and reactions that are involved in cellular function are ___ by ____

A

mediated by proteins

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3
Q

3 Models of Protein Structure

A
  1. ball- and - stick model
  2. ribbon model
  3. space-filling model
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4
Q

Proteins are linear polymers of a combination of ____

A

20 amino acids

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5
Q

Protein function…

A

is related to structure.

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6
Q

Amino acids are the…
and made up of…

(4 components)

A

building blocks of proteins
Four components (each component is bound to the alpha carbon):
1. carboxyl group (-)
2. amino group (+)
3. hydrogen
4. side chain/ R group
- make each amino unique
- responsible for chemical and physical properties of each amino acid monomer

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7
Q

Amino Acid Classification

A

R groups are grouped according to their properties
Based on:
- how they interact with water (hydrophobic or hydrophilic)
- basic or acidic
- polar or non polar

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8
Q

Hydrophobic Amino Acids

A
  • tend to buried in interior of folded proteins
  • hydrophobic R groups aggregate together away from the water
  • Weak van der Waals forces help with stability by causing hydrophobic R groups to be attracted to each other
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9
Q

Hydrophilic Amino Acids

A
  • contain EN elements like N and/or O
  • results in unequal charge, allows R groups to interact with each other or with H2O via H-bonding
  • Basic AA tend to be + charged
  • Acidic AA tend to be - charged
  • charged groups can form ionic bonds with one another and other charged molecules
  • typically found on “outer” surface of proteins
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10
Q

Glycine

A

Gly, G
- has H as R group
- not asymmetric
- small and nonpolar, allows free rotation around C-N bond
- this increases the flexibility of the polypeptide backbone

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11
Q

Proline

A

Pro, P
- makes a pentagon with 3 CH2s
- linkage restricts rotation of the C-N bond, limits amount of protein folding around proline

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12
Q

Cysteine

A

Cys, C
- CH2 bonded to SH for R group
- allows two cysteines to form a S-S disulfide bond, forms a cross bridge
- the cross-bridges can connect different parts of the same protein or different proteins together

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13
Q

Linking Amino Acids

A
  • adjacent amino acids are joined by peptide bond (between amino of one AA and carboxyl of another AA)
  • this is a dehydration (or condensation) reaction
    – releases H2O
  • free AA group at end of peptide forms the N- terminus
  • carboxyl group at end is C-terminus
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14
Q

A polymer of AA connected by peptide bonds is a ____, used synonymously with ____

A

polypeptide
protein

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15
Q

Protein Structure

A

amino acid in a protein gives the structure and thus the function
- proteins fold a certain way based on sequence of AA and the order of the R groups
- 4 levels of organization:
primary, secondary, tertiary, quaternary
- the three-dimensional structure of a protein is the protein conformation, this is described by 2’, 3’, 4’

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16
Q

Primary Structure

A
  • specific linear sequence of amino acids that make up the polypeptide chain, from amino to carboxyl end
  • most polypeptides contain many amino acids, these are coded for by the genome
  • primary structure determines 2’, 2’, 4’ structure of the protein
  • sequence of primary structure can be written either as three letter or one letter abbreviations
  • R groups alternate position on either side of the chain of amino acids
    – this affects protein folding and interaction of R group
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17
Q

Secondary Structure

A
  • describes conformation of portions of the polypeptide chain
  • two types, alpha helix & beta sheet
  • results from H-bonding between neighbouring amino acids of the polypeptide backbone, occur between functional groups
  • R groups are not involved
18
Q

Alpha Helix

A
  • very stable structure
  • right handed helices, let molecules that are not nearby in main structure interact with one another
  • forms due to H-bonds to the 4th amino acid neighbour above and below in the spiral
  • the carbonyl group of the one AA and the amide group of the 4th AA
19
Q

Beta Sheet

A
  • segments of the polypeptide lying side by side, assumes a pleated (folding) conformation
  • can be parallel and antiparallel
  • structure is stabilized by H-bonds formed between carbonyl groups in one chain and amide groups in the other chain within the same polypeptide
20
Q

Tertiary Structure

A
  • describes the conformation of the entire protein, single polypeptide chain folded into 3’ structure
  • ultimately this is how the regions of 2’ conformations are oriented
  • results in its functional form, unless part of protein with multiple subunits
  • structure determined by:
    – spatial distribution of hydrophilic and hydrophobic R groups
    – chemical bonds and interactions that form between R groups
    – H-bonds, hydrophobic, ionic, disulfide bonds
  • overall shape of (3’) functional protein may result in areas of protein that form active sites for enzymes, exterior R groups may impact how protein interacts with other molecules or proteins
21
Q

Quaternary Structure

A
  • Many proteins are made up of more than one polypeptide chain, subunit
  • the spatial arrangement of these subunits is the 4’ structure
  • these arise due to the same bonds as found in 3’ structure
  • polypeptide chains in each subunit may be:
    – identical - Homodimer
    – non-identical - heterodimer
22
Q

In transcription the sequence of DNA is used as…

A

a template, it makes the mRNA

23
Q

In translation the sequence of bases in mRNA is used to…

A

specify the order of amino acids to be added to the growing polypeptide, its the final stage of the central dogma

24
Q

Components of Translation:

A
  1. mRNA (messenger)
  2. Ribosome
  3. tRNAs (transfer)
  4. Aminoacyl tRNA synthetases
  5. Initiation factors, elongation factors & release factors
25
Q

Ribosomes

A
  • protein factories
  • this is where translation takes place
  • complex structure of RNA and protein
    – consist of small subunit and large subunit
  • eukaryotic ribosomes are larger than prokaryotic ribosomes
  • the mRNA is bound by the large and small ribosomal subunits, then moves through center of ribosome
  • 5’ to 3’ reading individual codons to incorporate the appropriate amino acids
26
Q

What is a codon?

A
  • a nucleotide combination that specifies the placement of an amino acid (codes for it)
  • Read in groups of 3
  • reading frame is where the ribosome begins reading the sequence of nucleotides
27
Q

Where does translation begin?

A
  • does not begin with the first 5’ RNA base on the mRNA
  • begins with start codon AUG
  • codes for methionine
28
Q

Ribosome Sites

A

3 functional sites
1. the aminoacyl tRNA is accepted in the A site
2. the peptide bond formation happens in the P site
3. the tRNA exits the ribosome in the E site

29
Q

Transfer RNAs

A
  • translation needs the transfer RNA molecule, i.e. tRNA
  • small molecules containing 70 -90 nucleotides (know are small)
  • each tRNA bonds with itself, forms base pairs
  • results in a structure that looks like a cloverleaf
  • two important sites on each tRNA
    – the 3’ hydroxyl site on the 5’-CCA-3’ end of the tRNA is where the specific amino acid attaches
    – three bases in the anticodon loop make up the anticodon
30
Q

How are amino acids attached to the tRNA?

A

specific amino acids area connected to specific tRNA molecules by enzymes called aminoacyl tRNA synthetases
- a tRNA without an amino acid attached is uncharged
- a tRNA with an amino acid attached is charged
- tRNA synthetases are very accurate

31
Q

The Genetic Code

A
  • during translation, the anticodon of the tRNA base pairs with the codon on the mRNA
  • base pairing is the specificity of DNA-RNA or codon-anticodon interactions
  • anticodons of tRNA base pair in antiparallel fashion
    – so first base of codon pairs with last base of anti-codon
  • genetic code has 20 amino acids but specified by 64 codons
  • many amino acids are specified by more then one codon, makes the genetic code redundant or degenerate
  • bases read 5’ to 3’ on mRNA chart
32
Q

Translation Stages

A

Has 3 stages
1. Initiation
- AUG codon is recognized and Met is the first amino acid
2. Elongation
- each successive amino acid is added to the growing polypeptide chain
3. Termination
- adding amino acids stops and the polypeptide chain is released from the ribosome

33
Q

Eukaryotic Translation Initiation

A
  • steps 2 & 3 of translation are similar between prokaryotes and eukaryotes
    – step 1 is different
  • in eukaryotes the initiation complex forms at the 5’ cap of the mRNA
    – the small ribosome and initiation factors will then “scan” the mRNA for the start codon on the mRNA -AUG
  • once start codon is reached the large ribosomal subunit is then recruited and translation can start
  • initiation factors are released
34
Q

Translation Elongation

A
  • after the ribosome is assembled, a new tRNA enters the A site, allows peptide bond to form
  • amino acid on the tRNA in the P site transfers to the tRNA in the A site during elongation
  • the reaction is catalyzed by an rRNA molecule in the large ribosomal subunit
  • ribosome then shifts one codon to the right
  • this moves uncharged tRNA (Met) to the E site
  • the peptide bearing tRNA moves to the P site
  • this frees the A site for the next charged tRNA in line to come in based on the next codon
35
Q

Translation Termination

A
  • process continues until one of 3 codons are reached
  • UAA, UAG, UGA these are stop codons, they don’t code for an amino acid
  • a protein release factor binds to the A site of the ribosome at the stop codon
  • causes bond that’s connected to polypeptide of the tRNA to break
  • creates the carboxyl terminus of the polypeptide, completes the chain
36
Q

Prokaryotic Translation Initiation

A
  • prokaryotes don’t have 5’ cap
  • initiation complex is formed at one or more internal sequences present in mRNA, Shine-Dalgarno sequence
  • elongation and termination are like in euks
37
Q

Regulating Protein Synthesis

A
  • not all genes are expressed in the cell all the time
  • many levels of regulation in cell
    – DNA accessibility
    – transcription factors
    – RNA processing
    – post-translational modifications
38
Q

Protein Sorting in Eukaryotes

A
  • mRNA is bound to a ribosome in the cytosol, where translation begins
    -what happens to the protein post translation depends on how its going to be sorted, specific signal sequences
  • no signal, stay in cytosol
  • amino terminal signal sends to chloroplast or mitochondria
  • internal signal sends to nucleus
39
Q

Some proteins have a specific amino terminal signal sequence for transport to the ____

A

ER
- it is bound by the signal recognition particle, SRP
- the ribosome with associated mRNA and newly formed polypeptide are transported to the ER

40
Q

Proteins produced by ribosomes on the rough ER could be found:

A
  • embedded in the ER membrane, inserted as it is synthesized
  • within the lumen of the endomembrane system
  • secreted out of the cell

Biol 130 (11 decks)

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