Protein Structure, Function, And Synthesis

Question 1

how many different amino acids are there?

Answer 1

Recall that proteins are linear polymers of a combination of 20 amino acids → like letters in an alphabet

Question 2

Components of amino acids:

Answer 2

• There are four components of an amino acid
• Each component is bound to the alpha (a) carbon
• Three components are identical for all amino acids:
  a. the carboxyl group
  b. the amino group
  c. a hydrogen
• At physiological pH the amino & carboxyl groups are charged (amino group is positive and carboxyl group is negative)
• The fourth component is the side chain → R group
• The R groups make each amino acid unique
• Are responsible for the chemical and physical properties of each amino acid monomer

Question 3

How are amino acids classified?

Answer 3

• The R groups of amino acids are grouped according to their properties
• Amino acids are classified based on:
• How they interact with water → hydrophilic or hydrophobic
• Whether they are basic or acidic
• Whether they are polar or nonpolar

Question 4

Hydrophobic Amino acids:

Answer 4

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

Question 5

Hydrophilic Amino Acids

Answer 5

• Recall that polar molecules contain electronegative elements → such as oxygen and nitrogen.
• Results in an unequal charge → allows the R groups to interact with each other or with H2O via H-bonding
• Basic amino acids tend to be → positively charged
• Acidic amino acids tend to be → negatively charged
• Charged groups can form ionic bonds → with one another & with other charged molecules
• Hydrophilic amino acids are typically found on the “outer” surface of proteins

Question 6

Special Amino Acids: Glycine

Answer 6

• The a carbon is bonded to two H atoms → glycine is not asymmetric
• It is small and nonpolar → allows free rotation around the C-N bond
• This increases the flexibility of the polypeptide backbone

Question 7

Special Amino Acids: Proline

Answer 7

Proline → R group links back to the amino group
- Linkage restricts rotation of the C-N bond → this limits the amount of protein folding around proline

Question 8

Special Amino Acids: Cytesine

Answer 8

Cysteine → R group contains a sulfhydryl group
- This allows two cystesine 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

Question 9

How does linking amino acids work?

Answer 9

• Adjacent amino acids are joined together in a peptide bond
• This is a dehydration reaction where the carboxyl group of one amino acid reacts with the amino group of another amino acid
• Releases a molecule of H20
• The free amino group is at the amino end of the peptide → forms the N-terminus
• The carboxyl group is at the carboxyl end → forms the C-terminus
• A polymer of amino acids connected by peptide bonds is a polypeptide → used synonymously with protein

Question 10

What are the proteins structures four level of organization?

Answer 10

Protein structure has four levels of organization → primary (1°), secondary (2°), tertiary (3°) and quaternary (2°)

• The three-dimensional structure of a protein is the protein conformation → this is described by 2º, 3°, and 4°

Question 11

Primary structure

Answer 11

• The primary structure is the specific linear sequence of amino acids that make up the polypeptide chain → from amino end to carboxyl end
• Most polypeptides contain many amino acids → these are coded for by the genome
• The primary structure determines 2°, 3°’, and 4° structure of the protein
• The sequence of the primary structure can be written as a sequence of the three letter or one-letter abbreviations
• e.g. Val-Gly-Ala-His or V-G-A-H
• The R groups alternate position on either side of the chain of amino acids
• This affects protein folding and the interaction of R groups

Question 12

Secondary Structures

Answer 12

• Secondary structure describes the conformation of portions of the polypeptide chain
• Two types → (a) alpha helix and (B) beta sheets
• Results from hydrogen bonding between neighbouring amino acids of the polypeptide backbone → occur between functional groups
• R groups are not involved
• It is a fixed configuration of the polypeptide backbone

Question 13

Secondary structure: alpha helix

Answer 13

• The alpha (a) helix is a very stable structure
• They are right-handed helices → let molecules that are not nearby in the main structure to interact with one another
• Form due to H-bonds to the 4th amino acid neighbour above & below in the spiral → the carbonyl group of one amino acid and the amide group of the 4”’ amino acid

Question 14

Secondary structure: beta sheets

Answer 14

• Segments of the polypeptide lying side-by-side → assumes a pleated (folding) conformation
• Can be parallel or antiparallel
• Structure is stabilized by H-bonds formed between carbonyl groups in one chain & amide groups in the other chain within the same polypeptide

Question 15

Tertiary structure

Answer 15

• a single polypeptide chain folded into 3° structure
• How regions of 2º conformations are oriented results in its functional form

Tertiary structure is determined by the following:
- Spatial distribution of the hydrophilic and hydrophobic R groups
- Chemical bonds and interactions that form between the R groups
- Includes:
- Hydrogen bonds, hydrophobic bonds & ionic bonds
- Disulfide bonds → covalent bond between two cysteine residues

• The overall shape (3° structure) of a functional protein may result in
• Areas of the protein that form active sites for enzymes
• Exterior R groups that may impact how a protein interacts with other molecules or proteins

Question 16

Quaternary structure

Answer 16

• Many proteins are made up of more than one polypeptide chain
• The spatial arrangement of these subunits is the 4° structure
• These arise due to the same bonds as found in 3° structure
• The polypeptide chains in each subunit may be:
• Identical → e.g. protein containing two identical polypeptide chains is known as a homodimer
• Non-identical → e.g. protein containing two non-identical polypeptide chains is known as a heterodimer

Question 17

What is translation? What are the components it requires?

Answer 17

sequence of bases in mRNA is used to specify the order of amino acids to be added in the growing polypeptide
- Final stage of the Central Dogma

• Translation requires several components:
• mRNA
• Ribosome
• Transfer RNAs → tRNAs
• Aminoacyl tRNA synthetases
• Initiation factors, elongation factors & release factors

Question 18

What are ribosomes?

Answer 18

• Ribosomes → protein factories
• This is where translation takes place
• Ribosomes are a complex structure of RNA and protein
• They consist of a small subunit and a large subunit
• Eukaryotic ribosomes are larger than prokaryotic ribosomes
• The mRNA is bound by the large and small ribosomal subunits → it then moves through the center of the ribosome
• The ribosome moves down the mRNA → from 5’ to 3’ and reads individual codons to incorporate the appropriate amino acids

Question 19

What is a codon?

Answer 19

A codon is a nucleotide combination that specifies the placement of an amino acid codes for the amino acid placement
- Each group of three adjacent nucleotides → arranged as a nonoverlapping series of nucleotide triplets
- The reading frame is where the ribosome begins reading the sequence of nucleotides

Question 20

Where does Translation begin?

Answer 20

• Translation does not begin with the first 5’ RNA base on the mRNA
• Translation begins with a start codon → AUG
• Codes for methionine

Question 21

Ribosome sites

Answer 21

• There are three functional sites within the ribosome
• The aminoacyl tRNA is accepted in the → A site
• The peptide bond formation happens in the → P site
• The tRNA exits the ribosome in the → E site

Question 22

Transfer RNAs (tRNA)

Answer 22

• Translation needs the transfer RNA molecules → tRNA
• They are small molecules containing 70-90 nucleotides
• 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 → where the specific amino acid attaches
• Three bases in the anticodon loop make up the → anticodon

Question 23

How are amino acids attached to tRNAs?

Answer 23

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

Question 24

How is genetic code read?

Answer 24

• During translation, the anticodon of the tRNA base pairs with the codon on the mRNA
• Like all nucleotide sequences, the anticodon of tRNAs base pair in an antiparallel fashion
• So, the first base of the codon pairs with the last base of the anti-codon
• The genetic code has 20 amino acids → specified by 64 codons
• Many of the amino acids are specified by more than one codon → most amino acids are encoded by more than one codon
• Bases are read 5’-3’ on the mRNA using the standard genetic code

Question 25

What are the translation stages?

Answer 25

1. Initiation → AUG codon is recognized & 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 & the polypeptide chain is released from the ribosome.

Question 26

Eukaryotic Translation Initialtion

Answer 26

- Steps 2 & 3 of translation are similar between prokaryotes & eukaryotes → however there are differences in step 1 - 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 the start codon is reached the large ribosomal subunit is then recruited → translation can start - The initiation factors are released

Question 27

Translation elongation

Answer 27

- After the ribosome is assembled, a new tRNA enters the A site → this allows the peptide bond to form - The 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 - The ribosome then shifts one codon to the right - This moves the 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 enter based on the next codon

Question 28

Translation Termination

Answer 28

- The process continues until one of three codons are reached → UAA, UAG, or UGA → these are stop codons - A protein release factor binds to the A site of the ribosome at the stop codon - This causes the bond that is connected to the polypeptide of the tRNA to break - This creates the carboxyl terminus of the polypeptide → completes the chain

Question 29

Prokaryotic Translation Initiation

Answer 29

- Recall the mRNA molecules have no 5' cap in prokaryotes - Thus, the initiation complex is formed at one or more internal sequences present in the mRNA → Shine-Dalgarno sequence (5’ -AGGAGGU-3’) - The ribosome binds to any Shine-Dalgarno sequence, with translation beginning at the first downstream AUG start codon, so one mRNA can code for several polypeptides. - Elongation and termination are similar to that of eukaryotes

Question 30

Regulating Protein Synthesis

Answer 30

- Not all genes are expressed in the cell all the time (Eye cells cant have stomach acid functions) - There are many levels of regulation in the cell including: DNA accessibility - DNA is locked away in nucleus Transcription factor - proteins to make DNA transcriptional-accessible does not exist RNA processing - RNA modifications such as poly-A-tails and splicing are not provided Post-translational modifications - chemical groups added or removed from the protein changes its on or off button

Question 31

how is protein sorted?

Answer 31

- Remember, mRNA is bound to a ribosome in the cytosol where translation begins - What happens to the protein after translation depends on how it will be sorted → specific signal sequences - No signal → stay in cytosol - Amino terminal signal → to chloroplast or mitochondria - Internal signal → to nucleus

Question 32

How are proteins with signal-anchor sequences transported?

Answer 32

- Some proteins have a specific amino-terminal signal sequence for transport to the ER - This specific amino-terminal sequence signal is bound by the signal recognition particle → SRP - The ribosome with associated mRNA and newly formed polypeptide is transported to the ER Proteins produced by ribosomes on the rough ER could be found: - Embedded in the ER membrane → inserted as it is synthesized - Within the lumen of the endomembrane system - Secreted out of the cell