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PMP101 > Proteins: Functions, Structure and Synthesis > Flashcards

Proteins: Functions, Structure and Synthesis Flashcards

1
Q

What are the main functions of proteins?

A

-Carry out enzymatic functions
-Generating movements of cells
-Carrying signals from cell to cell and within individual cells
-Providing support to cells and tissues

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2
Q

What are the main features of proteins?

A
  • Proteins are linear chains of amino acids arranged in a 3D structural hierarchy
  • Diversity of structures, resulting in a wide range of functions. Functions depend on the 3D protein structure. Its 3D structure is determined by a proteins amino acid sequence.

Without its normal conformation (native folding), the protein loses its biological activity.

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3
Q

What are IDSs? Intrinsically disordered Proteins?

A

Are proteins that have lost their native, functional folding, resulting in an insoluble aggregation in many organs (causing many diseases)

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4
Q

What can the accumulation lead to?

A

the neurotoxic effects in neurodegeneration diseases: Beta amyloid protein is one of the IDPs associated with neurodegenerative diseases like Parkinsons, prion disease and Alzheimers diseases.

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5
Q

What are amino acid monomers?

A
  • Proteins are assembled essentially from a set of 20 different amino acids
  • Amino acids have in common: Carbon a(alpha), amino (-NH2) and carboxyl (-COOH) functional groups
  • R group or side chain is specific for each amino acid
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6
Q

What makes up an amino acid?

A

-Alpha carbon, amino and carboxyl

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7
Q

What are peptide bonds between amino acids called?

A

Polypeptides

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8
Q

What do the peptide bonds between amino acids do? diagram

A
  • In a protein, amino acids are linked together by covalent peptide bonds formed between carboxylic acid and amino groups of two consecutive amino acids.
  • The continuous peptide bonds between amino acids form linear, unbranched polypeptides and the backbone of the protein.
  • The R groups are protruding the outside
  • Every proteing has a unique sequence of amino acids with a carboxyl end (C-term) and an amino end (N-term)
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9
Q

What is the four level protein structure?

A

he architecture of proteins has four levels of organisation: Primary, Secondary, Tertiary and Quaternary

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10
Q

What is the Primary structure of proteins?

A
  • The unique sequence of amino acids in a polypeptide chain, with no folding

Based on the length of the sequence:

  • Peptide=short chain(<50 amino acids)
  • Protein=longer chain (>50 amino acids)

Also referred to polypeptides. Both are composed of repetition of amino acids.

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11
Q

What is the Secondary Structure of proteins?

A
  • Secondary structure consists of stable spatial coils and folds of segments within a polypeptide chain. They are formed by H-bonds between the backbone amino and carbonyl groups and often involving repeating structural patterns (helices and sheets)
  • Typical secondary structures are:

-Coil called (alpha a) helix

-Folded structure called B (beta) pleated sheet related to its amino acid sequence

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12
Q

What is the Tertiary Structure of Proteins ?

A
  • Tertiary structure is the three-dimensional folding pattern determine by interactions among various side chains. It determines the overall folding/conformation of a polypeptide chain subunit.
  • It is stabilised primarily by:

-Hydrophobic interactions (weak and reversible) between non-polar side chains

-Ionic bonds and strong covalent bonds called disulfide bridges (of cysteines) between non-polar side chains.

-Hydrogen bonds involving polar side chains and backbone amino/carboxyl groups

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13
Q

What is the Quaternary Structure of Proteins?

A
  • Quaternary structure is the result of the association of two or more polypeptide chain subunits into a closely packed arrangement. For example:

1) Haemoglobin, to transport oxygen in red blood cells, consisting of four polypeptide chains: two a (alpha) and two (B beta)

2) Tubulin, the component of microtubules, consisting of 2 polypeptide chains: a (alpha) and B(beta)

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14
Q

How do you recognise DNA structure?

A

deoxyribose lacking OH-at 2’, nucleotide sugar (Pentose)

-double stranded

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15
Q

How do you recognise RNA structure?

A

RNA-Ribose having OH- at 2’’, nucleotide sugar (Pentose)

-single stranded

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16
Q

What is protein synthesis in Eukaryotic cells?

A

Protein synthesis (or gene expression) consists in two phases-transcription and translation (separated by the RNA maturation in the eukaryotic cells)

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17
Q

Where does Transcription take place?

A
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18
Q

Where does Translation take place?

A
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19
Q

What is Transcription?

A

The process of converting DNA (double stranded) to mRNA(single stranded)
-It occurs in the nucleus

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20
Q

Why does Transcription take place inside the nucleus?

A

DNA is too large to leave the nucleus (RNA can pass through the nuclear pores)

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21
Q

What is the process of Transcription?

A

RNA polymerase uses one of DNA strands as a template to produce pre-messenger RNA (pre-mRNA-codes for proteins) with a complementary sequence to DNA.

  • It adds nucelotides (complementary base pairing -U INSTEAD OF T) in the 5’-3’ direction.
  • Only 1 strand of the 2 strands of DNA is transcribed.
  • DNA transcription consists of 3 stages
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22
Q

What are the 3 stages of Transcription?

A

-Initiation
-Elongation
-Termination

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23
Q

DNA Transcription -Initiation

A

Initiation step - RNA polymerase, with the help of transcription factors, binds to a specific sequence of DNA (promoter-just before the start site of a gene). Each gene has its own promoter. This ensures that the genetic region will be transcribed into RNA.

  • RNA polymerase separates the double strands and use a single strand as a template
  • 2 initial RNA nucleotides are joined together to begin the complementary RNA strand synthesis
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24
Q

DNA transcription -strand elongation and termination steps

A

Elongation step - RNA polymerase moves along the DNA coding sequence in 5’-3’ direction. It melts duplex DNA whilst it adds ribonucleotides to the growing RNA (by phosphodiester)

Termination step- The RNA polymerase encounters a specific termination sequence (stop site). This releases the RNA strand. The newly RNA transcript is a precursor of mRNA (or pre-mRNA)

25
Q

What RNA complementary strand will be made from the following sequence?
DNA- TAC GCA TGA CTA ACT

A

RNA -AUG CGU ACU GAU UGA

26
Q

What are the complementary base pairs for DNA,
T, A, C, G

A

-T with A
-C with G

27
Q

What are the complementary base pairs from a DNA sequence to an RNA sequence?
T,A,C,G ? U?

A

-Use U instead of T

-U with A
-C with G

28
Q

What is RNA Processing ?

A

The pre-mRNA must undergo RNA processing steps, before it can be exported to the cytosol

29
Q

What are the 3 RNA processing steps?

A
  • Capping at 5’ end
  • Polyadenylation at 3’ end
  • splicing
30
Q

What is Capping at 5’ end?

A

A modified nucleotide 5’ cap, a 7-methylguanylate is added to the ribonucleotide at 5’ by a usual 5’-5’ triphosphate linkage (this will allow the attachment to the ribosome later)

31
Q

What is Polyadenylation?

A
  • A repetition of poly-A (100-250bp of ribonucleotide A) is added to the 3’ end
  • Its functions includes: increasing the stability of mRNA molecules (preventing its degradation) and facilitates its migration to the cytosol
32
Q

What is splicing?

A

Splicing is a large assembly of RNA and protein (spliceosome) excises (cuts out) introns and exons are joined together.

33
Q

Splicing - What are INTRONS ?

A

internal sequences that do not code for proteins, junk RNA

34
Q

Splicing - What are EXONS?

A

segments that DO code for proteins, expressed.

35
Q

What happens after RNA processing?

A

After RNA processing, pre-mRNA becomes a mature mRNA and is exported to the cytoplasm to start the translation.

36
Q

What is Translation?

A
  • (RNA to protein) is the conversion of the information from RNA (4 nucleotides) into protein (20 amino acids).

-It occurs in the cytoplasm on the ribosomes.

37
Q

Where does Translation occur?

A

In the cytoplasm on the ribosomes.

38
Q

During the process of Translation what does the mRNA do?

A

mRNA carries information from DNA in groups of these consecutive nucleotides, Codons. Each Codon specifies one amino acid (Universal Genetic Code), except stop codons.

39
Q

What is RNA made up of?

A

RNA is made of 4 different nucleotides, 64 combinations of three nucleotides are possible for 20 amino acids. Some amino acids being specified by more than one codon.
-Which is why we use a codon table

40
Q

What are the steps of Translation?

A
41
Q

What is a STOP codon?

A
42
Q

What is a codon table ? How do I read it ? diagram / practise

A
43
Q

What are tRNA molecules ?

A

adaptors between amino acids and codons

  • A charged tRNA carrying the next amino acid binds to A site on the ribosome and interacts with the mRNA codon.
  • The C-term of the polypeptide chain forms a peptide bond to the NH2 group of the amino acid at A site
  • mRNA is translated in the 5’ to 3’ direction
  • The protein is growing from N-term to C-term direction
  • The ribosome translocates along the mRNA to the next codon
  • The spent tRNA is ejected and A site is open to bind the next charged tRNA
  • -Short RNA folded into a 3D structure
  • Adaptors between codons of mRNAs and the corresponding amino acid
  • ensure that the genetic code is applied

-Two structures to mediate this adaption: Anticodon, 3 nucleotides that bind the complentary mRNA codon.

-3’ end (acceptor stem) attached to the specific amino acid that matches the codon

  • Some amino acids are linked to >tRNA
  • Many tRNAs can pair with >1 codon (’wobble’ base pairing - non perfect complementary)
44
Q

What is a codon?

A
45
Q

What is an Anticodon?

A
46
Q

Ribosomes as Protein Synthesising machines

A
  • Machinery to synthesise proteins
  • In eukaryotes, ribosomes (80S) consist of a small (40S) and a large subunit (60S)
  • Each subunit contains three binding sites for tRNA molecules A, P and the E site.
  • During Translation, tRNAs move through sites A to P to E.
47
Q

What is A site?

A

Where the incoming charged tRNA bind to mRNA

48
Q

What is P site?

A

Binds to the tRNA holding the growing polypeptide chain of amino acids

49
Q

What is the E site?

A

Where the spent tRNA is ejected

50
Q

What is a ribosomal subunit ? diagram

A
51
Q

What are the 3 phases of Translation?

A
  • Initiation
    -Elongation
    -Termination
52
Q

What is translation Initiation ?

A

the ribosome gets together with the mRNA and the first tRNA.

  • tRNA carrying methionine (linked to the start codon) binds the small subunit
  • Ribosomes bind to the mRNA 5’ end by recognising the 5’ GTP cap 9RNA processing)
  • Ribosomes slide along the mRNA (direction 5’-to-3’) until the start codon (AUG), which matches the anticodon of the linked tRNA
  • The large subunit attaches to the small one so that the tRNA is aligned on site P, completing the formation of an 80S initiation complex
53
Q

Translation Elongation step

A

amino acids are brought to the ribosome by tRNAs and linked together to form a chain.

  • A charged tRNA carrying the next amino acid binds to A site on the ribosome and interacts with the mRNA codon.
  • The C-term of the polypeptide chain forms a peptide bond to the NH2 group of the amino acid at A site
  • The ribosome translocates along the mRNA to the next codon
  • The spent tRNA is ejected and A site is open to bind the next charged tRNA
  • mRNA is translated in the 5’ to 3’ direction
  • The protein is growing from N-term to C-term direction
54
Q

Translation - Termination step

A

1) Translation halts at a stop codon (UAA, UAG, and UGA)

2) The stop codons are not recognised by a tRNA and do not specify an amino acid

3) Release factors bind to any stop codons that reached the A site

4) The ribosome releases the mRNA and dissociates into its two subunits

55
Q

Proteins exert a variety of what?

A

Essential biological functions within human cells

56
Q

Each protein has a unique what? which determines?

A

Unique amino acid sequence, which determines both its three-dimentional shape and its biological activity. The correct folding is essential for their activities.

57
Q

DNA is transcribed into what? and where?

A

pre-mRNA in the nucleus

58
Q

Pre-mRNA is processed where ? and matured into what?

A

In the nucleus (RNA processing) and matured into mRNA, in order to leave the nucleus and enter the cytoplasm.

59
Q

mRNA is transcribed to what? and where?

A

Proteins (translation process) in the cytoplasm on ribosomes following the genetic code

PMP101 (23 decks)

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