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Molecular biology > Proteins > Flashcards

Proteins Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What are the main uses of proteins? Give some examples of each

A
  • Enzymes (e.g., DNA polymerase, RUBisCO)
  • Transport (Bacteriorhodopsin - found in the phospholipid membrane used for light driven proton transfer across)
  • Structural support (cells and organelles)
  • Immunity (immune system)
  • Cell-cell communication
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2
Q

What are proteins?

A

Linear polymers of amino acids linked together by covalent peptide bonds in a specific sequence

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3
Q

What is amino acid structure?

A
  • An amine group
  • A carboxylic group
  • An R-group (this varies between amino acid)

These are all covalently bonded to a central alpha carbon

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4
Q

How many essential amino acids are there?

A

20

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5
Q

What are the three different groups of amino acid?

A
  1. Hydrophobic (these contain a benzene ring so can absorb light)
  2. Polar (concentration charge within the molecule and are therefore typically embedded within a lipophilic environment)
  3. Acidic/basic
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6
Q

What are the structures of a protein?

A
  1. Primary (amino acid sequence)
  2. Secondary (form alpha helix or beta pleated sheets)
  3. Tertiary (hydrogen bonds between R-groups, forming 3D structure)
  4. Quaternary structure (interactions between 3D monomers (tertiary shapes interact) - essentially several protein chains held together forming dimers, trimers, or tetramers)

If all of these structures are present, then the loss of just one will stop the protein from functioning.

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6
Q

How are amino acids typically named? In terms of what they are most commonly referred to.

A

Most typically referred to using their three letter name

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7
Q

What is the typical tertiary structure of a GFP protein?

A

Form beta-cans, which combine together to form a tetramer

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8
Q

What is the central dogma?

A

A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

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9
Q

What is required for protein production?

A

Gene expression - via transcription and translation.

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10
Q

What are the three main steps of protein production (brief)?

A
  1. Transcription (DNA -> mRNA) -> processing occurs before the next stage
  2. Translation (mRNA -> amino acid sequence using tRNA)
  3. Folding (of the protein)
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11
Q

What is a gene?

A

A gene is a DNA molecule that encodes a polypeptide chain

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12
Q

What are exons and introns?

A

Exons are sequences that encode the protein. These are separated by introns, which do not encode protein synthesis but are still required for gene function

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13
Q

What is a promoter region?

A

A region which triggers gene expression/ transcription and is found at the start of a gene (this can be used to locate genes)

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14
Q

What is a UTR?

A

An Untranslated Region (introns -> cut before translation from mRNA)

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15
Q

What is found in the interfaces between introns and exons in a eukaryotic gene?

A

The interfaces are formed of key nucleotides and sequences that will tell which parts need to be removed before transcription/translation

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16
Q

Describe transcription in eukaryotes.

A

The copying of the DNA sequence onto mRNA.

Pre-mRNA is produces first, before processing removes the introns and forms a mature mRNA. This processing is also known as RNA splicing, which removes the introns and splices the exons back together.

17
Q

What is the start codon on mRNA? What does it encode?

A

AUG -> this encodes methylamine

18
Q

What are the three stop codons on mRNA?

A

UAA, UGA, UAG

19
Q

Where does each stage of protein expression occur in eukaryotes?

A

DNA is transcribed to form pre-mRNA in the nucleus. This is then processed to form mature mRNA before it is exported across the nuclear envelope and into the cytoplasm.

Translation occurs in the cytoplasm (at the rER), using mRNA and tRNA. The resulting amino acid chain is then folded as it is transcribed.

20
Q

What is a codon?

A

A group of three RNA nucleotides that encode one amino acid.

21
Q

What does tRNA stand for? What is the structure?

A

transfer RNA

One end of each tRNA has a sequence of three nucleotides called an anticodon, which binds to specific mRNA codons. The other end of the tRNA carries the amino acid specified by the codons (via an amino acid attachment site)

22
Q

Which steps give rise to a mature mRNA in eurkaryotes?

A

Transcription, processing and export

23
Q

What are the different types of RNA?

A
  • mRNA -> messenger RNA
  • Ribosomal RNA (rRNA) -> forms parts of ribosomes which composed the large subunit (60S) and the small subunit (40S)
24
Q

What is an open reading frame?

A

The length of RNA through which the ribosome can synthesise an amino acid chain without reaching a stop codon.

25
Q

How many open reading frames can you have?

A

Three (due to the three RNA nucleotides in a codon)

26
Q

Which strand is the non-coding strand and which is the coding strand in DNA? (use the terms sense and antisense)

A

non-coding strand = the template strand which is also known as the antisense strand (the RNA is complementary to this strand?). This is in a 3’ to 5’ direction

coding strand = the strand that is “the same” as the mRNA. This is in the 5’ to 3’ direction

27
Q

How does protein expression differ in prokaryotes?

A
  • There are fewer steps (for example there is no processing)
  • There are is no split across a membrane (all occurs in the cytoplasm)
28
Q

What can be studied in isolated proteins?

A
  • Physical properties
  • Sequences (via sequencing)
  • 3D structure - Crystallisation and x-ray structure
29
Q

What can be used to determine the function of a protein?

A
  • Gene expression (why and when?)
  • Location
  • Solubility properties
30
Q

What is Proteomics?

A

Used to study all the proteins in an organism at one time using mass spectrometry

31
Q

What are the three main steps required for studying proteins in the lab?

A
  1. Sample preparation (depends on material and DNA)
  2. Protein separation -> electrophoresis
  3. Detection -> Immunoblot
32
Q

What is different about proteins that means that electrophoresis separation differs?

A

The charge is not always negative, instead varying based on the protein composition (R-group, structure etc.). This means proteins can be separated based on their size AND charge.

33
Q

How does the gel electrophoresis of proteins differ?

A
  • Uses thinner gel
  • Polyacrylamide gel electrophoresis (PAGE) can be used instead of agarose gel as it has a smaller pore size
  • SDS (an ionic detergent) can be added to denature the proteins and bind to them so that they are all negatively charged and are therefore separated only due to their mass

This is known as SDS-PAGE.

34
Q

What is SDS-PAGE?

A

A type of gel electrophoresis that separates proteins based on their mass instead of their charge.

Staining is carried out using different techniques, such as silver or fluorescent stains.

35
Q

What is carried out after gel electrophoresis when studying the presence of proteins in a lab setting?

A

Western Blotting - a further detection technique.

Whilst the gel electrophoresis can be used to determine that the wanted protein is present based on size, it is not sufficient for proper detection. This is carried out in tandem with staining (need two gel electrophoresis’s, one for staining and one for blotting)

36
Q

What are the main steps of Western Blotting?

A
  1. Blotting (transfer of proteins from the gel to a membrane such as nitrocellulose -> achieved using an electric current)
  2. Membrane blocking (blocks the membrane off using non-antibody reactive proteins)
  3. Probing with a primary antibody (antibody binds to the required protein)
  4. Probing with a secondary antibody (secondary antibody containing a visualisation such as fluorochrome feature binds to the primary antibody)
  5. Visualisation (using chemiluminescence, for example)
37
Q

What are multimeric structures?

A

The quaternary structure of a protein (e.g., dimers, trimers, tetramers etc.)

38
Q

How many tRNA molecules are there?

A

Approximately 64 -> 61 for the different amino acids and 3 for the stop codons?

39
Q

Why is the code said to be redundant?

A
  • This is because a single amino acid can be coded for by more than one codon. This means that certain mutations will not change DNA code function.

Molecular biology (10 decks)

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