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Diagnostic Molecular Biology > Ch. 3 - Proteins and the Genetic Code > Flashcards

Ch. 3 - Proteins and the Genetic Code Flashcards

1
Q

Proteins

A

Polymers of amino acids

Products of transcription and translation

Polypeptides that can reach sizes of more than a thousand amino acids in length

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2
Q

Amino acid side chain

A

The portion of an amino acid that determines its characteristic biochemical properties

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3
Q

What are the four groups of amino acids based on polarity?

A 
Nonpolar (hydrophobic; water insoluble)
Uncharged polar (hydrophilic; water soluble) 
Negatively charged polar
Positively charged polar
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4
Q

What determines the shape and biochemical nature of a protein?

A

The properties of the amino acids that make up the protein

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5
Q

Domains and example

A

Functional part of a protein

A single protein can have separate domains with different properties

Ex: Transmembrane proteins have hydrophobic regions positioned inside the lipid membrane of the cell and hydrophilic or charged extracellular regions (positioned outside of the cell membrane)

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6
Q

How many amino acids are there?

A

20

There is an unusual 21st amino acid, selenocysteine

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7
Q

How does the amino acid proline differ from the others?

A

It has a cyclic side chain (5C ring)

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8
Q

What are the two ways in which amino acids are classified?

A
  1. Based on polarity - nonpolar, uncharged polar, negative polar, positive polar
  2. Based on their biosynthetic origins or similar structures based on a common biosynthetic precursor
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9
Q

Zwitterions

A

Molecule that can become + or - charged at a given pH

Amino acids are zwitterions

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10
Q

L-stereochemistry

A

Amino acids are synthesized in vivo by stereospecific enzymes so that naturally occurring proteins are made up of amino acids of L-stereochemistry

Central C atom attached to a carboxyl group (COO-), an amino group (N3H+), a H atom, and a side chain (R)

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11
Q

Peptide (definition and structure)

A

A polymer of a few amino acids

At one end of the peptide will be an amino group (amino terminal or NH2 end) and the carboxyl group (carboxyl terminal or COOH end) on the opposed end

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12
Q

Peptide bond

A

-C-C-N- substituted amide linkage

Water is lost and the C from the COOH group binds to the N from the NH2 group

Amino and carboxyl groups are linked by peptide bonds to form the protein backbone

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13
Q

Dipeptide

A

Two amino acids joined together by a peptide bond

Additional units include tri-, tetra-, pentapeptides, etc.

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14
Q

In what direction do peptides grow?

A

Like the 5’ to 3’ of nucleic acids, from the amino to carboxyl terminus

NH2 to COOH

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15
Q

The most abundant macromolecules in calls are _______.

A

proteins

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16
Q

Proteome

A

The collection of proteins encoded in all of an organism’s DNA

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17
Q

Primary structure of proteins

A

The sequence of amino acids that determines the nature and activity of that protein

Read from amino end to carboxyl end

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18
Q

How is the secondary structure of a protein determined?

A

Interactions between amino acid side chains fold the protein into predictable configurations

Beta-pleated sheets and alpha helices or random coils

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19
Q

Tertiary structure of proteins

A

The secondary structure is further folded into a tertiary structure

Important to function

If a protein loses the tertiary structure, it is denatured

20
Q

What causes denaturing of a protein?

A

Mutations in DNA that substitute amino acids in the primary structure, which alters the tertiary structure
Heat
Conformations forced on innocuous peptides by infectious prions

21
Q

Prions

A

Unnaturally folded proteins that are capable of transferring their configuration to normal proteins

Cause transmissible spongiform encephalopathies such as Creutzfeldt-Jakob disease and bovine spongiform encephalitis (mad cow disease)

22
Q

Proteins bond to form _______.

A

Dimers, trimers, tetramers, etc.

23
Q

Oligomer

A

Proteins that bond together in order to function

Each component protein is a monomer

Quaternary structure of proteins

24
Q

Quaternary structure of proteins

A

Oligomers

25
Q

How are proteins classified?

A

According to function as enzymes and as transport, storage, motility, structural, defense, or regulatory proteins

26
Q

Enzymes and transport, defense, and regulatory proteins are usually _______ in nature, making them _______ and allowing them to freely _______ across the membrane.

A

globular; soluble; diffuse

27
Q

Structural and motility proteins are _______ and _______.

A

fibrous; insoluble

28
Q

Simple proteins

A

Have no other components other than amino acids

29
Q

Conjugated proteins

A

Have components other than just amino acids, which is nonprotein in nature, called prosthetic groups

I.e. lipoproteins, glycoproteins, and metalloproteins

I.e. hemaglobin

30
Q

Prosthetic group

A

The nonprotein component of conjugated proteins

31
Q

Lipoprotein

A

Conjugated protein covalently attached to lipids

I.e. low-density lipoprotein (LDL) and high-density lipoprotein (HDL)

32
Q

Glycoprotein

A

Conjugated protein covalently attached to carbohydrate moieties

I.e. sugars

33
Q

Metalloprotein

A

Proteins with associated metal atoms

I.e. ferratin

34
Q

Gene

A

The ordered sequence of nucleotides on a chromosome that encodes a specific functional product

Fundamental physical and functional unit of inheritance

Contain structural sequences that code for an amino acid sequence AND regulatory sequences that are important for the regulated expression of the gene

35
Q

Loss of _______ will result in an abnormal phenotype, even though there may be no changes in the _______ of the gene.

A

controlled expression of genes; structural sequence

36
Q

Genetic code

A

The relationship between DNA and the amino acid sequence

The dictionary that translates the four-nucleotide sequence info in DNA into the 20-amino acid sequence into in proteins

Read in triplets

37
Q

Codon

A

Three nucleotide sequence that will guide the insertion of a specific amino acid into protein

Triplet (64 in total)

38
Q

Nonsense codons

A

Three codons that terminate protein synthesis

UAG aka amber
UAA aka ocher
UGA aka opal –> also codes for selenoproteins, which is needed for protein synthesis to continue

39
Q

How do you get from DNA to protein?

A

DNA –> RNA

Nucleic acid –> amino acid –> phenotype

40
Q

What molecular factor can recognize both nucleic acid and protein sequences?

A

tRNA

41
Q

tRNA charging

A

Activation of amino acids by covalent attachment to tRNA
Dependent on Mg++
Starts protein synthesis

42
Q

Aminoacyl tRNA synthetase

A

Enzyme that catalyzes tRNA charging

Requires 20 for the reaction

43
Q

What are the two steps of the tRNA charging reaction?

A
  1. The amino acid is activated by addition of AMP
    amino acid + ATP –> aminoacyl-AMP + PPi
  2. The activated amino acid is joined to tRNA
    aminoacyl-AMP + tRNA –> aminoacyl-tRNA + AMP
44
Q

Anticodon

A

x

45
Q

Suppressor tRNA

A

x

46
Q

Ribosome

A

Translation occurs here

Diagnostic Molecular Biology (22 decks)

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