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1
Q

How works the condensation of amino acids?

A

The peptide bonds are formed by condensation of free amino acids, when the peptide bond is formed a water molecule is released

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2
Q

What is a peptide?

A

Is short chains of aminoacides linked by peptide bonds (covalent bonds)
Peptide bond: chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein chain.

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3
Q

How is described the catalysis by enzymes?

A

Is representes through a model that describes the enzyme kinetic (rate of an enzymatic reaction), wherem:
Vmax= maximum rate achieved at saturating substrate concentration
S=substrate concentration

The michaelis constant= substrate concentration where Vmax is the half

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4
Q

N-acetylation of proteins needs _______as donor molecule

A

Acetyl-CoA

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5
Q

Glucose, fructose and manosse molecules are attached in the process of O-glycosylation (True or false?)

A

True

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6
Q

How is called a sugar molecule containing 6 carbon atoms?

A

Hexoses

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7
Q

Which are the types of glycosylation of proteins?

A

N-glycosylation
O-glycosylation
GPI anchor
C-mannosylation
Monoglycosylation of serine and threonine

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8
Q

For what is useful the Protein
crystallography?

A

Allows to see crystal structure of molecules

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9
Q

What is the genetic code?

A

Describes how cells
translate information encoded within
genetic material (DNA or mRNA
sequences) into proteins

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10
Q

What is the function of the ribosomes?

A

links aminoacids in an
order specified by messenger mRNA
small ribosomal unit= reads mRNA
large ribosomal unit=joins aminoacids to form the polypecptide chain

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11
Q

What is the general structure of aminoacids?

A

Aminoacids are chiral molecules (Carbon is attached to 4 different molecules, proteins=L-isomer)
1. Amino group (H3N+)
2. Carboxyl group (COO-)
3. Side chain
4. H

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12
Q

What are the essential aminoacids?

A

Amino acids are synthesized from molecules of glycolysis and citric acid cycle. Those that can’t be synthesized by the human body and must be supplied with the diet:

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13
Q

Which are the aminoacids with small non-polar side chains? (Hydrophobe)

A

Glycin (Gly, G)
Alanin (Ala, A)

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14
Q

Which are the aminoacids with non-polar side chains? (Hydrophobe)

A

Valin (Val, V) - Essential aa
Leucin (Leu, L) - Essential aa
Isoleucin (Ile, I) - Essential aa
Methionin (Met, M) - Essential aa
Prolin (Pro,P)

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15
Q

Which are the aminoacids with aromatic side chains?

A

Phenylalanin (Phe, F)- Essential aa
Tyrosin (Tyr, T)
Tryptophan (Trp, W) - Essential aa

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16
Q

Which are the aminoacids with polar side chains uncharged and hydroxyl group? (Hydrophile)

A

Serin (Ser, S)
Threonin (Thr, T) - Essential aa

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17
Q

Which are the aminoacids with polar side chains uncharged and amides group? (Hydrophile)

A

Asparagin (Asn, N)
Glutamin (Gln, Q)

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18
Q

Which are the aminoacids with polar side chains (uncharged) and thiol group? (Hydrophile)

A

Cysteine (Cys, C)

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19
Q

Which are the aminoacids with polar side chains (charged) and amines group? (Hydrophile-Bases + )

A

Lysine (Lys, K) - Essential aa
Arginine (Arg, R)
Histidine (His, H) - Essential aa

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20
Q

Which are the aminoacids with polar side chains (charged) and R group? (Hydrophile-Acid - )

A

Aspartatic acid
Glutamic acid

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21
Q

How can be done the degradation of aminoacids?

A

The amino group is degraded to urea in the liver

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22
Q

Mention some features of peptide bond and linear structure of proteins

A

First AA in the peptide chain is always methionine, because the codon AUG serves also as an initiation site

The peptide bond has partial double bond character as shown by the resonance and is planar

Many proteins have a short signal peptide on N terminus that is used for protein targeting. It is cleaved off by signal peptidases

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23
Q

How is characterized the primary structure of proteins?

A

By its linear sequence of
amino acids (Starting with N-terminus NH3+ and ending with C-terminus COOH-) and the location of disulfide S-S bridges

Have cis and trans peptide bonds, and they can not rotate

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24
Q

How is characterized the secondary structure?

A

Local folded segments with
well defined structures

Are stabilized by a regular pattern of hydrogen bonds

Alpha-helix: coiled coil: Formed by hydrogen bonding between backbone carbonyl oxygen and the amide hydrogen four residues ahead.

Beta-sheet: The peptide chain is
more extended than in helices.
Hydrogen bonds are formed
between the strands. Parallel and antiparallel formations of beta sheets are possible

Typically spontaneously form as an intermediate before three dimensional tertiary structure

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25
Q

How is characterized the tertiary structure?

A

Represents the folded polypeptide chain, It is defined by the three dimensional arrangement of the amino acids, is composed of alpha helix and beta sheets

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26
Q

How is stabilized the structure of a protein?

A

Disulfide bonds Covalent bond between two cysteine residues

Hydrophobic effect Water forces hydrophobic groups together

Charge charge interactions (electrostatic): Between positively and negatively charged groups

Hydrogen bonds : Hydrogen atom is sandwiched between two electron attracting atoms (nitrogen or oxygen)

Van der Waals interactions : weak bonding interaction due
to fluctuating electrical charges

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27
Q

How is denaturated a protein?

A

High salt concentrations (ionic strength)
High and low pH
Organic solvents
Detergents
High temperature
= Cleavage of disulfide bonds

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28
Q

How is the process of protein folding?

A

The primary structure contains all the information necessary to specify the folded state, sometimes assisted by chaperones (prevent the unwanted association of the unfolded or partially folded forms of that protein with itself or with others)

The stably folded and functional form is called native state

Is driven by the “hydrophobic effect”, causing the protein to be compact

Nonpolar groups tend to self associate in water and thereby
minimize their contact surface area with the polar solvent—> it means the core of the folded conformation is hydrophobic (nonpolar side chains) and the polar side chains outside can form hydrogen bonds with water

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29
Q

What is a protein domain?

A

Is a compact region of a protein, the domains have specific functions ejp: enzymes

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30
Q

How is characterized the quaternary structure?

A

Is the arrangement of individual
polypeptide chains and can be very flexible

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31
Q

For what is used the reverse genetics?

A

To study the gene function by moving from a gene to the phenotype

Uses targeted mutagenesis

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32
Q

Why the transcriptome is more complex than genome?

A

Alternative splicing, alternarive promoters, RNA editing

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33
Q

For what is the human genome?

A

It contains approximately 20.000 genes
Is diploid
Contain less genes that the water flea

34
Q

What can regulate pos translational modifications?

A
  • Stability of proteins
  • Interaction with other proteins and nucleic acids
  • Localization of proteins
  • Function of proteins
  • Signal transmission
35
Q

Why the proteome is highly dynamic and diverse?

A

Due to:
- Variable transcription rate
- Alternative splicing
- Post-translational modifications

36
Q

What are the posttranslational modifications (PTMs)?

A

Are covalent chemical modifications allow the cell to
expand its protein structural and functional repertoire

37
Q

How many different 3-base codons combinations are possible?

A

64

38
Q

Chaperone proteins are typically needed to stabilize and form secondary structures?

A

True

39
Q

The first amino acid in every protein is?

A

Methionine

40
Q

What is released when a peptide bond is formed?

A

A water molecule

41
Q

Human cells can synthesize more than 50% of types of amino acids?

A

True

42
Q

The peptide bond can freely rotate in all axis?

A

False

43
Q

How is defined the primary structure of a protein?

A

By the linear sequence of amino acids, an amino-terminus and a carboxyl-terminus

44
Q

Thiol groups can be found in polar AA side chains?

A

True

45
Q

What groups can be found in polar AA side chains?

A

a central carbon atom, an amino group, a carboxyl group and an interchangeable side chain

46
Q

How can be degraded the aminoacids?

A

Urea, glucose, acetyl-coA

47
Q

Van der Waals interactions increase with the distance between molecules?

A

False

48
Q

Hydroxyl groups are found in non-polar AA side chains?

A

False

49
Q

Catalysis speed by enzymes…?

A

Is dependent on substrate concentration

50
Q

Protein domain typically show a hydrophobic core?

A

True

51
Q

A molecule (protein) made of few amino acids up to hundred amino acids is called?

A

A peptide

52
Q

Mention the PTMs:

A

-Proteolytic cleavage: cleavage at internal peptide bond, activates and deactivates proteins

-Phosphorylation: Addition of phosphate groups.

-Sulfation:Addition of a sulfate group to tyrosine. Used in signalling, coagulation cascade, hormones

-Lipidation: Covalent attachment of lipids. Used in protein targeting, vesicular transport, protein fixation to membranes.

-Methylation: Attachment of methyl group to lysine/arginine by methyltransferases. Used in protein-protein interaction, gene expression. by different
methyltransferases. Removal of methyl group by demethylases

-N-acetylation: Covalent addition of an acetylgroup from acetylcoa. Used in gene expression

-ADP-ribosylation: Enzymatic transfer of ADP ribose from NAD+ to arginine. Used in cell signaling, DNA repair and apoptosis. Catalyzed by ADP ribosyltransferases

-Ubiquitination and sumoylation: Attachment of a smallprotein ubiquitin orSUM multienzyme. Used in protein regulation and degradation.

-Hydroxylation: Attachment of hydroxyl group to prolyne or lysine. Leads to stabilization of structural proteins.

-Carboxylation: Addition of a carboxyl group to glutamate residues to form y-carboxyglutamate. Used in calcium binding proteins.

-Oxydation of aa chains: Chemical degradation of proteins by ROS, leads to the reduction of biological activity.

-Deamidation: Chemical degradation of proteins by pH at high levels and temperature.

Cofactors: small, non-protein molecule bind in the functional site of a protein and assist in ligand binding or catalysis.

53
Q

In what consist the phosphorylation?

A

Is the addition of phosphate groups to the proteins, turns enzymes and receptors on/off. Kinase: transfer phosphate groups, phosphatase: removes phosphate groups (dephosphorylation). Change activity and protein-protein interactions.

Biological activities: signaling cascades, cell motility, open/close membrane channels, gene transcription, inhibitor of tyrosine-kinases

54
Q

What is glycosylation?

A

Process by which a carbohydrate is covantly attached to a target macromolecule: proteins or lipids.

The process of adding, and the occurrence of, sugars on lipids
and proteins.

Leads to heterogeneity

55
Q

What is the difference between monosaccharides, oligosaccharides and polysaccharides?

A

Monosaccharides are the building blocks of oligo and polysaccharides

Oligosaccharides :few units, synonym of glycans

Polysaccharides: many units

56
Q

What are glycoproteins?

A

Proteins with attached (oligo)saccharides

57
Q

What is the difference between N-glycans and O-glycans?

A

N-glycans: oligosaccharides attached to protein via
nitrogen
O-glycans: oligosaccharides attached to protein via
oxygen

58
Q

What are the proteoglycans?

A

Proteins with many attached glycosaminoglycans

59
Q

What are glycolipids?

A

lipids with a glycan moiety

60
Q

What are glycosidic bonds?

A

Are covalent bonds linking a sugar to another group

61
Q

What are glycome?

A

The sum of glycans

62
Q

What is the difference between Glycosyltransferase and Glycosidase?

A

Glycosyltransferase: Is an enzyme transferring a sugar (mon-oroligosaccharide ) from an activated sugar to another molecule

Glycosidase: an enzyme that removes a sugar, either exo (just one sugar removed) or endo (in the middle of the glycoconjugate, so many
sugars removed in one step)

63
Q

Which are the types of glycosylation?

A
  • N glycosylation (N-linked): N glycosidic bond formed between GlcNAc and Asparagine , large oligosaccharides bound to the proteins

-O glycosylation (O-linked): O glycosidic bond formed between sugar and serine or threonine , mostly small oligosaccharides or
monosaccharides

-GPI Anchor (bond between C terminal carboxyl group and
mannose 6 phosphoethanolamine)

-C mannosylation of tryptophan

-Monoglycosylation of serine and threonine : regulation of
phosphorylation, less monoglycosylation is perhaps correlated with uncontrolled growth in tumor cells

64
Q

What are the functions of N-glycosylation and the types?

A

The protein folding and prevention of protein degradation. The types are high mannoes, complex and hybrid.

65
Q

What are the properties of O-glycosylation?

A

Prevents proteolytic degradation, helps immune recognition, protein to cell targeting. Also contributes to the stability, denaturation, degradation and biological activity.

66
Q

What is edman degradation?

A

A method of sequencing of aminoacids and peptides. The amino terminal residue is labeled and then removed (cleaved) from the peptide without disrupting the peptide bonds between all other amino acid residues

67
Q

How can be done the protein purification?

A

-Precipitation: adding high concentrations of salts, leading to destruction of hydrogen bonds -> aggregation and precipitation

-Dialysis: diffusion of small molecules through a membrane with molecular weight cut off

-Filtration:Removal of small molecules through a membrane by centrifugation, pressure or vacuum

-Gel filtration: proteins migrate faster through a porous gel than small molecules do

68
Q

How are proteins stabilized in solution?

A

Low temperature, pH, ionic strength, protease inhibitors, correct redox potential, necesssary metal ions and correct ionic strength

69
Q

What is the function of electrophoresis?

A

The separation of ions in an electric field according to their charge and dimension. Agarose: for DNA, SDS-page: for proteins

70
Q

O-glycosylation are sugar molecules attached to the protein chain via the amino acids asparagine and threonine?

A

TRUE

71
Q

What is the donor molecule in N-acetylation?

A

AcetylcoA

72
Q

How is called the enzyme that transfers phosphate groups to specific proteins?

A

Kinase

73
Q

ubiquitination of proteins changes the cellular localization of the modified proteins?

A

Yes

74
Q

Glycosylation can protect proteins from immunological recognition and/or proteolytic
degradation

A

True, O-glycosylation

75
Q

Oxidation of proteins can lead to?

A
  • Reduction of the catalytic activity of the protein

-Degradation of the protein

-Cross-linking of proteins

-fragmentation of the backbone of proteins

76
Q

How is defined the blood group of each’s person?

A

By glycosylation

77
Q

Scientists can find the same glycosylation pattern when comparing different eucaryotic
species?

A

False

78
Q

Glucose, Fucose and Mannose molecules are attached in the process of O-glycosylation?

A

True

79
Q

A Glycosidic bond is a covalent but reversible link between sugar molecules?

A

True

80
Q

Glycosylation decreases the solubility of proteins and can thereby lead to protein
aggregation?

A

False

81
Q

An endopeptidase is a?

A

Protease

82
Q

An endopeptidase is a?

A

Protease

Protein chemistry (2 decks)

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