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Introduction To Biochemistry And Metabolism > Proteins > Flashcards

Proteins Flashcards

1
Q

Name 2 structural proteins

A

keratin

Collagen

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2
Q

What is the function of transcription factors?

A

Regulate cell activities by switching genes on and off

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3
Q

What is the role of enzymes in metabolic reactions?

A

Speed up the rate of reaction

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4
Q

Explain the structure and role of K-channels

A

K-channels have 4 multipass subunits, cental selectivity pore

Determine what molecules enter and leave the cell

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5
Q

Explain the role and structure of ferritin and hemoglobin

A

Ferritin:

24 subunits, up to 4500 iron atoms

Haemoglobin:

4 subunits, 4 haem groups, 4 iron atoms

Both store essential molecules and transport them across the body

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6
Q

Explain the structure and role of insulin

A

Insulin is a signaling molecule and receptor

It has 6 subunits, coordinated by a central Zn 2+ cation

Communication between and within cells

Binding and regulation of other proteins

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7
Q

Explain the structure and role of antibodies - Immunoglobulin G

A

Immunoglobulin G has 4 peptide chains, 2 heavy chains, and 2 light chains

Immune response to invasion by viruses, bacteria, allergens and other toxins (antigens)

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8
Q

Explain the 2 motor proteins - Kinesin and Myosin

A

Kinesin moving along a microtubule

Myosin sliding on an actin filament

Common structure: catalytic core (head) + neck + coiled-coil

Transport of molecules and organelles across the cell

Membrane fusion/fission, exocytosis/endocytosis

Cell contraction/motility

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9
Q

Name some of the functions of proteins

A

Defense

Signaling

Transport

Catalysis

Movement

Structure

Regulation

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10
Q

Explain why side chains of amino acids are either polar or non-polar

A

polar or hydrophobic

Polar side chains - hydrophilic, wtaer-loving

Non-polar side chains - hydrophobic, water-fearing

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11
Q

Name the 2 ways amino acids are distributed and what it depend on

A

Amino acid distribution depends on the protein environment

Cytosolic proteins - Mostly polar on the outside and mostly hydrophobic on the inside

Membrane proteins - Most hydrophobic on the outside and mostly polar on the inside

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12
Q

Name the 2 main hydrophobic amino acids and explain their structure/bonding

A

Glycine - Local flexibility

Cysteine - disulfide bonds

Proline - helix breaker

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13
Q

Name the 5 polar charge amino acids

A

Lysine

Arginine

Histidine

Aspartic acid

Glutamic acid

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14
Q

Name the 5 polar uncharged amino acids

A

Serine

Threonine

Tyrosine

Asparagine

Glutamine

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15
Q

Name the amino acid the following are modified into and how they modified into these amino acids

A

Lysine into hydroxylysine

Serine into phosphoserine

Formed by post-translational modification

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16
Q

Deptide are linked with what bond (give both names) what molecule is removed

A

Peptide bond or amine bond

Water molecule is removed when the 2 amino acids join together to form a dipeptide

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17
Q

What formation are peptide bonds and give the exception

A

Almost all peptide bonds are in trans configurations

Only for proline, the two configurations have similar energies - trans form and cis form

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18
Q

Explain the resonance structure of proteins

A

Peptide bond has a partial double bond character and exist as two resonance structures

There is no rotation around the peptide bond, only around the alpha-carbon

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19
Q

Explain the structure of amino acids

A

All amino acids have the following groups linked to the carbon alpha atom: amino group, carboxyl group, hydrogen atom, and side chain (R group)

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20
Q

Side chains of amino acids can be:

A

Hydrophobic

Polar charged

Polar uncharged

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21
Q

Explain the primary structure of amino acids

A

Read from the amino terminus to the carboxyl terminus

Encoded by the nucleotide sequence of DNA

unique characteristic of the protein

Alteration of even a single amino acid can cause disease

Stabilization by peptide bonds

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22
Q

Explain the secondary structure of amino acids

A

Results of local folding of the polypeptide chain and formation of hydrogen bonds between C=o and N-H groups in the backbone (chain without groups)

23
Q

Name the 4 main types of secondary structures

A

Alpha helix

Beta pleated sheet

Beta turns

Loops

24
Q

Explain alpha helix

A

Most common type of helix

3.6 residues per turn

Hydrogen bonds between the carbonyl group ( C=O) of reside X and the N-H group of the residue X+4

Right-handed (clockwise)

Has a dipole moment corresponding to a partial positive charge at the N-terminus and a partial negative charge at the C-terminus

25
Q

Explain what a 3 10 - helix is

A

Occurs mostly at the ends of alpha helices

3 residues per turn

H-bonds between residue X and the X+3

Called 3 10 helix because the H bond closes a loop of 10 atoms containing 3 residues

26
Q

Explain what a pi-helix is

A

Very rare

Occurs mainly at the ends of alpha-helices

4.4 residues per turn

H-bonds between residue X and X+5

27
Q

Explain what a beta-pleated sheet is

A

Peptide chains fully extended - pleated shape

Stabilized by H-bonds between C=O and N-H groups of the backbone (flanking regions)

Side chains project above and below the sheet

28
Q

Name and explain the 2 types of beta-pleated sheets

A

Parallel B-sheets:

Two polypeptide strands running in the same direction

Non-linear hydrogen bonds, less stable, parallel B-sheets with less than five parallel strands are rare

Antiparallel B-sheets:

Two polypeptide strands running in opposite directions

Well oriented hydrogen on bonds

Strong and stable

29
Q

Explain what beta-turns are

A

B-turns (or reverse turns) reverse the direction of the polypeptide chain

In standard turns the C=O group of residue X is bonded to the N-H group of residue X+3

Most turns contain at least one residue of glycine or proline

30
Q

Explain what loops are

A

Various lengths, irregular shapes, very flexible

Connect other elements of the secondary structure

31
Q

Explain what super secondary structure is

A

A simple combination of a few secondary structure elements with a specific geometric arrangement

Often perform a particular function

32
Q

Explain tertiary structure

A

Over\ll three-dimensional structure of a protein molecule

Spatial relationship of the secondary structure elements to one another

Stabilized by bonds and interactions between side chains

33
Q

Give an example of a protein with a tertiary structure and explain the structure

A

Lysozyme

Alpha+beta fold

Five helices (three alpha, of which one is closer to the pi-helix, two intermediate alpha/310)

Three standard antiparallel beta sheets

34
Q

Explain the quaternary structure and give 2 examples

A

Spatial arrangements of subunits in a protein composed of more than one polypeptide chain

Stabilized by interactions between side chains (same types as in tertiary structure)

Subunits can be identical or different

Examples:

Neurotrophin-4: two identical subunits

Haemoglobin - two alpha and 2 beta subunits

35
Q

Explain simply the following:

Primary structure

Secondary structure

Supersecondary structure

Tertiary structure

Quaternary stcruture

A

Primary structure - Amino acid sequence of the protein stabilized by peptide bonds

Secondary structure - local rearrangement of residues in helices, sheets, turns, and loop stabilized by H-bonds between C=o and N-H groups of the backbone

Spersecondary structure - Combination of a few secondary structure elements usually performing a particular function

Tertiary structure - Overall 3D structure of the protein stabilized by interactions between side chains

Quaternary stcrture - Arrange,elements of subunits in a protein made of ore that one chain and stabilized by interactions between side chains

36
Q

Explain what protein domains are explain how they are organised

A

Proteins domains are spatially distinct fragments of a polypeptide chain

Protein domains are organised in functional and/or structural units that all called domains

37
Q

Explain the domains number of domains in eukaryotic proteins

A

Most proteins have multiple domains

80% of eukaryotic proteins are multidomain proteins

Only 20% or eukaryotic proteins are single domain proteins

38
Q

Explain domains and subunits

A

A single polypeptide chain can form several domains but only ONE subunit

39
Q

Explain what domain shuffling is - domain shuffling theory

A

Some domains appear in more than one protein

It is though that many multidomain proteins have arisen during evolution bu the fusion of genes that encoded separate proteins in an ancestor

40
Q

Explain Domain movement

A

Flexible connections between domains allows their movement in relation to each other

41
Q

Name the 3 different types of cofactors in enzymes and give examples

A

Prosthetic groups (covalently bound to the protein, e.g. haem in haemoglobin)

Metal ions ( Zn2+, Fe3+, etc.)

Coenzymes (often vitamins)

42
Q

Explain what the active site of an enzyme is

A

A cleft or groove in the protein containing residues that bond the substarte and residues that perform the catalytic reaction

Active site is complementary to the substrate in terms of size, shape, charge and hydrophobicity

43
Q

Explain the lock and key model

A

According to this model the active site is rigid and the substarte fits the active site like a key fits a lock

The model cannot explain why some enzymes act on a large range of substrates

44
Q

Explain the induced fit model

A

According to this model, the substrate induces a change in the enzyme structure that allows fitting

Enzymes are not rigid but flexible and mould to fit the substarte molecule

This model explains why sone enzymes can act on a very large range of substrates

45
Q

Explain the role of Hexokinase in the induced fit model

A

Hexokinases phosphorylates glucose to glucose 6- phosphate

Conformational changes in hexokinase are associated with glucose biding to the active site

46
Q

Explain the function of Phosphofructokinase 2 (PFK2)

Give the equation

A

PFK2 is a bifunctional enzymes wit 2 domains:

a. Kinase domain

b. Phosphate domain

Fructose 6-phopshate makes fructose 2,6-bisphospahate using kinase

Reversible reaction going from fructose 2,6-bisphopstae to fructose 6-phophaste using phosphate

47
Q

Explain the 3-point attachment model

A

Two chemically identical groups in the substarte, a1 and a2 can be distinguished by an enzyme because the substrate binds in the active site at three or more points

48
Q

Explain what sickle cell anaemia is and the difference with RBC’S

A

Normal red blood cells live ~ 120 days in the bloodstream, but sickle cells die after 10-20 days

Sickled cells cause blockage that deprive organs and tissues of oxygen

Not enough red blood cells in the bloodstream to carry oxygen resulting in anaemia

49
Q

Explain the molecular mechanism of sickle cell anaemia and what happens during glutamate to valine mutation in haemoglobin

A

Glu is hydrophilic whereases Val is hydrophobic

In deoxygenated HbS a hydrophobic picket with Phe and Leu is exposed on the surface

Val is attracted to Phe and Leu on another HbS molecule by hydrophobic interactions

Many HbS molecules aggregate into HbS fibres

These fibres cause red blood cells to become stiff and assume a distorted shape that can block blood vessel

Frequent episodes of sever pain, organ damage (oxygen deprivation), serious infections or ven stroke

50
Q

Explain what Goucher disease is

A

Most common lipid storage disease

Caused by mutations in acid-beta-glucosidase that break down glucosylceramide:

Glucosylceramide makes glucose + ceramide

Intracellular accumulation of glucosylceramide, particularly in the spleen, liver and bone marrow

51
Q

Explain the structure of acid-beta-glucosidase

A

Some of the known mutations are in a surface loop that forms part of the active site of the enzyme

They appear to stabilize the conformation that limits access to the active site

These mutations reduce enzyme catalytic activity

52
Q

Explain the molecular mechanism of acid-beta-glucosidase

A

Open conformation with access to the active site

Closed conformation with restricted access to the active site

53
Q
A

Introduction To Biochemistry And Metabolism (4 decks)

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