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Cell Biology > Basics and Proteins for Exam 1 > Flashcards

Basics and Proteins for Exam 1 Flashcards

1
Q

Main six atoms most living systems contain

A

H, C, N P, O, S

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2
Q

Bond Energy

A

Amount of energy required to break 1 mole of such bonds

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3
Q

Carbon Compounds are Stable in what kind of light?

A

Visible Light

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4
Q

Carbon-containing molecules are:

A
  • Very stable
  • Diverse
  • Can form stereoisomers
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5
Q

What is a Carboxyl group?

A

Carbon with 3 bonds: double with 1 Oxygen and single with 1 negative Oxygen, one bond with nothing

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6
Q

What is a Phosphate group?

A

Phosphorus with 4 bonds: double with Oxygen, single with negative Oxygen, single with negative Oxygen, singe with Oxygen with bond coming off.

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7
Q

What is an Amino group?

A

-NH3+

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8
Q

What is a Hydroxyl group?

A

-OH

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9
Q

What is a Sulfhydryl group?

A

-SH

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10
Q

What is a Carbonyl group?

A

C = O with two bonds coming off of C

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11
Q

W/hat is an Aldehyde group?

A

C = O and C - H with a - off of C

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12
Q

Hydrocarbons

A

Molecules containing only hydrogen and carbon

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13
Q

Stereoisomers

A

Mirror-image forms of the same compound

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14
Q

Strength of Hydrogen Bonds

A

2 - 5 kcal/mol

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15
Q

Selectively permeable membranes

A
  • Readily permeable to nonpolar molecules
  • Impermeable to most polar molecules
  • Highly impermeable to ions
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16
Q

Condensation Reaction

A

2 molecules become 1 with water as a product

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17
Q

Hydrolysis Reaction

A

1 molecule becomes 2 requiring water as a reactant

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18
Q

Does polymerization have an inherent directionality?

A

YES, polymerization has an inherent directionality

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19
Q

Protein Denaturization

A

Unfolding of the protein (Non-covalent bonds break, covalent bonds DO NOT break)

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20
Q

Most proteins are…

A

…enzymes. Most proteins are enzymes.

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21
Q

What is a protein?

A

A protein is a sequence of amino acids held together via covalent bonds.

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22
Q

How many amino acids are used in protein synthesis?

A

20 amino acids are used in protein synthesis

23
Q

Every amino acid has the same basic structure (4)

A
  • Carboxyl group
  • Amino group
  • Hydrogen
  • R group
24
Q

What kind of amino acids are in proteins?

A

Left hand or L - amino acids are in proteins

25
Q

R-group determines? It can be… (3)

A 
The chemical properties of each amino acid.
It can be:
1) Hydrophobic/nonpolar
2) Hydrophilic/polar uncharged
3) Hydrophilic/polar charged
26
Q

The first amino acid used when making a protein

A

Methionine (Met) is almost always the first amino acid in a protein

27
Q

Peptide bond

A
  • The covalent C - N bond linking two amino acids together is called a peptide bond
  • Nitrogen of Amine Group bonds with Carbon of Carboxyl group
28
Q

Directionality of amino acid chain

A 
Amino group (N - terminus) and Carboxyl group (C - terminus)
-Proteins constructed from N - to C - terminus via stepwise condensation reactions
29
Q

Disulfide bond (Covalent bond)

A

Covalent bond between two non-linked Cysteine (Cys) amino acids

30
Q

Non-covalent bonds in proteins

A
  • Hydrogen bonding
  • Ionic bonding
  • Van der Waals interactions
  • Hydrophobic interactions
31
Q

Hydrogen bonds in proteins

A
  • Hydrogen bonds form between an EN atom (O or N) and a hydrogen
  • Stabilize helical and sheet structures
  • Become strong in large numbers
32
Q

Strength of Covalent Bonds

A

70 - 100 kcal/mol

33
Q

Strength of Ionic Bonds

A

3 kcal/mol

34
Q

Ionic bonds in proteins

A
  • Act over longer distances

- Disrupted by changes in pH or high salt concentrations

35
Q

Strength of Van der Waals Interactions

A

0.1 - 0.2 kcal/mol

36
Q

Van der Waals Interactions in proteins

A
  • Interaction of nonpolar molecules
  • Atoms must be within 0.2 nm of each other
  • Result of dipoles
37
Q

Hydrophobic Interactions

A
  • Tendency of hydrophobic molecules to be excluded from interaction with water
  • Amino acids with hydrophilic R groups on outside of folding
  • Amino acids with hydrophobic R groups on inside of folding
38
Q

Primary Protein Structure

A

The Primary Structure is simply the sequence of amino acids of the polypeptide/protein
-All 3 higher levels dictated by primary structure

39
Q

Secondary Protein Structure

A
  • Involves repetitive patterns of local structure
  • Structure result of H-bonding b/w amino acid residues
  • Local interactions yield alpha helicies and beta pleated sheets
40
Q

Alpha Helix

A
  • Has 3.6 amino acids per turn
  • Peptide bonds of every fourth amino acid are close together
  • H-bond forms b/w NH of one peptide bond and the CO of the other
  • Spiral shape with R groups of amino acids jutting out
41
Q

Beta Pleated Sheet

A
  • Extended sheet-like conformation
  • Characterized by maximum of H-bonding
  • All amino and carboxyl groups of amino acids involved
  • H-bonds form perpendicular to plane of sheet
  • Carbon atoms jut out making sheet “pleated”
42
Q

Diagram of Protein Structure

A
  • Alpha helix is spiral or cylinder
  • Beta sheet is flat ribbon or arrow with head pointing to C-terminus
  • Looped segment connecting helicies and/or sheets is called a RANDOM COIL and is shown by narrow ribbon
43
Q

Tertiary Protein Structure

A
  • Depends almost completely on R group of amino acids interactions
  • Structure not repetitive or predictable
  • Hydrophobic R groups group up in interior of protein
  • Polar R groups drawn to surface by affinity for each other and water
  • Proteins fold into a NATIVE CONFORMATION, most stable state for a particular string of amino acids
  • Secondary and tertiary structure contribute to overall folding of protein, varying by primary structure
44
Q

Molecular chaperones

A
  • Assist protein folding in tertiary stage, although some folding will occur spontaneously
  • PREVENT MISFOLDING
45
Q

Two Main Categories of Proteins

A

Fibrous and Globular Proteins

46
Q

Fibrous Proteins

A
  • Extensive secondary (helix/sheet) structure, so highly ordered and repetitive
  • Secondary structure determines shape more than tertiary
  • Examples: Keratins (skin and hair), Elastins (ligaments and vessels), Collagen (tendons and skin)
47
Q

Globular Proteins

A
  • Most proteins involved in cellular structure are globular
  • Fold into compact structure
  • Small local regions of helicies or sheets
  • Every globular protein has unique tertiary structure
48
Q

Domains

A

A discrete, locally folded unit of tertiary structure that usually has a specific function…many globular proteins consist of 1 or more domains

ONE PROTEIN, DISTINCT PARTS

49
Q

Quaternary Strucutre

A
  • Concerned with subunit interactions and assembly
  • Only applies to multimeric proteins
  • H-bonding, electrostatic forces, hydrophobic interactions, Van der Waals interactions, and disulfide bonds are responsible for this structure
50
Q

Homotetrameric Protein

A

4 copies of same gene product (protein)

51
Q

Heterotetrameric Protein/Heterotetramer

A

4 gene products of different kinds

52
Q

Cofactors

A

bind to proteins, but not proteins themselves but are necessary for the protein to function (Ex. iron)

53
Q

Hierarchy of Proteins

A
  • Proteins are made up of subunits (which are proteins themselves)
  • Subunits are made up of domains
  • Domains are made up of amino acids

Cell Biology (9 decks)

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