Lecture 1: Biochemistry and Protein Structure Review Flashcards Preview

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Flashcards in Lecture 1: Biochemistry and Protein Structure Review Deck (34):
1

Kilocalorie

the amount of energy need to raise the temperature of one liter of water one ˚C

2

Relative strength of bond types

Covalent > Ionic (electrostatic interactions) > Hydrogen > Van der Waals

3

Electrostatic attractions are ____ in aqueous solutions

weakened

4

Hydrogen Bonds

Highly directional, unlike a typical electrostatic interaction, and is strongest when a straight line can be drawn between all three atoms involved 

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5

Amino acids that form a protein are often ___ bonded together

Hydrogen

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6

___ bonds exist between the G and C bases in a DNA double helix

Hydrogen

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7

Hydrophilic molecules

composed of ions or polar molecules that attract water molecules through electrical charge effects

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8

Hydrophobic Molecules

Molecules that contain a preponderance of nonpolar bonds. Insoluble in water. Most hydrocarbons are hydrophobic molecules.

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9

Van der Waals Interactions

weak attractive force generated by induced flickering dipoles in neighboring atoms

10

Hydrophobic Forces

Non really a “bond”, but interactions that push nonpolar surfaces out of hydrogen bonding water networks where they would otherwise physically interfere with the highly favorable interactions between water molecules 

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11

Which of the following represent covalent interactions?

 a) peptide bond formation during the translation of epidermal growth factor (EGF)

 b) hydrogen bond formation during folding of the newly translated EGF

 c) ionic bond formation during folding of the newly translated EGF 

d) disulfide formation during folding of the newly translated EGF 

e) binding of EGF to the EGF receptor

a) peptide bond formation during the translation of epidermal growth factor (EGF)

d) disulfide formation during folding of the newly translated EGF 

12

What are the four basic building blocks of the cells? And what larger units do they make up?

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13

Phospholipid structure

Polar head group (choline is common), phosphoric acid, glycerol backbone, fatty acid tails

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14

Amino acid structure

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15

Nucleotide structure

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16

Difference between a nucleotide and a nucleoside

nucleotides are the constituents of DNA and RNA not nucleosides

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17

Which of the following accurately describe the molecule shown below? 

 

CH3(CH2)7CH=CH(CH2)7COOH 

 

a) Hydrophilic 

b) Hydrophobic 

c) Polyunsaturated 

d) Saturated 

e) Unsaturated 

B) Hydrophobic

E) Unsaturated

18

Most macromolecules fold into ___ stable shape or conformation

One

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19

_____ bonds specify shape and interaction properties of macromolecules

Non covalent

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20

Most work in the cell is done by ___

protein

21

Proteins are:

-enzymes that catalyze specific reactions 

-structural components that give cells shape and allow them to move 

-signals and signal receivers 

22

The shape and properties of a protein is determined by its _____

amino acid sequence 

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23

Environmental pH determines the charged state of some amino acid side chains 

• Five amino acids side chains can carry a charge 

– D, E, H, K, R 

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24

Proteins are structurally polar 

• Polypeptide sequences are always written in an Amino terminal (N, NH2) to Carboxyl terminal (C, COOH) direction 

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25

Protein conformations are restricted by __ interactions 

steric

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26

What three noncovalent interactions help shape protein conformations?

Electrostatic interactions, Hydrogen bonds, Van der Waals attractions

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27

___ interactions also regulate protein conformation 

Hydrophobic

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28

The 3D shape of a protein is determined by its amino acid sequence. What proves this?

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29

What secondary structure is this and how is it formed?

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-Alpha Helix

-Particular sets of phi/psi angles and main chain hydrogen bonds between peptide bond can result in the common fold. 

30

What secondary structure is this?

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Beta sheet

31

Which beta sheet is parallel and which is antiparallel?

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A) antiparallel

B) parallel

32

What secondary structure is this and how is it formed?

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Coiled coil- alpha helices wrap around eachother to minimize exposure of hydrophobic amino acid side chains to the aqueous environment.

33

What is this an example of?

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Secondary structure elements combining to form tertiary structure

34

Src family kinases are an example of?

The fact that many large proteins are composed of several to many smaller independent modules 

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