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Flashcards in Exam 1 Deck (60):
1

What four elements make up 99% of all atoms in living organisms?

Carbon, Nitrogen, Oxygen, Hydrogen

2

What are the four major classes of biological molecules?

Proteins, Nucleic Acids, Lipids, Carbohydrates

3

Explain the central dogma of biology

DNA transcribed into RNA
RNA translated into Protein
DNA can also be replicated to inherit genetic information

4

although all cells in an organism have the same DNA, tissues differ due to selective _______

expression

5

the most common carbohydrate fuel

glucose

6

List the three roles of proteins in biological membranes

Control the permeability of molecules across the membrane
Relay information across the membrane
Generate biochemical energy using a molecular gradient across the membrane

7

Movement of particles due to the random fluctuations of energy content of the environment is known as

Brownian motion

8

What is meant by the phrase "water is a polar molecule?"

The electrons are not shared equally over the covalent bonds of the water molecule. This creates an electrical dipole over the molecule, with the oxygen atom being more electronegative and the hydrogen atoms being more positive.

9

Describe the hydrophobic effect and the driving force behind it

the hydrophobic effect is an organizing principle of non polar/hydrophobic molecules in an aqueous solution. there is an apparent attractive force between hydrophobic molecules that is spontaneous and driven by an increase in entropy. this entropy increase is due to the release of water molecules at the surface of the hydrophobic molecules as they come together

10

List the possible organizations of amphiphilic molecules in aqueous solution

bilayer membrane, micelle, vesicle

11

How is protein folding driven?

the nonpolar/hydrophobic residues are driven together by the hydrophobic effect to form the core of the protein's 3D structure. As they come together water is excluded from the interior of the protein and the outer surface of the protein tends to contain more hydrophilic residues that will interact favorably with the aqueous solution.

12

Why are weak bonds important in biochem?

weak bonds allow for flexibility in biological molecules due to their transient nature. however, these weak interactions provide great strength in numbers

13

what is the distance range of a hydrogen bonds?

1.5 - 2.6 angstroms

14

atoms commonly found in biological molecules that are often hydrogen bond acceptor

oxygen & nitrogen

15

Describe the basis for the van der waals attractive force between two atoms

Non polar atoms without a partial or formal charge can induce a transient dipole. When these atoms are adjacent to one another at an optimal distance (3-4 angstroms) then complementary transient dipoles can provide a small attractive force between the atoms

16

Explain why pH is an important parameter of biological systems

The pH of the solution affects the electrostatic interactions among biological molecules. Because the numerous and important weak interactions (electrostatic, hydrogen bonds) among biological molecules rely on a charge component, these interactions will be altered if the pH is changed. This will have (negative) consequences for the function of these biological molecules if a stable pH cannot be maintained.

17

define pKa

a measure of ionization tendency. it is the pH at which an acid molecule is 50% protonated/50% deprotonated (or dissociated) into its conjugate base

18

an acid ionizes to form a proton and its

conjugate base

19

naturally occurring isomer in proteins (L or D)

L-isomer

20

Which amino acid has a pKa near neutral pH

histidine

21

Is valine an essential or nonessential amino acid for humans

essential

22

is aspartate negatively or positively charged at neutral pH

negatively charged

23

a dipolar ion (opposite charges on the same molecule)

zwitterionic

24

the amino acid with the smallest-size side chain allowing greatest flexibility in a protein is

glycine

25

which amino acid has a side chain that connects both the alpha carbon and the nitrogen of the amino group in the peptide bond

proline

26

an amino acid with a hydrophobic side chain containing a thioether

methionine

27

What is the three letter abbreviation for tryptophan

Trp

28

In what pH range is zwitterionic alanine the predominate structure

2-9

29

Interactions between side chains of Aspartate and Arginine at neutral pH would be

ionic

30

which amino acid has a carboxyl group in its side chain

glutamate

31

What is the advantage of having multiple functional groups in proteins?

the diversity of the physical and chemical properties of the functional groups contribute to the overall diversity of protein function

32

A gene is mutated such that the amino acids glycine and glutamate are now alanine and leucine, respectively. What are the potential results of each of these mutations? Assume that the mutations are not near each other in the primary sequence and have no impact on the other.

The glycine-to-alanine mutations are similar and will have little or no effect (unless the flexibility of the glycine is essential at that position). Glutamate and leucine have very different chemistries and will impact the function and structure of the protein, as one is charged and water soluble and the other is hydrophobic and nonpolar.

33

What are the three aromatic amino acids?

Tyrosine, Phenylalanine, Tryptophan

34

Serine, Threonine, and Tyrosine all have what in common?

hydroxyl functional groups

35

Which amino acid is responsible for stabilizing the structure of a protein by forming pairs of sulfhydryl groups?

Cysteine

36

Even though malnourished, children with Kwashiorkor display a distended stomach, giving the illusion of being full. Why does this happen

This is a nutritional state where there is an extremely low or poor protein intake in the diet. The osmolar shift of the blood, which is poor in protein content, causes water to flow into the tissues. Low protein content of the blood causes problems with fluid distribution in the body.

37

What is the difference between nonessential and essential amino acids?

Essential amino acids cannot be made by the body and must come from food

38

this molecule is made when a peptide bond is formed

water

39

this amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restricts bond rotations

proline

40

the plot that allows one to investigate the likely orientation of certain amino acid pairs is called

Ramachandran plot

41

Due to the side group steric clash, almost all peptide bonds are _____ in their configuration

trans

42

Every third residue in the protein collagen is

glycine

43

Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as

Beta-mecaptoethanol

44

this beta-sheet structure occurs when the two strands are oriented in opposite directions

antiparallel

45

a protein is considered to be _____ when it is converted into a randomly coiled structure without its normal activity

denatured

46

do all cysteines participatein disulfide bond formation

no

47

what is the hydrogen bonding pattern for helices in proteins

i, i +4

48

which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein

phenylalanine

49

the folding of a protein into its native shape can be described as

a series of repeatable random events where the lowest energy structure is maintained

50

the amino acid sequence from the N-terminus to the C-terminus

primary structure

51

what is the predominant screw sense for helices in proteins

right-handed

52

How are the amino acid R groups arranged relative to the plane of a β-sheet structure?

The R-groups of amino acids in a β-sheet protrude perpendicular (above and below) the sheet plane.

53

what determines a protein's tertiary structure

the amino acid sequence

54

How does the protein backbone add to structural stability?

The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.

55

Why are amino acids with a branch at the β-carbon problematic for helices

The branched-chain R groups result in steric clashes within the compact structure of the α helix.

56

Why are all the theoretical combinations of phi and psi not possible

steric hindrances of the side chains make certain combinations and angles impossible

57

name of the modified amino acid in collagen

hydroxyproline

58

Molecular basis of scurvy

Scurvy is a deficiency in vitamin C, which humans must acquire from the diet, and causes defects related to collagen function in the body. The protein collagen contains the modified amino acid hydroxyproline. The enzyme that converts proline to hydroxyproline, prolyl hydroxylase, depends on Vitamin C for its activity. So, without Vitamin C, the proline in collagen cannot be efficiently converted to hydroxyproline, which leads to detrimental consequences in collagen structure and function.

59

Describe the Anfinsen ribonuclease experiment and what conclusions were drawn about protein folding.

Purified and active Ribonuclease A was treated with urea and β-mercaptoethanol to completely denature the protein. With these reagents all tertiary structure was lost and any disulfide bonds were reduced. At this point Ribonuclease lost all of its enzyme activity. The concentrations of these denaturants were slowly decreased (removed from solution) and the ribonuclease regained activity. The final renatured protein had the same characteristics as the original protein. Anfinsen concluded that the primary sequence of amino acids contained all of the necessary information to generate the three-dimensional tertiary structure of the enzyme.

60

proteins that can assume a new protein structure that is self-propagating

prions