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Spring 2013 / Biochemistry > Lecture 7 - Proteins > Flashcards

Lecture 7 - Proteins Flashcards

0
Q

What is an Amino Acid?

A

An Amine (subunit monomer) that builds proteins.

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1
Q

What are the three major nitrogen-containing building blocks?

A

Amino Acids, Porphyrins and Nucleotides

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2
Q

What is a prophyrin?

A

nitrogen-containing ring structure that chelate a metal ion in the center of the ring, specialized to hold the ion in place without bonding it.

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3
Q

What is a nucleotide?

A

subunit/monomer for nucleic acid which provides information storage and molecules for building DNA and RNA

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4
Q

What is the structure of a amino acid?

A

carboxylic acid (carboxyl group) and an amine group

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5
Q

What is a single amino acid called?

A

monopeptide

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6
Q

What are two joined monopeptides called? Three? more than three?

A

dipeptide
tripeptide
polypeptides

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7
Q

Once a polypeptide develops its secondary and tertiary structure by folding, what does it become?

A

a protein

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8
Q

amide bond looks like what?

A

O=C-N

this is an amide bond, also a peptide bond

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9
Q

What does and amide or peptide bond do?

A

joins two amino acids

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10
Q

are amides proteins?

A

yes, since they are joined by a peptide bond

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11
Q

through what reaction is an amide/peptide bond formed?

A

dehydration synthesis

-similar to sugars and carb bonding

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12
Q

what is an essential tripeptide used in biological systems and a cell’s major antioxidant molecule?

A

Glutathione

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13
Q

What is Glutathione composed of?

A

glutamic acid, cysteine and glycine (3 amino acids - tripeptide)
it also has a thiol (sulfhydrul) group - which gives it its ROS (reactive oxidant species) properties.

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14
Q

Where is Glutathione found and how abundant is it?

A

FOund in the cytoplasm to relieve oxidative stress from toxins, the most abundant molecule in cytoplasm besides water.

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15
Q

How many amino acids found in humans?

A

20 specific types

other types found in other animals

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16
Q

How many of the 20 specific amino acids found in humans can we synthesize our selves?

A

12 can be synthesized

8 (called essential) must be taken in through diet

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17
Q

Amino acids are found with enantiomeric and chiral conformations - which form can be incorporated into proteins in humans?

A

L-form enantiomer amino acids and

∂-chiral amino acids

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18
Q

What characteristics give aminos the properties for multiple, divers possibilities of protein conformation (folding)?

A
  • sulfur-containing aminos (cysteine and methionine) give integrity to the protein folding by forming disulfide bridges.
  • charged or uncharged molecules causes attraction and repulsion when the polypeptide folds into a protein.
  • hydrogen bonds form between some aminos affecting conformation and stability.
  • Hydrophobic and hydrophilic aminos attract or repel with each other as the protein folds, creating space inside the protein for enzymatic actions
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19
Q

What are the various and diverse roles that proteins play in the body?

A
  • enzymes
  • structural proteins: connective tissue, skin, collagen
  • movement: tendon, muscle, actin, myosin
  • messengers/hormones/regulatory
  • transport: channel proteins
  • defense: immunoglobulins
  • nutrient storage: milk protein, albumin
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20
Q

What is the primary structure (or conformation) (1°) of a protein?

A

polypeptide produced by a ribosome is a linear, unfolded chain of amino acids linked with peptide bonds

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21
Q

What does the secondary structure (2°) of a protein look like?

A

hydrogen bonding occurs, folding in the protien

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22
Q

What does the tertiary (3°) conformation of protein look like?

A

disulfide bridges, positive/negative charge attractions and hydrophobic/phyllic interactions form creating curves and spaces creating areas for enzymatic actions and storage.

23
Q

What is a Quaternary Structure?

A

When two or more tertiary structure proteins hydrogen bond together. Hemoglobin has a quaternary structure.

24
Q

What is an active site and where is it found?

A

Active site is where the catalytic work of the enzyme takes place. It is found as cavities within a tertiary protein.

25
Q

What is a substrate?

A

molecules that enter the active site to be “worked upon” by the enzyme. There can be one or multiple substrates.

26
Q

What are some examples of actions that take place in the active site?

A

splitting or joining molecules and flipping conformation occur in the active sites.

27
Q

What are coenzymes and cofactors?

A

ATP, vitamins, ions and porphyries are often part of or introduced into the site, facilitating reactivity.

28
Q

What are porphyrins?

A

complex heterocyclic amine molecules that perform important roles in enzymes and enzyme related processes. Noted form their ability to chelate metal ions onto their structure and hence utilize the electron cloud properties of the captured metal ion. Found in the active sites of enzymes.

29
Q

True or False: Many vitamins have nucleotides as part of their structure.

A

True

30
Q

What is the nucleotide chain composed of?

A

phosphate-sugar backbone of either ribose or deoxyribose sugars and phospate

31
Q

Do Nucleic Acids branch?

A

no. They form an unbranched chain

32
Q

What are the 3 subunits of Nucleotides?

A

nitrogenous base, monosaccharide (simple sugar), phosphate group

33
Q

Where in the cell are nucleotides formed?

A

in the cell nucleolus

34
Q

What are the two different nitrogenous bases found in nucleotides?

A

purine or pyrimidine

35
Q

What is a purine?

A

heterocyclic acid with two rings which contain nitrogen

guanine, adenine

36
Q

What is a pyrimidine?

A

a heterocyclic acid of one ring containing nitrogen.

cytosine, thymine, uracil

37
Q

What are the two sugars found in nucleic acids?

A

ribose and deoxyribose

38
Q

Does the double bond in a phosphate group have fixed or unfixed double bonds?

A

Unfixed, the phosphate group has five bonds: three single and one double bonds with oxygen. The moving of the one double bond releases energy.

39
Q

What is the second step in the building of Nucleotides?

A

NucleoSides. They are the nitrogenous base plus a ribose or deoxyribose.

40
Q

What process needs to occur for the nucleoSide to become a nucleoTide?

A

phosphorylation - the bonding of a phosphate group to the nucleoside to complete the formation of a nucleotide.

41
Q

What are some important molecules that have the nucleotide Adenosine as their base?

A

ATP (adenosine triphosphate)
NADH
cAMP (cyclic adenosine monophosphate)
ADP & AMP (intermediaries of ATP in metabolism)

42
Q

cAMP is a messenger molecule used in the cytoplasm, regulating cell metabolism by stimulating energy use. What happens at higher and lower concentrations of cAMP?

A

Higher concentration causes the cell’s metabolism to increase.
Lower concentrations slows cellular metabolism.

43
Q

Caffein inhibits and enzyme called phosphodiesterase. What is the normal function of phosphodiesterase?

A

phosphodiesterase breaks down cAMP - slowing down the cells metabolism. Caffein inhibits phosphodiesterase resulting in higher than natural cellular activity.

44
Q

What are the base pairing rules for DNA and RNA?

A

Adenine - Thymine
Cytosine - Guanine
for RNA (which has no Thymine)
Adenine - Uracil

45
Q

What attracts the DNA nucleotide bases to their complementary pair to form the helix?

A

Hydrogen bonding

46
Q

When RNA forms a double helix, is it from one strand of RNA or two strands?

A

Always one strand - looped back on itself. DNA forms a double helix from two strands.

47
Q

What is the function of DNA?

A

Storage molecule for genetic data

48
Q

What are the three distinct types of RNA?

A

rRNA - ribosomal RNA (often bonded to itself)
tRNA - transfer RNA ( “ “)
mRNA - messenger RNA (usually open, unbonded)

49
Q

Where is rRNA made?

A

in the cell nucleus

50
Q

How is mRNA formed?

A

it is TRANSCRIBED from DNA in the nucleus and carries the protein code (from the DNA) from the nucleus to the cell’s manufactories - ribosomes.

51
Q

What is the job of tRNA?

A

to carry amino acids into the protein synthesis process in the ribosome.

52
Q

How many different kinds of tRNA are there?

A

There are 20 different tRNA’s which code for each of the 20 amino acids - specific tRNA for each amino

53
Q

What is a codon?

A

3-base grouping of nucleotides which act as an information packet in the mRNA when building proteins

54
Q

Which aminos contain sulfur? Why is this important?

A

Methionine and cysteine online?

These aminos for sulfur bridges and are important in protein folding.

Spring 2013 / Biochemistry (13 decks)

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