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Cell Biology > Lecture 4 - Exam 1 > Flashcards

Lecture 4 - Exam 1 Flashcards

1
Q

Steroid hormones are derivatives of…?

A

Cholesterol

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2
Q

Steroid hormones act as…?
Can they cross cell membranes?

A

They act as chemical long distance messengers among cells.
They can cross cell membranes.

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3
Q

What are nucleic acids?
What is the structure of nucleic acids?

A

Principal informational molecules of the cell.
Are made up of many nucleotides together. Nucleotides are a Sugar molecule (Ribose or Deoxyribose), a phosphate, and a nitrogenous base.

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4
Q

What is Deoxyribonucleic acid (DNA)?
What is Ribonucleic acid (RNA)?

A

DNA: The genetic material
RNA: several types (mRNA, rRNA, and tRNA)

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5
Q

What is messenger RNA (mRNA)?
What is ribosomal and transfer RNA (rRNA & tRNA)?

A

mRNA: Carries information from DNA to the ribosomes.
rRNA & tRNA: Are involved in protein synthesis.
Other RNAs are involved in regulation of gene expression, and processing and transport of RNAs and proteins.

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6
Q

Are there other RNAs other than mRNA, rRNA, tRNA?

A

YES!

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7
Q

What are the two types of bases that comprise a nucleotide with deoxyribose as the sugar? What about with ribose as the sugar?

A

Purines (adenine and guanine) & Pyrimidines (cytosine and thymine).
With ribose, you will have uracil instead of thymine.

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8
Q

What are nucleosides?

A

When the bases (A, C, T, G, or U) are linked just to sugars. (no phosphate)

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9
Q

What are nucleotides?

A

Have a sugar, a base, and a phosphate that is linked to the 5’ carbon of the sugars.

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10
Q

What are phosphodiester bonds?

A

Form between the 5’ phosphate of one nucleotide and the 3’ hydroxyl of a sugar of another nucleotide.

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11
Q

What are oligonucleotides?

A

Are polymers of a few nucleotides.

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12
Q

RNA and DNA are _______ and may contain thousands or millions of nucleotides.

A

Polynucleotides

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13
Q

Polynucleotides (like DNA or RNA) have a sense of direction. One end terminates in a __ phosphate group and the other in a __ hydroxyl group.

A

5’ ; 3’
Hence, polynucleotides are always synthesized in the 5’ to 3’ direction.

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14
Q

DNA is made up of two polynucleotide chains running in _______ directions.

A

Opposite

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15
Q

Complementary base pairing allows…?

A

It allows one strand of DNA (or RNA) to act as a template for synthesis of a complementary strand.
Thus, nucleic acids are capable of self-replication.

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16
Q

DNA is made up of two polynucleotide chains running in opposite directions. The bases are where?

A

The bases are on the inside, joined by hydrogen bonds between complementary base pairs:
G w/ C
A w/ T

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17
Q

What is a hydrogen bond?

A

Weak electrostatic attraction between a proton in one molecule and an electronegative atom in the other.

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18
Q

What is the most diverse macromolecule?

A

Proteins.

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19
Q

Proteins are…?

A

Polymers of 20 different amino acids

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20
Q

What is the structure of an amino acid?

A

alpha carbon bonded to a carboxyl group (COO-), an amino group (NH3+), a hydrogen, and a distinctive side chain.

21
Q

How are amino acids grouped?

A

Based on characteristics of their side chains:
Nonpolar side chains
Polar side chains
Side chains w/ charged basic group
Acidic side chains terminating in carboxyl groups

22
Q

Supposed to memorize the single letter nomenclature for amino acids. Most are self-explanatory, here are the ones that are funky:
Phenylalanine
Tryptophan
Tyrosine
Asparagine
Glutamine
Lysine
Arginine
Aspartic Acid
Glutamic Acid

A

F
W
Y
N
Q
K
R
D
E

23
Q

What are the amino acids with basic groups (charged)?
What are the amino acids with acidic side chains terminating in carboxyl groups?

A

Basic: Lysine, Arginine, & Histidine
Acidic: Aspartic Acid & Glutamic Acid

24
Q

What are the standout nonpolar amino acids?
What are the standout polar amino acids?

A

Cysteine
Serine, Threonine, & Tyrosine

25
Q

What are amino acids joined by?

A

Peptide bonds

26
Q

What are polypeptides?

A

Are chains of amino acids, hundreds or thousands of amino acids in length.

27
Q

What are the two termini?

A

N and C terminus

28
Q

What are the different levels of protein structure?

A

Primary: the sequence of amino acids in the polypeptide chains
Secondary: regular arrangements of amino acids within localized regions
Tertiary structure: the polypeptide chain folds due to interactions between side chains of amino acids in different regions of the chain.
Quaternary: interactions between different polypeptide chains in proteins composed of more than one polypeptide

29
Q

Describe the primary structure of a protein.

A

Linear sequence of amino acids.
Held together by covalent bonds of peptide backbone.
The two ends of the structure are referred to as the amino terminus (N) and carboxyl terminus (C).

30
Q

Describe the secondary structure of a protein.

A

The alpha and beta sheet secondary structures are held together by hydrogen bonds between the CO and NH groups of peptide bonds.
Alpha: Every four amino acids the CO of one peptide bond forms a hydrogen bond with NH of another peptide bond.
R groups are sitting on the outside.
Beta sheet: Two parts of a peptide chain lie side by side either parallel or antiparallel.

31
Q

Describe the tertiary structure of a protein.

A

Regions of a alpha helix and beta sheet secondary structures, connected by loop regions, are folded into the tertiary structure.

32
Q

What is in the interior of a tertiary structured protein that is critical?
What are some other properties of this critical component?

A

The hydrophobic amino acids.
Hydrogen-hydrogen bonds in alpha helices and beta sheets makes them more hydrophobic.

33
Q

What is found on the surface of a tertiary structured amino acids?
What do these things contain?

A

Loops.
They contain polar amino acids.

34
Q

What are disulfide bonds?

A

Are covalent linkages (not weak hydrostatic interactions) between the sulfur-containing side chains of cysteines, contribute to the tertiary structure. I.e. the sulfur atoms are sharing electrons.
In tertiary structure, these bonds act as “safety pins”

35
Q

Can you find disulfide bonds in tertiary and secondary structures?

A

YES!

36
Q

Each of the subunits in a quaternary proteins have their own what?
The subunits are held together by what?

A

Each of the subunits has its own primary, secondary, and tertiary structure. The subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains.

37
Q

What are some conditions that can disrupt the bonds in proteins and cause them to denature?

A

Temperature : high temps disrupt weak hydrogen bonds
pH : can disrupt ionic bonds between acidic/basic R groups
Reducing environment: breaks disulfide bonds

38
Q

What is the thermodynamic hypothesis?

A

Proteins fold into their native states by minimizing their free energy.

39
Q

Do some proteins fold spontaneously?

A

Yes, mostly small globular proteins.

40
Q

What did Cyrus Levinthal note about polypeptide chains?

A

Noted that polypeptide chains have an astronomical number of conformations.

41
Q

The average protein is how long?
And how many potential folds?

A

248 amino acids.
10^200 potential folds.

42
Q

If proteins were to sample all possible configurations, it would take longer than the age of the universe to arrive at its correct native conformation. What is the paradox?

A

The paradox is that most small proteins fold spontaneously on a millisecond or even microsecond time scale.
SOLUTION: local interactions happen fast then these lead to more global interactions.

43
Q

What is the energy landscape theory?

A

The folding funnel model is a specific version of the energy landscape theory of protein folding. The native state is a deep free energy minimum, giving a well-defined tertiary structure.
A driving force for protein folding is the stabilization associated with the sequestration of hydrophobic amino acid side chains in the interior of the folded protein.

44
Q

Folding is ________.

A

co-translational

45
Q

Describe misfolded proteins.

A

Misfolded proteins are stuck in a local energy well.
Enzymes are needed for the rescue.
Chaperons help fold the proteins.
Chaperonines are chaperones with specific structure and use ATP.
Both bind to and stabilize unfolded or partially folded polypeptides.

46
Q

Chaperons often bind to?

A

Polypeptide chains that are still being translated on ribosomes. Chain must be protected until synthesis of an entire domain is complete.

47
Q

What are Heat Shock Proteins (HSP)?

A

(A type of chaperone!!) Produced when cells are put at elevated temperatures.
They stabilize and facilitate refolding of proteins that have been partially denatured as a result of elevated temperatures

48
Q

Describe HSP60.

A
  1. Hydrophobic interaction with misfolded proteins (client proteins)
  2. Enclosed environment allows protein to refold.
  3. Protein repair (requires energy of ATP)
  4. Released of folded protein.
49
Q

Describe HSP100.

A

Refolds misfolded proteins
Dissolved aggregates
Disaggregation requires HSP70

Cell Biology (33 decks)

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