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MSAP Biochem > Week 1 Biochem > Flashcards

Week 1 Biochem Flashcards

1
Q

Describe the flow of genetic information:

A

DNA contains the info (genes) used to transcribe RNA, which is then translated into proteins built up of amino acids. (Central Dogma)

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2
Q

What are the three main components of Nucleotides:

A
  1. Sugar
  2. Triphosphate
  3. Base (A,C,T,G)
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3
Q

What is the importance of the 3’ hydroxyl group?

A

It is necessary for the formation of new phosphodiester bonds between nucleotides in a strand of DNA, by binding with the 5’ phosphate groups of new nucleotide triphosphates.

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4
Q

What is a nucleosome?

A

A complex of 8 histones around which DNA is wrapped twice to yield “quaternary structure”.

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5
Q

What are the 3 basic levels of Eukaryotic packaging smaller than chromosomes:

A
  1. Nucleosomes
  2. Loops-of-Fibers
  3. 30 nm Fibers
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6
Q

What is another name for the 30 nm fiber?

A

Solenoid Structure

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7
Q

What is DNA wrapped around in the Nucleosome?

A

Histone Octamers

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8
Q

Each histone core has _______ base pairs of DNA wrapped around it to form a nucleosome.

A

146

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9
Q

How many BP’s of DNA does each linker region contain?

A

54

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10
Q

What is H1?

A

The histone protein that holds the core particle down to secure the DNA wrapped around the octamer.

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11
Q

Solenoid structures are also called:

A

Chromatin Fibers

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12
Q

What is the main difference between euk. and prok. DNA?

A

Euk is linear

Prok. is circular

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13
Q

Describe the 2 steps that prokaryotes use to compress DNA:

A
  1. Negative Supercoiling: Opening up the closed DNA loop to allow negative supercoiling of the DNA.
  2. Use of HU protein core to loop the negatively supercoiled DNA around it.
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14
Q

In E. Coli, there are about _______ HU proteins that form the core around which negatively supercoiled DNA is looped.

A

60,000

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15
Q

How many ORI’s does prokaryotic DNA contain?

A

1

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16
Q

Prokaryotic replication continues towards the ________ until completion, when the _________.

A
  1. Replication Forks

2. Termini signal is received.

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17
Q

What are two things about eukaryotic rep. that are not true about prok. rep.?

A
  1. Many ORI’s

2. No Termini Signal

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18
Q

What are the 2 important sequences of the OriC in E. Coli?

A
  1. Consensus Sequence: 3 tandem-arrayed 13-Nucleotide Sequences.
  2. An additional FOUR 9-nucleotide sequences.
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19
Q

What do the 9-nucleotide sequences do?

A

Serve as high affinity binding sites for the protein dnaA

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20
Q

What is the function of dnaA? How does it achieve this function?

A

To help open up the parental double stranded DNA. It does so by breaking hydrogen bonds between base pairs.

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21
Q

How does the opening of closed prokaryotic DNA begin?

A

When enough dnaA proteins bind the 9-nucleotide sequences, they use ATP to begin opening the parental strands.

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22
Q

What is DnaB and what does it do?

A

Helicase: 2 are needed and one associates with each replication fork to open up the double HELIX. Hence the name.

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23
Q

What is DnaC and what does it do?

A

DnaC is a transport protein that complexes with DnaB proteins to deliver them to the replication forks, with the use of ATP, to allow them to separate the double helix.

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24
Q

Where does strand separation begin in prokaryotic DNA?

A

At the consensus sequence, once enough DnaA proteins form a barrel that is activated by ATP.

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25
Q

What is another name for DnaC?

A

Helicase Inhibitor

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26
Q

Helicase acts by binding to _______ and then _______.

A
  1. SINGLE strands of parental DNA

2. Unwinding it in opposite directions away from the origin.

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27
Q

DnaB binds to ______ at the replication forks to form ______.

A
  1. Primase

2. Primosome Protein complex

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28
Q

What are ssb’s and what do they do?

A

Single-Stranded-Binding Proteins: They bind to the opened single strands of DNA near the primosome in order to stabilize the DNA and prevent the reforming of secondary structure (the re-binding of the 2 parental strands.

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29
Q

Where do DnaA, DnaB, and DnaC bind to respectively?

A
  1. 9-Nucleotide sequences at the OriC
  2. The left and right replication forks
  3. Binds to DnaB and delivers it
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30
Q

What is the function of DNA Polymerase?

A

To use the parental strand of DNA to synthesize a new daughter strand.

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31
Q

How does DNA Polymerase 3 work and in which type of cells does it work?

A

Prokaryotic Cells. It uses the parental strand as a template and forms phosphodiester bonds between the free -OH groups on the 3’ end of the PRIMER strand and the phosphate groups of incoming nucleotide triphosphates.

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32
Q

What is the by-product of adding a new nucleotide triphosphate to the primer strand?

A

Pyro-phosphate: The two remaining phosphates from the incoming nucleotide triphosphate.

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33
Q

How can base mispairing occur?

A

A tautomer of one of the bases can form, possessing a different configuration that resembles another base.

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34
Q

How does DNAPOL3 recognize and remove mispaired bases?

A

When the tautomeric configuration changes back from an Imine to an Amine, the 3’ -OH group will be in the wrong position to form new phosphodiester bonds. So DNAPOL3 has 3’ to 5’ Proofreading Exonuclease activity to cleave off bases with improper orientation of the 3’ -OH group.

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35
Q

In terms of DNAPOL3 activity, explain the difference between the “P” and “E” sites.

A

The “P” site is the active site of DNAPOL3 when it is polymerizing, or synthesizing new DNA in the 5’ to 3’ direction. The “E” site is the active site of DNAPOL3 when it is editing mispaired bases in the 3’ to 5’ direction.

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36
Q

What is DNA Primase?

A

A polymerase required for DNAPOL to begin elongation of daughter strands.

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37
Q

What is DNAPOL3?

A

A multi-subunit protein used for elongation, and the synthesis of DNA leading and lagging strands.

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38
Q

What does DNAPOL1 do?

A

It removes the original RNA primer laid down by DNA Primase, and replaces it with DNA.

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39
Q

What does DNA Ligase do?

A

It joins Okazaki fragments together

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40
Q

What do Helicases do?

A

Untwist the double helix at replication forks.

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41
Q

What does Topoisomerase do?

A

It corrects overwinding ahead of the replication fork by breaking, swiveling, and rejoining DNA strands in order to relieve the tension caused by supercoiling.

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42
Q

How does DNA Primase function?

A

It uses the template strand to synthesize a short segment of complimentary RNA bases, leaving a free 3’ -OH, for DNAPOL3 to use as a substrate to begin elongation (continue replication).

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43
Q

DnaA ______ in double stranded parental DNA, while DnaB _____ in the double stranded parental DNA.

A
  1. Breaks Hydrogen bonds between base pairs

2. Untwists the double helix at the replication fork

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44
Q

List the 7 enzymes important in DNA Replication:

A
  1. DNA Primase
  2. DNA Pol 3
  3. DNA Pol 1
  4. Helicase
  5. DNA Ligase
  6. SSB’s
  7. Topoisomerase
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45
Q

As each molecule of _____ joins the DNA strand via DNAPOL3 activity, it loses _____.

A
  1. dNTP

2. Pyrophosphate

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46
Q

Describe Lagging Strand Synthesis:

A

The lagging parental strand is synthesized by DNAPOL3 in the 5’ to 3’ direction AWAY from the replication fork, resulting in the formation of many okazaki fragments as DNA Primase must continually lay down more RNA primers for elongation to continue as the replication bubble opens wider towards the 3’ end of the parental lagging strand template. The primers of these fragments are then removed by DNAPOL1 and replaced with DNA nucleotides, and the fragments are then joined by DNA Ligase which REESTABLISHES the backbone with phosphodiester bonds.

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47
Q

Define Transcription:

A

The synthesis of a single stranded RNA copy of a SEGMENT of DNA.

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48
Q

Define Translation:

A

The conversion of the messenger RNA base sequence into the amino acid sequence of a protein polypeptide.

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49
Q

List 5 differences in RNA Transcription that are not true of DNA Replication:

A
  1. Transcript is composed of RNA, not DNA.
  2. Uses RNA Polymerase
  3. RNA Pol. doesn’t use a Primer
  4. Adds NTP’s, not dNTP’s, which have a C-2 -OH group instead of a hydrogen at C-2.
  5. Uracil pairs with Adenine, not Thymine.
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50
Q

Antisense strand:

A

The only strand of DNA used to make the RNA Transcript, as opposed to DNA Replication in which both single strands of DNA are used to make new daughter strands.

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51
Q

Sense Strand:

A

The strand NOT used as a template, meaning it has the SAME sequence as the RNA transcript because it pairs perfectly with the antisense strand.

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52
Q

What is the difference between the Sense strand and the RNA transcript?

A

The RNA transcript will have Uracil instead of Thymine

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53
Q

Describe the 4 Types of RNA molecules:

A
  1. mRNA: Messenger RNA. ENCODES the amino acid sequence of a polypeptide. They ARE the transcripts of protein-coding genes.
  2. tRNA: Transfer RNA. TRANSFERS amino acids to the ribosome during translation.
  3. rRNA: Ribosomal RNA. COMBINES with ribosomal proteins to form the ribosome, at which mRNA is translated into protein.
  4. snRNA: Small Nuclear RNA. Combines with certain proteins and is involved in RNA processing, such as mRNA splicing, in eukaryotes.
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54
Q

What are the 2 main components of bacterial RNA transcription? These two carry out bacterial translation.

A
  1. A core RNA polymerase

2. A protein called Sigma Factor

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55
Q

Describe the 3 eukaryotic RNA Polymerases:

A
  1. RNA Polymerase 1: Synthesizes rRNA
  2. RNA Polymerase 2: Synthesizes mRNA and some snRNA as well
  3. RNA Polymerase 3: Synthesizes tRNA and some snRNA as well
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56
Q

What are the 3 regions of a prokaryotic gene?

A
  1. Promoter: Located upstream of the RNA coding sequence, it ensures the proper location of transcription initiation.
  2. RNA coding sequence: The region that will actually be transcribed into RNA.
  3. Terminator: Downstream of the RNA coding sequence, specifies where transcription will stop.
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57
Q

Where do RNA Polymerases bind to initiate transcription of RNA?

A

To the promoter of a gene.

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58
Q

What is the transcription initiation site and how is it designated?

A

It is the site of the first base that is transcribed and is designated +1.

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59
Q

What does a negative designation imply on a DNA template strand?

A

It implies that the designated base lies in the promoter region, UPSTREAM of the RNA coding sequence.q

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60
Q

Whate are the two most common PROKARYOTIC promoter locations?

A
  1. The -35 consensus sequence: 5’-TTGACA-3’

2. The -10 consensus sequence: 5’-TATAAT-3’ also called the Pribnow box

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61
Q

What does the term “consensus sequence” imply? Why is this important?

A

That it refers to an average sequence structure, which may vary slightly between prokaryotes. These slight differences between sequences allow for regulation of the RATE of transcription, because some may signal for faster/slower transcription than other sequences.

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62
Q

After about 8-9 ribonucleotides have been transcribed in prokaryotic RNA transcription, what happens? What does this tell us?

A

The sigma factor disengages and RNA Polymerase continues elongation of the transcript. It tells us that the Sigma Factor is only necessary for initiation of transcription, but not elongation of the RNA.

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63
Q

Once the RNA polymerase has transcribed the Terminator sequence, what happens?

A

RNA Polymerase disengages, the RNA transcript will break off, and the DNA will reform its double strand.

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64
Q

Give the Cis element, the DNA sequence, and the approx. location of each of the 3 common EUKARYOTIC promoter sequences:

A
  1. GC Box: GGGCGG: -70 to -200
  2. TATA Box: TATAAA: -20 to -35
  3. CAAT Box: CCAAT: -80
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65
Q

Describe the 5 transcription initiation proteins that build the Basal Transcription Machinery:

A
  1. TATA Box Binding Protein: A subunit of TF2D. Binds to the TATA Box of the promoter.
  2. TF2D: Distorts DNA Helix to allow recruitment of other transcription factors.
  3. TF2B: Involved in RNA Polymerase start site recognition.
  4. TF2H: Contains a DNA Helicase and phosphorylates RNA Polymerase.
  5. TF2E: Positions RNA Polymerase.
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66
Q

What are Cis-regulatory elements and how do they work?

A

Silencers and enhancers that bind to the template DNA and fold it so they can interact with the Basal Transcriptional Machinery in order to regulate the rate of transcription.

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67
Q

Transcription of DNA results in ____ supercoils behind the RNA Polymerase which are relieved by ______, and ____ supercoils in front of the RNA Polymerase which are relieved by _______.

A
  1. Negatively
  2. Topoisomerase
  3. Positively
  4. Gyrase
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68
Q

What are the two important regions of the prokaryotic Terminator?

A
  1. Palindromic Sequences: That form hairpins because they have internal complementarity to form hydrogen bonds with each other.
  2. G-C rich regions within the loops that form strong bonds and make them very stable, which are followed by a string of U’s.
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69
Q

Intrinsic Termination:

A

Formation of the stem loop structure that causes dissociation of RNA Polymerase and the RNA transcript from the template.

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70
Q

Extrinsic Termination:

A

STEM LOOP FORMATION IS NOT SUFFICIENT FOR TERMINATION OF TRANSCRIPTION. So Rho protein (a helicase) attaches to its recognition site on the RNA transcript, moves along RNA transcript following RNA Polymerase, and separates the template strand from the transcribing strand.

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71
Q

Describe the 5 main components of mRNA structure:

A
  1. 5’ UTR: Untranslated region leading the mRNA.
  2. Translation start site: 3 base sequence (AUG) that binds the mRNA to signal the ribosome to start translating it at that position.
  3. Protein-coding sequence: The sequence that will actually be translated by the ribosome.
  4. Translation stop site: 3 base sequence that binds the mRNA to signal the ribosome to STOP translating.
  5. 3’ UTR: Untranslated region flanking the coding sequence.
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72
Q

Why are the 5’ and 3’ UTR’s important if they don’t code for anything?

A

They have regions within them that allow for RNA post-transcriptional modification which can determine WHEN an mRNA actually gets translated by the ribosome, possibly not until it is modified later on.

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73
Q

The 5’ UTR of an mRNA has a ______, while the 3’ UTR contains a _____.

A
  1. Cap

2. Poly-A Tail

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74
Q

In eukaryotes, what are the two different sequences within the RNA-coding region?

A
  1. Introns: Nonprotein-coding sequences

2. Exons: Protein-coding sequences.

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75
Q

What is the difference between a Pre-mRNA and a mature mRNA?

A

A Pre-mRNA is one that has recently been transcribed and still possess both introns and exons, a mature RNA has been modified to prepare it for translation by:

  1. Addition of a 7-methyl guanasine cap on the 5’ end because the ribosome will NOT bind to the mRNA to translate it without this cap (in eukaryotes).
  2. Polyadenylation: The addition of a string of “A”'’s on the 3’ end of the mRNA because proteins will bind that tail during translation to interact with the 5’ cap to recruit the translation initiation complex.
  3. RNA splicing: Removal of the introns, the joining together of the exons so it can be read by the ribosome properly.
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76
Q

What ability of DNA Polymerase does RNA polymerase lack? Why is this important?

A

The proofreading exonuclease activity to fix mispaired bases. This is important because if DNA polymerase lacked that activity it would result in a heritable mutation, whereas improperly translated proteins are tolerable for the cell.

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77
Q

What is the difference in location of RNA transcription and translation between prokaryotes and eukaryotes?

A

Eukaryotes: Transcription occurs in the nucleus, translation occurs on the ribosome (in cytoplasm).
Prokaryotes: Both occur in the cytoplasm. And translation can actually start before transcription is even finished.

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78
Q

Why can prokaryotes exhibit co-transcriptional translation?

A
  1. The ribosome is in such close proximity to the transcription site.
  2. The mRNA does not require post-transcriptional modification to be translated.
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79
Q

Describe the general structure of an amino acid:

A

A central carbon possesses an Amino group (terminus), a Carboxyl group (terminus), and an “R” group which varies between AA’s.

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80
Q

The ______ terminus of an amino acid joins with the ______ terminus of another to form a _______.

A
  1. Carboxyl
  2. Amino
  3. Peptide Bond
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81
Q

How did Nirenburg decipher the genetic code?

A

He conducted lab experiments using synthetic mRNA sequences to perform in vitro translation and determined which proteins were formed.

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82
Q

List the 6 features of the genetic code:

A
  1. Triplet Code
  2. No commas
  3. Non-overlapping
  4. Almost universal
  5. The code is degenerate: Multiple codons can code for the same amino acid
  6. The code has start and stop codons
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83
Q

What are the 2 exceptions to the non-degenerate rule of the genetic code?

A
  1. Only UGG codes for Tryptophan

2. Only AUG codes for methionine

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84
Q

What are the most common start and stop codons?

A

START: AUG (is also methionine)
STOP: (3) UAG, UGA, UAA

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85
Q

What is base-pair wobble? When does it occur?

A

It occurs when a cell doesn’t possess enough of the tRNA’s that match to a particular codon. tRNA’s possess an anticodon that pairs precisely with a certain codon on the mRNA being translated and determines which protein will be delivered to the polypeptide chain. If the proper tRNA is not present, the ribosome will allow a tRNA anticodon with the same FIRST TWO bases as the proper codon to bind with the transcript and add that amino acid, even though the third base of the codon is wobbling and not binding.

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86
Q

Frameshift Mutation:

A

Addition or deletion of a single base that cause the reading of the genetic code to be shifted over by one nucleotide, thereby changing the resulting amino acids transcribed.

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87
Q

What gives tRNA their stem loop structure?

A

The internal complementarity also exhibited by the terminator sequence of prokaryotic DNA during transcription (RNA synthesis).

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88
Q

Where are amino acids being delivered to the translating mRNA located with respect to the tRNA? What is the process of adding amino acids to these tRNA called?

A

They are attached to the 3’ end of the tRNA. When they are added it is called CHARGING a tRNA.

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89
Q

What enzyme is responsible for “charging” tRNA?

A

Aminoacyl-tRNA synthetases serve to add amino acids to tRNA, producing charged tRNA.

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90
Q

How does Aminoacyl-tRNA synthetase facilitate the addition of amino acids to tRNA?

A

The amino acid is activated by adding AMP to its Carboxyl group VIA ATP HYDROLYSIS, forming aminoacyl-AMP. It then transfers the Carboxyl group FROM the AMP to the -OH group at the 3’ end of the tRNA.

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91
Q

The ribosome has ______ subunits:

A
  1. TWO

2. The Small and Large Subunits

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92
Q

The complexing of the small and large ribosomal subunits forms 2 pockets called the ______ and the ______.

A
  1. Peptidyl Site

2. Aminoacyl site

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93
Q

What important activity does the large ribosomal subunit possess?

A

It possess peptidyl transferase activity. An amino acid will be each of the P and A sites of the subunit and the peptidyl transferase will link them with a PEPTIDE BOND in order to lengthen the polypeptide chain.

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94
Q

The ribosome has _____ binding sites. One is for ______ and the other two are for ______.

A
  1. The mRNA

2. tRNA anticodons

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95
Q

What is the first step in preparation for translation in prokaryotes?

A

Recruitment of GTP and translation factors to the small ribosomal subunit, forming the INITIATION COMPLEX.

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96
Q

What happens after formation of the initiation complex in prokaryotic translation?

A

The initiation complex binds to the mRNA near the Shine-Delgarno sequence (just upstream of the start codon) and the first tRNA anticodon (Methionine) will bind with the start codon.

97
Q

What happens after the binding of the 1st fMet in prokaryotic translation?

A

The large ribosomal subunit joins with the initiation complex and places the fMet (1st tRNA anticodon) into the P site.

98
Q

What structure in eukaryotes is the Shine-Delgarno sequence of prokaryotes comparable to?

A

The 5’ cap of mRNA. This is because the Shine-Delgarno sequence is responsible for positioning and recruiting the mRNA for translation without it requiring post-transcriptional modification as in eukaryotes.

99
Q

What happens after the 1st tRNA anticodon fMet binds to the P site in prokaryotic translation?

A

Elongation Factors (EF-Tu) AND GTP work to recruit the next appropriate tRNA into the A site of the large subunit.

100
Q

What happens once tRNA anticodons have bound both the A and P sites during prokaryotic translation?

A

The large subunit’s peptidyl transferase activity will form a peptide bond between the two amino acids AND break the bond between the P site amino acid and the 3’ end of the tRNA that delivered it.

101
Q

What happens after a tRNA is severed from the amino acid it has delivered to the P site?

A

Once a tRNA dissociates from the amino acid it has delivered to the P site, the tRNA in the A site is TRANSLOCATED to the P site, and a new tRNA anticodon binds to the A site to continue translation.

102
Q

What is a polysome?

A

A number of ribosome all translating the same strand of mRNA sequentially

103
Q

What are releasing factors and how do they function?

A

Releasing factors are translation factors that recognize the stop codon, to which no amino acids have anticodons. When they enter the A site, they cause peptidyl transferase to release the polypeptide chain from the P site tRNA and disassemble the translation machinery. Essentially because it cannot form a bond between the P site amino acid and the releasing factor lacking an amino acid.

104
Q

What are the prokaryotic and eukaryotic releasing factors?

A
  1. Eukaryotic: eRF
  2. Prokaryotic:
    RF1-Recognizes UAA and UAG
    RF2-Recognizes UAA and UGA
    RF3-Stimulates termination
105
Q

What structure connects polypeptides to one another in quaternary structure?

A

Disulfide bridges

106
Q

What is an INTRA-disulfide bridge?

A

A disulfide bridge formed within a single polypeptide

107
Q

What is an INTER-disulfide bridge?

A

A disulfide bridge formed between two polypeptide chains

108
Q

What type of bonds are disulfide bridges?

A

Covalent bonds

109
Q

What is the only way to break peptide bonds?

A

Prolonged exposure to acid or base at high temperature

110
Q

Describe the nomenclature rule for naming polypeptides:

A

Begin at the Amino terminus, and each amino acid along the chain has -yl added to the end of its name except for the final amino acid in the chain. Ex: Valylglycylleucine

111
Q

Describe the 3 main characteristics of a peptide bond:

A
  1. Lack of rotation: Partial double bond, rigid and planar, between the alpha-C and either the amino or carboxyl terminus
  2. Allows for trans- configuration to minimize steric hinderance
  3. Uncharged BUT polar, separation of charge creates dipole moment (Gives the possibility of forming hydrogen bonds)
112
Q

Through what process are peptide bonds formed?

A

Through a condensation reaction (dehydration) between two amino acids in which a molecule of water is eliminated.

113
Q

What is the difference between cis- and trans- configuration and how is this achieved?

A

Cis- configuration means that both functional groups are in the same plane, trans- means they are in opposite planes. This is possible because there is still rotation about the single bonds within each amino acid.

114
Q

Describe the first step in determination of the composition of a polypeptide:

A
  1. Acid Hydrolysis of a polypeptide sample by strong acid at 110 degrees C for 24 hours. This cleaves peptide bonds and gives COMPOSITION but not sequence.
115
Q

After determining the composition of a polypeptide sample, what is the next step in determining the sequence of amino acids?

A
  1. Cation-exchange chromatography to separate individual amino acids. All of the amino acids will have + charge already from acid hydrolysis, and will bind to an anion-exchange column when applied to it, from which they can be eluted by application of buffers of increasing ionic strength and pH.
116
Q

After eluting amino acids from an anion-exchange column, what is the next step in determining polypeptide composition?

A
  1. After elution from the anion-exchange column, Ninhydrin will be applied to tag the amino acids in order to produce a certain colorimetric change that can be read as they pass through a photometer, indicating the type of amino acid present.
117
Q

What is the 1st step in SEQUENCING a polypeptide, once composition is known? What is the 2nd step?

A
  1. Subject it to a reaction using Edman’s Reagent (Phenylisothiocyanate) which will only react with the FREE AMINO terminus of the whole polypeptide. This reaction will destabilize the peptide bond of the 1st amino acid in the sequence and subjection to MILD acid hydrolysis will cleave the first amino acid.
  2. Repeat this process to yield all amino acids in the sequence sequentially.
118
Q

What is an alternative way of determining an amino acid sequence besides Edman’s degradation?

A

DNA sequencing. If you know the gene sequence, you can simply use the genetic code to predict the proteins that would result from the amino acid sequence encoded in its genome.

119
Q

What stabilizes the SECONDARY structure of a polypeptide?

A

INTRACHAIN Hydrogen bonds linking peptide bonds between amino acids form either:

  • alpha helices
  • beta pleated sheets
  • random non-repetitive chains
120
Q

Approximately how many amino acids per turn are exhibited by an alpha helix?

A

4 amino acids

121
Q

What enables the formation of hydrogen bonds between every 4th AA residue in an alpha helical structure?

A

The polar characteristic of the peptide bonds between those amino acids

122
Q

How are the R groups of each amino acid involved in the secondary structure of a polypeptide?

A

They determine the overall polarity of the entire polypeptide. They are fanned out, pointing away from any hydrogen bonding existing in the secondary structure. HOWEVER, the more polar R groups existing in the polypeptide will give the polypeptide greater polar character overall.

123
Q

Which 2 amino acids most often disrupt the alpha helical secondary structure and why?

A
  1. Proline (P) and Glycine (G)

2. Proline: Because of its amino side chain. Glycine: Because of its very small size.

124
Q

What 2 things other then Proline and Glycine can disrupt the alpha helical secondary structure?

A
  1. Large numbers of similarly charged residues will create repulsion effects that disrupt the alpha helix.
  2. The presence of large, bulky R groups (such as Tryptophan’s) because there is not enough space for so many of them in sequence to form that structure.
125
Q

Describe Tertiary Structure:

A

The folding of a polypeptide’s secondary structures (DOMAINS) to create a different 3D shape for the molecule.

126
Q

How does the hydrogen bonding of Beta pleated sheets differ from that of alpha helices? How are Beta pleated sheets designated?

A
  1. In Beta sheets, every peptide bond of every amino acid is involved in hydrogen bonding, forming a stretched out sheet structure.
  2. They are designated by an ARROW in which the beginning of the arrow represents the N-terminus, while the point of the arrow represents the C-terminus.
127
Q

What must be present for beta pleated sheets to form?

A

At least TWO polypeptides or segments of polypeptides that can be EITHER parallel or antiparallel

128
Q

Describe Beta Bends:

A

The presence of Proline or Glycine in a polypeptide involved in a beta sheet (or sometimes presence of a charged group) will produce a short 4 amino acid or so segment that will be corrected by ionic interactions and hydrogen bonding to produce an antiparallel polypeptide in the sheet.

129
Q

Describe SuperSecondary Structure and give 6 examples:

A 
Not quite tertiary structure, but involves multiple small aggregates of secondary structures exhibiting local folding. 
Ex: 
B-A-B Loops
A-A Corners
Beta Barrels
Twisted Beta Sheets
Greek Keys
Beta Meanders
130
Q

Define Native Conformation:

A

The final, active, and functional form of a polypeptide. Most commonly is the tertiary structure.

131
Q

What are globular proteins? (4 characteristics)

A

A type of polypeptide tertiary structure in which the folding of secondary structures gives a globular shape that has:

  • High Water Solubility
  • A Variety of Secondary Structures Within it
  • Spherical Shape
  • A catalytic/regulatory/transport role i.e. Dynamic metabolic function
132
Q

What are fibrous proteins? (4 characteristics)

A

A type of polypeptide tertiary structure that has:

  • Poor Water Solubility
  • A Long, narrow, rod-like structure
  • One dominating type of secondary structure
  • A role in determining tissue/cellular structure
133
Q

What is the main difference in the roles of globular versus fibrous proteins?

A

Globular proteins serve a functional purpose, while fibrous proteins serve a structural purpose.

134
Q

What 4 TYPES of bonds hold tertiary structures together?

A
  1. Hydrogen Bonds
  2. Disulfide Bonds
  3. Van der Waals Forces (Hydrophobic Interactions)
  4. Electrostatic Interactions (Ionic/Polar Forces)
135
Q

Which is the ONLY covalent force that holds tertiary structures together?

A

Disulfide bonds formed between two neighboring Cysteine molecules

136
Q

What is the main determinant of the Hydrophobic and Electrostatic interactions that will exist in a proteins tertiary structure?

A

The folding of R groups in such a way that particular R groups are in close proximity to one another.

137
Q

What is the difference between Hydrophobic interactions (Van der Waals forces) and electrostatic interactions?

A

Hydrophobic interactions exist between Non-polar R groups of amino acids, while Electrostatic interactions exist between Polar R groups of amino acids (acidic and basic coming together).

138
Q

Hydrogen bonds within a protein exist between _______.

A

Polar side chains of amino acids

139
Q

Define Domain: (Give an example)

A

A fundamental, functional, and 3-D structural unit of a polypeptide created AFTER the tertiary structure is formed, yielding a pocket or groove (the Domain) that allows the protein to serve its purpose.
Ex: An enzyme active site, can be formed from multiple components of the tertiary structure lining and forming that pocket.

140
Q

What are Chaperones?

A

Proteins that assist in the folding of polypeptides to help them achieve their Native (functional) form.

141
Q

Define Denaturation: (List 6 ways of denaturing Native Forms of proteins)

A

Destruction of all but primary structure of a protein

  • Heat
  • Organic Solvents
  • Mechanical Shearing
  • Heavy Metals
  • Detergents
  • Chaotropic Agents
142
Q

Denaturation results in _________, and can be both ______ or ______.

A
  1. Loss of biological activity
  2. Reversible
  3. Irreversible
143
Q

What protein exhibits reversible denaturation?

A

Ribonuclease

144
Q

What is protein mis-folding and what causes it?

A

When an alternative tertiary structure is formed, rather than the intended optimally efficient structure. Caused by either spontaneous misalignment of certain residues or due to the mutation (loss/addition) of a certain amino acid involved in folding.

145
Q

Give an example of how protein mis-folding can be dangerous:

A

The mis-folding of the transmembrane protein B-amyloid can lead to the cleavage of its extracellular domain that then causes the formation of plaques, which may contribute to Alzheimer’s disease.

146
Q

Quaternary proteins are considered _________, and are held together by ________. Specifically: (3)

A
  1. Multimeric
  2. Non-covalent
  3. Hydrogen Bonds, Van der Waals forces, Electrostatic Interactions
    * There are NO disulfide bridges in between proteins in quaternary structure.
147
Q

Give an example of a multimeric protein exhibiting quaternary structure:

A

Hemoglobin: Has 4 subunits (2 alpha and 2 beta) that are required for it to function.

148
Q

_______ bonds are NOT disrupted during denaturation.

A

Peptide

149
Q

Give 3 reasons why are enzymes important?

A
  1. They control the rate of reactions
  2. They can be used as diagnostic tools by measuring their amount in the bloodstream
  3. Almost all prescription drugs target enzymes to elicit their effect
150
Q

Enzymes are considered _______ and almost ALL are _______.

A
  1. Biological Catalysts

2. Proteins

151
Q

List and describe the 6 classes of enzymes:

A
  1. Oxido-reductases: Catalyze Oxidation-Reduction reactions (Removal or addition of an H+ to/from an O)
  2. Transferases: Catalyze the transfer of C-, N-, and P- containing groups (Transfer entire groups)
  3. Hydrolases: Catalyze cleavage of bonds by ADDITION of water (Water is a reactant)
  4. Lyases: Catalyze cleavage of bonds WITHOUT water (Typically C-N, C-C, or C-S)
  5. Isomerases: Catalyze racemerization of molecules (Rearrange them without changing total carbon number)
  6. Ligases: Catalyze formation of bonds between C and O, S, and N. (Joins two molecules together)
152
Q

What are 2 other “transferases” that are almost considered separate classes of enzymes?

A
  1. Kinases: Require ATP to transfer a phosphate group from a triphosphate to an enzyme to form a Phospho-enzyme. (Phosphorylate enzymes to change how they work, particularly on threonine, serine, and tyrosine residues).
  2. Phosphatases: Remove phosphate groups (the opposite kinases)
153
Q

Define Turnover Number:

A

The number of substrate molecules converted to product per enzyme per second

154
Q

Define Enzyme Specificity:

A

Enzymes are highly specific and bind one molecule (or similarly structures group of molecules) to complete one type of reaction

155
Q

What is a Cofactor?

A

An inorganic component required for an enzyme to function (Typically metals)

156
Q

What is a Coenzyme?

A

An organic, non-protein molecule required for an enzyme to function

157
Q

What is the difference between cofactors and co-enzymes?

A 
Cofactor= Inorganic
Co-Enzymes= Organic, but non-protein
158
Q

Most _______ are often used as (to derive) coenzymes in the body.

A

Vitamins

159
Q

Define Holoenzyme:

A

Enzyme + Cofactor

*Most FUNCTIONAL enzymes

160
Q

Define Apoenzyme:

A

Enzyme - Cofactor

161
Q

Define Prosthetic group:

A

A coenzyme that’s very tightly (usually covalently) attached to its enzyme (protein)
*Essentially same as coenzyme (non-protein)

162
Q

What are Simple enzymes?

A

Composed SOLELY of protein (Single OR multiple subunits)

163
Q

What are Complex enzymes?

A

AT LEAST a Holoenzyme (Enzymes with a cofactor and maybe a coenzyme)
Can be Apoenzyme + Coenzyme + Cofactor
Some may catalyze, some may regulate activity

164
Q

What is a zymogen?

A

The inactive form of an enzyme

165
Q

Explain what is meant by “Proteolytic cleavage to activate enzymes”:

A

Enzymes are initially synthesized/secreted in an inactive form, which is activated by truncation of the amino terminus.

166
Q

What is covalent modification (in terms of enzyme regulation)?

A

Addition of a group, most often phosphorylation, to an enzyme to increase/decrease its activity.

167
Q

Define Sequestration:

A

Many enzymes come together to form a polymer in which some enzymes will become INACTIVE, while others will become MORE active.

168
Q

Define Allosteric Regulation of enzymes:

A

A molecule that is distinct/different from the substrate binds to a distinct site (not the active site) on the enzyme and changes its catalytic activity.

169
Q

Define Induction of enzymes:

A

Also considered”Up-regulation”. Increasing gene expression (and therefore increasing synthesis) of specific enzymes.

170
Q

Define Repression of enzymes:

A

The opposite of Induction. Decreasing the gene expression of specific enzymes so fewer will be produced per cell.

171
Q

What are two kinds of enzymes used in covalent modification?

A
  1. Kinases

2. Phosphatases

172
Q

List 3 types of covalent modification:

A
  1. Phosphorylation/De-phosphorylation
  2. Adenylation
  3. Methylation
173
Q

Allosteric regulation occurs most often with ______ enzymes. The allosteric modulators bind to the ______ subunit, not the _____ subunit.

A
  1. Complex
  2. Regulatory
  3. Catalytic
174
Q

Describe an example of induction (of enzymes):

A

Steroid hormones enter the cell across the membrane and bind their receptor, that complex then goes into the nucleus and binds to an “enhancer” region in the gene for a specific protein. This binding activates the gene expression for that protein (enzyme).

175
Q

Which method of enzyme regulation is the slowest?

A

Induction/Repression: Because they must modify gene expression, leading to transcription, translation, and processes that will take hours-days, rather than seconds-minutes.

176
Q

Define Isozymes:

A

Enzymes can exist in multiple forms. Some have a different molecular size, but perform the same catalysis.
Different polypeptide composition yields different size, but same reaction is carried out with same substrate

177
Q

Give an example of an enzyme that exists in multiple isozymes:

A

Creatine Kinase: CK-1, CK-2, CK-3 all make creatine phosphate from creatine but have slightly different subunits.

178
Q

Why might it be important for an enzymes to exist as multiple isozymes? (Give an example)

A

This means they can have different tissue distribution.
Ex: CK-2 is highest in heart tissue, so it can be used DIAGNOSTICALLY. If you experience an MI, heart cells die and will release their contents into the bloodstream. So after a cardiac event, they will have HIGH CK-2 in the bloodstream.

179
Q

_________ is also very important in enzyme regulation because it determines _______.

A
  1. Enzyme location in the cell

2. The proximity of the enzyme to its substrate and their ability to bind

180
Q

The cell membrane possess a ________. This is important for TWO reasons:

A
  1. Phospholipid Bilayer
  2. Two Reasons:
    - It creates a demarkation of the cell, separating inside from outside since it is impermeable to aqueous material.
    - Many protein components of the cell membrane play a role in transport of small molecules, and many are receptors that recognize extracellular signals.
181
Q

How do enzymes catalyze reactions?

A

Enzymes increase the rate of reaction by reducing the activation energy needed to achieve a transition state between substrate and product.

182
Q

Describe the 4 steps of enzymatic reaction:

A
  1. Enzyme binds substrate to form ES complex
  2. ES complex goes through a transition state
  3. A complex of the Enzyme and Product is produced (EP)
  4. The enzyme and product separate
183
Q

All steps of enzymatic are _______, meaning that ________.

A
  1. In Equilibria

2. They are dependent on the rate constants for each step involved

184
Q

Differentiate between the binding and catalytic sites:

A

The binding site is a large domain (pocket) that functions to bind the substrate, whereas the catalytic site is a smaller domain WITHIN the binding site that directly facilitates the transformation of the substrate into product

185
Q

What does the active site consist of?

A

BOTH the binding site and the catalytic site

186
Q

Describe the Induced-Fit model:

A

The enzyme (lock) and substrate (key) have a lock and key fit in which the lock is dynamic and not rigid in shape, so it can interact with a substrate of complimentary shape

187
Q

What are 3 factors that influence enzyme activity?

A
  1. Environmental factors: pH, temperature, etc.
  2. Cofactors: Metal ions
  3. Effectors: Species that alter activity (like allosteric regulators)
188
Q

Most enzymes possess an optimal ________, usually related to ______.

A
  1. pH range in which they function

2. The environment in which they function

189
Q

Define Enzyme Kinetics:

A

The study of the rate of conversion of a substrate into a product as catalyzed by an enzyme

190
Q

Define velocity versus rate with respect to enzyme kinetics:

A

Velocity (v): The change in CONCENTRATION of substrate or product per unit time
Rate (k): The change in TOTAL QUANTITY of reactant or product per unit time

191
Q

Define Initial Velocity with respect to enzyme kinetics:

A

Same as velocity, but referring to the change in concentration seen during the LINEAR PHASE of the reaction before a lot of product is formed

192
Q

What are the 3 main assumptions of Michaelis-Menten Kinetics?

A
  1. ES complex is in a steady state and REMAINS CONSTANT during the initial phase of the reaction.
  2. The enzyme is SATURATED when all enzyme is in form of the ES complex.
  3. Rate of product formation is MAXIMAL when all enzyme is in the form of ES complex.
    i. e. Vmax=K2[ES]
193
Q

Enzymes following Michaelis-Menten Kinetics (most enzymes) exhibit a ________ shape on a graph, whereas _______ enzymes exhibit a ______ shape on a graph.

A
  1. Hyperbolic
  2. Allosteric
  3. Sigmoidal
194
Q

Allosteric regulators specifically increase/decrease ____________ (meaning that the reaction _______), therefore increasing/decreasing _________ and shifting the curve _______.

A
  1. The affinity of the enzyme for the substrate
  2. Requires more/less substrate to occur at the same speed
  3. The Vmax of the reaction
  4. Left/Right
195
Q

What does the Michaelis-Menten Equation do?

A

It relates the velocity of any enzyme (at any ONE time) to its Vmax, [S] at any one time, and Km.

196
Q

What is Km a measurement of? What does it tell you specifically?

A
  1. The affinity of the enzyme for its substrate. It relates all three of the other rate constants.
  2. It tells you the [S] at which the enzyme will operate at 1/2 Vmax.
197
Q

How is Km determined?

A

By finding the 1/2 Vmax and recording the [S] at that point on the x-axis.

198
Q

Does a smaller or higher Km imply a greater affinity of the enzyme for its substrate?

A

A smaller Km implies that, since the enzyme requires LESS substrate to operate at 1/2 Vmax.

199
Q

How does the Lineweaver-Burk Plot differ from a Michaelis-Menten Plot?

A

Their double reciprocal equation yields a linear graph of the reciprocals of [S] and Vmax.

200
Q

In a Lineweaver-Burk Plot, what do the X- and Y- axes represent?

A

X-axis: -1/Km
Y-axis: 1/Vmax
Don’t forget the minus in Km reciprocal
Ex: -1/Km=-4 –> Km=-1/-4 or 1/4 = 0.25

201
Q

List 4 things that can inhibit enzyme activity and explain what they do to inhibit:

A
  1. Substrate Analogs: Compete with the substrate
  2. Toxins: Modify the active site
  3. Drugs: Modify active site as well
  4. Metal complexes: (Heavy metals) Bind so tightly to enzyme active sites that they inactivate them
202
Q

What are the two processes through which enzymes can be inhibited?

A

Reversible Inhibition and Irreversible Inhibition

203
Q

Describe Reversible Inhibition:

A

Small organic molecules bind the enzyme NON-COVALENTLY and inhibits it only while it is bound, when it is removed the enzyme will function again.

204
Q

Describe Irreversible Inhibition:

A

Formation of strong, covalent bonds to the enzyme that permanently inhibit the enzyme as they cannot be broken

205
Q

What are the 3 subclasses of reversible inhibitors?

A
  1. Competitive Inhibitors
  2. Non-competitive Inhibitors
  3. Uncompetitive Inhibitors
206
Q

What are competitive inhibitors?

A

Molecules that structurally resemble the normal substrate and compete for the same site

207
Q

What are non-competitive inhibitors?

A

Molecules that bind to an allosteric site on the enzyme that changes its catalytic behavior

208
Q

What are uncompetitive inhibitors?

A

Molecules that bind to an allosteric site, like noncompetitive inhibitors, but ONLY bind to the ES complex

209
Q

What are two examples of irreversible inhibitors?

A

Organophosphates and Heavy Metals

210
Q

Describe how do each of the 3 types of reversible inhibitors alter the enzyme kinetics:

A
  1. Competitive Inhibitors: INCREASE the Km, but no effect on Vmax
  2. Non-competitive Inhibitors: no effect on Km, but DECREASE the Vmax
  3. Uncompetitive Inhibitors: DECREASE BOTH
211
Q

What are the 2 components of metabolism?

A

Catabolism and Anabolism

212
Q

Explain Catabolism:

A

Oxidizing large macromolecules (Carbs, protein, and lipids) into smaller REDUCED energy molecules (CO2, H2O, and NH3) to yield energy in the form of ATP

213
Q

What 4 types of energy molecules does catabolism yield?

A

ATP
NADH
NADPH
FADH2

214
Q

Explain Anabolism:

A

Oxidizing energy molecules to REDUCE and form larger complex molecules that carry out bodily functions at the expense of ATP and other energy sources

215
Q

Catabolism is considered ________, because it involves making a select few energy molecules from a variety of macromolecules. Similarly, Anabolism is considered ______ because it uses only a select few energy molecules to form a variety of complex molecules.

A
  1. Convergent

2. Divergent

216
Q

When an energy molecule is reduced, it _______ a hydrogen ion. This occurs in ______ metabolism.

A
  1. Gains

2. Catabolism

217
Q

Describe the 3 stages of Catabolism:

A
  1. Hydrolysis of complex macromolecules into their smaller building blocks.
  2. Conversion of building blocks into AcetylCoA (or other simple intermediates).
  3. OXIDATIVE PHOSPHORYLATION: Oxidation of AcetylCoA to yield ATP.
218
Q

Where does Oxidative Phosphorylation occur and what is it (in simple terms)?

A

It occurs in the mitochondria and is the entrance of AcetylCoA into the Citric Acid Cycle to yield ATP and CO2 as a byproduct.

219
Q

What two factors does regulation of metabolism depend on?

A
  1. Intercellular Signals: HORMONES sent from one cell to a receptor on another.
  2. Intracellular Signals: SIGNAL TRANSDUCTION caused by binding to hormone receptor that causes a change within the cell.
220
Q

Describe the 3 types of Intercellular Signals involved in metabolism:

A
  1. Synaptic Signaling: Neurotransmitters
  2. Endocrine Signaling: Hormones
  3. Direct contact: Via Gap Junctions
221
Q

Define Signal Transduction:

A

The process by which extracellular signals are converted to intracellular signals to elicit an effect

222
Q

List the 4 basic types of signal transduction pathways:

A
  1. Steroid Receptors
  2. Ion-Gated Channels
  3. Receptor Enzymes (Catalytic Receptors)
  4. GPCR’s that produce 2nd messengers
223
Q

Explain the Steroid Receptor pathway of signal transduction:

A

Steroid hormones cross through the cell membrane and bind receptors in the cytoplasm that allow them to move into the nucleus to bind to enhancer/repressor regions of a gene to up/down-regulate the expression of that specific gene by enhancing/repressing it promoter activity, thereby altering its transcription and translation rate.

224
Q

What is an HRE?

A

Hormone responsive element: Enhancer/Repressor regions of a gene that steroid hormones bind in order to elicit their effect.

225
Q

Explain the Ion-Gated Channel pathway of Signal Transduction:

A

Neurotransmitters bind a cell surface receptor that is linked to a Ligand OR Voltage-gated ion channel. This binding causes a conformational change in the receptor the allows entry of Cations (often Na+ ions) into the cell which DEPOLARIZE the membrane and propagate the signal
Ex: ACh and its Nicotinic Cholinergic Receptor

226
Q

Explain the Receptor Enzyme pathway of signal transduction:

A

An receptor that is ALSO an enzyme, such as the INSULIN receptor. Once bound by its hormone/ligand (insulin in this case) to the alpha subunit, it causes a conformational change in the beta subunit. This activates the intrinsic activity of the Tyrosine kinases of the beta subunit which auto-phosphorylate. They then begin phosphorylating other protein that elicit intracellular effects.

227
Q

What are two reasons that GPCR’s are important?

A
  1. Nearly 50% of all pharmaceutical drugs target these receptors.
  2. They exhibit a high degree of specificity
228
Q

GPCR’s are transmembrane receptors that span the membrane _______ times.

A

7

229
Q

Explain the GPCR pathway of signal transduction:

A

A hormone/neurotransmitter binds the extracellular domain, activating the G-protein coupled to the intracellular domain, which then activates an effector enzyme to increase production of second messengers like cAMP. These second messengers then trigger a cascade of intracellular events.

230
Q

What are the two main examples of GPCR second messenger systems?

A
  1. Adenylate cyclase system increases cAMP

2. Calcium/Phosphotidylinositol system increases IP3, DAG, and Ca2+

231
Q

Define second messengers:

A

Small molecules produced within the cytoplasm in response to activation of a cell surface receptor (most likely a GPCR)
Ex: cAMP, DAG, IP3, Ca2+, NO, etc.

232
Q

Describe the Adenylate Cyclase System:

A
  1. Catecholamines bind the B-adrenergic receptor.
  2. Activation of alpha-S subunit of the G-protein allows it to bind GTP and exchange it for GDP to bind an activate the effector enzyme, Adenylate Cyclase.
  3. Adenylate Cyclase increase cAMP production via ATP cyclization.
  4. cAMP binds and activates Protein Kinase A to phosphorylate proteins/enzymes intracellularly to elicit the effect of epinephrine/norepinephrine.
233
Q

What other hormone, besides Catecholamines, has a GPCR that utilizes the Adenylate Cyclase system?

A

Glucagon and its Glucagon receptor

234
Q

How is the epinephrine induced Adenylate Cyclase system terminated once the signal has achieved its effect?

A

Phosphodiesterase hydrolyzes cAMP to 5’ AMP

235
Q

What is an example of a GPCR that elicits the Calcium/Phosphotidylinositol Pathway? What activates it?

A
  1. The Alpha-1-Adrenergic Receptor

2. Also Catecholamines

236
Q

What is PIP2 and why is it important?

A

A membrane phospholipid associated with GPCR’s that utilize the Phosphoinositide Pathway. It serves as the substrate for the effector enzyme in this system, Phospholipase C (PLC).

237
Q

What is the function of PLC?

A

PLC cleaves PIP2 to generate IP3 and DAG

238
Q

After PLC cleaves PIP2, where do each of the products go?

A

IP3 is highly water soluble and goes into the cytoplasm, while DAG remains in the membrane.

239
Q

Explain the Alpha-1-Adrenergic receptor pathway:

A
  1. Catecholamines bind the GPCR’s extracellular domain, activating the intracellular G-Alpha-Q subunit.
  2. G-alpha-Q exchanges GTP for GDP to bind and activate PLC.
  3. PLC then hydrolyzes PIP2 into IP3 and DAG.
  4. IP3 then binds to the ER and causes the release of Ca2+ into the cytoplasm.
  5. BOTH Ca2+ and DAG then activate PKC which will phosphorylate protein/enzymes to elicit their response.

MSAP Biochem (4 decks)

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