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Biochemistry > Module 10 > Flashcards

Module 10 Flashcards

1
Q
  • if you leave any part of your body (hair, blood, skin), it can be used to identify you using this method
A

DNA finger printing

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2
Q

Why Is Gene Expression Important?

A
  1. Almost all nucleated cells in the body contains the same DNA
  2. Cell specificity (phenotype) is determined by gene expression
  3. Modifications in Gene Expression allow the cell to adapt to changes in the environment
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3
Q

Almost all cells are nucleated except __

A

RBCs

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4
Q

Lymphocytes don’t posses the exact same DNA because they have something called __ which is needed to recognize new diseases, viruses and bacteria

A

Gene Rearrangement

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5
Q
  • choosing which information in this DNA to utilize to create a specific proteins that can create a specific cells
A

Gene expression

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6
Q

Central Dogma of the Molecular Biology

A
  1. DNA (the cookbook)
  2. RNA (the recipe)
  3. Proteins (the actual dish)
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7
Q
  • can undergo REPLICATION to form another DNA
A

DNA

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8
Q

Part of DNA is __ to form an RNA

A

Transcribed

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9
Q

The transcribed RNA is __ in to proteins

A

Translated

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10
Q

In viruses, __ can also happen. RNA to DNA

A

Reverse Transcription

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11
Q
  • has all the information to create muscle, neurons and everything needed by the body like enzymes
  • its complete
  • distributed in 46 chromosome in the human body
  • will make up 3 billion base pairs
A

DNA

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12
Q

How many mRNA can you use in that 3 billion genes?

A

20,000 proteins (reason why so small? most of the DNA is non encoding)

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13
Q

What is therefore Gene Expression?

A
  • choosing which recipe to turn into a dish

- choosing which in those 20,000 proteins your going to create

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14
Q
  • Made up of nucleotides A, T, C, G
  • Each nucleotide is made up of:
    1. Base (Nitrogenous)
    2. Sugar (5 Carbon)
    3. Phosphate Group
  • Contains the genetic information
  • contains of 3 billion base pair long distributed into 46 chromosomes
  • has a negative charge due to the presence of the PHOSPHATE group
A

DNA (Deoxyribonucleic Acid)

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15
Q
  • Building block of DNA

- composes of Adenine, Thymine, Cytosine, Guanine

A

Nucleotides

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16
Q

The 5 carbon sugar from the DNA comes from __

A

Pentose Phosphate Pathway/Hexose Monophosphate Shunt

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17
Q

Where is DNA located in the Cell?

A
  • Some in the mitochondria (because its used to be an entire different microorganism)
  • Most of the DNA is found in the NUCLEUS
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18
Q

How can DNA (which is very long) fit into something that is very small?

A

Packing (wrap the DNA around core proteins that is called HISTONES, by wrapping them around it para syang nacocompress)

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19
Q
  • DNA wrapped around histones
A

Chromosomes

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20
Q
  • are positively charged proteins because they are rich with lysine and arginine (which are basic alkaline amino acids)
A

Histones

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21
Q
  • is a simpler organism that only have a single circular chromosome
A

Bacteria

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22
Q
  • Made up of nucleotides also – A, U, G, C
  • 3 Types:
    1. mRNA
    2. rRNA
    3. tRNA
  • Only portions of the DNA are transcribed
A

RNA

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23
Q
  • one that is transcribed; largest (Massive)
A

messenger RNA (mRNA)

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24
Q
  • the one found in the ribosomes; most common/predominant (most Rampant)
A

ribosomal RNA (rRNA)

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25
Q
  • the one that transfers amino acid to the mRNA by the process of translation; smallest/ Tiniest
A

transfer RNA (tRNA)

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26
Q
  • Made up of amino acids
  • Each amino acid has:
  • Amino Group
  • Carboxylic Acid Group
  • Hydrogen
  • Side Chain (determine what type of amino acid)
  • Protein’s amino acid sequence will ultimately determine its shape which will ultimately determine its function
A

Proteins

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27
Q

COMPOSITION: Nitrogenous Base, 5C Sugar, Phosphate Group
STRUCTURE: Double-stranded, Negatively-Charged, long sequence
LOCATION: Nucleus or Nucleoid Body
PROCESSES: Replication (DNA Polymerase)

Genes, Cistrons, Operons

A

DNA

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28
Q

COMPOSITION: Similar to DNA (U instead of T)
STRUCTURE: Single-stranded, short sequence
LOCATION: Nucleus and Cytoplasm
PROCESSES: Transcription, Post-transcriptional modifications, Translation

Low, High, Constant rate of transcription

A

RNA

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29
Q

COMPOSITION: 4 Levels – Primary, Secondary, Tertiary, Quaternary

STRUCTURE: Intracellular – enzymes, regulatory proteins, structural proteins; Extracellular – Hormones, structural proteins
LOCATION: Ribosomes and Golgi Apparatus

A

Proteins

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30
Q
  • a portion of a DNA that will encode for a specific mRNA (the one that will go to the ribosome to create proteins)
  • its in the sequence of DNA
A

Gene

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31
Q
  • Expression of a gene is increased by a factor (Activator)

- specific gene will be activated/turn on to create proteins

A

Positive Regulation

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32
Q
  • the factor that stimulate the gene to be activated
A

Activator

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33
Q
  • Expression of a gene is decreased by a factor (Repressor)
A

Negative Regulation

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34
Q
  • the factor that will decrease the expression of the gene
A

Repressor

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35
Q
  • general term for either activator or repressor
A

Effector

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36
Q

Signals that may induce gene expression is divided into 3:

A
  • Type A Response
  • Type B Response
  • Type C Response
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37
Q
  • Increased Gene Expression DEPENDENT upon the continued presence of the inducing signal; CONDITIONAL
A

Type A Response

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38
Q
  • Commonly observed in prokaryotes in response to sudden changes in the intracellular concentration of the nutrient; seen also in eukaryotes after exposure to inducers such as hormones, nutrients or growth factors
A

Type A Response

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39
Q
  • Increased Gene Expression that is TRANSIENT despite the continued presence of the inducing signal
A

Type B Response

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40
Q
  • Characterizes the action of many drugs; commonly occurs during the development of the organism
A

Type B Response

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41
Q
  • Increased GENE Expression that PERSISTS and is IRREVERSIBLE even after the termination of the signal; once the signal is present, the gene expression will last forever even though sometimes the signal is already gone
  • a transient signal will produce an IRREVERSIBLE response
A

Type C Response

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42
Q
  • Typically occurs during the development of differentiated function in tissue or organ
A

Type C Response

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43
Q
  • simpler; composed of bacteria and archaea
  • More primitive than eukaryotes; made up of single chromosome
  • No nucleus, no post-transcriptional modifications
  • Most of its DNA is CODING
  • Maybe POLYCISTRONIC
A

Prokaryotes

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44
Q 
- model for study of gene expression in humans
MECHANISM
*Control of transcription (MAINLY)
*“on-off” switching is usually seen
- Examples:
*Lac Operon
*Genetic Switch of Bacteriophage Lambda
A

Prokaryotic Gene Expression

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45
Q

What is an operon?

A
  • It is a linear group of related genes (made up of 2 or more unit) involve in metabolism
  • some of genes will be turned on and others will be turned off
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46
Q

Why does bacteria need lac operon?

A
  • involve in metabolism; it is activated with low levels of glucose and high levels of lactose
  • activated by bacteria so that it can utilize the lactose
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47
Q

What is bacteriophage?

A
  • virus that can destroy bacteria
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48
Q

Why switch the bacteriophage lambda good for the virus but bad for the bacteria?

A
  • favorable for the bacteriophage because the virus will increase their number; bad for the bacteria because the bacteria will die and it will undergo lysis
  • increases the number of bacteriophage; decreases the number of bacteria
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49
Q
  • usual source of energy of bacteria
A

Glucose

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50
Q
  • neither prokaryote or eukaryote
  • doesn’t have their own mitochondria
  • uses the host enzymes to insert their DNA so that it can be translated and transcribed
  • it’s the ultimate parasite
A

Virus

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51
Q

2 enzymes needed in the metabolism of Lactose

A
  1. Lactase Permease

2. B-Galactosidase

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52
Q
  • enzyme needed for the lactose to enter into the bacteria
A

Lactase Permease

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53
Q
  • enzyme that breakdown lactose into monosaccharides
A

B-Galactosidase

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54
Q

Lac Operon is composed of

A
  • LacI
  • lacZ
  • lacY
  • lacA
  • Promoter site
  • Operator ste
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55
Q
  • inhibition; creates the repressor protein that prevents the creation of the creation of permease and B-galactosidase
A

lacI

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56
Q
  • gene responsible for the creation of the enzyme B-galactosidase (GalactoZdase)
A

lacZ

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57
Q
  • gene responsible for the creation of the enzyme Permease (permYase)
A

lacY

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58
Q
  • gene responsible for the creation of enzyme Transacetylase (Ala/ function unknown yet)
A

lacA

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59
Q
  • an enzyme that will cause transcription of genes
A

RNA polymerase

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60
Q

In a condition with no lactose or with lactose but with high glucose, what will happen?

A
  • RNA polymerase will only transcribe lacI and it will not transcribe lacZ, lacY, lacA
  • when you transcribe lacI, you will create repressor proteins (which will bind to the operator region that will prevent the transcription of the lacZ, lacY, lacA)
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61
Q

In Repressed state (no lactose or with lactose but high glucose), what gene will be transcribe?

A

only lacI

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62
Q

What will happen in the activated state (high lactose and no glucose)?

A

high lactose will serve as an inducer&raquo_space; this inducer will bind to the repressor protein > causing disintegration of the repressor protein (wala nang nakaharang sa operator region)

  • LACTOSE and nagtanggal ng harang
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63
Q

During low glucose

A 
low glucose (fasting state, glucagon) >> cAMP (cyclic AMP) will bind to a CAP protein >> 
CAP-cAMP complex will stimulate the RNA polymerase to further work the transcription lacZ, lacY and lacA)

the one that stimulate the RNA polymerase (CAP-cAMP protein from low glucose)

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64
Q

Promoter and Operator Region

A

Promoter region - where the CAP-cAMP will bind

Operatior Region - where the repressor protein will bind

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65
Q
  • Found in the genes of the intestinal E.Coli
  • An example Type A response
  • Maximal when 2 things happen: Glucose levels are low, lactose levels are high
  • Uses both positive and negative regulators
A

Lac Operon

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66
Q
  • Negative Regulator
  • high affinity with an inducer (HIGH GLUCOSE LEVELS)
  • Binding of inducer derepresses the lac operon
A

LacI

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67
Q
  • Positive Regulator (Causes attachment of RNA polymerase to the promoter region to begin transcription)
  • cAMP increases during LOW GLUCOSE LEVELS (Remember: glucose inhibits adenylate cyclase which converts ATP to cAMP)
A

CAP-cAMP

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68
Q

2 types of pathway that happens after the bacteriophage enter into the host

A
  1. Lysogenic Pathway

2. Lytic Pathway

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69
Q
  • the dormant pathway
  • the DNA virus that is inserted into the host will not do anything
  • will only be activated under certain conditions, eg UV radiation
A

Lysogenic Pathway

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70
Q
  • active pathway
  • unregulated proliferation/replication of the viral DNA; the proteins needed by the viruses are synthesize in the ribosomes
  • produces viruses inside the bacteria using the bacteria’s ribosomes, enzymes and ATP which will further cause lysis of the cell and spread to the other cells
A

Lytic Pathway

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71
Q
  • responsible for the lysogenic pathway
  • will produce repressor proteins (it would lock the operator region similar to lac operon and will will prevent the RNA polymerase from transcribing)
A

Gene for Repressor

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72
Q
  • the one responsible for the lytic pathway

-

A

Gene for Cro

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73
Q
  • in between the Gene for Repressor and Gene for Cro

- divided in to 3 parts: Or3, OR2, OR1

A

Operator Region

74
Q

UV radiation can cause synthesis of __ (it will destroy repressor proteins which will cause the transcription of Cro gene which will lead to the Lytic Pathway. This is an example of Type C response.

75
Q
  • Due to a virus that infects bacteria
  • When the repressor gene is on, the Cro gene is off
  • When the Cro gene is on, the repressor gene is off
A

Bacteriophage Lambda

76
Q

The __ is both a positive regulator (promotes itself) and a negative regulator (inhibits Cro gene)

A

repressor gene

77
Q

(Bacteriophage Lambda)

  • If the repressor protein concentration becomes too __, it will attach to OR3 and diminish transcription of repressor gene until repressor protein concentration drops. It is responsible for dormancy of virus
78
Q

(Bacteriophage Lambda)

When Cro gene is activated, the lytic pathway is irreversible or __

A

Type C response

79
Q
  • Have a nuclei, histones and chromosomes
  • RNA undergoes post-transcriptional processes
  • Transcription is not a simple “on-off” switch
  • Signals from a number of complex environmental stimuli may converge on a single gene and a positive or negative response can be dominant.
A

Eukaryotes

80
Q
  • More complicated than prokaryotic gene expression with several mechanisms for control
  • Less-understood than prokaryotic gene expression
  • can happen at several levels (replication, transcription, translation and post-translation)
A

Eukaryotic Gene Expression

81
Q
  • Some regions of the chromatin are transcriptionally active, others are transcriptionally inactive or potentially active
A

Chromatin Remodeling

82
Q

Chromatin Remodeling: Mechanism

A
  • Scaffolding proteins that condenses chromatin regions and inactivates it
  • Having different regions of the chromatin available for transcription in cells from various tissues (e.g. B-globin gene is in the “active” chromatin in reticulocyte but in the “inactive” chromatin in the muscle cell)
  • Histone Acetylation and deacetylation – acetylation decreases binding of histone to DNA allowing access to transcription factors; a variety of CHONs have acetylase and deacetylase activity
  • Methylation of deoxycitidine residues – may cause gross changes in chromatin which inhibits transcription
  • Binding of specific transcription factors – may disrupt nucleosomal structure
  • Moving particular genes in or out of different subnuclear components
83
Q
  • Enhancers are DNA sequences that are different from promoters
  • DNA sequences found further away from promoter region that can activate or in activate genes
A

Use of Enhancers/Silencers

84
Q

Characteristics of Enhancers

A
  • Work when located long distances from the promoter
  • Active only when it exists within the same DNA molecule as the promoter
  • Work when upstream or downstream from the promoter (work in either direction
  • Can work with homologous or heterologous promoters
  • Work by binding to one or more proteins
  • Work by FACILITATING BINDING OF THE BASAL TRANSCRIPTION COMPLEX TO THE PROMOTER
  • MEDIATES TISSUE-SPECIFIC GENE EXPRESSION
  • PREVENTED FROM TRIGGERING TRANSCRIPTION RANDOMLY BY LOCUS-CONTROL REGION WITH ASSOCIATED BOUND PROTEINS AND INSULATORS WHICH IS ONCE AGAIN BOUND TO PROTEINS

(DNA sequences that can inhibit or stimulate other genes)

85
Q
  • a DNA sequences that will have a positive effect on the expression of gene
86
Q
  • a DNA sequences that will have a negative effect on the expression gene; decreases gene expression
87
Q
  • Transcription factors and their respective genes are called TRANS-REGULATORS (Cis-regulators would include promoters, enhancers, HREs)
  • Transcription Factors are activator proteins that bind to response elements (promoters, HREs, etc)
A

Regulatory Proteins/Transcription Factors

88
Q

(Regulatory Proteins/Transcription Factors)

2 recognizable domains:

A
  1. DNA-binding domain
  2. Activation domain (binds to other transcription factors, interacts with RNA polymerase to stabilize initiation complex, recruits histone-acetylases/deacetylases)

*The domains are independent and non-interactive

89
Q

(Regulatory Proteins/Transcription Factors)

DNA-binding domain has 3 unique motifs:

A
  • Helix-Turn-Helix
  • Zinc Finger
  • Leucine Zipper
90
Q

(Control of Nuclear RNA Processing)

Use of __ would yield different proteins such as mouse amylase, myosin light chain kinase, rat glucokinase, drosophila alcohol dehydrogenase and actin

A

alternative transcription start sites

91
Q

(Control of Nuclear RNA Processing)

  • used in immunoglobulins
A

Alternative polyadenylation sites

92
Q

(Control of Nuclear RNA Processing)

  • used to create 7 unique alpha-tropomyosin mRNAs in seven different tissues (regulatory mechanism is currently unknown)
A

Alternative splicing and processing

93
Q
  • mRNAs are stabilized or destabilize through interaction of proteins in the cytoplasm. These protein in turn maybe affected by hormones
  • The amount of mRNA determines the amount of translation and consequently the amount of protein produced
A

Control of mRNA Stability

94
Q

Stable vs Unstable mRNA

A

Stable mRNA - increase proteins

Unstable mRNA - decrease proteins

95
Q

(Gene Amplification and Rearrangement)

  • During development or in response to drugs, hundreds of rRNA and tRNA genes can be used to produce hundreds of copies of rRNA and tRNA
  • it will increase protein production
A

Amplification

96
Q

(Gene Amplification and Rearrangement)

  • seen in IgG genes; DNA will be rearranged to produce a DNA that is exact mirror image of the virus that’s why the next time you meet the virus you now have antibody what will attach to the virus&raquo_space; it will be phagocytose by the neutrophils and macrophages
  • enable us to adjust to foreign organism
A

Rearrangement

97
Q
  • E.g. Heme increases the translation of B-globin translation
A

Control the Rate of Protein Translation

98
Q
  • E.g. ALA synthase has a half-life of one hour in the hepatocyte
A

Control the Rate of Protein Degradation

99
Q
  • E.g. Barr bodies in women (inactivation of one X chromosome)
A

Inactivation of a Specific Chromosome of Chromosome Region

100
Q

The __ biosynthetic pathways in cells can be considered to be one large sorting system. Many proteins carry signals (usually but not always specific sequences of amino acids) that direct them to their destination, thus ensuring that they are delivered to the appropriate membrane or cell compartment; these signals are a fundamental component of the sorting system.

101
Q

A __ is made early in protein biosynthesis, when specific proteins are synthesized either on free or on membrane-bound polyribosomes.

A

major sorting decision

102
Q

proteins synthesized on membrane-bound polyribosomes contained an __ which causes them to become attached to the membranes of the ER (membrane bound polyribosomes), and facilitates protein transfer into the ER lumen.

A

N-terminal peptide extension (N-terminal signal peptide)

103
Q

polyribosomes synthesizing proteins lacking the signal peptide would retain free movement in the __ (cytosolic polyribosomes )

104
Q

__ have the same structure, and that the distinction between membrane bound and free ribosomes depends solely on the former carrying proteins that have signal peptides.

A

all ribosomes

105
Q

ER regions containing attached polyribosomes are called the __

106
Q

distinction between the two types of ribosomes results in two branches of the protein-sorting pathway, called the __

A
  1. cytosolic branch

2. rough ER (RER) branch

107
Q

Proteins synthesized by __ are directed to mitochondria, nuclei, and peroxisomes by specific signals, or remain in the cytosol if they lack a signal.

A

cytosolic polyribosomes

108
Q

(Cytosolic)

Any protein that contains a targeting sequence that is subsequently removed is designated as a preprotein. In some cases, a second peptide is also removed, and in that event the original protein is known as a __

A

preproprotein

109
Q

Proteins synthesized and sorted in the __ include many destined for various membranes (eg, of the ER, Golgi apparatus [GA], plasma membrane [PM]) as well as lysosomal enzymes, and also those for export from the cell via exocytosis (secretion). These various proteins may thus reside in the membranes or lumen of the ER,or follow the major transport route of intracellular proteins to the GA.

A

RER branch

110
Q

In the __, proteins are transported from the ER → GA→ PM and then released into the external environment.

A

secretory or exocytotic pathway

111
Q

Proteins destined for the GA, the PM, certain other sites, or for secretion are carried in __. transport of vesicles occurring continuously through the secretory pathway is referred to as “constitutive transport.

A

transport vesicles

112
Q

Certain other proteins destined for secretion are carried in secretory vesicles. These are particularly prominent in
the pancreas and certain other glands. Their mobilization
and discharge are switched on and off when required and
often referred to as __.

A

regulated secretion

113
Q

GA plays two major roles in protein synthesis

A

First, it is involved in the processing of the oligosaccharide chains of membrane and other N-linked glycoproteins and also contains enzymes involved in O-glycosylation.

Second, it is involved in the sorting of various proteins prior
to their delivery to their appropriate intracellular destinations.

*All parts of the GA participate in the first role, whereas the
trans-Golgi network (TGN) is particularly involved in the
second and is very rich in vesicles.

114
Q
  • are proteins which stabilize unfolded or partially folded intermediates, allowing them time to fold properly, and prevent inappropriate interactions, thus combating the formation of nonfunctional structures.
  • exhibit ATPase activity and bind ADP and ATP.
  • required for the correct targeting of proteins to their subcellular locations.
A

Molecular chaperones

115
Q

__ are the second major class of chaperones. They form complex barrel-like structures in which an unfolded protein is sequestered away from other proteins, giving it time and suitable conditions in which to fold properly.

A

Chaperonins

116
Q

Targeting Sequence or Compound: N-terminal signal peptide

Organelle Targeted: __

A

Endoplasmic Reticulum

117
Q

Targeting Sequence or Compound: Carboxyl-terminal KDEL sequence (Lys-Asp-Glu-Leu) in ER-resident proteins in COPI vesicles
Organelle Targeted: __

A

Lumen of ER

118
Q

Targeting Sequence or Compound: Di-acidic sequences (eg, Asp-X-Glu) in membrane proteins in COPII vesicles
Organelle Targeted: __

A

Golgi membranes

119
Q

Targeting Sequence or Compound: Amino terminal sequence (20-50 residues)
Organelle Targeted: __

A

Mitochondrial matrix

120
Q

Targeting Sequence or Compound: NLS (eg, Pro2-Lys3-Arg-Lys-Val)
Organelle Targeted: __

121
Q

Targeting Sequence or Compound: PTS (eg, Ser-Lys-Leu)

Organelle Targeted: __

A

Peroxisome

122
Q

Targeting Sequence or Compound: Mannose 6-phosphate

Organelle Targeted: __

123
Q

The structure of the __ has been studied in detail. It is polymeric, has two ring-like structures, each composed of seven identical subunits, and again ATP is involved in its action. The heat shock protein Hsp60 is the equivalent of GroEL in eukaryotes.

A

bacterial chaperonin GroEL

124
Q

Some Properties of Chaperone Proteins

A
  • Present in a wide range of species from bacteria to humans
  • Many are so-called heat shock proteins (Hsp)
  • Some are inducible by conditions that cause unfolding of newly synthesized proteins (eg, elevated temperature and various chemicals)
  • They bind to predominantly hydrophobic regions of unfolded proteins and prevent their aggregation
  • They act in part as a quality control or editing mechanism for detecting misfolded or otherwise defective proteins
  • Most chaperones show associated ATPase activity, with ATP or ADP being involved in the protein-chaperone interaction
  • Found in various cellular compartments such as cytosol, mitochondria, and the lumen of the endoplasmic reticulum
125
Q
  • contains many proteins. Thirteen polypeptides (mostly membrane components of the electron transport chain) are encoded by the mitochondrial (mt) genome and synthesized in that organelle using its own protein-synthesizing system. However, the vast majority (at least several hundreds) are encoded by nuclear genes, are synthesized outside the mitochondria on cytosolic polyribosomes, and must be imported.
A

Mitochondria

126
Q

__ have proved to be a particularly useful system for analyzing the mechanisms of import of mitochondrial proteins, partly because it has proved possible to generate a variety of mutants that have illuminated the fundamental processes involved. Most progress has been made in the study of proteins present in the mitochondrial matrix, such as the F1 ATPase subunits.

A

Yeast cells

127
Q

__ must pass from cytosolic polyribosomes through the outer and inner mitochondrial membranes to reach their destination. They have an amino terminal leader sequence (presequence), about 20 to 50 amino acids in length, which is not highly conserved but is amphipathic and contains many hydrophobic and positively charged amino acids (eg, Lys or Arg).

A

Matrix proteins

128
Q

Passage through the two membranes is called __. It occurs posttranslationally, after the matrix proteins are released from the cytosolic polyribosomes.

A

translocation

129
Q

Two distinct translocation complexes are situated in
the outer and inner mitochondrial membranes, referred to
(respectively) as __.

A

TOM (translocase-of-the-outer membrane) and TIM (translocase-of-the-inner membrane)

130
Q

Each complex has been analyzed and found to be composed of a number of proteins, some of which act as __ (eg, Tom20/22 ) for the incoming proteins and others as components (eg, Tom40 ) of the transmembrane pores through which these proteins must pass.

131
Q

Proteins must be in the __ to pass through the complexes, and this is made possible by ATPdependent
binding to several chaperone proteins including Hsp70

A

unfolded state

132
Q

A __ across the inner membrane is required for import; it is made up of the electric potential across the membrane (inside negative) and the pH gradient

A

proton-motive force

133
Q

The presequence is split off in the matrix by a __

A

matrix-processing protease (MPP)

134
Q

Interaction with __ ensures proper import into the matrix and prevents misfolding or aggregation

A

mt-Hsp70 (mt = mitochondrial; Hsp = heat shock protein; 70 = ∼70 kDa)

135
Q

interaction with the __ ensures proper folding. The interactions of imported proteins with the above chaperones require hydrolysis of ATP to drive them.

A

mt-Hsp60–Hsp10 system

136
Q

Some General Features of Protein Import

to Organelles

A
  • Import of a protein into an organelle usually occurs in three stages: recognition, translocation, and maturation.
  • Targeting sequences on the protein are recognized in the cytoplasm or on the surface of the organelle.
  • The protein is generally unfolded for translocation, a state maintained in the cytoplasm by chaperones.
  • Threading of the protein through a membrane requires energy and organellar chaperones on the trans side of the membrane.
  • Cycles of binding and release of the protein to the chaperone result in pulling of its polypeptide chain through the membrane.
  • Other proteins within the organelle catalyze folding of the protein, often attaching cofactors or oligosaccharides and assembling them into active monomers or oligomers.
137
Q

Molecules smaller than about 40 kDa can pass through the channel of the NPC by __, but special translocation mechanisms exist for larger molecules

138
Q

The general picture that has emerged is that proteins to be imported (cargo molecules) carry a __.

A

nuclear localization signal (NLS)

139
Q
  • Transport of macromolecules involves localization signals
  • Histones, ribosomal CHONS, ribosomal subunits, transcription factors, mRNA molecules
  • Bidirectional
  • Occurs through Nuclear Pore Complexes (NPCs
140
Q
  • involved in aspects of the metabolism of many molecules
  • fatty acids, plasmalogens, cholesterol, bile acids, purines, amino acids, and hydrogen peroxide
  • single membrane ;more than 50 enzymes
  • Marker enzymes: catalase and urate oxidase
  • Its proteins are synthesized on cytosolic polyribosomes and fold prior to import.
A

Peroxisomes

141
Q
  • Mutations in genes involved in biogenesis of peroxisomes
  • Apparent at birth and is characterized by profound neurologic impairment, victims often dying within a year.
  • # of peroxisomes can vary
A

Zellweger Syndrome

142
Q

Zellweger Syndrome: Biochemical findings

A
  • accumulation of very-long-chain fatty acids,
  • Abnormalities of the synthesis of bile acids
  • marked reduction of plasmalogens
143
Q
  • Mutations
  • genes encoding certain proteins—the PEX family of genes (peroxins) —involved in various steps of peroxisome biogenesis
  • genes encoding certain peroxisomal enzymes
A

Zellweger Syndrome

144
Q

Two closely related conditions are neonatal adrenoleukodystrophy and infantile Refsum disease. Zellweger syndrome and these two conditions represent a spectrum of overlapping features, with Zellweger syndrome being the most severe (many proteins affected) and __ the least severe (only one or a few proteins affected).

A

infantile Refsum disease

145
Q
  • N-terminal signal peptides
  • synthesized on membrane-bound polyribosomes
  • translocated into the lumen of the rough ER prior to further sorting
A

rough ER sorting branch

146
Q

Translocation of proteins to the ER

A
  • Co-translational

- Posttranslational

147
Q
  • process occurs during ongoing protein synthesis
  • nascent CHONs are transferred across the ER membrane into the lumen
  • process of elongation of the remaining portion of the CHON being synthesized probably facilitates passage of the nascent CHON across the lipid bilayer
  • unfolded state
A

Cotranslational pathway

148
Q

The Cotranslational pathway involves a number of specialized proteins and proceeds in 5 steps

A

Step 1: As the signal sequence emerges from the ribosome, it is recognized and bound by the signal recognition particle (SRP).
Step 2: The SRP escorts the complex to the ER membrane where it binds to the SRP receptor (SR).
Step 3: The SRP is released, the ribosome binds to the translocon, and the signal sequence is inserted into the membrane channel.
Step 4: The signal sequence opens the translocon. Translation resumes and the growing polypeptide chain is translocated across the membrane.
Step 5: Cleavage of the signal sequence by signal peptidase releases the polypeptide into the lumen of the ER.

149
Q
  • Proteins synthesized on free ribosomes and maintained in an unfolded conformation by cytosolic chaperones
  • Does not require SRP
  • Signal sequences are recognized by the Sec62/63 complex
  • Sec63 protein is also associated with a chaperone protein (BiP), which acts as a molecular ratchet to drive protein translocation into the ER.
  • Binding of polypeptide chains to BiP is needed to drive the posttranslational translocation of proteins into the ER
A

Posttranslational pathway

150
Q

Routes CHONs follow to be inserted into the membranes of the ER

A
  • Cotranslational insertion
  • Posttranslational insertion
  • Retention in the GA followed by retrieval to the ER
  • Retrograde transport from the GA.

Involved in assembly of the proteins of the ER membranes

151
Q

ER: Quality Control

A
  • Newly synthesized proteins attempt to fold with the assistance of chaperones and folding enzymes
  • folding status is monitored by chaperones and enzymes
152
Q

Proteins may enter the ER membrane posttranslationally
through the lateral gate in the translocon in a similar way to
cotranslationally sorted molecules. An example is __, which appears to enter the ER membrane subsequent to translation, assisted by several chaperones

A

cytochrome b5

153
Q

The chaperone __ is a calcium-binding protein located in the ER membrane. This protein binds a wide variety of proteins, including major histocompatibility complex
(MHC) antigens and a variety of plasma proteins. It binds the monoglucosylated species of glycoproteins that occur during processing of glycoproteins, retaining them in the ER until the glycoprotein has folded properly.

154
Q

__, which is also a calcium binding protein, has properties similar to those of calnexin, but it is not membrane-bound. In addition to chaperones, two enzymes in the ER lumen are concerned with proper folding of proteins.

A

Calreticulin

155
Q

__ promotes rapid formation and reshuffling of disulfide bonds until the correct set is achieved.

A

Protein disulfide isomerase (PDI)

156
Q

__ accelerates folding of proline-containing proteins by catalyzing the cis–trans isomerization of X-Pro bonds, where X is any amino acid residue

A

Peptidyl prolyl isomerase (PPI)

157
Q

Misfolded or incompletely folded proteins interact with
chaperones, which retain them in the ER and prevent them
from being exported to their final destinations. If such interactions continue for a prolonged period of time, the misfolded proteins are usually disposed of by __. This avoids a harmful build-up of misfolded proteins

A

endoplasmic reticulum-associated degradation (ERAD)

158
Q

The accumulation of misfolded proteins in the ER is referred to as __.

159
Q

The cell has evolved a mechanism termed the unfolded protein response (UPR) to sense the levels of misfolded proteins and initiate intracellular signaling mechanisms to compensate for the stress conditions and restore ER homeostasis. The UPR is initiated by __, which are transmembrane proteins embedded in the ER membrane.

A

ER stress sensors

160
Q

Activation of these stress sensors causes three principal effects:

A

(1) transient inhibition of translation to reduce the amount of newly synthesized proteins,
(2) induction of a transcription leading to increased expression of ER chaperones and to
(3) increased synthesis of proteins involved in degradation of misfolded ER proteins

161
Q

A target protein which is misfolded undergoes retrograde transport through the ER membrane into the cytosol, where it is subjected to __. It then enters a proteasome, inside which it is degraded to small peptides that exit and may have several fates.

A

polyubiquitination

162
Q

(Protein Degradation)

There are two major pathways of protein degradation in eukaryotes. One involves lysosomal proteases and does not require ATP, but the major pathway involves __ and is ATP-dependent.

163
Q
  • is particularly associated with disposal of misfolded proteins and regulatory enzymes that have short half-lives. - is known to be involved in diverse important physiologic processes including cell-cycle regulation (degradation
    of cyclins), DNA repair, inflammation and the immune
    respons, muscle wasting, viral infections, and many others . - is a small (76 amino acids), highly conserved protein that plays a key role in marking various proteins
    for subsequent degradation in proteasomes.
A

ubiquitin pathway

164
Q

Ubiquitin pathway involves three enzymes:

A

an activating enzyme (E1),
a conjugating enzyme (E2), and
a ligase (E3)

165
Q
  • protein complexes with a relatively large cylindrical structure
  • composed of 4 rings with a hollow core containing the protease active sites
  • 1 or 2 caps or regulatory particles that recognize the polyubiquinated substrates and initiate degradation
A

Proteosomes

166
Q

Vesicular Transport

A
  • CHONs&raquo_space; transport vesicles&raquo_space; GA or PM
  • Clathrin-coated vesicles are destined for exocytosis and lysosomes
  • Coat proteins I and II are associated with COPI and COPII vesicles&raquo_space; responsible retrograde and anterograde transport
167
Q
  • Involved in intra-GA transport and retrograde transport from the GA to the ER
168
Q
  • Involved in export from the ER to either ERGIC (ER-GA intermediate compartment) or the GA
169
Q
  • Involved in transport in post-GA locations including the PM, TGN (trans-Golgi network) and endosomes
170
Q
  • Involved in regulated secretion from organs such as the pancreas (eg, secretion of insulin)
A

Secretory vesicles

171
Q
  • They carry proteins to the PM and are also involved in

constitutive secretion

A

Vesicles from the TGN to the PM

172
Q

The basic concept is that each transport vesicle is loaded with specific cargo and also one or more __ proteins that direct targeting. Each target membrane bears one or more complementary t-SNARE proteins with which the former interact, mediating SNARE protein-dependent vesicle–membrane fusion.

173
Q

Model of the steps in a round of anterograde transport involving COPII vesicles

A
  1. Budding
  2. Binding of various coat proteins to Sar1-GTP
  3. Bud pinches off – formation of coated vesicle
  4. Coat disassembly
  5. Vesicle targeting
  6. V-SNARES pair with cognate t-SNARES in the target membrane to dock the vesicles and initiate fusion.
  7. Fusion of vesicle with acceptor membrane
  8. Deliver vesicle and its contents to appropriate site
174
Q

2 major roles in protein synthesis

A
  1. Glycosylation - All parts of golgi apparatus

2. Sorting - Trans- golgi network; Very rich in vesicles

175
Q

Some Transport Vesicles Travel via the

Trans Golgi Network

A

Cisternal Maturation - Cisternae move and transform into one another

TGN : sorted for transport to the PM, secretion, or lysosomes

176
Q

Some proteins are carried from the Golgi to the plasma membrane by a __, which accounts for the incorporation of new proteins and lipids into the plasma membrane, as well as for the continuous
secretion of proteins from the cell

A

constitutive secretory pathway

177
Q
  • Complex
  • lipid bilayer structure similar in all membranes
  • differ : specific protein and lipid content
A

Membrane Assembly

178
Q

Asymmetry is maintained during fusion of transport vesicles with the PM:

A
  • Inside of the vesicles after fusion&raquo_space; outside of the PM

- Cytoplasmic side of the vesicles remains facing the cytosol.

179
Q

Some Major Features of Membrane Assembly

A
  • Lipids and proteins are inserted independently into membranes.
  • Individual membrane lipids and proteins turn over independently and at different rates.
  • Topogenic sequences [eg, signal (amino terminal or internal) and stop-transfer] are important in determining the insertion and disposition of proteins in membranes.
  • Membrane proteins inside transport vesicles bud off the endoplasmic reticulum on their way to the Golgi; final sorting of many membrane proteins occurs in the trans-Golgi network.
  • Specific sorting sequences guide proteins to particular organelles such as lysosomes, peroxisomes, and mitochondria.
180
Q
  • Diseases of Proteostatic deficiency

- Mutations in genes or other factors affecting the folding of proteins

A

Conformational Diseases

Biochemistry (9 decks)

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