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Finals I

Terms in this set (44)

Nucleus
a specialized double membraned organelle that houses the DNA / genome of the cell.

Also where ribosomes are assembled (sub units), where transcription occurs
Nucleolus
Specialized region in which ribosomes are assembled, including transcription of rRNA and ribosome subunit assembly

-- functions in rRNA synthesis and ribosome production.
Nuclear Envelope
The _____________ separates the nuclear contents from the cytoplasm.
• It controls traffic of proteins and RNAs through nuclear pore complexes, and plays a critical role in regulating gene expression.

- Helps control gene transcription by regulating movement of proteins, such as transcription factors, to and away from DNA

-- it is continuous with rough ER
The nuclear envelope consists of:
▪ two nuclear membranes,
▪ an underlying nuclear lamina,
▪ nuclear pore complexes.
• Outer membrane is continuous with the endoplasmic reticulum (ER).
• Inner membrane has proteins that bind the nuclear lamina.
The Nuclear envelope structurally consists of:
Structure and function of nuclear pore complex

Protein filaments extend from the rings, forming a basket-like structure on the nuclear side.
They contribute to the membrane's selectivity.

are the only channels for small polar molecules, ions, proteins, and RNA.
1. to small nonpolar molecules.
2. small polar molecules like proteins and mRNA
1. The nuclear membranes are phospholipid bilayers permeable only______

2. ______ molecules enter through the nuclear pore complex
1. mRNA and ribosomal sub units. The transcribed RNA in the nucleus enter through the nuclear pore complex for translation in the cytoplasm.
2. Proteins, Why ? for gene regulation, transcription, DNA replication, ribosome assembly.
1. molecules exported out of the nucleus?
2. Molecules that constantly enter into the uncle through the nuclear pore complexes
nuclear lamina
• The ______is a fibrous mesh that provides structural support.

binding to the inner nuclear envelop membrane and the chromatin, supporting structure and may involved in gene regulation

• It consists of fibrous proteins called lamins, and other proteins.
-- mutations in the genes that code for this structure cause several different inherited tissue-specific diseases such as Progeria
DNA binding and Protein-protein interaction domain

1. DNA binding domain

2. Protein-protein interaction domain
Two major domains of a transcription factor:

1. Part of an activation factor. is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA.

2. a transcription factor scaffold domain which contains binding sites for other proteins such as transcription coregulators. Interact with Mediator proteins and general. Interact with coactivators to modify chromatin structure.
Chromatin remodeling, transcriptional, RNA processing (post-transcriptional) , translation, post-translational
Different levels of gene regulation
by the rate of transcription, translation and modification of protein
The amount of protein is controlled 3 major ways
transcription
_________is the first step in gene expression, and the initial level at which gene expression is regulated.

• RNAs in eukaryotic cells are then modified and processed in various ways.
constitutively expressed genes
Genes that are actively transcribed (and translated) under all experimental conditions, at essentially all developmental stages, or in virtually all cells
1.inducible genes

2. repressible genes
1. Genes that are transcribed and translated at higher levels in response to an inducing factor


2. Genes whose transcription and translation decreases in response to a repressing signal
enhancer
cis-acting element.
• They are required for maximal transcription of a
gene.
can be upstream or downstream of the transcription initiation site
-contain short sequence elements, some similar to promoter sequences.

-Activators bind these sequences and other protein complexes form, postulated to bring activating- complex close to the promoter and increasing transcription.
Chromatin structure
The packaging of eukaryotic DNA in chromatin has important consequences for transcription, so _______ is a critical aspect of gene expression.
1. from N-temrinus to C-terminus
2. From 5' to 3'
directionality of polymerization

1. Proteins
2. DNA/RNA
1. mRNA
2. rRNA
3. tRNA
The 3 roles of RNA in Translation

• ____________) encodes amino acid sequence of polypeptides (RNA polymerase II)

• _______________ organizes protein in ribosomes and catalyzes protein synthesis (RNA polymerase I)

•_____________shuttles amino acids for protein synthesis (RNA polymerase III)
tRNA
has an amino acid attachment site

and an anti-codon region

-invovled during translation of mRNA to protein



• The anticodon loop binds to the appropriate codon by complementary base pairing.
aminoacyl tRNA syntheses

- tRNA, ATP, Amino acid
Attachment of amino acids to specific tRNAs is mediated by enzymes called

- this reactions involves 3 different molecules
-Translation involves an interpretation of one language into another. From mRNA to Protein

-In genetics, the nucleotide language of mRNA is translated into the amino acid language of proteins
-This relies on the genetic code
-The genetic information is coded within mRNA in groups of three nucleotides known as codons

The code is degenerate - More than one codon can specify the same amino acid

Codon is a three- nucleotide base sequence on the mRNA that code for a specific amino acid.
Define genetic code, codon, anti codon.

What are the start and stop codon in translation

**Translation progress)
1. initiator tRNA, Methionine

2. The initiator tRNA carrying met, enters the p-site, all subsequent tRNA enter to the A-site, then move to P-site to add the amino acid to the growing chain, peptide bond is made at the P-site, E- site is exit
1. _________ tRNA carries the first amino acid, which is ____ in eukaryotes.

2. Roles of E, P, A sites involved in translation
Translation produces a polypeptide sequence or a protein based on the genetic sequence carried by mRNA. The genetic sequence carried by the mRNA is translate amino acid sequenced by the complementary base parking action of codons from the mRNA and anticodons from the tRNA.

Translation occurs in the cytoplasm where the ribosomes attach to mRNA. site of translation. where mRNA codons are translated to amino acid sequecne building up a protein.
tRNA carrying an amino acid (bounded by tRNA synthetase) binds to specific mRNA codon according to the tRNA's anticodon complementary base pairing.
During initiation, the tRNA carrying the first amino acid binds to the start codon which signal the start of translation. (AUG), the ribosome holds the complex in place
during elongation, one tRNA at a time adds an amino acid to the growing polypeptide chain
Terminatin occurs when a stop codon is reached signaling termination, release factor occupies the A site
Describe the process of translation. Include major molecules involved.
primary structure
The four levels of protein structure, and ________ refers to the amino acid sequence in a polypeptide, which determines higher levels of structure
Chaperone proteins
________: helping in protein folding, and first identified as heat-shock proteins

-- are proteins that facilitate folding of other proteins.

They act as catalysts that assist the self- assembly process without becoming part of the folded protein.

They bind to and stabilize unfolded or partially folded polypeptides.

bind to polypeptide chains that are still being translated on ribosomes.

The chain must be protected from aberrant folding or aggregation with other proteins until synthesis of an entire domain is complete.
post translational
mRNA processing such as:

1. Alternative splicing

• 60-70% of human genes undergo alternative splicing • Human cells have a higher number of distinct proteins than actual genes • By splicing a mRNA from one gene in different ways, the cells produce more kinds of proteins

and


2. 5'cap 3' poly a tailing

are method of gene regulation at what level?
translational
level of gene regulation at which regulation at mRNA occurs . Translation repressor proteins bind to the mRNA to prevent translation. Acts on the mRNA
phosphorylation
One of the most important and common regulatory mechanisms utilized in cells. Used as a signaling mechanism in cells by activating and de-activating enzymes.
- _________is the process of covalently adding a phosphate group to a protein's amino acid (Tyr, Thr, Ser)
1. kinase
2. phosphatase
1. enzyme that catalyze the addition of a phosphate group, activating the protein

2. enzyme that catalyses dephosphorylation, deactivating the protein

Phosphorylation enzymes are involved in many complex signal cascades that regular cellular activities such as cell cycle and cell division
inhibition of protein production, increase of chaperone production, and increased activity of proteasome.
The unfolded protein response can involve ___, ____, ___
1. ubiquitin

2. ubiquitination
1. is a small protein which gets appended to another protein as a "label" • The labeled protein is targeted for destruction in the proteasome pathway

2. a multi-step process that involves the addition of multiple ubiquitin to a specific protein targeted for degradation by a proteasome.
E1 - ubiquitin activation enzyme
E2 - ubiquitin conjugate enzyme
E3 - Ubiquitin legase enzyme
what are specialized enzymes involved in ubiquitination?
Proteasome
a multi-enzyme complex that function as garbage disposals by degrading proteins tagged with ubiquitin.

Misfolded proteins are identified, returned to the cytosol, and degraded

destroys proteins by unfolding and cutting down poly peptides.
Proteins are processed into short peptides, followed by hydrolysis of these peptides via cytoplasmic exopeptidases into amino acids for the cells' use
5
Acidic hydrolytic enzymes in lysosomes: PH ??
lysosomes
Transport vesicles carrying acidic hydrolase fuse with late endosomes to form ____
1. unfolded protein respond
2. cell death
If an excess of unfolded proteins accumulates, a signaling pathway called the ________ (UPR) is activated.

It leads to expansion of the ER and production of more chaperones.

If protein folding can't be adjusted to a normal level, the cell undergoes programmed______.
M6P tag: phosphorylated mannose
Lysosomal proteins are marked by ______
how is M6P recognized, by an M6P on the membrane of the trans golgi network. The M6P labeled protein binds to a specific region of the trans membrane golgi with M6P receptors. The M6P labeled protein is transported by a receptor-dependent transport vesicle.

the M6P receptor shuttles between the trans golgi network and the lysosome. the receptor is recycled.
How is M6P Recognized?
rough ER and free ribosomes in cytosol
Proteins synthesized by ribosomes on____ and ____ are delivered to different locations, respectively ( specific locations)
1. Rough ER

2. smooth ER
The ER has two domains that perform different functions: •

1. _______ is covered by ribosomes on the outer surface. It functions as a region where membrane bound ribosomes synthesize proteins. This is also where proteins fold and get modified for transport to the golgi.

2. _____ has no ribosomes and is involved in lipid metabolism.
Golgi Apparatus
This is where proteins from the ER are processed and sorted for transport to *endsomes, lysosomes, plasma membrane, or secretion

is composed of flattened membrane- enclosed sacs (cisternae) and associated vesicles. It process and sorts proteins. proteins and lipids are transported to the Golgi body for shipment to other locations in the cell.

modifies existing sugars and proteins, sorts proteins, adds new sugars to proteins




responsible for transporting, modifying, and packaging proteins from ER, to other destination
It has polarity: proteins from the ER enter at the cis face, usually oriented toward the nucleus. They exit from the trans face.

Cis compartment - receives molecules from the ERGIC (er to golgi intermediate compartment)
medial and trans compartments — most modifications are done
trans golgi network - the sorting and distribution center
Discuss the structure of the golgi
Protein sorting overview

• Proteins synthesized on rough ER and processed through Golgi are targeted to:

- Cell membrane - Lysosomes - Secretion from cell

• Proteins synthesized in cytosol:

- Cytosol - Mitochondria - Nucleus
Protein sorting overview

• Proteins synthesized on rough ER and processed through Golgi are targeted to:

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• Proteins synthesized in cytosol:
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The sequence of KDEL serves as an ER retention signal for proteins by binding to KDEL receptor that transport the proteins from the Golgi apparatus back to the ER
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