MCB exam3

Nuclear envelope

It controls traffic of proteins and RNAs through nuclear pore complexes, and plays a critical role in regulating gene expression.

What the nuclear envelope consists of

-two nuclear membranes
-an underlying nuclear lamina
-nuclear pore complexes

Outer membrane of the nuclear envelope is continuous with the:

Endoplasmic reticulum (ER)

Inner membrane of the nuclear envelope has proteins that bind the:

Nuclear lamina

Nuclear lamina is:

a fibrous mesh that provides structural support, consists of fibrous proteins (lamins) and other proteins

Lamins

intermediate filament proteins that associate to form higher order structures.

Two lamins interact to form

a dimer: the α-helical regions wind around each other to form a coiled coil

Hutchinson Gilford progeria

Inherited tissue-specific disease caused by mutations in lamin genes

Nuclear pore complexes

Composed of about 30 different pore proteins (nucleoporins)

Molecules pass through pore complexes by two mechanisms:

-Small molecules and protein (<40kd) pass freely in either direction.
-Proteins and RNAs are selectively transported; recognized by specific signals.

Nuclear pore structure

Eight spokes are connected to rings at the nuclear and cytoplasmic surfaces, surrounding a central channel. Protein filaments extend from the rings, forming a basketlike structure on the nuclear side.

Nuclear localization signals

Proteins that must enter the nucleus have amino acid sequences called

Nuclear transport receptors

Nuclear localization signals are recognized by

T antigen nuclear localization signal is

a single stretch of amino acids rich in basic amino acid residues –lysine and arginine.

Nuclear localization signals (NLS) are recognized by receptors called

importins,which carry proteins through the nuclear pore complex.

Importins work in conjunction with

the GTP-binding protein Ran, which controls directionality of movement.

Proteins are targeted for export from nucleus by

amino acid sequences called Nuclear export signals (NES).

NES are recognized by

receptors in the nucleus (exportins), which direct protein transport to the cytoplasm.

Many importins and exportins are members of

a family of nuclear transport receptors known as karyopherins

Karyopherin exportins transport

tRNAs, rRNAs, miRNAs–function in cytoplasm

Helicase on the cytoplasm side

releases the mRNA and ensures unidirectional transport.

snRNAs are complexed with 6–10 protein molecules to form

small nuclear ribonucleoprotein particles (snRNPs)

Euchromatin in interphase cells

Is decondensed and transcriptionally-active, and is distributed throughout the nucleus

Heterochromatin in interphase cells

Is highly condensed and not transcribed, and is often associated with the nuclear envelope or periphery of the nucleolus

LADs

Lamina-associated domains

NADs

Nucleolus-associated domains. DNA sequences found in NADs substantially overlap with those in LADs

Nuclear bodies

organelles within the nucleus that concentrate Proteins and RNAs that function in specific nuclear process. They are not enclosed by membranes.

Nucleolus

Functions in rRNA synthesis and ribosome production

Nucleolar organizing regions

Nucleolus is organized around the chromosomal regions that contain the
5.8S, 18S, and 28S rRNA genes

Nuclear speckles

Recruited to actively transcribed genes where pre-mRNA processing occurs.

Endoplasmic reticulum (ER):

network of membrane-enclosed tubules and sacs (cisternae)-extends from nuclear membrane throughout cytoplasm.
•Rough ER: ribosomes on the outer surface.
•Smooth ER: lipid metabolism.

Secretory pathway:

Rough ER → Golgi → secretory vesicles → cell exterior

✓Proteins synthesized on free ribosomes

stay in the cytosol or are transported to the nucleus and other organelles.

✓Proteins synthesized on membrane-bound ribosomes

are translocated directly into the ER through translocon

➢Cotranslational translocation:

Proteins move into the ER during their synthesis on membrane-bound ribosomes

➢Posttranslational translocation:

Proteins move into the ER after translation has been completed on free ribosomes

Cotranslational pathway:

•Ribosomes are targeted to the ER by a
signal sequence at the amino terminus which is removed when the growing polypeptide chain enters the ER.
•The role of signal sequences in targeting proteins to correct locations was determined by in vitro preparations of rough ER.

Proteins destined for incorporation into membranes:

1. Initially inserted into ER membrane instead of being released into lumen.
2. The membrane-spanning regions: Usually α helical regions with hydrophobic amino acids.
3. Orientations vary—the amino (N) or the carboxy(C) terminus is on the cytosolic side

The lumen of the ER is topographically equivalent to

The exterior of the cell

Some proteins have an amino terminal signal sequence

Cleaved by signal peptidase during translocation through translocon

A transmembrane α helix in the middle of the protein

halts translocation and anchors the polypeptide in the membrane

Many proteins are inserted directly into the ER membrane by

Internal transmembrane sequences

The cytosol is a

Reducing environment, most cysteine residues are in their reduced (--SH) state

The ER is what type of environment

Oxidizing environment, produces disulfide (S–S) bond formation, facilitated by protein disulfide isomerase

Proteins are glycosylated on specific
asparagine residues (N-linked glycosylation)

as they are translocated into the ER.

Some proteins are attached to the plasma membrane by glycolipids called

glycosylphosphatidylinositol (GPI) anchors

Misfolded proteins:

removed from the ER by
ER- associated degradation (ERAD)

If an excess of unfolded proteins accumulates, a signaling pathway is activated called the

unfolded protein response (UPR). It leads to expansion of the ER and production of more chaperones

If protein folding cant be adjusted to a normal level

the cell undergoes programmed cell death

PERK

a protein kinase that phosphorylates translation factor eIF2, which inhibits general translation and reduces the amount of protein entering the ER.

Hydrophobic, membrane lipids are synthesized in association with

already existing membranes rather than the aqueous cytosol.

Most lipids are synthesized:

in the smooth ER.

Eukaryotic membranes are made of 3 lipid types:

Phospholipids, glycolipids, and cholesterol

Most phospholipids are synthesized on the

cytosol side of the ER membrane from water-soluble precursors (glycerol).

New phospholipids are added only to the

cytosolic half of the ER membrane

Some phospholipids must be transferred to the other half of ER membrane

requires passage of polar head groups
through the membrane–flippases

The ER is the major site of synthesis of:

Cholesterol and ceramide

Ceramide is converted to

Glycolipids or sphingomyelin in the golgi apparatus

Smooth ER is abundant in

Cells with active lipid metabolism

Steroid hormones are synthesized from

cholesterol in the ER; abundant smooth ER is found in cells of the testis and ovary

In the liver, smooth ER contains

enzymes that
metabolize lipid-soluble compounds. Enzymes inactivate some drugs

KDEL or KKXX

Protein targeting sequence at the carboxy terminus that directs retrieval back to the ER

Golgi apparatus

Proteins from the ER are processed and sorted for transport to endosomes, lysosomes, the plasma membrane, or secretion

Most glycolipids and sphingomyelin are synthesized

In the Golgi

Proteins from the ER enter where on the golgi

The convex cis face (entry face)

Proteins transported through the Golgi exit from

The concave trans face (exit face)

The Golgi has 4 regions:

•cis compartment—receives molecules from the ERGIC
•medial and trans compartments—most modifications are done here
•trans-Golgi network—the sorting and distribution center

Glycolipids and sphingomyelin are synthesized from

ceramide in the Golgi.

Sphingomyelin is synthesized by

transfer of a phosphorylcholine group from phosphatidylcholine to ceramide.

In polarized cells of epithelial tissue, plasma membranes are divided into

Apical domains and basolateral domains, each with specific proteins

Transport vesicles with secretory proteins are coated with

Coat proteins

COPII-coated vesicles carry proteins

from the ER to the ERGIC and on to the Golgi apparatus.

COPI-coated vesicles bud from the

ERGIC or Golgi and carry their cargo back, returning proteins to earlier compartments

Clathrin-coated vesicles

transport in both directions between the trans Golgi network, endosomes, lysosomes, and plasma membrane

Interaction between transport vesicles and target membranes is mediated by

Tethering factors and small GTP binding proteins (Rab proteins)

Transmembrane proteins called

SNAREs- fusing vesicles and membrane

inner mitochondrial membrane

Impermeable to most ions and small molecules-helps maintain proton gradient

Outer mitochondrial membrane

Highly permeable to small molecules, constants porins that form channels allowing free diffusion

High-energy electrons from NADH and FADH2 are transferred through a series of carriers in the membrane to

molecular oxygen

First step of oxidative catabolism

Glycolysis

In anaerobic conditions, the NADH is reoxidized to

NAD+ by the conversion of pyruvate to lactate or ethanol

In an aerobic organism NADH

•serve as an additional source of energy•the NADH donates electrons to the electron transport chain

In eukaryotic cells, pyruvate is then transported into the

Mitochondria–completely oxidized

Pyruvate undergoes oxidative decarboxylation in the presence of

coenzyme A (CoA-SH), forming acetyl CoA; generation of NADH. 2 pyruvates generate 2 NADH

Acetyl CoA enters the

citric acid cycle (Krebs cycle)

✓2 carbons of citrate:

•2 CO2
•1 oxaloacetate
•1 GTP
•3 NADH and
•1 FADH2

Oxidation of glucose:

6 molecules of CO2, 4 ATP, 10 NADH, 2 FADH2

Most energy from the breakdown of carbohydrates or fats is derived by

Electron transport and oxidative phosphorylation

Components of the electron transport chain are organized into

Four complexes in inner mitochondrial membrane

Electrons from NADH enter the electron transport chain at

Complex I

Electrons are transferred to complex III by

Coenzyme Q (ubiquinone)

Cytochrome c carries electrons to

complex IV (cytochrome oxidase) where they are transferred to O2

Complex II

receives electrons from the citric acid cycle intermediate succinate

The energy derived from electron transport is coupled to

The generation of a proton gradient across the inner mitochondrial membrane

how many protons per pair of electrons are transported at each complex

4

Electrochemical gradient:

pH gradient and electric potential drive protons back to matrix across inner membrane

Energy in the electrochemical gradient harnessed and converted to ATP in

Complex V (ATP synthase)

Mitochondrial genomes

Usually circular DNA molecules, present in multiple copies

U in the tRNA anticodon can pair with

any of the four bases in the third codon position of mRNA;
four codons are recognized by a single tRNA

Leber’s hereditary optic neuropathy:

blindness; mutations in mitochondrial genes for electron transport chain