BMS 300- Unit 1

Cellular functions take place in an

Aqueous environment

Dipole Moment

A measure of the separation of partial positive and partial negative charges within a molecule, determined by the magnitude of the charges and the distance between them.

Hydrogen Bonding in Water

The electrostatic attraction between a hydrogen atom covalently bonded to an electronegative atom (such as oxygen) and a small electronegative atom on a neighboring polar molecule.

Hydrophilic Interactions

Interactions involving polar or charged molecules that dissolve readily in water by forming ionic or hydrogen bonds with water molecules.

Hydrophobic Interactions

Interactions involving nonpolar, uncharged molecules (such as fats or oils) that do not dissolve in water due to an inability to form favorable bonds with water molecules.

Amphipathic Molecules

Molecules containing both hydrophilic (polar/charged) and hydrophobic (nonpolar) regions, such as phospholipids.

Phospholipid structure

•Modified triglyceride

•R group

•Has amphipathic properties

Micelle

Single layer lipid sphere

Liposome

Two layer liped sphere (more stable)

Integral membrane proteins can serve

–In cellular communication

–as ionic pathways

–To maintain ion concentrations

Peripheral proteins

Sit loosely on the inner or outer surfaces

How does the body extract energy from food?

–Anaerobic and aerobic pathways

–Beta-oxidation

–Deamination

Metabolism

Sum of cellular reactions required to sustain life

• Our bodies extract energy (contained in the bonds between atoms of a molecule) and convert it to a form that our cells can use.

Cells extract usable energy from carbohydrate via four main pathways

•Glycolysis

•pyruvate to acetyl CoA

•the citric acid cycle

•the electron transport chain

In glycolysis how does the body decide to convert pyruvate to lactate or acetyl CoA?

When limited oxygen is avalible pyruvate is shuanted to form lactate.

When oxygen is readily avalible and energy is needed, pyruvate is converted to acetyl CoA.

Citric Acid Cycle

• Acetyl-CoA combines with oxaloacetate to form citric acid

•Oxaloacetate is regenerated

• One glucose molecule produces two acetyl-CoA molecules; the citric acid cycle will occur twice

• NADH and FADH2 deliver their cargo of high-energy electrons to the electron transport chain (ETC)

Electron transport chain

• As electrons are passed down the chain, they move from a higher to a lower energy level, releasing energy.

• Some of the energy is used to pump H+ ions out of the matrix and into the intermembrane space, establishing an electrochemical gradient.

• H+ ions flow down the gradient, powering ATP synthase

The electron transport chain (ETC) consists of a series of protein complexes & sits in the

Inner mitochondrial membrane

A drug selectively permeabilizes the inner mitochondrial membrane, allowing protons (H+) to leak freely down their electrochemical gradient into the mitochondrial matrix bypassing ATP synthase. Assuming glucose is readily available, what will be the physiological status of Glycolysis versus the Electron Transport Chain (ETC) in these cells?

Glycolysis will accelerate, and the ETC will continue to pump protons.

Carbohydrates Metabolism - Steps

Extracting Energy from Fat

Starts with lipid digestion into glycerol and free fatty acids (FFA)

• Lipids break down into glycerol (to glycolysis anaerobic in the cytoplasm) and fatty acids (beta-oxidation aerobic in the mitochondria)

Beta-oxidation of fatty acids

• Breakdown (beta-oxidation) of fatty acids takes place inside the mitochondria

• Acetyl-CoA, which enters the Krebs (TCA) cycle to generate NADH and FADH2 for transferring pairs of high-energy electrons to ETC to fuel ATP synthesis

Extracting Energy from Proteins

• During starvation, the body breaks down protein and extracts energy from the amino acids

• Deamination strips down the amino acid to a "carbon skeleton“ while producing a nitrogen byproduct that becomes urea

• The carbon skeleton structure determines where it enters the catabolic pathways

Nucleus

• Contains DNA

• Nuclear membrane is continuous with Endoplasmic Reticulum

• Nuclear pores allow selective transport

  • Complex of proteins that span nuclear membrane

Orientation & Base Pairing of DNA

• Strands of a DNA double helix always run in opposite directions

  • Antiparallel orientation

• Bases-pairs interact via hydrogen bonds

  • A – T: two H-bonds

  • C – G: three H-bonds

Transcription

The process by which information in a DNA strand is copied into an mRNA

• Initiated by transcription factors binding to a promoter region

What does RNA polymerase do in transcription?

• Unwinds DNA

• Reads template strand 3’ to 5’

• Synthesizes RNA strand 5’ to 3’

• Catalyzes phosphodiester bonds

• mRNA is complementary to DNA sequence (U replacing T)

Post-transcriptional Modifications

5’ Capping

• Protects from 5’-3’ exonuclease degradation

• Ribosome binding site

3’ poly adenylation

Protects from 3’ to 5’ exonuclease degradation

Splicing

• Removes non-coding regions

  • Small nuclear RNAs (snRNAs) are components of the spliceosome that aid in splicing

  • Alternative splicing: multiple proteins are possible from one gene

RNA

• RNA is single-stranded, but it can fold into secondary structures

  • Hydrogen bonds between bases

• Complex structures that function as ribozymes – catalytic activity

  • Found in spliceosomes, which edit mRNA

  • Found in ribosomes, which aid protein synthesis

Messenger RNA (mRNA)

Forms a template for protein synthesis

Transfer RNA (tRNA)

Carries amino acids to ribosomes for protein synthesis

• Brings amino acids to the ribosome for the growing polypeptide chain

Ribosomal RNA (rRNA)

Structural core of ribosomes

Small nuclear RNAs (snRNA)

Involved in processing of DNA and RNA in nuclei

Where are mRNA, tRNA, and rRNA made?

Nucleus

Where do mRNA, tRNA, and rRNA function?

Cytosol

Translation

The process by which a protein is synthesized from the information contained in a molecule of messenger RNA (mRNA)

Small Ribosomal subunit

Binds and reads mRNA

Large subunit

Docking site for tRNAs & Catalyzes peptide bonds between amino acids released from tRNAs

Aminoacyl-tRNA

Synthetase facilitates linking tRNA to new amino acid

Charging tRNA

• Aminoacyl-tRNA synthetase facilitates linking a tRNA to a new amino acid

• ATP cleavage provides energy to link the amino acid to tRNA via an ester bond

• tRNA can drop off an amino acid at a ribosome

Post-translational Modifications (PTM)

• Some are reversible and some are irreversible

  • Mostly addition of a group or molecule

  • Can also remove a group or cleave a protein

• PTMs are important for proper protein functions in cells

• Failure to properly modify proteins causes problems in multiple organ systems

Primary Protein Structue

Sequence of a chain of amino acids

Secondary Protein Structure

Local folding of the polypeptide chain into helices or sheets

Tertiary Protein Stucture

3D folding pattern of a protein due to side chain interactions

• are formed mainly by hydrophobic interactions between amino acid side chains

Quaternary Protein Structure

• Protein consisting of more than one amino acid chain

• Defined by the interactions between different polypeptides (subunits)

Amino Acids

• Proteins are constructed of long chains of amino acids.

• All amino acids contain a carboxyl group and an amino group linked by a carbon

• an R group is attached to this carbon.

• The R group is characteristic of each of the 20 amino acids

• Some R groups are hydrophobic while others are hydrophillic

Peptide bonds

• Amino acids are linked one to another by the formation of a peptide bond

• Peptide bonds form when the carbon on the carboxyl group forms a covalent bond with the nitrogen in the amine group in the adjacent amino acid

α-helices

• polypeptide backbone forms a very compact corkscrew

• i + 4 H bonding

  • Hydrogen bonding between the carbonyl oxygen (C= O) of one amino acid and the hydrogen on the amide (N—H ) of a nearby amino acid

• Side chains face outward from the helix axis

β-sheets

• More extended than an alpha helix

• Hydrogen bonds are formed between the peptide bond C=O and N—H groups of polypeptides that lie side by side

The charge and orientation of R groups on amino acids are important in determining all of the following protein characteristics except

The secondary structure within the protein

Polypeptide backbone Determinants of Shape

• Type of Amino Acids

• Order of Amino Acids

• interactions/bonds between Amino Acids

• Environmental factors – temperature, pH, etc.

Prions

Protein Infectious Agents (PRP)

In the cell membrane, ____________________ normally form the ion

channels

Alpha Helices

Smooth Endoplasmic Reticulum

• Lacks ribosomes

• Location of functions including cellular detoxification (abundant in liver cells) storage of calcium ions (sarcoplasmic reticulum in muscle cells).

Rough Endoplasmic Reticulum

• ER is responsible for proteostasis (protein homeostasis)

  • Biosynthesis, folding, maturation, stabilization, and trafficking of transmembrane and secretory proteins

• The rough ER contains ribosomes on its surface

• With the assistance of chaperones, nascent proteins fold and undergo other functional modifications, including glycosylation, disulfide bond formation, and oligomerization.

• Properly folded and modified proteins are then packaged into vesicles to be shipped to the Golgi apparatus and other locations in the cell.

• Chaperones identify improperly folded proteins and facilitate degradation in the cytosol by proteasomes

SR-SRP complex process

1. SR-SRP complex brings a hydrophobic polypeptide to the ER

2. SR-SRP complex leaves. The hydrophobic polypeptide is looped into the translocon, and it binds a recognition site.

3. The polypeptide loop pushes open the plug

4. The signal peptide leaves the translocon by a lateral gate, where the signal peptidase degrades it

5. The polypeptide is released into the ER lumen at the end of translation for PTM

Insertion of multi-pass trans- membrane proteins in RER

• The signal recognition particle (SRP) and its receptor (SR) are required to initiate the translocation of the first transmembrane domain

• The threading of subsequent transmembrane domains is managed by

  • the ribosome- translocon assembly

  • the hydrophobicity of the translated domain.

Golgi apparatus

• The Golgi apparatus is a major sorting and dispatch station for the products of the ER

• Vesicles enter via the cis face and are transported through membrane- enclosed cisternae.

Protein modifications include phosphorylation, glycosylation, and tags that define their cellular destinations

1. Lysosomes –contain proteolytic and degradative enzymes

2. Plasma membrane -receptors, channels, Single or multi-pass proteins

3. Extracellular fluid (Secreted proteins)- hormones, antibodies

Recap of organelles involved in the central dogma

Nucleus: DNA replication, RNA transcription, and RNA editing

Rough ER: Following cotranslational translocation, proteins are further processed

Golgi apparatus: Proteins are further processed and sent to various destinations (cell membranes, secreted out of the cell or degraded)

The presence of a signal peptide in a protein sequence indicates that it will LEAST likely be processed in the

Cytoplasm

Hydrogen bonding is NOT required for?

 The primary structure of proteins

What type of bond is responsible for the dipole moment of a water molecule?

Polar bonds

Which of the following are responsible for hydrophobicity?

Nonpolar particles

What is the result of translation?

Protein

Consider the primary structure of proteins. What type of bonds connects two amino acids together?  

Covalent bond

In eukaryotic cells, enzymes that form phosphodiester bonds between nucleotides function in the:

nucleus

What is the name of the motor protein associated with actin filaments?

Myosin

What is the function of glycolysis?

 Breakdown of a 6-carbon glucose to two 3-carbon pyruvate molecules

Botulinum toxin is a protease that cleaves vesicular associated membrane protein (VAMP) into smaller pieces, rendering it nonfunctional. What will occur due to exposure to botulinum toxin?

Disruption of the formation of the SNARE complex

ER-associated degradation (ERAD) pathway

• Degrades troubled proteins by ubiquitin- proteasome system (UPS)

• Cell recognizes protein as misfolded

• Protein is ubiquinated

• Protein is retrotranslocated from ER cytosol to cytoplasm

• Protein is degraded by proteosome

The Unfolded Protein Response(UPR)

• if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding pathways in the cell.

  • inhibit protein translation

  • Increase folding capacity of the ER by causing more chaperones to enter the ER

What is the last resort for ER stress due to unfolded proteins?

Autophagy

What is a Vesicle?

• Enclosed lipid bilayer

• Contains cytoplasm

• Carries materials

• Formed by budding off an existing membrane

  • plasma membrane

  • organelle membrane

How to vesicles get transported?

Through coated vesicles

COPII

From ER to Golgi

COPI

From Golgi to ER membrane

Clathrin

From the plasma membrane

• an example of receptor- mediated endocytosis

Exocytosis –SNARE Complex Steps

1. v-SNAREs in the vesicle bind to

   t-SNARES in the target membrane

2. Water is squeezed from between the two membranes

3. Stalk formation

4. Hemi-fusion

5. Fusion

Trafficking of Vesicles and Cytoplasmic Proteins

• Requires roads and vehicles

  • Roads are the cytoskeleton

  • Vehicles are the motor proteins

Cytoskeleton Intermediate filaments

Structureal only

Cytoskeleton microtubules

• Structural and transport

• Long-distance transport

Cytoskeleton F - actin

• Structural and transport

• Short-distance transport

Actin filaments

Double stranded; made of globular (G) actin

Polar

• plus end – toward membrane

• minus end – toward nucleus

Microtubules

Tube-like, made from dimers

Polar

• plus end – toward the membrane

• minus end – toward nucleus

Motor Proteins/Molecular Motors

• ATPases

• Bind and cleave ATP → ADP

• Energy released powers movement along cytoskeleton

• Motor protein types:

  • Kinesin

  • Dynein

  • Myosin

Kinesin moves towards the

Plus (+) end on microtubules

Dyenin moves towards the

Minus (-) end on microtubules

Myosin V moves towards the

Plus (+) end on F-actin

Myosin VI moves towards the

Minus (-) end on F-actin

How are cells connected to each other and the extra-cellular matrix?

• Gap junctions

• Tight junctions

• Anchoring junctions

How do we classify epithelial tissue?

• Cell shape

• Number of layers

Gap junction

Mediates cell-to- cell communication

• They are aggregates of intercellular channels that permit direct cell–cell transfer of ions and small molecules

• Connect the cytoplasm in adjacent cells

• Couple cells both electrically and metabolically

• Found in most cells (e.g., bone, nerves, muscles, etc.

Gap-junctional channels are composed of hexamers of integral proteins

Connexins

Isoforms

Same type of protien seen in multiple tissues

Different combinations of connexins create channels that differ in

permeability and regulation

• Regulation can be mediated by changes (pH, [Ca 2+ ] ) or signals (neurotransmitters)

• Turnover of connexons is rapid

New connexons are inserted into the plasma membrane by

Exocytosis