Structure and Function - Bio1A

Basic units of structure define the function of all living things

Structure and Function

• At each level of the biological hierarchy we find a correlation between structure and function

• Analyzing a biological structure gives us clues about what it does and how it works

• Conversely, knowing the function of something provides insight into its structure and organization

Life can be defined by the laws of physics and chemistry

All biological processes are dictated by the atomic and molecular constituents of cells and organisms

Life depends on water and the search for extraterrestrial life may hinge on discovering water on exoplanets

Life on earth relies on a subset of elements principally hydrogen, oxygen, carbon, nitrogen and phosphorus

Atomic forms of matter

Atomic elements are the foundation of molecules and can not be broken by chemical reactions

Compounds form by the combination of atoms in a fixed ratio - e.g. NaCl – one atom of sodium and one of chlorine

Molecules are atoms held together by chemical bonds; in biological molecules these bonds are covalent (strong) and hydrogen bonds (weak)

Ionic bonds

Involve the transfer of one or more electrons to the outer shell of one element to another

Ions

A positively charged ion is called a cation; a negatively charged ion is called an anion

Water: The essential element of life

Cells are surrounded by water and are composed of 70-95% of water

One oxygen and two hydrogens share electrons to form a covalent bond

The water covalent bond is polar because oxygen is more electronegative and the electron of each hydrogen is drawn closer to the oxygen atom

Properties of water of importance in life

Hydrogen bonds hold water molecules together: Cohesion allows water molecules to help plants to transport water against gravity

Adhesion allows water molecules to remain attracted to other polar molecules

Ability to moderate temperature: High specific heat, high heat of vaporization

Versatile solvent: Dissolves many molecules, acid/base properties

Properties of water (high specific heat)

Cohesion - Adhesion

High specific heat (1 cal/ g / C)

• high temperature retention

• Stabilizes ocean temperatures

• Stabilizes organismal temperatures

Carbon is the basis of most biological molecules

Carbon is especially versatile in covalent bonding to other abundant elements

Carbon is the backbone of many large and complex biological molecules including metabolic intermediates, proteins, nucleic acids, carbohydrates, fats and sterols

Carbon bonds in organic molecules form structural isomers, cis-trans isomers and enantiomers with distinct biological roles

Cis-trans isomers

Trans isomer

Enantiomers

Mirror image isomers of same molecule

Sugars: Monosaccharides

Monosaccharides such as glucose serve as an energy source and provide carbon units for amino acid and lipid production

Sugars: Disaccharides and Polysaccharides

Disaccharides and polysaccharides serve as a storage reservoir of sugar units

Polysaccharides serve a structural role in plant and microbial cell walls and as a tissue storage form of glucose

Sugars: Oligosaccharides

Oligosaccharides are covalently bound to lipids such as in the blood group antigens, and covalently bonded to secreted proteins such as on antibody molecules

Monosaccharides in equilibrium between linear and ring form

Isomers of glucose

Dehydration reaction: synthesizing a polymer

Hydrolysis: breaking down a polymer

Lipids are structural building blocks of membranes and signaling molecules

• Lipids are built from hydrophobic long chain fatty acids usually attached to a glycerol linker

• Saturated fatty acid chains with no double bonds pack tightly and are in a solid state at room temperature

• Fatty acids with double-bonded carbons - unsaturated –pack less tightly and are liquid at room temperature

• Phospholipids in membranes create a bilayer

• Sterols stiffen the membrane and also serve as hormone signals transmitted between cells

Attachment of a fatty acid to a carbon of glycerol to create an ester bond

Fat droplets contain triglycerides - 3 fatty acids attached to a glycerol backbone

Protein composition, structure and function

• Proteins consist of linear chains of amino acids that fold into 3-dimensional structures that dictate the function of the molecule

• Amino acids combine, as dictated by the genetic code, with the release of water to create a peptide bond

• Polypeptides are synthesized by a ribosome and fold according to the rules governed by the atomic interactions of the amino acid sequence

• Proteins fold in three phases to form secondary, tertiary and quaternary interactions

Amino acid structure

• All amino acids have amino and carboxy groups

• Amino acids are distinguished by their “R” group side chains

Nonpolar, hydrophobic, amino acids

Polar, hydrophilic, side chains

Electrically charged, hydrophilic, side chains

Determinants of protein folding

• Some unfolded proteins spontaneously refold correctly based on the complex chemical and physical interactions of sidechain and peptide bond interactions

• In cells, proteins fold as they are made by the ribosome in the amino-to carboxy- terminal direction

• Many polypeptides have more than one independently folded domain

• Some genetic diseases produce misfolded proteins and some build up aggregates to produce toxic effects

Basic folding units and sequence of interactions

Quaternary structures

Nucleic acids and their constituent bases

• DNA strands are arranged in an antiparallel orientation with purine and pyrimidine bases in complementary H-bonds facing inward

• DNA strands unwind to permit one DNA strand to be transcribed to make a complementary RNA strand in the 5’-3’ direction

• RNA is decoded by the ribosome which reads information in the 5’-3 direction to produce a polypeptide from the amino- to the carboxy-terminus

• DNA is replicated by unwinding the helix at a replication fork to expose single strands which are copied to produce complementary strands in the 5’-3’ direction; one strand continuous, the other not

The flow of information in the cell

DNA→ RNA→ Protein

DNA replication

• One strand, the leading strand, copied continuously, the lagging strand copied discontinuously

DNA replication fork

• strands unwind and new bases are added at the 3’ terminus by the DNA polymerase

The principle tools of discovery in the life sciences

• visualization of cells, cell structures (cell biology) and molecules (structural biology) has advanced microscopy from a descriptive craft to a molecularly precise tool

• Cell and molecular fractionation has allowed us to discover the function of cell organelles, proteins and nucleic acids

• Genetics and genomics allows life scientists to discover novel functions and ascribe roles to known molecules

Fractionation of soluble and membrane proteins is used to understand cellular processes

• Biochemical pathways may be understood at a molecular level through the fractionation of soluble proteins to separate them from other unrelated activities

• The thousands of different proteins in a cell may be distinguished on the basis of size, shape, surface charge and selective binding affinitie

• Proteins embedded in membranes must first be solubilized with a gentle detergent and kept in the presence of the detergent

mRNA

mRNA read from one DNA strand in 5’-3’ direction

DNA replication fork

stands unwind and new bases are added at the 3’ terminus by the DNA polymerase

DNA replication:

One stand, the leading strand, copied continuously, the lagging strand copied discontinuously

The principle tools of discovery in the life sciences

• Visualization of cells, cell structures (cell biology) and molecules (structural biology) has advanced microscopy from a descriptive craft to a molecularly precise tool

• Cell and molecular fractionation has allowed us to discover the function of cell organelles, proteins and nucleic acids

• Genetics and genomics allows life scientists to discover novel functions and to ascribe roles to known molecules

Fractionation of soluble and membrane proteins is used to understand cellular processes

• Biochemical pathways may be understood at a molecular level through the fractionation of soluble proteins to separate them from other unrelated activities

• The thousands of different proteins in a cell may be distinguished on the basis of size, shape, surface charge and selective binding affinitie

• Proteins embedded in membranes must first be solubilized with a gentle detergent and kept in the presence of the detergent

X-ray crystallography has been used to determine the atomic structure of many large molecules

New techniques using the electron microscope has allowed rapid structure determination of macromolecular complexes

Membrane compartments separate unique functions in cells

• Major functions such as RNA synthesis in the nucleus, respiration in the mitochondrion and protein degradation in the lysosome are physically segregated from the cytoplasm

• Single or double bilayer membranes capture and enclose specific sets of proteins that define an organelle’s functions

• Each organelle membrane boundary has specialized proteins that govern the selective uptake or export of proteins or nucleic acids

• Some compartments form a boundary by phase separation not involving a membrane boundary

Nuclear pores mediate traffic of proteins and RNA into and out of the nucleus

Ex: from discussion 3

Nuclear pores are size and protein/particle selective

Endoplasmic reticulum

• a vast network within the cell that organizes lipid, secretory and cell surface membrane protein synthesis

Ribosomes

• Tethered on the cytoplasmic surface of the ER synthesize proteins for secretion and membrane insertion

Secretory proteins

• synthesized with a signal that directs the ribosome to a channel in the ER membrane

Secretory and membrane proteins

• transit in vesicles from the ER through the Golgi apparatus into granules that fuse at the cell surface

Fusion of Insulin

• containing secretory granules in a pancreatic beta cell

Lysosome

• Acidic compartment fro the degradation of macromolecules

• Engulf organelles and invading pathogens by autophagy

Mitochondria

• have a two-membrane envelope and a separate chromosome

Chloroplasts

• have a two-membrane envelope and internal thylakoid membranes for photosynthesis

The endosymbiont hypothesis for the origin of mitochondria and chloroplasts

ATP

• high energy phosphate linkages bonded to base that is also part of RNA

The muscle protein actin and motor protein myosin promote movement of cells and intracellular organelles

Microtubules promote organelle and chromosome movement mediated by different motor proteins

Cilia have an organized set of microtubules that slide back and forth mediated by a motor protein

Membrane structure and function

Membrane structure and its influence on function

• Membranes are largely 2-dimensional fluids with lipids and proteins free to move laterally, to spin, but not to flip-flop.

• Membranes are asymmetric with the polarity of membrane proteins and glycans determined by their insertion in the ER

• Selective transport of ions and small molecules is dictated by the geometry of a membrane channel and the concentration gradients of transport substrates and charged ions.

• Membrane receptors bind ligands on the cell surface and some are then internalized to control metabolism.

Phospholipid with a saturated and an unsaturated fatty acid

Packing of phospholipids in membranes influenced by saturation, unsaturation and cholesterol

Lateral diffusion of fluorescently labeled molecules in a membrane measured by fluorescence recovery after photobleaching (FRAP)

Organization of an integral membrane glycoprotein of the red blood cell membrane

Alpha helical transmembrane domain

• Most integral membrane proteins have at least one membrane- spanning domain that forms an alpha helical structure with hydrophobic amino acids facing the phospholipid fatty acid chain interior of the membrane

Glycans attached to lipids and proteins on the lumenal surface of the ER

Inner surface of the red cell membrane showing a cytoskeleton responsible for the shape of the cell

Osmotic pressure: Water moves across a membrane to achieve an equilibrium of free water molecules

Membrane proteins that mediate the transit of ions and small molecules across a membrane

Ion concentrations on the inside and outside of a typical mammalian cell

Ion-coupled transport by a glucose-Na+ symporter

ATP – high energy phosphate linkages bonded to base that is also part of RNA

Energy released by hydrolysis of the terminal phosphate ester bond of ATP

Sodium- K+ ATPase:

• Step 1 – 3 Na+ ions bind and ATP is used to add a phosphate to the enzyme

• Step 2 – 3 Na+ ions ejected outside, 2 K+ ions bind to sites exposed in the open channel

• Step 3 – Phosphate cleaved from enzyme which returns to the resting state exposing K+ to cell interior

Ion channels in nerve cells

Voltage-gated channels: cycle of closed – open – inactivated – relaxed and clos

Structure of the voltage-gated K+ channel – selectivity channel discriminates K+ from Na+

A better fit of anhydrous K+ to carbonyl oxygens in the selectivity filter

Activation of a ligand-gated channel at the synapse

Low density lipoprotein (LDL) binds to a cell surface receptor

Skin cells from normal and FH disease patients show a profound defect in LDL uptake by mutant cells

Thermodynamics and life

• First law of thermodynamics: The energy of the universe is constant. Energy can be transferred and transformed but it cannot be destroyed

• During every energy transfer or transformation, some energy

  is unusable, and is often lost as heat

• Second law of thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universe

Life and the transformation of matter

• Living cells unavoidably convert organized forms of energy

  to heat

• Spontaneous processes occur without energy input; they

  can be fast or slow

• Life does not violate the 2nd law of thermodynamics:

Entropy may decrease locally (in an organism) but the

total entropy of the universe increases

Definition of free-energy change, ∆G

• The change in free energy (∆G) during a process is related

to the change in enthalpy, or change in total energy (∆H),

change in entropy (∆S), and temperature in Kelvin (T):

∆G = ∆H – T∆S

• Only processes with a negative ∆G are spontaneous

Spontaneous processes can be harnessed to perform work

Actions that result in a negative ∆G

Exergonic vs Endergonic