lecture 3 notes

How are non-covalent bonds able to provide stability to macromolecules in spite of being weaker than covalent bonds?

are attractive forces between atoms of opposite charge. Do not depend on shared electrons Weaker than covalent bonds (bonds are broken and re-formed) Important for dynamic cellular processes and molecular interactions Attractive forces are additive: provide stability

What are polysaccharides? What are some examples of nutritional polysaccharides? Would you expect these to be use before or after disaccharides? Why?

are polymers of sugars joined by glycosidic bonds Glycogen and starch are nutritional polysaccharides (surplus energy storage) before

Which amino acids are more likely to be located on the surface of a cytosolic protein? Why?

asparagine, serine, threonine hydrophilic side chains

Why do sugars tend to be water soluble?

because of their large numbers of hydroxyl groups

What are molecular chaperones? How do they help proteins acquire their correct three dimensional conformations?

bind short stretches of hydrophobic amino acids to help unfolded proteins achieve the correct 3D conformation Some (Hsp70) bind as polypeptides emerge from the ribosome (prevent binding to other molecules in the cytosol) Chaperonins provide a folding environment

What are the 2 main types of tertiary structure a polypeptide can adopt? Where is each type more likely to be found in a multicellular organism?

globular or fibrous Fibrous proteins are elongated: extracellular materials Globular proteins are compact: most proteins within cells Most globular proteins contain both α helices and β sheets

Why are hydrophobic interactions not considered true bonds?

occur when nonpolar (hydrophobic) molecules associate to minimize their exposure to polar (hydrophilic) molecules Result from an energetic drive to exclude water from the hydrophobic surfaces, rather than from attractive forces

What characteristics would you expect a soluble protein to have? (i.e. what arrangement of amino acids would you expect to see in a soluble protein?

polar residues at the surface of the protein (to associate with water = increased solubility) AND nonpolar residues tightly packed inside the protein (exclude water molecules) Polar residues may project into nonpolar regions (in enzymes) Increased reaction rates due to decreased competition with water

. What are free radicals? How are these produced?

unstable atoms or molecules with unpaired electrons May result from breaking of covalent bonds or from oxidation-reduction reactions Formed during normal metabolism Highly reactive (can damage macromolecules like DNA) May play a role in aging

What are the 2 most common secondary structure conformations found in polypeptides? How are these similar? How are they different? Why do you think these 2 conformations are favored over others?

α-helix β-pleated sheet

Which type of secondary structure would you expect to be more predominant in a protein like silk, which must be able to resist tensile forces (pulling)

β-pleated sheet:

Which types of bonds stabilize tertiary structure?

non-covalent bonds

Fatty acids are amphipathic molecules, what does this mean?

Fatty acids are unbranched hydrocarbons with one carboxyl group

What are protein subunits? How are these different from protein domains?

Most proteins have more than one chain Linked by noncovalent bonds or covalent disulfide bonds Proteins composed of subunits have quaternary structure they are diff bc protein . domain deal with tertiary structures

What is the difference between acids and bases?

Acids release protons (H+) Bases accept protons Acids and bases exist in pairs (conjugates) The acid always contains one more positive charge than its conjugate base

What are the two most common types of posttranslational modifications? What impacts can these modifications have on proteins?

Addition of a phosphate group to serine, threonine, or tyrosine residue Lysine acetylation Alterations to the side chains of the 20 basic amino acids after their incorporation into polypeptides modify a protein's 3D structure, level of activity, localization within the cell, life span, and/or its interactions with other molecules.

In addition to serving as genetic material, what are other functions of nucleic acids?

Adenosine triphosphate (ATP): key role in cellular metabolism Guanosine triphosphate (GTP): switch to turn on some proteins

What is a peptide bond?

Amino acids are linked together by peptide bonds into a polypeptide chain to make a protein. Peptide bonds: Linkage of the carboxyl group from one amino acid to the amino group of another (releases H2O)

Do cells use different stereoisomers (D and L) of amino acids equally for protein synthesis? If not, which stereoisomer do cells use?

Amino acids used in protein synthesis are L stereoisomers

How are phospholipids similar to tryglycerides? How are they different?

Amphipathic lipids that are major components of cell membranes Diacylglycerol: 2 fatty acid chains But a triglyceride contains three fatty acids attached to the glycerol backbone, while a phospholipid has two fatty acids plus a phosphate group attached to the glycerol.

Why are buffers important for preventing sharp fluctuations in pH in organisms?

Buffers protect organisms from fluctuations in pH React with free hydrogen or hydroxyl ions, resisting changes in pH Usually contain a weak acid with its conjugate base they can absorb excess H+ ions or OH- ions

. Which types of bonds can these amino acids form?

Can be found within protein cores Associate with each other through van der Waals forces and hydrophobic interactions

Which types of bonds can these amino acids form?

Can form hydrogen bonds with water and other molecules

Which types of bonds can these amino acids form?

Can form ionic bonds due to charges

Which type of atoms are likely to be absent from these amino acids?

Cannot form electrostatic bonds or interact with water

Why are free ionic bonds relatively unlikely to form in living organisms?

Cells are composed mostly of water, which interferes with ionic bonds between free ions.

What are the 2 major functions of cholesterol? Under which category of lipids does cholesterol fall?

Cholesterol: found in animal cell membrane & precursor to steroid hormones Largely absent in plant cells found under steriods hormone production

What usually accompanies changes in protein activity?

Conformational changes are non-random movements triggered by the binding of a specific molecule

Both mad cow disease and Alzheimer's disease are characterized by the presence of misfolded proteins. How does the presence of these misfolded proteins lead to neuronal cell death?

Contains more β sheets Aggregates into insoluble fibrils, cannot be digested by enzymes

protein folding steps

Denaturation (unfolding) can be brought about by various agents. Removal of denaturing agents could lead to refolding Information of the final 3D conformation contained within the primary sequence (proteins are capable of self-assembly)

What are other functional differences between DNA and RNA?

Deoxyribonucleic acid (DNA) holds genetic information of all cells and some viruses Ribonucleic acid (RNA) is the genetic material of some viruses Bases are purines or pyrimidines Purines: adenine and guanine in both DNA and RNA Pyrimidines: cytosine and uracil in RNA; uracil is replaced by thymine in DNA

In addition to proteins having different subunits, which other type of protein "arrangement" would be considered to have quaternary structure? Which types of bonds are important for these arrangements?

Different proteins can become physically associated to form a Multiprotein complex. Noncovalent bonds stabilize interactions

What is a protein domain? Can a single domain have different types of secondary structure? Can a single polypeptide have more than one domain?

Domains occur when proteins are composed of 2 or more distinct regions that fold independently of one another. Each domain is a functional region

Most functional groups contain electronegative atoms, why is this important?

Exert greater attractive force Electrons attracted to the more electronegative atom of a molecule Nitrogen and oxygen are strongly electronegative Strongly electronegative atoms can capture electrons from other atoms during a chemical reaction. Results in the formation of charged ions.

Why are free radicals capable of altering molecules, like proteins and nucleic acids?

Free radicals attack important macromolecules leading to cell damage and homeostatic disruption. unstable atoms or molecules with unpaired electrons

Which portions of a polypeptide would be likely to have the greatest biological activity?

Hinges, turns, loops, finger-like extensions Most flexible, sites of greatest biological activity

What property do the side chains (R groups) of these amino acids have?

Histidine: partially charged at pH 7.0; often important in enzyme active sites (it can gain or lose a proton at physiological pH ranges acts has an acid or base

What is the difference between a homodimer and a heterodimer? Would proteins composed of homodimers be considered to have quaternary structure? What about proteins composed of heterodimers?

Homodimer: 2 identical subunits Heterodimer: 2 non-identical subunit

Which amino acids are considered polar, charge?

Hydrophilic R groups (side chains) Most are fully charged (Asp, Glu, Lys, and Arg) at pH 7.0 (side chains are relatively strong organic acids & bases)

Given that fatty acids and glycerol both contain hydrophilic portions, why are fats hydrophobic?

It is known as a phospholipid. The carboxyl end of the fatty acid is highly polar and therefore water soluble (hydrophilic meaning attracted to water). Hydrocarbon chain of the fatty acid is highly non-polar and therefore water insoluble

Which type of molecules found in cells may not have any real function?

Metabolic intermediates Formed along the pathways leading to end products

Why can glycine form hinges within polypeptides?

More flexible than other amino acids bc side chain is hydrogen

Why do polysaccharides made of the same sugar subunit have different structures?

Polysaccharides are polymers of sugars joined by glycosidic bonds. Glycogen and starch are nutritional polysaccharides (surplus energy storage) Glycogen is an animal product made of branched glucose polymers Starch is a plant product made of both branched and unbranched glucose polymers because of the different ways the monomers are linked

Which types of macromolecules are considered polymers? Which are not? Why?

Proteins, nucleic acids, and polysaccharides are polymers composed of low-molecular-weight building blocks, or monomers lipids are not

Which amino acids are considered polar, uncharged?

R groups have a partial negative or partial positive charge

What property do the side chains (R groups) of these amino acids have? (These are also hydrophilic)

R groups have a partial negative or partial positive charge makes them very reactive

How does the increase in the concentration of hydrogen ions affect pH?

React with free hydrogen or hydroxyl ions, resisting changes in pH Hydrogen ions are positively charged and can take up a lone pair of electrons from another compound to form a covalent bond. So the more hydrogen ions you have, the more electron pairs you can accept and the more acidic it become

What name do we use to describe amino acids that have been incorporated into a polypeptide?

Residues

What are the differences between saturated and unsaturated fatty acids?

Saturated fatty acids lack C=C double bonds and are solid at room temperature. Unsaturated fatty acids have one or more C=C double bonds and are liquid at room temperature (oils).

Which amino acids would you be likely find buried within the core of a protein, at sites distinct of the active site? Why?

nonpolar ones Ala, Leu, Phe

Where do multicellular organisms store fat (i.e. what is the name of cells that store fat)? What special characteristic do these cells have that allow the accumulation of fat over time?

Stored in adipocytes (fat cells) Contain one or a few large lipid droplets Can alter their volume to accommodate more fat

List the precursor molecules of cellular macromolecules (building blocks)

Sugars: precursors of polysaccharides Amino acids: precursors of proteins Nucleotides: precursors of nucleic acids Fatty acids: incorporated into lipids

Why do some proteins need assistance to acquire their tertiary conformation?

Tertiary structure can be predicted by threading Aligning the amino acid sequence to that of a closely related protein (similar amino acid sequence) of known tertiary structure.

What is the primary structure of a protein? What information is contained in the primary structure of a protein?

The specific linear sequence of amino acids that constitute a polypeptide chain. Provides the information required to determine the protein's 3D shape and thus function. The degree to which changes in primary sequence are tolerated depends on the degree to which the shape of the protein is critical for its function.

Why are unsaturated fatty acids liquid at room temperature?

Unsaturated fats tend to be liquid at room temperatures: the double bond is, in the normal cis configuration, asymmetric and so forces a kink or bend into the carbon chain. As a result the unsaturated fatty acids are unable to pack so closely together,

Why is glycine likely to be found in sites where 2 polypeptides are in close association with each other?

Usually at sites were 2 polypeptides (in the same or different proteins) are in close association side chain is hydrogen The R group (side chain) is a hydrogen atom (small size) More flexible than other amino acids (can form hinges)

How can 2 proteins that have different primary structures have similar tertiary structures? What would similarities in tertiary structure suggest?

Usually indicates similar functions (tertiary structure dictates interactions and enzymatic activities)

Which portion of an amino acid gives each one its unique properties?

amino acid sequence

Does protein denaturation affect the primary structure of a protein?

nope they remain the same denaturation reactions are not strong enough to break the peptide bonds

What are the components of nucleic acids? How are these similar between DNA and RNA? How are they different?

a 5-carbon sugar, a phosphate group, and a nitrogenous base polymers of nucleotides that store and transmit genetic information

In general, why have free radicals been associated with aging?

aging is caused by accumulation of damage inflicted by reactive oxygen species (ROS). Superoxide Dismutase (SOD): enzyme that destroys the superoxide radical SOD protects cells from damage caused by the superoxide radical. Bacteria and yeast are unable to grow without SOD. SOD2 knockout mice die one week after birth. Mice with higher levels of catalase live 20% longer than controls. However, some studies showed an association between increased oxygen radicals and longer lifespan Multiple genes are involved in the aging process: programmed aging.

Which portion of a phospholipid is polar/hydrophilic?

negatively-charged polar head, which is hydrophilic

What are disaccharides? What primary function do disaccharides serve in cells?

composed of 2 sugar units Used as a source of readily available energy Sucrose and lactose short term energy storage mole

What unique property does proline possess? How does this property affect where proline is found in a polypeptide?

creating kinks in polypeptide chains and disrupting ordered secondary structure

ALPHA

cylindrical, twisting spiral Backbone lies inside, side chains project outward Stabilized by H-bonds between atoms from adjacent peptide bonds

When thinking about cells and their components, where would you expect to find ionic bonds? Why?

deep in a protein's core where water is excluded

What are the 2 most important functions of carbohydrates in the cell?

energy and digestion simple sugars (monosaccharides) and sugar polymers Serve as energy storage molecules and some are structural

Why is cysteine important for tertiary and quaternary protein structure?

forms covalent bond with another cysteine to form disulfide link Because it has a very reactive sulfhydryl group at its side chain. This puts cysteine in special position that cannot be replaced or substituted by any other amino acid.

BETA

has several segments of polypeptide lying side by side, forming a folded or pleated conformation Extensive H-bonding (perpendicular to long axis, projecting from one part of the chain to another) Parallel or anti-parallel Extended, resists tensile forces

Integrins are a group of receptor proteins that are important for cell adhesion. These proteins are composed of two different polypeptides, thus they are considered to be _____. The presence of 2 subunits in these receptor proteins is an example of _____.

heterodimeric, quaternary structure

Which amino acids would you be likely find in the active site of an enzyme? Why?

histiidine, polar charged

Which type of bond would be most important for enhancing the solubility of macromolecules in water?

hydrogen bonds

What property do the side chains (R groups) of these amino acids have?

hydrophobic side chain of C - H atoms

Why are disordered segments of protein biologically important? What usually happens to these segments as a result of interactions with other proteins or molecules?

lack a defined conformation These regions can play vital roles in cellular functions Often bind to DNA and other proteins Often undergo physical transformation once they bind to an appropriate partner

Which type of bond is associated with interactions between macromolecules that have complimentary surfaces, such as an antibody and the antigen it binds?

non-covalent bonds

If you decided to fast for a 24 hour period, which macromolecule (carbohydrates or lipids) would be used first as a source of energy?

lipids

. What is a tryglyceride (or fat)?

made of glycerol linked by ester bonds to three fatty acids

What are stereoisomers? Are cells able to distinguish between stereoisomers? Do cells use stereoisomers equally?

mirror images with the same chemical reactivities. Sugars can have many asymmetric carbons, but are designated D- or L- according to the arrangement around the carbon farthest from the carbonyl group. D-sugar: OH group projects to the right L-sugar: OH group projects to the left Cells can distinguish between D and L forms and typically only use one form.

In terms of energy, which conformation is a polypeptide more likely to adopt?

most thermodynamically favorable structure

What is a prion? How is it different from a viroid? Would you be able to tell the difference between these 2 by how they react to different treatments/compounds?

progressive neurodegenerative disorders Viroids are small, naked infectious RNA molecules Prions are infectious protein particles causing neurological degenerative diseases in humans and animals.

What is the difference between secondary and tertiary protein structure?

refers to the conformation of portions of the polypeptide chain describes the conformation of the entire polypeptide

What are oligosaccharides? What is the primary function of oligosaccharides in cells? Given, their primary function, where would you expect to find oligosaccharides?

short chains of sugar units Found bound to cell surface proteins and lipids May be used for cell recognition.

Which amino acids are considered polar, uncharged?

side chains Made almost entirely of C and H atoms Generally lack O and N

What are monosaccharides?

simple sugars glucose (dextrose), fructose (levulose) and galactose

2 categories of lipids

steriods and phosoplipids Phospholipids: Amphipathic lipids that are major components of cell membranes Steroids: lipids built around a four-ringed hydrocarbon skeleton

How do prions cause disease propagation?

transmitting their misfolded protein state structure of the brain or other neural tissue

Besides serving as energy storage, what is another important function of polysaccharides?

structural support

In cells, where would hydrophobic interactions be more likely to occur?

the core of a water-soluble protein

What does quaternary structure refer to? Do all proteins have quaternary structure? Why or why not?

the number and arrangement of multiple folded protein subunits in a multi-subunit complex. All proteins have primary, secondary and tertiary structures but quaternary structures only arise when a protein is made up of two or more polypeptide chains.