sci-of-large-molecules

lecture 3

What is the only biomolecules that is not made of repeating units of monomers?

lipids

What are important properties of biomolecules?

• involved in biological processes that are basic to living organisms

• necessary for all forms of life

• contribute to the structural integrity of cells and organisms

• have been conserved throughout evolution due to their important roles

• carry out a variety of different types of functions

• complex and have diverse structural variations

What is the polymer of an amino acid?

polypeptide (protein)

What is the polymer of a monosaccharide?

polysaccharide (carbohydrate)

What is the polymer of a nucleotide?

nucleic acid (DNA,RNA)

What are proteins made up of?

long chains of amino acids that folded into three-dimensional structures

What is the function of DNA polymerase?

important enzyme in DNA replication

What is the function of proteases?

catalyze the breakdown of proteins in the cell

What is the function of actin?

part of the cytoskeleton

What is the function of collagen?

fibrous protein in connective tissue, like bone and tendons

What is function of transferrin?

transport of iron in the bloodstream

What is the function of hemoglobin?

transport of oxygen in the bloodstream

What is the function of insulin?

signals cells to take up glucose

What is the function of growth factor receptors?

bind and respond to extracellular signals

What is the function of antibodies?

recognize invaders

What is the function of major histocompatibility proteins (MHC)?

recognition of self vs non-self cells

What does the basic structure of amino acids contain?

side chain (R group), carboxyl group (COOH), central carbon, hydrogen atom, amino group (NH2)

How many different amino acids make up proteins?

20

What does the charge of an amino acid depend on?

the pH

What are the different types of side chains that an amino acid can be classified by?

nonpolar side chains and polar side chains

What does it mean to have nonpolar side chains?

no electrically charged regions are formed, hydrophobic, do not participate in hydrogen bonding

What does it mean to have a polar, negatively charged, acidic side chain?

donate protons at neutral pH and what remains is negatively charged

What does it mean to have a polar, positively charged, basic side chain?

accept protons at neutral pH and what remains is positively charged

What does it mean for amino acids to be essential or non-essential?

essential (we need them in our diet), non-essential (we produce them on our own)

What kind of amide bonds are amino acids linked by?

peptide bonds

What are the different shapes that proteins can fold into?

primary, secondary, tertiary, and quaternary

What happens to a proteins side chains when folded in an aqueous environment?

polar side chains go on the outside of the molecule and can form hydrogen bonds to water, hydrophobic core region contains nonpolar side chains

What characterizes the primary structure of proteins?

sequence of amino acids

What characterizes the secondary structure of proteins?

folding pattern where short stretches of amino acids interact with each other

Which type of secondary structure is this?

alpha helix

What type of secondary structure is this?

beta pleated sheet

What is the common pattern in secondary structure alpha helixes?

hydrogen bonding in which the carbonyl oxygen (C=O) of an amide group forms a hydrogen bond with the hydrogen on the amide group (N-H) of another amine group four residues ahead (I to i+4), along with the polypeptide backbone

What is the common pattern in beta pleated sheets?

hydrogen bonds form between amino acids that may be far from each other in the primary sequence but are close in the folded protein, hydrogen bonds can also form between the oxygen on the carbonyl groups

What characterizes a tertiary structure?

further folding of the chain, residues with hydrophobic side chains tend to be found on the inside of a protein, while hydrophilic residues tend to be on the outside

What characterizes a quaternary structure?

some proteins consist of multiple polypeptides that come together as one protein

What protein structure is hemoglobin an example of?

four polypeptides

What is cytochrome p450 (Cyp450)?

family of enzymes that have important roles in drug metabolism

What are G protein coupled receptors?

proteins involved in cell signaling

What do beta blockers target?

G protein couples receptors

What are beta blockers used to treat?

hypertension, angina, and other conditions

What are antibodies essential for?

immune responses

What are antibodies produced for?

to treat disease

What is the monoclonal antibody used to treat Her2 positive breast cancer?

Herceptin

What do carbohydrates include?

simple sugars (ex. glucose, fructose), complex carbohydrates (starch, glycogen)

What do all monosaccharides have in terms of molecular structure?

carbonyl group (C=O), chiral center (central carbon), terminal carbon (at the end)

What is the second chiral center in a monosaccharide called?

penultimate carbon

What is a structure of monosaccharides with 3 carbons called?

triose

What is a structure of monosaccharides with 4 carbons called?

tetrose

What is a structure of monosaccharides with 5 carbons called?

pentose

What is a structure of monosaccharides with 6 carbons called?

hexose

What kind of monosaccharides are examples of hexoses?

glucose and fructose

What are the different forms that monosaccharides can cycle through?

linear and cyclic (if 5 or 6 carbons)

What is the linear way that monosaccharides can be illustrated?

fischer projection

What are the circular ways that monosaccharides can be illustrated?

chair conformation, haworth projection

What could glucose be broken down into to use for energy?

ATP

Plants can make what types of energy sources from glucose?

starch and cellulose

What monosaccharide is obtained mostly by food, such as fruits and honey, a role in energy production?

fructose

What monosaccharide is important for synthesis of glycoproteins and glycolipids?

mannose

What monosaccharide is a component of lactose, the sugar in milk?

galactose

What monosaccharide is a component of RNA?

ribose

What monosaccharide is a component of DNA?

deoxyribose

What monosaccharide plays a crucial role in carbohydrate metabolism, specifically in glycolysis and gluconeogenssis?

glyceraldehyde (a triose)

What monosaccharide is uncommon and an intermediate in some metabolic pathways such as the pentose phosphate pathway?

erythrose (a triose)

What monosaccharide is not common in mammalian cells, found in cell walls of plants, found in microorganisms, and obtained in diet in beans and peas?

arabinose

What monosaccharide is found in plants and microbes?

xylose

What monosaccharide is found at low levels in plants and microbes?

lyxose

What monosaccharide is not common in nature and used industrially (cosmetic, tanning)?

erythrulose (a ketotertrose)

What are disaccharides?

two monosaccharide units

What are lactose and sucrose examples of?

disaccharides

What are oligosaccharides?

3-10 monosaccharides

What are polysaccharides?

more than 10 monosaccharides (can be thousands)

What are glycogen, cellulose, and starch examples of?

polysaccharides

What kind of bond are disaccharides bound by?

glycosidic

What is the term for the addition of carbohydrates to proteins, lipids, and other sugars?

glycosylation

What are TAGs?

tumor associated glycoproteins in cancer cells

What are exciptients?

vehicle for drug delivery that often contains carbohydrates

What kind of ingredients are in excipients?

inactive ingredients

What is the use of glucose for energy, or storage of glucose in the form of glycogen?

metabolism

What are the basic components of DNA?

genetic information storage

What are the basic components of RNA?

transcription of genes and translation of proteins

What do nucleotides consist of?

5 carbon sugar, phosphate group, nitrogen base (nucleobase)

What are a nitrogen base and sugar together called?

nucleoside

What are the major bonds in DNA?

phosphodiester bonds (backbone) and hydrogen bonds (base pairing)

How does DNA fit in the cell?

condensed by being packaged with histones, coiled around the histones to become super coiled, takes the form of a chromosome

What is an antisense drug that alleviates symptoms of SMA (Spinal Muscle Atrophy)?

spinraza

What condition is caused by a mutation in the SMN1 (survival of motor neuron 1) gene?

SMA (Spinal Muscle Atrophy)

What is SMN2?

gene that can make SMN, but at lower levels and often truncated, due to alternative splicing

What binds the SMN2 RNA (but not the SMN1 RNA) and prevents splicing at the junction between exon 7 and the intron?

hnRNP (heterogeneous nuclear ribonucleoproteins)

What kind of nucleotide is Spinraza (nusinersen)?

oglionucleotide

What does Spinraza do?

binds RNA and prevents binding of the hnRNP, restores a splice site so that exon 7 is not removed, then full length SMN can be produced from the SMN2 gene to compensate for the lack of SMN1 gene

What is characteristic of lipids?

include fats, oils, and steroids such as cholesterol, hydrophobic molecules, long hydrocarbon chains or ring systems

What are lipids in terms of energy?

major source of energy storage in the body and stored in adipose tissue as triglycerides (TAG)

What forms the lipid bilayer of the cell membrane?

phospholipids

What do lipids do in terms of insulation and protection?

help to regulate body temperature and cushion organs and tissues

What do lipids do in terms of cell signaling?

regulate cell growth, differentiation, and apoptosis

What do lipids do to apoptotic cells?

remove

What is the simplest form of lipids?

fatty acids

What do fatty acids generally contain?

a carboxyl group (COOH)

What is characteristic about saturated fatty acids?

no double bonds, saturated with H atoms, more difficult to melt, high MP

What is characteristic about cis unsaturated fatty acids?

monosaturated or polyunsaturated, easier to melt because they don’t pack together well