Chapter 3: Biological Molecules-- The Carbon Compounds of Life

atherosclerosis

"Hardening" of the arteries from accumulation of cholesterol and saturated fats over time. This narrowing of the arteries can lead to HYPERTENSION (high blood pressure) and CARDIOVASCULAR DISEASE, a heart attack, or stroke. Saturated fats have been implicated in the development of atherosclerosis. A disease in which arteries, particularly those serving the heart, become clogged with fatty deposits. Plaque builds up in the walls of the arteries which supply oxygenated blood to body tissues. Plaque reduces the internal diameter of the arteries, restricting or even completely blocking the flow of blood. This can severely impair heart function and in extreme cases leads to heart attack.

Sucrose

(carbohydrate)(table sugar) Consumed in large quantities as an energy source in the human diet.

glycosidic bonds

carbons on adjacent sugar units are bonded to the same oxygen atom like links in a chain (combines monosaccharides).

SREBP

(in textbook)

glycogen

(carb) (polysaccharide) Energy-providing carbohydrates are stored in animal cells as glycogen. Animal starch stored in liver and muscle.

cellulose

(carb) (polysaccharide) One of the primary constitutes of plant cell walls. Cellulose in breads, cereals, and veggies is not digestible and passes through our digestive system as "fiber," and does not provide energy. Fiber aids in the digestive process. It also has an important role in helping to lower "bad" cholesterol. Additionally, fiber helps regulate blood sugar levels. Most organisms lack the enzymes that break down the bond between glucose subunits in structural polysaccharides.

dissaccharide

(carb) Two monosaccharides polymerize to form a disaccharide. "Two sugars." Disaccharides typically are assembled from two monosaccharides covalently joined by a dehydration synthesis reaction. Chemical formula of a disaccharide = C12H22O11 (all isomers) Ex: maltose, sucrose, and lactose

unsaturated

(for lipids) One or more double bonds link that carbons, reducing the number of hydrogen atoms bound. The chain is then not saturated with hydrogen. Monounsaturated: fatty acid with one double bonds Polyunsaturated: more than one double bond. Tend to bend at a double bond. This kink makes the chains more disordered and thus more fluid at biological temperatures. Found in plant sources like vegetable oils (canola oil). Considered healthier than saturated fats.

saturated

(for lipids) The hydrocarbon chain of a fatty acid binds the maximum possible number of hydrogen atoms, so that only single bonds link the carbon atoms. All SINGLE carbon-carbon bonds. The fatty acid is "saturated" with as many hydrogen atoms as Carbons can hold. Usually found in SOLID animals fats (butter). Packs down straight to form solids. The more saturated, the less fluid the triglyceride

Waxes

(lipids) Protective coating from water, prevents dehydration (surface of leaves and fruits, inside ears) Fatty acids may combine with long-chain alcohols or hydrocarbons structures to form waxes, which are harder and less greasy than fats. Waxy coatings help keep skin, hair, or feathers of animals protected, lubricated, and pliable. Many plants secrete waxes that form a protective exterior layer, which greatly reduces water loss from the plants and resists invasion by infective agents such as bacteria and viruses.

phospholipids

(phosphate containing lipids) Make up the major part of cell membranes. They make an excellent barrier because the molecule in NONPOLAR and won't dissolve in water. Composed of ONE glycerol + TWO fatty acids + ONE phosphate group (triglyceride but phosphate group instead of fatty acid) The phosphate group is hydrophilic (polar) and the fatty acids are hydrophobic (nonpolar). A cell membrane is composed of a phospholipid bilayer, where the hydrophobic tails face in towards each other, creating a barrier. (phosphate heads and fatty acid tails) The primary lipids of cell membranes. In the most common phospholipids, glycerol forms the backbone of the molecule as in triglycerides, but only two of its binding sites are linked to fatty acids. The third site is linked to a polar phosphate group, which binds to yet another polar unit. The end of the molecule with the fatty acids is nonpolar and hydrophobic, and the end with the phosphate group is polar and hydrophilic.

cholesterol

(steroid/lipid) Soft waxy substance made in the liver and consumed in our diet! -It is used to make steroid hormones (testosterone, cortisone, estrogen). -Also used in nerve tissue and in CELL MEMBRANE STRUCTURE! -Found in ANIMAL products (meat, butter, cheese, cream, eggs) (Cholesterol made by the body is good. Cholesterol eaten in out diet is bad.) The basic structure of cholesterol has FOUR CARBON RINGS.

Energy

1. CHEMICAL ENERGY in a molecule is stored in THE CHEMICAL BONDS! (more bonds = more stored energy) 2. Energy is released from a molecule by breaking the bonds 3. The body's 1st nutrient choice to use for energy is carbohydrates. When these molecules are all used up, the body will break the bonds contain in lipids. A calorie is a measure of energy in food content. (carb = 4, protein = 4, lipids = 9). This means lipids have more than double the number of bonds.

How does DNA code for proteins?

1. DNA is a specific order of nucleotides. 2. Transcription is a process that copies the DNA into RNA in the nucleus. 3. mRNA is a copy of the DNA. 4. Translation is a process that "reads" the RNA and 'translates" the message into amino acids. This occurs on ribosomes. 5. A protein is created which is a specific order of amino acids.

What are some genetic disorder caused by gene mutation?

1. Diabetes (Type 1): Mutation in insulin (blood glucose regulation!) 2. Sickle cell disease: Mutation in Hemoglobin (blood protein that delivers oxygen to cells) 3. Hemophilia: Mutation in a clotting protein (protein that allows us to stop bleeding)

What can cause a protein to denature?

1. Temperature -Too hot can PERMANENTLY denature a protein (ex: Cooking an egg or meat is permanent, reversible is blow drying hair.) -Too cold can slow down protein function, but is usually reversible. (ex: Refrigerating foods slows down enzymes that would spoil the food faster at room temperature) 2. Changes in pH -Proteins usually have an "optimum pH" where is functions best (ex: Blood pH must be within 0.2-0.4 of 7.4 for the proteins to function properly. Changes beyond this result in death, but stomach enzymes work best as acidic pH's) 3. Salts -Ions/charges attract parts of the protein, pulling it out of shape (ex: "Perming" or permanently straightening one's hair through chemicals, changes the existing proteins and will not reverse with washing.)

Glycerol

3-carbon alcohol with an -OH attached to each carbon. Forms the backbone of the triglyceride. In free state, it is a polar, water-soluble, sweet-tasting alcohol.

peptide bond

A COVALENT BOND BETWEEN THE CARBOXYL GROUP OF ONE AMINO ACID AND THE AMINO GROUP OF THE NEXT AMINO ACID (on test)! Covalent bonds link amino acids into the chains of subunits that make proteins. The link, a peptide bond, is formed by a dehydration synthesis reaction between the amino group of one amino acid and the carboxyl group of a second.

glycosidic link

A covalent bond formed between two monosaccharides by a dehydration reaction. BETWEEN SUGARS IS A GLYCOSIDIC LINK (BOND) WHICH IS ALPHA. Alpha can be broken down but beta cannot. (look in textbook)

polymer

A molecule assembled from subunit molecules called monomers into a chain by covalent bonds. The process of assembly from monomers is called polymerization. These reactions are dehydration synthesis reactions. (The breakdown of polymors to monomers- opposite- occurs by hydrolysis.) Each polymeric biological molecule contains one type of monomer, which can all be identical or vary. The variations among monomer structures are responsible for the highly diverse and varied biological molecules. (For proteins there are 20 different amino acids - which are monomers).

gene

A specific sequence of base pairs in a section of a long DNA chain. A specific order of nucleotides which, in turn, codes for a specific order of amino acids. Genome = All the genes that make up and organism (the human genome has 19,000-20,000 human protein coding genes) Genes are found on physical structures we call chromosomes. There are 100 genes on each chromosome.

Carbohydrate Function - Useable Energy

A) "Immediate" Energy: Goes into the bloodstream. Comes from simple sugars (mono or disacc). (Taste sweet - fruit, honey, candy) B) "Stored" Energy: LONG CHAINS OF GLUCOSE. Comes from starches (polysaccharides) which taste bland. -In humans (animal starch): glycogen - stored in liver and muscle -In plants: starch/amylose (veggies/grains)

Carbohydrate Function - Structural Carbohydrates (not used for energy)

A) Cellulose: Structural polysaccharide (found in plant cell walls) B) Chitin: Structural polysaccharide (found in fungi cell walls like mushroom and in the exoskeleton of insects and shellfish making them crunchy)

hydrolysis reaction

Breaking down a polymer The components of a water molecule are ADDED to functional groups as molecules are broken into smaller subunits and it BREAKS a bond. Ex: the breakdown of a protein molecule into individual amino acids in the digestive processes of animals. Hydroxyl groups are formed as part of these.

carbonyl

C=O Aldehydes and Ketones; Found in sugars Major building blocks of carbs Participate in the reactions supplying energy for cellular activities

Monomer (single units/building blocks) and Polymer (many units) for each macronutrient

Carbohydrates: monosaccharide and polysaccharide Lipids: 3 fatty acids + glycerol and triglyceride Proteins: amino acids and polypeptide Nucleic Acids: nucleotide and polynucleotides Synthesis Reactions build monomers to polymers. Hydrolysis reactions break them down.

Why Carbon?

Carbon is small and has 4 valence electrons, which allows carbon to make 4 covalent bonds. These properties allow limitless sizes and arrangements of organic molecules, especially when carbon bonds to itself! Hydrocarbons are compounds composed of only carbon and hydrogen. They contain a lot of energy because of all the bonds! (the more bonds the more energy released) They are ALWAYS NONPOLAR.

Hormonal Proteins (signaling)

Carry regulatory signals between cells. (Chemical messengers). Allows coordination of an organism's activity. Insulin is a protein hormone that regulates sugar in the bloodstream. Ex: -Insulin regulates sugar levels in the bloodstream -growth hormone regulates cellular growth and division.

Neutral lipids

Commonly found in cells as energy-storage molecules. Called "neutral" because at cellular pH they have no charged groups, so they are nonpolar. Oils (liquid at room temp) and fats (semisolid at room temp) are the two types of neutral lipids. Almost all neutral lipids are formed by dehydration synthesis reactions involving glycerol and three fatty acids (makes a tryglyceride).

lipids

Contain Carbon, Hydrogen, and (very little) Oxygen. They are a diverse group of water-insoluble, primarily nonpolar biological molecules composed mostly of hydrocarbons. (Not considered to be polymers). Dissolve much more readily in nonpolar solvents. Their insolubility in water underlies their ability to form cell membranes, the thin molecular films that create boundaries between and within cells. Also, some lipids are stored and used in cells as an energy source. Other lipids serve as hormones that regulate cellular activities. The three most common lipids that occur in living organisms are neutral lipids, phospholipids, and steroids.

Carbohydrates

Contain only carbon, hydrogen, and oxygen atoms. Ratio of 1C:2H:1O Most names end in -ose

fatty acid

Contains a single hydrocarbon chain with a carboxyl group (_COOH) at one end. The carboxyl group gives it its acidic properties. It is an "organic acid."

Protein

Contains carbon, hydrogen, oxygen and NITROGEN. The monomer: Amino acid (20 different types) Each amino acid has 4 "groups" surrounding a central carbon. -The "R" group is the variable side chain. It gives the amino acid its chemical properties (polar/nonpolar or acidic/basic)

double helix

DNA has two strands that are twisted into a double helix. In cells, DNA takes the form of a double helix, first discovered by Watson and Crick in 1953, in collaboration with Wilkins and Rosalind Franklin. In the double helix, two nucleotide chains are wrapped around each other in a spiral that resembles a twisted ladder. The sides of the ladder are the sugar-phosphate backbones of the two chains, which twist around each other in a right-handed direction to form the double spiral. The rungs of the ladder are the nitrogenous bases, which extend inward from the sugars toward the center of the helix. Each rung consists of a pair of nitrogenous bases held in a flat plane roughly perpendicular to the long axis of the helix. The two nucleotide chains of a DNA double helix are held together primarily by hydrogen bonds between the base pairs. Slightly more than 10 base pairs are packed into each turn of the double helix. A DNA double-helix molecule is also referred to as double-stranded DNA.

DNA (deoxyribonucleic acid)

DNA is the universal GENETIC CODE for ALL living things! DNA actually codes for THE SEQUENCE OF AMINO ACIDS (PROTEINS)! These proteins make up not only our entire structure and physical traits, but they also allow all metabolic functions to occur in our cells. Stores the hereditary information responsible for inherited traits in all eukaryotes and prokaryotes and in a large group of viruses. In terms of information flow, genes in the DNA are expressed to produce proteins and RNAs that, together, specify and control the functions of cells. Each nucleotide of a DNA chain contains deoxyribose and one of the four bases A, T, G, or C.

Defensive Proteins (immune defense)

Defend against invading molecules and organisms. Antibodies (specific proteins) are special proteins made by white blood cells that inactivate and destroy viruses and bacteria. ANTIBODIES ARE SPECIFIC for pathogens. Ex: -Antibodies recognize, bind, and help eliminate essentially any protein of infecting bacteria and viruses, and many other types of molecules, both natural and artificial.

starch

Energy-providing carbohydrates are starches. Animal starch is glycogen. (in animals glucose stored as glycogen in liver and muscles for long term energy. Plant starch is amylose. There are stored sugars used for energy.

amylase

Enzyme in saliva that breaks the chemical bonds in starches. Animals have an enzyme that can break down alpha glycosidic links.

Do fats are carbs have more stored energy?

Fats have more stored energy than carbs because the molecule has more BONDS. It takes much more energy to burn a fat molecule (9 cal/g) than a carbohydrate (4 cal/g).

Structural Proteins

For support. Collagen (skin, wounds, tendons) and keratin makes up hair and nails. Ex: -Microtubule fibers and microfilament fibers inside cells -collagen and other proteins of animal cells -cell wall proteins of plant cells.

chemical evolution

Formation of the organic molecules that allowed the first form of life on Earth to originate. Chemical evolution occurred as a result of reactions involving inorganic molecules present on primordial Earth, and the condition of the Earth at the time. The conditions were very different-- the atmosphere lacked oxygen, and contained hydrogen, methane, ammonia, and water. Energy for the chemical evolution reactions came from solar energy and other natural sources (lightning and volcanic activity).

deoxyribonucleic acid

Found in the NUCLEUS of every eukaryotic cell in LINEAR form. Prokaryotes don't have a nucleus but that all have DNA in CIRCULAR form. It contains the "genetic code" which is all the traits and metabolic function in an organism. The four DNA nitrogen bases are Adenine bonding with Thymine and Guanine bonding with Cytosine. The two strands of DNA are complementary because the nitrogen bases always pairs up in a specific way. These are referred to as "base pairs."

maltose

Germinating seeds and major sugar in brewing industry. glucose + glucose

RNA (ribonucleic acid)

In all organisms, one major type of RNA carries the instructions for assembling proteins from DNA to the sites where the proteins are made inside cells. Another major type of RNA forms part of ribosomes, the structural units that assemble proteins, and a third major type of RNA brings amino acids to the ribosomes for their assembly into proteins. Each nucleotide of an RNA chain contains ribose and one of the four bases A, U, G, or C.

RNA nucleotide chain

In contrast to DNA, RNA molecules exist largely as single, rather than double, polynucleotide chains in living cells. That is, RNA is typically single-stranded. All RNAs are expressed from genes in DNA. Once synthesized, the linear RNA molecules can fold and twist back on themselves to form double-helical regions. The patterns of these fold-back double helices are as vital to RNA function as the folding of amino acid chains is to protein function.

deoxyribose and ribose

In nucleotides, the nitrogenous bases link covalently to deoxyribose in DNA and to ribose in RNA. Nucleotides containing deoxyribose are called deoxyribonucleotides and nucleotides containing ribose are called ribonucleotides. Deoxyribose and ribose are sugars with five carbons.

bilayer

In polar environment, such as water solutions, phospholipids assume arrangements in which only their polar ends are exposed to the water. One of these arrangements, the bilayer, is the structural basis of membranes. In a bilayer (film of phospholipids just two molecules thick) the phospholipid molecules are aligned so that the polar groups face the surrounding water molecules at the surfaces of the bilayer. The hydrocarbon chains of the phospholipids are packed together in the interior of the bilayer, where they form a nonpolar, hydrophobic region that excludes water. This bilayer remains stable because, if disturbed, the hydrophobic, nonpolar hydrocarbon chains of the phospholipids become exposed to the surrounding watery solution, and the molecule returns to its normal bilayer arrangement.

trans fatty acids (trans fat)

In the food industry, unsaturated vegetable oils are often processed to solidify the fats. The partial hydrogenation process adds hydrogen atoms to unsaturated sites, eliminated many double bonds. Usually he hydrogen atoms at a double bond are positioned on the same side of the carbon chain, producing a cis (Latin, "on the same side") fatty acid. In a trans (Latin, "across") fatty acid, the hydrogen atoms are on different sides of the chain at some double bonds. Found in many vegetable shortenings, some margarines, cookies, cakes, donuts, and other foods made with or fried in partially hydrogenated fats. Trans fatty acids raise LDL cholesterol levels nearly as much as saturated fatty acids do.

Enzymatic Proteins

Increase the rate of biological reactions. These are organic catalysts. They start and speed up chemical reactions; enzymes are not used up in a reaction, they are recycled and used over and over again. Enzymes are specific! (each reaction requires a different one) Ex: -DNA polymerase in DNA replication -RuBP (ribulose 1,5-bisphosphate) carboxylase/oxygenase (rubisco) in photosynthesis -digestive enzymes.

Hemoglobin

Iron-containing protein in red blood cells that carries oxygen for delivery to cells. Hemoglobin contains 4 polypeptides, each with an iron atom in the center (on test)! It has a quaternary structure.

nucleic acids

Long polymers assembled from repeating monomers called nucleotides. Two types are DNA and RNA. Contain carbon, hydrogen, oxygen, phospherous, and nitrogen. (They serve as the blueprints for proteins.)

Steroids

Made from cholesterol. They are hormones (chemical signals) like cortisone, testosterone, estrogen, and growth hormone. A group of lipids with structures based on a framework of four carbon rings. Small differences in the functional groups of steroid hormones have vastly different effects in animals.

Stereoisomers

Molecules that are mirror images of one another are an example of these. Often, one or more carbon atoms link to four different atoms or functional groups. This is called an asymmetric carbon. They can take either of two fixed positions in space with respect to other carbons in a carbon chain. One of the stereoisomers is the L isomer (left). The other is called the D isomer (D=dexter (right)).

nucleotide

Monomer of nucleic acids. Consists of three parts linked together by covalent bonds: 1. Nitrogenous Base: A nitrogen-containing molecule that accepts protons, formed from rings of carbon and nitrogen atoms 2. A five-carbon, ring-shaped sugar 3. One to three phosphate groups HYDROGEN BONDS HOLD THE NITROGEN BASES TOGETHER. Perform many functions in addition to serving as the building blocks of nucleic acids. Two ribose-containing nucleotides in particular, adenosine triphosphate (ATP) and guanosine triphosphate (GTP), are the primary molecules that transport chemical energy from one reaction system to another. The same nucleotides regulate and adjust cellular activity. Molecules derived from nucleotides play important roles in biochemical reactions by delivering reactants or electrons from one system to another.

Ring formation of carbs

Monosaccharides with four or more carbons can fold back on themselves to assume a ring form. Folding into a ring occurs through a reaction between two functional groups in the same monosaccharide, as occurs in glucose (Figure 3.6). The ring form of most five- and six-carbon sugars is much more common in cells than the linear form.

sucrose

Most plentiful sugar in nature (transported through leafy plant and makes table sugar) glucose + fructose

Amino

NH2 Acts like an organic base by accepting a proton (H+) in aq solutions, converting it from a non-ionized to an ionized form.

carboxyl

O=C-OH Organic Acids Gives organic molecules acidic properties (-OH group readily releases the H as a proton in aq solutions, converting it from a non-ionized to an ionized form.)

hydroxyl

OH- Alcohols Polar Hydrogen bonds with water, facilitating dissolving of organic molecules. Enables an alcohol to form linkages with other organic molecules through dehydration synthesis reactions. ALCOHOL IF YOU SEE OH.

What determines the order of amino acids on a protein?

ON TEST The order of the nucleotides determines the order of amino acids.

Organic vs Inorganic

Organic Compounds: -Contain carbon and hydrogen -Form large and complex molecules -C to C bonds -MAKE UP AND ARE MADE BY LIVING THINGS -Ex: 4 macronutrients of life Inorganic Compounds: -Do not contain carbon (and hydrogen together) -Not as large and complex -Ex: water, minerals, O2, CO2

phosphate

PO4 Very electronegative (very polar); Found in "energy" molecule ATP React as weak acids (one or both -OH groups readily release Hydrogen as H+ in aq solutions, converting them from a non-ionized to an ionized form). Can bridge two organic building blocks to form a larger structure (Ex: DNA) Added or removed from biological molecules as part of reactions that conserve or release energy, or, for many proteins, to alter activity.

Hydrogenation

Plant oils are converted commercially to fats- that is, adding hydrogen atoms to increase the degree of saturation. (Ex: vegetable oils to margarines) This process turns unsaturated fats more saturated by adding hydrogen and removing some of the double bonds. Companies doe this because it creates a better texture and taste and increases shelf life. However, hydrogenation forms trans-fats. This structure is different from most natural fats because it is more stable making it difficult for the body to digest. This can clog up arteries over time.

secondary structure of protein

Polypeptide either is coiled into an alpha helix or folding into a pleated sheet. These structures are stabilized by hydrogen bonds (between the amino and carboxyl groups of amino acids). Produced by hydrogen bonding between different amino acids in a segment of amino acids within a polypeptide chain. The result is coiling or folding of the segment. Most proteins include coils and many also include folds.

polysaccharides

Polysaccharides are the macromolecules formed by polymerization of monosaccharide monomers through dehydration synthesis reactions. They are not sweet but they are made up of hundreds of glucose monomers bonded together. Ex: plant starch, animal starch, cellulose, chitin

Prevention and treatment for atherosclerosis

Prevention: 1. Exercise, healthy diet low is saturated fats/cholesterol. 2. Eat ANTIOXIDANTS (blueberries, purple grapes, dark chocolate, cranberries). Substances that can prevent or slow damage to cells cause by "free radicals" or damaging chemicals. Treatments: 1. Medication (like Lipitor) 2. Angioplasty (Compression of the plaque build up in the arteries) (Balloon that flattens plaque against walls) 3. Bypass Surgery (removal of the clogged vessel - opens chest and cuts out artery. They take a vessel usually from the leg and insert in to bypass the clog. For worst type.)

lactose

Primary sugar of milk. glucose + galactose It has a beta bond so amylase cannot break down, instead the enzyme is lactase. The body makes lactase to break it down but many people lose it with age.

Motor/Contractile Proteins (motile)

Produce cellular movements. For muscles movement actin and myosin help. Movement of cilia and flagella also. Ex: -Myosin acts on microfilaments to produce muscle movements -kinesin acts on microtubules involved in cell division and in movement of some materials within the cell.

amino acid

Proteins are polymers consisting of one or more unbranched chains of monomers called amino acids. These are molecules that contains both an amino and a carboxyl group. The amino acid composition and sequence of a protein determines its structure and its function. Some proteins have single functions, whereas others have multiple functions.

quaternary structure

Proteins that contain 2 or more polypeptide chains to make the whole protein. Some proteins are comprised of two or more polypeptide chains bonded together. Each of those polypeptide chains has a tertiary structure. The combined arrangement of the bonded polypeptide chains in a protein formed from more than one chain is its quaternary structure.

Ribonucleic Acid

RNA copies the DNA and brings it to the ribsomes so the proteins can be synthesized. This means that it "copies" the genes and helps synthesize the proteins from the genetic code. Every 3 bases is called a CODON and codes for a single amino acid. The shape is a single strand and the monomer is a nucleotide. The nitrogen bases are Guanine, Adenine, Cytosine, and Uracil. (U replaces T)

Amylose

Simplest form of starch (in plants). Pasta, bread, potato, rice AMYLASE: Enzyme that breaks down amylose in the saliva and mouth (The digestive system breaks down amylose and packs some glycogen in liver and muscles and slowly releases sugars back in the bloodstream for 4-5 hours.)

monosaccharides

Smallest carbs. Simple or single sugars. 1. Glucose (C6H12O6): #1 energy source for most organisms. 2. Fructose (C6H12O6): Sweetest one (honey, fruits, flower nectar). 3. Galactose (C6H12O6): Usually found combined with glucose to make lactose

Membrane Transport Proteins

Speed up movement of substances across biological membranes. They carry molecules into or out of the cell membrane or throughout the body. Hemoglobin is the protein in red blood cells that carries oxygen to all cells. Its made of 4 polypeptides 1 alpha chains and 2 beta chains. Ex: -Ion transporters move ions across membranes -glucose transporters move glucose into cells -aquaporins allow water molecules to move across membranes

dehydration synthesis reaction (condensation reaction)

Synthesizing a polymer The components of a water molecule are REMOVED during a reaction FORMING a new bond. (Usually as part of the assembly of a larger molecule from smaller subunits). Ex: individual sugar molecules combine to form a starch molecule. Hydroxyl groups readily enter these. Carboxyl groups readily enter, giving up hydroxyl groups. Amino groups readily enter, releasing H+ as it links subunits into larger molecules.

polypeptide

The chain of amino acids formed by sequential peptide bonds is a polypeptide, and it is only part of the complex structure of proteins. That is, once assembled, an amino acid chain may fold in various patterns, and more than one chain may combine to form a finished protein, adding to the structural and functional variability of proteins. (dipeptide is two amino acids)

Macronutrients

The classification of nutrients that provide calories or energy for normal body functions. Proteins: Supplies amino acids (growth and repair of tissue), proper immune system functioning, fullness between meals. (meats, fish, legumes, dairy) Carbohydrates: Main source of fuel for CNS and brain, fast energy to the muscles, 2 categories are simple and complex. (vegetables, fruits, bread, pasta, rice, sugar) Fats: Protection and insulation to tissue, maintains body temp, fullness, aids body in transporting fat-soluble vitamins. (meats, dairy, veggie and fish oil)

What is the relationship between the amino acid sequence of a protein and its conformation?

The information for determining the three-dimensional shape of ribonuclease is in its amino acid sequence. Tertiary structure determines a protein's function. That is, a protein's tertiary structure buries some amino acid side groups in its interior and exposes others at the surface. The distribution and three-dimensional arrangement of the side groups, in combination with their chemical properties, determine the overall chemical activity of the protein. Tertiary structure also determines the solubility of a protein. Water-soluble proteins have mostly polar or charged amino acid side groups exposed at their surfaces, whereas nonpolar side groups are clustered in the interior. Proteins embedded in nonpolar membranes are arranged in patterns similar to phospholipids, with their polar (hydrophilic) segments facing the surrounding watery solution and their nonpolar surfaces embedded in the nonpolar (hydrophobic) membrane interior. These dual-solubility proteins perform many important functions in membranes, such as transporting ions and molecules into and out of cells.

Nucleotide pairing

The nucleotide sequence of one chain is said to be COMPLEMENTARY to the nucleotide sequence of the other chain. The complementary nature of the two chains underlies the processes when DNA molecules are copied—replicated—to pass hereditary information from parents to offspring and when RNA copies are made of DNA molecules to transmit information within cells. In DNA replication, one nucleotide chain is used as a template for the assembly of a complementary chain according to the A-T and G-C base-pairing rules.

tertiary structure of a protein

The overall 3-D shape. Results from the interactions among the R-Groups! Hydrophobic interactions, hydrogen bonds, covalent bonds, ionic interactions, disulfide bridges (covalent bonding) which causes bending, twisting, etc. Often proteins are described as GLOBULES! (includes the alpha helices and pleated sheets.) The folding of the complete amino acid sequence of a polypeptide chain, with its secondary structures, into the overall three-dimensional shape. When only a single polypeptide chain comprises the functional protein, tertiary structure is the highest level of structure the protein has.

primary structure of protein

The particular and unique linear sequence of amino acids linked to each other by peptide bonds to form a polypeptide. A specific sequence of amino acids (which is determined by the order of nucleotides in DNA)! Stabilized by peptide bonds.

shape and function of protein

The primary structure of a protein—the sequence in which amino acids are linked together by peptide bonds—underlies the other, higher levels of structure. Changing even a single amino acid of the primary structure alters the secondary, tertiary, and quaternary structures to at least some degree and, by so doing, can alter or even destroy the biological functions of a protein. For example, substitution of a single amino acid in the blood protein hemoglobin produces an altered form responsible for sickle-cell anemia; a number of other blood disorders are caused by single amino acid substitutions in other parts of the protein.

How does a polypeptide become a functional protein?

There must be... 1. A minimum of 50 amino acids (although most are many hundreds long) 2. A specific shape/conformation: determined by level of structure (primary, secondary, etc.)

What happens if there is a change in the order of nucleotides?

This is called a mutation! It can be caused by environmental factors, like smoking, or it can be genetic - an inherited mutation in the gene) This causes a change in the order of amino acids of a protein. Which causes a change in the SHAPE of the protein. Which means the protein will not function properly!

structural isomers

Two molecules with the same chemical formula but atoms that are connected in different ways. (ex: glucose and fructose)

isomers

Two or more molecules with the same chemical formula but different molecular structures. (Ex: All the monosaccharides of glucose, fructose, and galactose have the same chemical formula of C6H12O6) Glucose and Galactose have a 6 sided ring. Fructose has a 5 sided ring.

What is the difference between L and D stereoisomers?

Typically, one of the two forms enters much more readily into reactions within a cell (enzymes fit best to one of the two forms).

denaturation

Unfolding a protein from its active conformation so that it loses its structure and function is called denaturation. If a protein changes shape and can no longer function, it is said to be denatured! It's especially important for enzymes to keep their shape! Primary sequence is not affected by denaturing. The peptide bonds do not break.

Are saturated or unsaturated fats better for the body?

Unsaturated! They are metabolized much faster due to their structure. They do not leave fatty streaks (plaques) in our arteries because they are liquid (saturated fats leave fat deposits!) Unsaturated fats LOWER cholesterol levels.

cholesterol and disease

Your body requires a certain amount of cholesterol, but the liver normally makes enough to meet this demand. Additional cholesterol is made from fats taken in as food. LDL cholesterol (bad one) contributes to plaque formation as atherosclerosis proceeds. HDL cholesterol (good one) removes excess cholesterol from plaques in arteries, thereby reducing plaque buildup. Diets high in saturated fats raise LDL cholesterol levels.

cis double bond vs trans double bond

a carbon-carbon double bond in which the hydrogen atoms are positioned on the same side of the double bond. This makes it unstable and bend so they cannot stack and the fat stays a liquid. (cis = same side) trans-fat double bond has hydrogen on the opposite side. This stabilizes the fat and makes it very hard to break down.

Triglycerides (what we eat - fats and oils)

glycerol + 3 fatty acids. Stored energy; heat insulation, padding. In the synthesis of a triglyceride, three dehydration synthesis reactions occur, each involving the carboxyl group of one fatty acid and one of the hydroxyl groups of glycerol. A covalent bond formed between a carboxyl group and a hyroxyl group is called an ester linkage. In the formation of the three ester linkages, the polar groups of glycerol are eliminated, resulting in the nonpolar tryiglyceride. Used widely as stored energy in animals. They yield more than twice as much energy as carbs do. A layer of fatty tissue just under the skin also serves as an insulating blanket in humans, other mammals, and birds.

alpha helix and beta pleated sheet

secondary structure of protein. Particularly stable and make an amino acid chain resistant to bending. Alpha helix: The backbone of the amino acid chain is twisted into a regular, right-hand spiral. Beta pleated sheet: The amino acid chain is folded into zigzags in a flat plane rather than being twisted into a coil. In many proteins, β strands are aligned side by side in the same or opposite directions to form a structure known as a beta (β) sheet (Figure 3.19).

functional groups

the components of organic molecules that are most commonly involved in chemical reactions. Each group has specific chemical properties (then found in larger molecules containing them). So the number and arrangement of functional groups in a larger molecule give it its particular function.