Proteins and Enzymes: Adv. Biology

Best sources of Protein

eggs, dairy foods, lean meats, poultry, meat alternatives such as dried beans, nuts, soy, peanut butter, BUT note that too much protein from animal sources increase saturated fat intake and can displace whole grains & vegetables which have been shown to reduce chronic diseases

specificity

enzymes are specific because of their shape (and thus the shape of their active site) and can only catalyze a very specific chemical reaction. The active site can only fit a specific substrate or substrates

Motor Proteins

keep cells moving and changing shape. they also transport components around inside cells. examples: 1.actin proteins - in muscles, have tiny myosin motors slide along them to c contract muscles 2.dyein and kinesin - carry vesicles and other cargo around the cell 3. a cellular motor made of 40 diff. proteins- in bacteria, attaches to a flagellum and spin to propel it forward.

What is the primary structure of the amino acid?

linear sequence of amino acids as encoded by the DNA. The amino acids are joined by polypeptide bonds which link a amino group and a carboxyl group. A water molecule is released each time a bond is formed.

Tertiary structure of amino acid?

proteins that fold into a compact globular shape. Hydrophobic side chains shelter inside away from surrounding water. The functions of many proteins rely on this structure. example: hemoglobin forms a pocket inside to hold heme a small molecule with an iron atom in the center that binds oxygen

Marasmic Kwashiorkor

1. A type of PEM from chronic deficiency in kilocalories & protein 2. symptoms: have edema in legs & arms; have a "skin and bones" appearance; with treatment the edema subsides and appearance becomes more like someone with marasmus

Characteristic of Incomplete proteins?

1. Low in one or more essential amino acid 2. usually plant sources are incomplete

substrate concentration effect

1. higher substrate concentration means more substrate is available for the enzyme to act on 2. lower substrate concentration means less to act on 3. At a point faster than the working rate of an enzyme, additional concentration no longer increases the reaction rate. The working rate of the enzyme is then the limiting factor not the amount of substrate. 4. therefore the graph for substrate concentration shows the rate LEVELING OFF when substrate concentration is high, instead of dealing when not in the optimal range 5. changes in substrate do not cause enzymes to denature

What are the different side chain characteristics?

1. hydrophobic- such as leucine & isoleucine, have carbon rich side chains that do not interact well with water 2. hydrophilic - such as serine & threonine, interact well with water 3. charged - such as glutamic acid & arginine, interact with oppositely charged amino acids or water

What are the characteristics of high quality protein source?

1. is digestible 2. contains all essential amino acids - a Complete Protein 3. provides sufficient protein to synthesize nonessential amino acids 4. usually animal sources

What happens to the amino acids in the liver?

1. used to synthesize new proteins 2. converted to energy, glucose & fat 3. released to the bloodstream and transported throughout the body

How many essential amino acids are there?

9

active site

A pocket formed by the folding of the protein where the substrates bind. The active site involves a small number of key residues that actually bind the substrate to react. The rest of the protein is needed to maintain these residues in position.

What are proteins made of?

All proteins are made out of the same twenty amino acids but are combined in different ways. Arrangement dictates the protein's shape and its shape is critical for it to do its job correctly since protein functions is based on their ability to recognize and bind to specific molecules.

How does the role of proteins in energy work?

Because proteins provide 4 calories per gram, they can be used as fuel or energy

macronutrients

Carbohydrates, Lipids, Proteins

Part 3 of protein digestion

Enzymes from the pancreas enter the small intestine and continue to cleave peptide peptide bonds, resulting in dipeptides, tripeptides, & single amino acids (Small intestine and pancreas)

activation energy

For a reaction to start, the substrate must collide with the enzyme with enough energy to break and form bonds. It's the minimum amount of energy needed to start the reaction, leading to the formation of a high energy intermediate. Enzymes act to LOWER the activation energies required for reactions to occur

Enzymes

Globular proteins that speed up or CATALYZE chemical reactions in organisms. They build and break down molecules. They are critical for digestions and many other processes in the cell. Without enzymes chemical reactions would happen too slowly to sustain life. Essentially every life process relies for every living thing relies on enzymes! examples: 1.DNA polymerase- builds DNA molecules 2.lactase - helps infants digest the sugar in their mother's milk 3.luciferase - makes fireflies glow

Part 2 of protein digestion

Hydrochloric acid denatures protein and activates pepsinogen to form pepsin. Pepsin breaks the polypeptide chain into smaller polypeptides (Stomach)

Two of the most important types of chemical reactions?

Hydrolysis and dehydration synthesis (condensation)

treatment for PEM

Medical and nutritional treatment can dramatically increase mortality rate but should be carefully & slowly implemented in 3 steps. 1. Address life-threatening factors like severe dehydration or fluid & nutrient imbalances 2. restore depleted tissue by gradually providing nutritionally dense kilocalories and high-quality protein 3. transition to foods and introduce physical activity

What effects the optimal reaction rate of an enzyme?

PH and temperature, and the concentration of substrate. The rate at which a reaction occurs when an enzyme is present will increase as the temperature or pH reach their optimal level. This is because temperature and PH changes the shape of an enzyme and thus its active site which is complementary to a substrate.

Soy plus and minuses

Plus: high-quality protein source, low in saturated fat, contains isoflavones, phytoestrogens, may reduce risk of heart disease, some research suggests it may reduce the risk of cancer, some concern it may promote breast cancer

What are the four levels of the Protein

Primary structure, secondary structure, tertiary structure, quaternary structure

What is PDCAAS?

Protein digestibility corrected amino acid score

How does the role of proteins in enzymes and hormones work?

Proteins are needed to make most enzymes that speed up reactions in the body and many hormones that direct specific activities, such as regulating blood glucose levels.

How does the role of proteins in structural and mechanical support and maintenance work?

Proteins are the body's building materials, providing strength & flexibility to tissues, tendons, ligaments, muscles, organs, bones, nails, hair, skin. Proteins are also needed for the ongoing maintenance of the body.

How does the role of proteins in antibodies & the immune response work?

Proteins create specialized antibodies that attack pathogens that may cause illness

Benefits of healthy vegetarian diet

Reduced risk of: heart disease, high blood pressure, diabetes, cancer, stroke, obesity

Structure of Proteins

The chains of amino acids are classified by the number of amino acids in a chain: a. Peptides: <50 amino acids 1. dipeptides = 2 amino acids 2. tripeptides = 3 amino acids 3. polypeptides = > 10 amino acids b. Proteins: > 50 amino acids (typically 100-1000)

What is the secondary structure of the amino acid?

The often fold into two types of secondary structures stabilized by hydrogen bonds: alpha helix and

How do cells make proteins?

They use the information encoded in their genes. Each gene in the DNA encodes information about how to make an individual protein.

Part 4 of protein digestion

Tripeptidases and dipeptidases on the surface of the small intestinal cells finish the digestion to yield single amino acids, which can then be absorbed. *occasionally proteins are absorbed intact

What is RNA?

a molecular message similar to DNA that is is produced in the cell nucleus and then moves into the cytoplasm of the cell where the ribosome reads the RNA message and produces the protein that the gene specified in the RNA. The protein then travels to where it is needed.

non-essential amino acids

can be synthesized by the body

Where are amino acids absorbed?

in the small intestines

essential amino acids

must be consumed in the diet

alpha helix

one of two secondary structures where a protein chain can fold into a rigid alpha helix forming regular patterns of hydrogen bonds between the backbone atoms of nearby amino acids

beta sheet

one of two secondary structures where backbone atoms can interact side by side to form beta sheets

metabolism

the chemical reactions in living things

Where are the amino acids transported via the portal vein?

the liver

product

the result of the reaction of the enzyme and substrate complex that is then released from the enzyme. For example: sucrose + H20 yields the product of glucose + fructose

What determines the property of the amino acid?

the side chain of the amino acid is the only part that varies from amino acid to amino acid.

How are the 3D shapes of proteins formed?

through attractions and interactions of side chains that cause the proteins to fold into precise 3-D shapes.

Risks of a vegetarian diet

underconsumption of certain nutrients like protein, iron, zinc, calcium, Vit. D, Riboflavin, Vit. A, Omega-3 fatty acids, & Vit. B12

denatured

when an enzyme's shape has changed due to: 1. heat/temperature 2. acids/pH 3. bases/pH 4. Salts 5. Mechanical agitation * primary structure is unchanged by denaturing ** any alteration in the structure or sequencing changes the shape and function of the protein

high energy intermediate stage

when the substrates are joined at the active site it is the highest level of progress of the reaction

what is the quaternary structure of an amino acid?

when two or more polypeptide chains can come together to form one functional molecule with several subunits. example: the 4 subunits of hemoglobin cooperate so that the complex can pick up more oxygen in the lungs and release it in the body

How many side chains are there on an enzyme?

20

How many unique amino acids are there?

20

Result of too little protein?

can lead to bone loss and ... 1. cells lining GI tract are not sufficiently replaced as they slough off 2. digestive function is inhibited 3. absorption of food is reduced 4. intestinal bacteria gets into the blood and causes septicemia 5. immune system is compromised due to malnutrition and cannot fight infection.

conditionally essential amino acids

cannot be synthesized due to illness or lack of necessary precursors ie. premature infants lack sufficient enzymes needed to create arginine

Amino Acids are made of ?

carbon, oxygen, nitrogen, hydrogen and sometimes sulfur. These atoms form a carboxyl group, a hydrogen, a nitrogen-containing an amino group and a unique side chain attached to a central carbon atom.

proteins

chains of amino acids

lipids

chains of fatty acids

carbohydrates

chains of glucose

Marasmus

1. a type of PEM from severe deficiency in kilocalories 2. symptoms: frail, emaciated appearance; weakened and appear apathetic; many cannot stand without support; look old; hair is thin, dry & lacks sheen; body temperature and blood pressure are low; prone to dehydration, infections, & unnecessary blood clotting

Kwashiorkor

1. a type of PEM with severe protein deficiency generally resulting from a diet high in grains and deficient in protein 2. Symptoms: edema in legs, feet, stomach; muscle tone & strength diminish; hair is brittle and easy to pull out; appear pale, sad & apathetic; prone to infection, rapid heart rate, excess fluid in lungs, pneumonia, septicemia, & water and electrolyte imbalances

pH effect on enzyme

1. enzymes are affected by pH 2. pH other than an optimal level causes denatured enzymes. 3. at less than optimal ph reaction time decreases until it is so denatured that it doesn't work 4. sometimes an enzyme can regain its shape after being denatured, if the PH returnes to an optimal range. 5. It does not make substrate move any faster or slower

How are peptide bonds formed and what do they do?

1. formed when the acid group (COOH) of one amino acid joins with the amine group (NH2) of a second amino acid 2. formed through condensation and a molecule : of water is released 3. broken through hydrolysis - OH (hydroxyl group) + H (hydrogen from water molecule)

Types of vegetarians

1. lacto-vegetarian, 2. lacto-ovo-vegetarian, 3. ovo-vegetarian, 4. vegan 5. semivegetarian

How does the body use proteins? (functions)

1. provide structural and mechanical support (also helping muscular contraction) 2. Maintain fluid balance 3. functions as enzymes and hormones (also promoting satiety and appetite control) 4. help maintain acid base balance 5. Transport nutrients 6. Assist the immune system 7. Serve as a source of energy when necessary

3oz serving of cooked meat, poultry or fish...

1. provides 21-25 grams of protein 2. about 7g/oz 3. is about the size of a deck of cards 4. is adequate amount for one meal

Why need enzymes?

1. reactions too slow to maintain life 2. can't increase temperature/pressure in cells (this is fatal)

Risks of eating too much protein

1. risk of heart disease 2. risk of kidney stones 3. risk of calcium loss from bones 4. risk of colon cancer 5. displacement of other nutrient-rich, disease preventing foods

Properties of enzymes

1. specific 2. Increase rate of reaction 3. unchanged at the end of the reaction

temperature effect on enzyme

1. substrates (molecules) move faster at higher temperatures because of kinetic energy. 2. faster moving substrates collide with the enzyme more, causing the reaction rate to increase until the OPTIMAL temperature is reached the rate is FASTEST. 3. Increasing temperature after the optimal point begins to cause denature because increase in vibration energy that breaks down the bonds and thus the shape of the enzyme 4. Denaturation of an enzyme by heat IS irreversible by lowering the temperature doesn't fix the enzyme's shape

PEM (Protein -energy malnutrition)

1. when protein is used for energy rather than its other functions in the body. 2. other important nutrients are in short supply 3. more prevalent in infants and children ( 17,000 children die each day as a result)

How many non-essential amino acids are there?

11

What is the induced fit model as it applies to enzyme action?

A model for the enzyme-substrate interaction to describe that only the proper substrate (the molecule that the enzyme acts on in a reaction) is capable of inducing the proper alignment of the active site that will enable the enzyme to perform its catalytic function. It suggests that the active site continues to change until the substrate is completely bound to it, at which point the final shape and charge is determined. The induced fit model, suggested by Daniel Koshland in 1958, is the more accepted model for enzyme-substrate than the lock-and-key model. Unlike, the lock and key model that describes the active site as like a keyhole and the substrate as the exact & only key that fits it, the induced fit model shows that enzymes are other flexible structures in which the active site continually reshapes itself by its interactions with the substrate until the time the substrate is completely bound to it (which is also the point at which the final form and shape of the enzyme is determined). When the substrate interacts with the enzyme it undergoes a chemical reaction that allows the atoms to move relative to each other, the bonds to possibly lengthen or shorten and themes reactive groups to move closer to each other, causing a shape change. This shape change makes the substrate more amenable to alteration, as it holds the substrate in a transitional state, which helps speed up the reaction that the enzyme catalyzes. With this model, they way that the substrate has to change its structure may be useful in terms of the catalysis itself. It may represent the beginning of the reaction that the enzyme is catalyzing. Conversely, in the lock and key model, the catalysis follows after the substrate fits into the enzyme.

Regulatory Proteins

Bind DNA to turn genes on and off. Active genres are used to build proteins. examples: 1.p53 protein- prevents cells from dividing when its DNA is damaged. 2.HOX protein - during development, tells a group of cells what organ to become. 3.Androgen and estrogen receptors- control genes that trigger the start of puberty in males and females.

How much protein does a person need?

Healthy people - need enough to replace what is used daily. >18yrs 0.8g/kg daily (10-35% total daily kilocalories) Pregnant, athletes (50-100% more), injured, or adolescents have additional needs. ** goal is NITROGEN BALANCE 1. healthy adult = nitrogen balance 2. pregnant woman, growing children & adolecsents & some athletes = positive nitrogen balance 3. injured or malnourished = negative nitrogen balance

Sensory Proteins

Help detect light, sound, touch, smell, taste, pain and heat. Some organisms can even detect electricity or magnetism. examples: 1. opsin- in the eye detect light 2. olfactory receptors- in the nose sense airborne chemicals 3. crypto chrome proteins- in monarch butterflies sense the earth's magnetic field 4.TRPA1 protein - in rattlesnake's pit organ senses body heat.

Relationship between shape and function of an amino acid?

Many proteins rely on the ability to recognize the shape of specific molecules in order to function correctly. 1.Defense - the flexible arms of antibodies allow it to recognize & bind to foreign molecules preventing it from entering the cell 2.Structure - collagen fors a triple helix that gives strong structural support throughout the body 3. Transport - calcium pump moves ions across cell membranes allowing the synchronized contraction of muscle cells 4. Communication - the hormone insulin is a small stable protein that can easily maintain its shape while traveling through the blood to maintain blood sugar levels 5. Enzymes - alpha-amylase is an enzyme with a catalytic site that begins the breakdown of carbohydrates in our saliva. 6. Storage - Ferritin forms a hollow shell that storages iron from our food.

Transport Proteins

Move molecules and nutrients around the body and in and out of cells. examples: 1.hemoglobin- in red blood cells, pick up oxygen from the lungs and delivers it to all the tissues of the body 2.cytochrome c proteins- in mitochondria, move electrons from one protein complex to another, generating energy to power the cell. 3.channels - in cell membranes help ions cross the membrane which allows heart cells to beat and nerve cells to fire.

What roles do proteins play in sending a pain signal?

Nerve networks are responsible for the sensation of pain. The "receptor Protein" at the receiving end of each cell in the line of end-to-end cells that transmit the pain signal are responsible for picking up the signal and passing it along to the next cell.

How does the role of proteins in fluid balance work?

Proteins play a major role in ensuring that the body fluids are evenly dispersed in the blood and inside and outside cells

How does the role of proteins in transport work?

Proteins shuttle substances such as oxygen, waste products, and nutrients (such as sodium and potassium) through the blood and into and out of cells

Dehydration Synthesis (condensation)

a type of chemical reaction that involves BUILDING (synthesizing) large molecules called POLYMERS by JOINING TOGETHER building blocks (Monomers). This happens in cells when they need to build molecules such as proteins, fats, nucleic acids, or complex carbohydrates.

hydrolysis

a type of chemical reaction that involves the BREAKDOWN of a large molecule called a Polymer into its building blocks (also known as Monomers). This is what enzymes in the body do when they breakdown food during digestion.

Signaling Proteins

allow cells to communicate with each other. Signals, receptors, and relay proteins work together to get information from outside a cell to the inside. Examples: 1.insulin receptor- signals muscle and fat cells to store blood sugar after it is activated by released insulin. 2.EGF (epidermal growth factor) receptor- At a wound site is signals skins cells to grow and divide during wound healing activated by the released of EGF. 3.adrenergic receptor- signals heart cells to beat faster and liver cells to release glucose, giving muscles a burst of energy when activated by a non-protein hormone called adrenalin.

Diet % Summary

healthy diet: 45-65% Carbohydrates 20-35% Fats 10-35 % Proteins

Defense Proteins

help organisms fight infection, heal damaged tissue, and evade predators. examples: 1. antibodies - battle the bacteria & viruses 2. Fibrin proteins - form blood clots and scabs 3.TD (threonine deaminase)- produced by tomato plant to make caterpillars sick if they try to eat it

What determines a proteins function?

its shape

Part 1 of protein digestion

mechanical digestion in the mouth by chewing, tearing and mixing food with salivary juices from the Bolus. (mouth and salivary gland)

protein bar vs peanut butter sandwich?

peanut butter sandwhich

Polymers, monomers, dimer

poly= many, mono = one, di =two

What are structural proteins

special proteins that are like bricks, stacking together to form column-like supports that give the cell its shape. like the branches of the nerve cells help extend and hold them in place. Structural proteins strengthen cells, tissues, organs and more. examples: 1.Collagen - strengthens our bones, cartilage, tendons, ligaments, & skin. It makes up about 1/4 of the body's total protein. 2.Tublin- forms hollow tubes, called microtubules that support the structure of the cell. 3.Fibroin - used by silkworms to build cocoons that people turn into silk.

Storage Proteins

store nutrients and energy-rich molecules for later use. examples: 1.casein- in milk of mammals, supply nutrients for babies to grow 2. ovalbumin - in egg whites, gives energy to growing bird embryo 3.gluten - stored in seeds of wheat, barley & rye, gives seedlings a fast start.

What is a protein?

the machines that make all living things function. Each cell contains thousands of different proteins that all look different and do separate jobs.

substrates

the reactants of enzyme-catalyzed reactions.

substrate concentration

the relative amount of substrate present in a solution