Biology Unit 7

This series of alternating rhythmic muscular contractions and relaxation that occurs in the esophagus, stomach and intestines is called peristalsis.

What is peristalsis?

The specificity is determined by the shape of the active site.

What is specificity of the enzyme to its substrate determined by?

The pancreas, located behind the stomach, produces enzymes (lipase, trypsin, amylase and DNA & RNA nucleases). The pancreas also produces sodium bicarbonate, a base that neutralizes stomach acid so that these enzymes can be effective.

What is the function of the pancreas:?

bile

A salty liquid that separates fats to increase the surface area for lipase

salivary glands, liver, gallbladder, pancreas

Accessory organs of the digestive system

Peptide bonds, polypeptides

Amino acids are joined by ________________ _______ to form ___________________.

Mechanical digestion begins when the teeth cut and grind food. Increases surface area

Describe how the teeth help with digestion

The amine group of one amino acid joins with the carboxyl group of another amino acid

Describe the dehydration synthesis reaction that creates proteins:

Water acts like a knife and breaks peptide bonds

Describe the hydrolysis reaction that breaks proteins apart:

As nutrients and water are absorbed from the matter in the colon, the matter solidifies into feces. Feces leave the body by passing through the rectum and the anal canal.

Describe the last stage of digestion

Alternating contractions of three smooth muscle layers churn the food to continue to it break up mix it with the gastric fluid. This process forms a mixture called chyme.

Describe the mechanical digestion that occurs in the stomach

specific

Enzymes are _________ to their substrates.

Make up structures such as hair, nails, collagen, muscle Act as enzymes, hormones, antibodies, transport proteins, and contractile fibers Play vital roles in cell function such as speeding up reactions, cell-to-cell communication, fighting infection, transporting materials, and contraction Generally not used for energy

Functions of proteins:

works and produced in small intestine, breaks maltose into two glucose molecules

Maltase

works in stomach, produced by chief cells, breaks proteins into peptides

Pepsin

globular

Round, sphere-shaped

Metal ions such iron and zinc Coenzymes are organic molecules that are needed by enzymes to help the reaction Many vitamins are coenzymes

Examples of cofactors:

Structures - hair, collagen, fibrin (blood clotting) Enzymes - amylase, lipase, ATP synthase Hormones - insulin, glucagon, growth hormone Antibodies - IgA, IgE, Transportation - hemoglobin, channel proteins Contraction - actin, myosin

Examples of proteins (structures, enzymes, hormones, antibodies, transportation, contractions)

Energy is RELEASED Often occur spontaneously but not always

Exergonic/Exothermic Reaction

Living things must carry out energy-requiring reactions in order to stay alive. As a result, every living thing must have a source of energy to carry out chemical reactions. For example, plants trap light energy to create energy-rich compounds; while humans obtain the energy to perform chemical reactions by eating and digesting food.

Explain chemical reactions in life: (why chemical reactions are important, what we need to provide the energy for them + examples)

consist of Nucleotides which contain Carbon,hydrogen, oxygen, nitrogen, phosphorus

Nucleic acids

Pepsin (stomach) = pH 2.5 Trypsin (small intestines) = pH 8

Optimal pH of pepsin and trypsin?

Linear chain of monomers (amino acids) Can be more than one thousand amino acids Order of amino acids is critical for proper folding

Primary structure of proteins:

alphabets are primary structure words are secondary structure sentences are tertiary structure paragraphs are quaternary structure

Protein structure letter analogy:

consist of Amino Acids which contain Carbon, hydrogen, oxygen, nitrogen, sulfur

Proteins

Quaternary structure occurs in only some proteins when two or more polypeptide folded chains come together to form a functioning protein

Quaternary structure

Substrate

Reactant(s) that enzyme works on the reactants that are activated by the enzyme.

works in mouth, produced by salivary glands, breaks amylose into disaccharides

Salivary amylase

active site

Site on the enzyme that substrate molecule fits into

products

The elements or compounds produced by a chemical reaction

proteins, carbohydrates, lipids, nucleic acids

What are the macromolecules?

Building molecules-Synthesis Breaking down molecules-Decomposition/Digestion

What are the two categories of chemical reactions that enzymes help with?

The polypeptide is held together by covalent bonds (disulfide bridge), hydrogen bonds, ionic bonds and hydrophobic interactions

What bonds are involved in tertiary structure?

A polypeptide can consist of hundreds or thousands of amino acids

What can a polypeptide consist of?

A protein can consist of one or more polypeptide chains.

What can a protein consist of?

If a protein does not fold correctly, the protein can not function. This can have devastating effects on the cell.

What can be an issue with protein folding?

Chemical reactions always involve changes in the chemical bonds that join atoms in compounds.

What do chemical reactions always involve?

Enzymes play key roles in: Regulating chemical pathways Making materials the cell needs

What do enzymes play key roles in?

Hydrogen bonds occur between oxygen of one amino acid and hydrogen of another amino acid

What do hydrogen bonds occur between?

Secondary structure depends heavily on hydrogen bonding to maintain its shape

What do secondary structures rely heavily on?

A dipeptide consists of two amino acids connected by a peptide bond

What does a dipeptide consist of?

Produces a globular mass that for many proteins is last level of folding

What does the folding of tertiary structure produce?

The shape and the chemical environment inside the active site permits a chemical reaction to proceed more easily.

What does the shape and chemical environment of the active site determine?

carbon, hydrogen, oxygen, nitrogen, (sometimes sulfur)

What elements make up proteins?

Tertiary structure involves less regular folding than secondary The polypeptide folds over on itself multiple times as a result of interactions between R-groups on amino acids

What happens during the folding into tertiary structure?

Denature protein = unfold = lose shape Molecules move slower Fewer collisions between enzyme & substrate

What happens if the temperature is increased (for enzymes)? What happens if the temperature is decreased?

When sulfurs attract each other a form a bond (disulfide bridge)

What is a disulfide bridge?

activation energy

What is a factor in whether the overall chemical reaction releases energy or absorbs energy?

These muscle contractions continue the mechanical breakdown of food started in the mouth and move the food through the esophagus and into the stomach.

What is the function of peristalsis?

Salivary glands secrete saliva, which moistens food and makes it easier to chew and swallow. Saliva is a mixture of water, mucus, and a digestive enzyme called salivary amylase which begins the chemical digestion of amylose - a carbohydrate aka starch

What is the function of salivary glands?

Bile is stored and concentrated in the gallbladder The gallbladder releases the bile through a common bile duct into the small intestine.

What is the function of the gallbladder?

The liver performs numerous function in the body including storing glucose (glycogen), making proteins, and breaking down toxic substances. The liver produces bile, which is vital to digesting fats.

What is the function of the liver?

In the induced fit model the enzyme must undergo a conformational change upon binding to the substrate before the shape of the active site and enzyme become complementary to one another.

What is the induced fit model?

In the lock and key model, the substrate and the enzyme are complementary to one another and fit perfectly like a key into a lock.

What is the lock and key model?

near the humans internal pH of 7.4 (usually 6-8) pepsin

What is the optimal pH of most enzymes in humans? What is an exception?

smooth muscle because the movement is involentary

What is the structure of the esophagus

The surface area of the small intestine is large due to the presence of many folds within the lining of the small intestine and the millions of villi that are also present. Microvilli are present on the surface of the villi. ~20 feet long (to in increase surface area) Capillaries and lymphatic vessels are inside villi to allow molecules to diffuse better.

What is the structure of the small intestine? Why?

The chyme from the stomach will further break down in the small intestine. Maltase, Sucrase, Lactase, Peptidase all secreted by the S.I. to continue hydrolysis and ultimately the digestion of the disaccharides and dipeptides.

What occurs in the small intestine?

All chemical reactions in living organisms require enzymes.

What reactions in living things require enzymes?

Activation energy is involved in nearly all chemical reactions, whether the overall reaction releases or absorbs energy.

What type of chemical reactions is activation energy involved in?

Digestion occurs in the gastrointestinal tract, or digestive tract, which is a long tube which begins at the mouth and winds through the body to the anus.

Where does digestion occur? What is this?

small intestine

Where does the Transport of the nutrients occurs mostly in?

The ball of food is then forced by swallowing action into the pharynx. The ball of food is then forced from the pharynx into the esophagus.

Where does the food go after the mouth? Where does it go after that?

Twenty different R groups so there are 20 different amino acids

Why are there 20 different amino acids?

Some chemical reactions that make life possible are too slow or have activation energies that are too high to make them practical for living tissue. Increasing the temperature makes molecules move faster and can increase the rate of reaction. However, biological systems are very sensitive to temperature changes. Enzymes increase the rate of the reaction without increasing the temperature.

Why do we need enzymes?

Proteins have a specific shape which allows them to perform a specific activity or function. For example, enzymes have an active site that must have a specific shape in order to fit the substrate. Enzymes that lose their shape and can no longer function are said to be "denatured".

Why is Enzyme Shape Important? Examples? What is denatured?

For most enzymes the optimum temperature is about 30°C (In humans the optimum temperature for most enzymes is 35°- 40°C (body temp = 37°C) or 98.6 °F) Many are a lot lower, cold water fish will die at 30°C because their enzymes denature A few bacteria have enzymes that can withstand very high temperatures up to 100°C Most enzymes however are fully denatured at 70°C

What is the optimal temperature for most enzymes (and specifically humans) and at what temperature do most enzymes denature? What are some exeptions?

increase surface area for enzymes

What is the point of mechanical digestion?

pepsin's optimal range, denatured proteins so pepsin can access the amino acids easier

What is the point of the high pH in the stomach?

cofactors

additional non-protein molecules that are needed by some enzymes to help the reaction

sphicter

circular ring of muscle that constricts a passage or closes a natural opening (found in stomach to prevent acid from getting into esophagus and SI and make sure stomach doesn't pop by letting)

microvilli

extensions of the cell membranes present on the villi.

collagen

has 3 subunits intertwined like a braid

hemoglobin

has 4 subunits

polar

hydrophilic

neutralizes the pH of the chyme

sodium bicarbonate in SI

catalyst

substance that speeds up the rate of a chemical reaction

works in small intestine, produced by pancreas, continues the breakdown of proteins

trypsin

Primary Secondary Tertiary Quaternary

what are the 4 levels of protein structure?

Some glands produce mucus, which lubricates and protects the stomach wall. Other glands (parietal cell) produce hydrochloric acid, which makes the stomach contents very acidic and cause denaturing of proteins. Other glands produce pepsin (chief cells), Pepsin breaks proteins into smaller polypeptide fragments.

Describe the glands in the stomach

Catalase and 2H2O One molecule of catalase can break 40 million molecules of hydrogen peroxide each second.

Example of An Enzyme-Catalyzed Reaction: what is significant about the reaction?

Many drugs and poisons are inhibitors of enzymes in the nervous system

Examples of inhibitors:

Because enzymes are specific and generally catalyze only one chemical reaction, the first part of an enzyme's name is usually derived from the substrate (element or compound) it works on. The ending of the enzyme's name typically ends in -ase. Examples: Sucrase breaks down the substrate sucrose into glucose and fructose. Lactase breaks down the substrate lactose into glucose and galactose.

How are enzymes named (plus examples)?

hydrolysis

How are proteins broken apart?

They fit into the enzyme and allow the substrate to fit better

How do cofactors work?

Enzyme: reaction rate increases as enzyme increases, The reaction rate is directly related to enzyme concentration. Substrate: reaction rate goes up as substrate increases until a certain point, The reaction rate can reach a maximum when the enzyme is saturated.

How does enzyme and substrate concentration affect reaction rate?

Extreme pH levels will produce denaturation The structure of the enzyme is changed The active site is distorted and the substrate molecules will no longer fit in it At pH values slightly different from the enzyme's optimum value, small changes in the charges of the enzyme and its' substrate molecules will occur. These changes will affect the binding of the substrate with the active site.

How does pH affect enzymes? (extreme and minor)

Enzymes have optimum temperatures at which the greatest number of collisions occur between enzyme & substrate. For chemical reactions the rate of the reaction typically doubles or triples with every 10°C rise in temperature.

How does temperature affect enzymes?

The substrate binds with the active site of the enzyme to create the enzyme-substrate complex

How is an enzyme-substrate complex created?

Cells can regulate the activities of enzymes. Most cells contain proteins that help to turn key enzymes "on" and "off" at critical stages in the life of the cell i.e. Feedback inhibition Enzymes can be affected by any variable that influences a chemical reaction. Enzyme/Substrate Concentration pH Temperature Inhibitors

How is enzyme action regulated? Hint: What kind of things affect how proteins work?

Reaction rate

Speed of which a chemical reaction occurs

dehydration synthesis

What process forms peptide bonds?

Food from the esophagus empties into the stomach.

Where does the food go after the esophagus?

chemical reaction

a process that changes one set of chemicals into another set of chemicals.

Energy is released or absorbed

whenever chemical bonds are made or broken...

No because not all enzymes need to be regulation (like ATP synthase)

Do all enzymes need cofactors or coenzymes?

Secondary structure of a protein

Specific patterns of folding that results in alpha helices and Beta-sheets

central C amino group (NH2) carboxyl group (-COOH) R group (variant)

Structure of amino acids:

Products

Substances produced as a result of the reaction

works and produced in small intestine, breaks sucrose into glucose and fructose

Sucrase

reactants

The elements or compounds that enter into a chemical reaction

Chaperonins

protein molecules that assist the proper folding of other proteins

Cells Reproduction Respond to stimuli Evolve DNA Homeostasis Obtain and use energy Growth and develop

What are Characteristics of Living Things?

An ulcer is a lesion of the surface of the skin or a mucous membrane of the stomach. An ulcer will result if the mucous layer is absent from the stomach lining.

What is an ulcer? What causes it?

a subunit

What is each polypeptide chain in the quaternary structure called?

Feedback inhibition occurs when the product of a series of enzymatic reactions begins to accumulate within the cell The product may then inhibit the action of the first enzyme Further production of the enzyme is then halted

What is feedback inhibition?

Amino acids that are in water can form ions Amino groups can gain a H+ to become NH3+ Carboxyl groups can lose a hydrogen to become COO-

What is special about amino acids in water? How does this happen?

bacteria that eat away at mucus lining

What is the cause of ulcers?

Proteins

What macromolecule accounts for over half of the body's organic matter?

change the temperature, [salt] or pH

When can proteins be denatured?

actuvation energy

an initial input of energy needed in chemical reactions

inhibitors

chemicals that reduce the rate of reaction.

chemical reactions also involve changes in energy.

Because chemical reactions involve the making and breaking of bonds...

Once a critical level is exceeded, then the change in shape of the enzyme is irreversible and the enzyme will forever lose its activity.

Can denatured enzymes be fixed?

consist of Sugars and starches which contain Carbon, hydrogen, oxygen

Carbohydrates

Polar, non-polar, positive charged, negative charged

Categories of amino acids:

Inhibitors are specific for an enzyme and work at low concentrations.

Characteristics of inhibitors:

Competitive inhibition interferes with the active site of the enzyme but they do not usually destroy it

Competitive inhibition

The stomach lining has millions of gastric glands that release substances into the stomach, including mucous, hydrochloric acid and pepsin.

Describe the chemical digestion in occur stomach

Carbohydrates: provide energy to the body (starch, glucose, glycogen) Protein: work as enzymes, transport, make up structures in the cell (pepsin, lipase, maltase) Nucleic acid: store genetic information, help make proteins, provide energy (ATP, DNA, RNA) Lipid: Storing energy (triglycerides, fat, oil)

Describe the functions and give some specific examples of each of the macromolecules.

Transport occurs when the end products of digestion are transported (diffusion, facilitated diffusion and active transport) into the circulatory system through the blood and lymph vessels. Most of the products of carbohydrate and protein digestion are transported into the capillaries which are hugging the villi. (See diagram) Molecules of undigested fat and fatty acid enter the lymph vessels directly.

Describe transport in the digestive system

Once absorption is complete in the small intestine, peristalsis will move the remaining contents into the colon or large intestine. ~ 5 feet long The colon has various sections, and all of these sections work together to finish the absorption of nutrients and water. The colon initiates contractions that move the material out of the body.

Digestion in the large intestine

absorbs energy will not occur without a source of energy

Endergonic/Endothermic Reaction:

works and produced in small intestine, breaks dipeptides into amino acids

peptidase

cofactor

Non-protein molecules that help the enzyme work

Digestion

The process of breaking down food into simpler molecules that can be absorbed and used by the cells of the body

Changes in temperature, pH and salinity (concentration of salt) can increase or decrease enzyme activity because the shape of the active site is affected.

How are enzymes denatured?

Enzymes are NOT used up or changed during the reaction.

How are enzymes effected by their chemical reactions?

Enzymes bind to their substrates and bring them together in the proper orientation for the reaction to begin. The binding and aligning of the substrates lowers the activation energy of the reaction.

How do enzymes lower activation energy?

yes

Is the tertiary structure of a protein a working protein?

consist of Fats and oils which contain Carbon, hydrogen, oxygen

Lipids

Enzymes

Molecules that act as biological catalysts that increase the rate of chemical reactions by lowering the activation energy.

amino acids

Monomer of proteins

Substrate-Enzyme Complex

Name given to the substrate and enzyme when joined

Non-competitive inhibition changes the shape of the enzyme so it can't bind with substrate

Non-competitive inhibition

pharynx

an open area that begins at the back of the mouth, and serves as a passageway for both air and food.

Non-polar

hydrophobic

works and produced in small intestine, breaks lactose into glucose and galactose

lactase

works in small intestine, produced by pancreas, breaks down lipids into fatty acids and glycerol backbones

lipase

alpha helix

looks like a spiral staircase

beta sheets

looks like the folds of an accordion

denatured

lose structure and therefore lose function due to conditions outside of their tolerance

accessory organs

organs that the food does not actually pass through but help with the process

works in small intestine, produced by pancreas, breaks amylose into disaccharides

pancreatic amylase