Unit 1: Biochemistry

Question 1

What do inhibitors do?

Answer 1

shut down the action of the enzyme

Inhibitors shut down the action of the enzyme.

Question 2

What are non-competitive inhibitors?

Answer 2

bind to locations other than the active site, called allosteric sites, thus preventing the substrate from binding to the active site by causing a conformation change that alters the active site so that it is no longer an ideal receptacle for the substrate

Non-competitive inhibitors bind to locations other than the active site, called allosteric sites.

Question 3

What are competitive inhibitors?

Answer 3

bind directly to part of or the entire active site by mimicking the shape of the substrate thus preventing the enzyme from accepting the true substrate

Competitive inhibitors bind directly to part of or the entire active site.

Question 4

What do activators do?

Answer 4

bind to allosteric sites enhancing the activity of the enzyme by conforming the shape of the enzyme so that the receptacle is a better fit for the substrate

Activators bind to allosteric sites enhancing the activity of the enzyme.

Question 5

What are cofactors?

Answer 5

located in the active site of the enzymes. they attract electrons from the substrate molecule bonds causing them to break

Cofactors are located in the active site of the enzymes.

Question 6

What are examples of inorganic ions as cofactors?

Answer 6

copper, zinc, and iron

Examples of inorganic ions as cofactors are copper, zinc, and iron.

Question 7

What are coenzymes?

Answer 7

organic, non-protein molecules

Coenzymes are organic, non-protein molecules.

Question 8

Factors Affecting Enzyme Function - Temperature

Answer 8

As temperature increases the activity of enzymes also increases up to a certain critical temperature beyond which enzyme function is impaired
Most human enzymes work best between 30-40℃ (close to body temperature)
When enzymes become too hot, they become denatured

Question 9

Factors Affecting Enzyme Function - pH

Answer 9

Most enzymes have an optimal pH range of 6 to 8. However, there are exceptions like pepsin, which works optimally at pH 2.

Additional information: Pepsin is the enzyme that digests protein in the stomach.

Question 10

Factors Affecting Enzyme Function - Concentration

Answer 10

Increasing substrate concentration increases the rate of reaction by promoting more collisions between substrate and enzyme molecules. Increasing enzyme concentration also boosts the reaction rate, but only up to a certain point before the rate decreases as substrate is used up.

Example sentence: The rate of reaction increases with higher enzyme concentration until a saturation point is reached.

Question 11

What is an enzyme?

Answer 11

An enzyme is a protein (or protein-based molecule).

(p. 50)

Question 12

What is the function of enzymes?

Answer 12

Enzymes act as catalysts, which speed up chemical reactions without being consumed in the process.

Question 13

Why are enzymes essential for life?

Answer 13

Without enzymes, life as we know it would not exist because metabolic processes would occur too slowly to maintain normal cellular function.

Question 14

What is the reactant upon which an enzyme acts called?

Answer 14

The reactant upon which an enzyme acts is called a substrate.

(p. 50)

Question 15

What are the depressions on enzymes’ surfaces called?

Answer 15

Enzymes have one or more depressions (dents) on their surface called active sites.

(p. 50)

Question 16

How is the substrate enzyme complex held together?

Answer 16

The substrate enzyme complex is held together by hydrogen bonds and weak ionic bonds.

Question 17

What is the induced fit in enzyme-substrate interaction?

Answer 17

When the substrate binds to the active site, the enzyme can make subtle changes in shape to accommodate the substrate (called an induced fit).

(p. 50)

Question 18

What are some ways enzymes speed up reactions?

Answer 18

An enzyme can speed up a reaction by causing stress on the bonds of the substrate, transferring H+ and OH- ions to or from the substrate, accepting electrons forming a temporary bond, and bringing 2 substrates together in the correct orientation for reaction.

Question 19

What is a non-spontaneous change?

Answer 19

a process that does not occur on its own under a given set of conditions. In order for it to happen, it requires an input of energy or external intervention.

Question 20

What is Adenosine Triphosphate?

Answer 20

Primary source of free energy of living cells
Composed of the purine nitrogenous base: adenine, a ribose sugar, and a chain of three phosphate groups
The collection of negative charges on the phosphate chain makes the terminal phosphate high;y unstable
Energy is stored in covalent bonds between the phosphates, with the greatest amount of energy between the terminal and second phosphate group
The free energy required of the many endothermic reactions that occur within a cell comes from hydrosis, with the aidest the enzyme ATP passes, of the terminal phosphate from the ATP molecule
This transfer of the phosphate group is called phosphorylation
Even though the human body consumes its own mass in ATP per day, a highly efficient recycling system exists in the body whereby catabolic processes provide the energy to reconnect the terminal phosphate to an ADP molecule as anabolic processes use the energy ATP releases.

Question 21

What is Adenosine Triphosphate composed of?

Answer 21

Composed of the purine nitrogenous base: adenine, a ribose sugar, and a chain of three phosphate groups

Adenosine Triphosphate is often abbreviated as ATP.

Question 22

What are buffers made up of?

Answer 22

Made up of a weak acid and its salt, or a weak base and its salt
Absorbs small additions of acids and bases without allowing a pH change to occur
Buffers resist pH change by shifting equilibrium

Applications
Human blood contains a buffer system that maintains the pH of blood at 7.4. You can eat/drink acidic foods without the blood becoming acidic and cause membrane cells to dissociate and dissolve
Soils act as a buffer to protect lakes

Question 23

What are hydrolysis reactions?

Answer 23

Addition of a water to break a molecule into two
Catabolic process (break down)
Releases energy (exergonic/exothermic)

Question 24

What are condensation reactions?

Answer 24

Removal of water molecule to bind two molecules together
Anabolic reaction (build)
Absorbs energy (endergonic/endothermic)

Question 25

What is phosphorylation?

Answer 25

Transfer of phosphate group
Even though the human body consumes its own mass in ATP per day, a highly efficient recycling system exists in the body whereby catabolic processes provide the energy to reconnect the terminal phosphate to an ADP molecule as anabolic processes use the energy ATP releases.

Question 26

What are anabolic reactions?

Answer 26

Reaction that produces large molecules from smaller subunits
Energy is absorbed
Anabolic steroids

Question 27

What are catabolic reactions?

Answer 27

Reaction that breaks macromolecules into subunits
Energy is released
Digestion

Question 28

What is a spontaneous change?

Answer 28

A spontaneous change occurs on its own once started and does not require a continual input of energy.

Example: Once a match is lit, it will continue to burn without the continual addition of energy.

Question 29

Isotonic in plants

Answer 29

Equilibrium

Question 30

Hypotonic in plants

Answer 30

Plants in a hypotonic environment have increased turgor pressure, a sign of a healthy plant

Question 31

Hypertonic in plants

Answer 31

Plants in a hypertonic environment wilt
The cell membrane shrinks away from the cell wall. The cell may die
Known as plasmolysis

Question 32

Isotonic in animal cells

Answer 32

Water concentration inside the cell is equal to the concentration outside the cell
Net movement = 0
Most living cells on earth, → ideal situation

Question 33

Hypotonic In animal cells

Answer 33

Water concentration outside the cell is greater than the water concentration inside the cell
As water keeps diffusing into the cell the cell expands and may burst
Net movement = outside → inside
Placing a single celled organism (98% water) into distilled water (100%)

Net movement: outside -> inside

Question 34

Hypertonic in animal cells

Answer 34

Water concentration inside the cell is greater than the water concentration outside the cell
As water keeps pumping out, the cell shrivels and may die (dehydrate)
Net movement = inside → outside
Placing freshwater amoeba into salt water

Question 35

Bulk Active Transport - Endocytosis

Answer 35

Active process by which cells ingest (import) materials
Cell membrane pinches (folds) in on itself to create a vesicle (membrane enclosed sac) which moves into the cell
Phagocytosis (cell eating)
Movement of large molecules into the cell
White blood cell engulf bacteria cell
Pinocytosis (cell drinking)
Transport of fluid droplets into the cell
Fat droplets entering a cell

Question 36

Bulk Active Transport - Exocytosis

Answer 36

Active process by which cells export materials (movement) out of the cells
maintain filled vesicles fuse with cell membrane & contents are released
Specialized cells in pancreas secrete hormone; insulin
Exocitosis restores the membrane removed by endocytosis

Question 37

Sodium-Potassium Pump

Answer 37

Protein pumps found in the membrane can move substances against the concentration gradient
These pumps utilize energy from metabolism, specifically in the form of adenosine triphosphate (ATP)
This pump is found in animal cells
3 Na ions within the cell bond to the transporter protein at the same time as 2 K ions bind on the outside of the cell (all are positively charged)
This binding causes protein to change shape
Its new shape forces the Na ions out and the K ions into the cell
Once ions are released, the protein changes back to its original shape
A high concentration on Na builds up outside the cell
Na diffuses back inside through a carrier protein
This carrier protein is shaped so that Na can only diffuse back inside if it has bonded with a glucose molecule
Na returns to the cell down the concentration gradient and this provides the means for glucose to enter the cell

Question 38

Active Transport

Answer 38

Movement across the cell membrane that requires the cell to expend energy and moves particles against the concentration gradient
Unlike passive transport it does not move with the concentration gradient
A cell often must maintain an internal environment vastly different from its external environment
Nutrients must be concentrated inside the cell, waste must be completely removed
The amount of energy the cell expends depends on the concentration gradient
Kidney cells need to pump glucose and amino acids into the blood
Intestinal cells need to pump nutrients out of the intestines and into the blood

Question 39

What is a Carrier Protein?

Answer 39

will only accept non charged particles

Question 40

What is a Channel Protein?

Answer 40

will accept charged particles
The proteins have a tunnel like shape and only allow ions that are small enough and with the correct charge to pass
A positively charged channel will only allow negatively charged ions to pass and vice versa

Question 41

What is Facilitated Diffusion?

Answer 41

the method of diffusion used y molecules that are simply too large to pass through the membrane by diffusing
Specialized transport proteins imbedded in the membrane move the molecule across
Transport proteins only recognize and move one type of dissolved molecule (very selective due to structure)
This process is still driven by a concentration gradient and molecules move from an area of high concentration to low concentration with no use of energy required

Question 42

What is Osmosis?

Answer 42

the diffusion of water molecules across a selectively permeable membrane from an area of high concentration to an area of low concentration
Solute → substance dissolves in water
Solvent → substance which the solute is dissolved in

Question 43

What is Passive Transport?

Answer 43

The movement of molecules across a semipermeable membrane that does not require the cell to expand any energy
Types of passive transport are: Diffusion, osmosis, and Facilitated diffusion
Diffusion → the movement of particle down a concentration gradient from an area of high concentration to an area of low concentration
Diffusion is caused by molecular collisions
As the particles collide they bounce around in all directions and move further apart with equal frequency
Areas of high concentration will have more collisions then areas of low concentration
Diffusion rates are affected by temperature and pressure (increased rates as temp or pressure increases)
Both oxygen and carbon dioxide are free to diffuse across a cell membrane

Question 44

Transportation Methods + The Particle Theory of Matter

Answer 44

Brownian Motion → the random movement of particles
Particle theory
All matter is made up of particles
There are spaces between particles
Particles are always moving

Question 45

What is the First Law of Thermodynamics?

Answer 45

Total amount of energy in the universe is constant
Energy cannot be created or destroyed but only converted from one form to another—change in states
If an object or process gain an amount of energy it does so at the expense of a loss of energy somewhere else in the universe

Question 46

What is the Second Law of Thermodynamics?

Answer 46

Entropy (randomness/disorder in energy or a collection of objects) of the universe increases with any change that occurs

Question 47

What is the Second Law of Thermodynamics?

Answer 47

Entropy (randomness/disorder in energy or a collection of objects) of the universe increases with any change that occurs

Question 48

What is an Exergonic (exothermic) Reaction ?

Answer 48

Chemical reaction in which the chemical potential energy of the product is less then the energy of the reactants (energy has been released)

Question 49

What is an Endergonic (endothermic) Reaction?

Answer 49

Chemical reaction in which the chemical potential energy of the products is more than the energy of the reactant (energy has been absorbed)

Question 50

What is a Redox Reaction?

Answer 50

oxidization reduction
Reactions involving a transfer of one or more electrons from one reactant to another
Oxidization is the loss of electrons
Reduction is the gain of electrons
Energy is always lost during oxidization and gained during reaction
Application
Oxidization of food molecules releases energy used to maintain body temperature and muscle contraction

Question 51

What is Water?

Answer 51

Water is a molecule that is essential to life that makes up 50-90% of nearly all organisms. Water is a polar covalently bonded molecule (uneven sharing of electrons).
The polar nature of water allows water molecules to form weak bonds with each other called Hydrogen Bonds

Question 52

Properties of water: What is Cohesion?

Answer 52

attachment to self
As a result of hydrogen bonding, water molecules tend to stick together
Allows for transport of water against gravity in plants
Allows for surface tension to occur on the surface of water

Question 53

Properties of Water: What is Adhesion?

Answer 53

Water molecules stick to other polar molecules

Question 54

Properties of Water: Explain High Specific Heat Capacity

Answer 54

Water requires a large amount of energy transfer to produce a change in temperature
Protects cells from rapid temperature change and provides stable environment for cell reactions

Question 55

Properties of water: Explain High Specific Heat of Vaporization

Answer 55

Hydrogen bonding causes liquid water to absorb a lot of thermal energy and turn into water vapour (gas)
Many organisms, including humans, dissipate body heat by evaporation of water to cool down (sweating)

Question 56

Properties of Water: Explain its density

Answer 56

Ice is less dense than liquid water (ice floats) due to its expansion upon freezing
Allows aquatic ecosystems to survive in the winter since bodies of water freeze from top to bottom

Question 57

Nucleotide Polymers:

Answer 57

DNA & RNA are nucleotide polymers
Adenine and thymine bond together
Apples in the trees
Cytosine and guanine bond together
Cars in the garage
Pyrimidines → nitrogenous bases with a single ring
Adenine and Guanine
Purines → nitrogenous bases with double rings
Cytosine and Thymine

Question 58

Phosphodiester and Hydrogen bonding of Nucleic Acids:

Answer 58

Phosphodiester bonds hold the phosphate group of one nucleotide and the hydroxyl group attached to the number 3 carbon of the sugan on the adjacent nucleotide
The two strands of DNA are held together by hydrogen bonds between the nitrogenous bases on adjacent strands
Hydrogen bonds only form properly if one strand is upside down.
Said to run antiparallel

Question 59

Explain the Structure of a Protein:

Answer 59

Protein Structure
Primary
The sequence of amino acids
Changes in the primary structure can alter the proper function of a protein molecule
Protein function is tied to their 3-D structure
Secondary
Due to the colliding/folding caused by hydrogen bonding between R-groups
This forms what is called α (alpha) helix or β pleated sheet
Tertiary
A folded individual peptide is formed
This is due to more bonding or replenish between the R-groups and the polypeptide and its environment
This is stabilized by:
Hydrogen bonds
Ionic bonds
Disulfide bridges
Quaternary
Formed by the interactions of 2 or more polypeptides (ex: hemoglobins)
Structure determines the Function

Question 60

Characteristics of Protein

Answer 60

Used to build cell structures and during chemical reactions (enzymes)
Not generally used for energy
Composed of hydrogen, carbon, oxygen, nitrogen and sometimes sulfur atoms
Proteins are found in chicken, nuts, beef, fish, and tofu
Proteins are the most common organic molecule in living things and are also the most diverse
Made up of subunits called amino acids. The sequence of amino acids determines the type of protein

Question 61

Amino Acids

Answer 61

Amino acids have
An amino group
Carboxyl group
Hydrogen
Side chain (R-group)
Many amino acids joined together are known as polypeptides.
The molecules are held together by bonds called peptide ponds
Peptide bond
Formed by the joining of amino end of the molecule to the carboxyl end of another by dehydration synthesis
8 amino acids are essential since our body cannot synthesize them (we get them from our diet). We can synthesize the other 12.
All 20 amino acids differ in their R-group. The R-groups make the amino acids polar, nonpolar, or electrically charged

Question 62

Cholesterol

Answer 62

a unique lipid (steroid)
Used by the body to produce hormones, both male and female sex hormones
Important part of the cell membrane
Too much cholesterol can combine with other fats to produce plaque with has the ability to block arteries
Compact hydrophobic molecule containing 4 fused hydrocarbon rings and one hydroxyl functional group

Question 63

Saturated and Unsaturated Fats

Answer 63

Saturated fats
Single bonds between carbon atoms (full of hydrogen atoms)
Lard & butter
Unsaturated fats
Have double bonds between at least two carbon atoms (loss of hydrogen atoms)
Oil

Question 64

What are Lipids composed of?

Answer 64

Lipids are composed of hydrogen, carbon and oxygen atoms.
There are three groups of lipids
Fats, oils, and waxes
Phospholipids
Steroids

Question 65

What are Lipids?

Answer 65

They are an energy source, in which it is more difficult to break down the carbohydrates. Thus 1 gram of lipids has twice as much energy as 1 gram of carbohydrates or proteins.
Lipids
Aid in vitamin absorption
Insulate the body
Protect internal organs
Cell membranes main component
Act as the raw materials when synthesizing hormones and other chemicals need by the body
Insoluble in water
Glycerol
3 carbon chain attached to a hydroxyl group
Fatty acid
Hydrocarbon chains containing a carboxyl group at one end
Lipids are produced via dehydration synthesis between the hydroxyl group on the glycerol with the carboxyl group on the fatty acid → producing an ester linkage
Triglycerides are the most common form of lipid and are composed of a glycerol molecule and three fatty acids

Question 66

Polysaccharides

Answer 66

Polysaccharides
Monosaccharide polymer composed of monosaccharide subunits held together by glycosidic linkages (ether)
Chitin, amylase, amylopectin (starch), cellulose
α (Alpha) glucose → the OH lies below the plane of the ring
β (Beta) glucose → the OH lies above the plane of the ring
There is a 50% chance that the OH will end up below or above the plane of the ring

Question 67

Disaccharides

Answer 67

2 simple sugars bonded together to form a glycosidic linkage (ether)
Sucrose

Question 68

Monosaccharides

Answer 68

Simple sugars, contain either a carbonyl aldehyde or carbonyl ketone and a hydroxyl function group
Glucose

Question 69

Carbohydrates

Answer 69

Carbohydrates are composed of carbon, hydrogen and oxygen atoms in the ratio of 1:2:1, (C6H12O6).
Composed of single sugar molecules or chains of such sugar molecules
Most important energy source of food which is obtained from the intake of food
Carbohydrate are found in potatoes, bread, corn, rice, fruit and pasta
The word ‘saccharide’ means sugar.
Most sugars end with ‘ose’
Glucose is found in all cells & is our primary energy source
Glucose and fructose are the common saccharide
Sucrose is the makeup of glucose and fructose

Question 70

Common Polysaccharides

Answer 70

Common polysaccharides
Starch → storage form of carbohydrates in plants
Cellulose → forms cell walls of plants
Glycogen → storage form in animals
All disaccharides and polysaccharides are formed by a process called dehydration synthesis (the removal of water) to join many monosaccharides
Maltose → glucose + glucose
Lactose → glucose + galactose
Sucrose → glucose + fructose

Question 71

Functional Groups

Answer 71

Group of atoms with characteristic properties.
Polar (made up of atoms with differing electronegativities)
Hydrophilic → water loving
Functional groups determine the overall physical properties of the molecule such as solubility, melting and boiling point.
Function groups make up the most reactive region of the molecule and will dictate how the molecule reacts chemically