EXAM 1 CBIO 2200 STUDY GUIDE

The branch of biology concerned with the study of the structure of organisms and their parts.

Chapter 1:

1. Why study Anatomy and Physiology?  

- We must understand normal structure and function so you’re able to  identify abnormal or incorrect function

-We must understand mechanisms of therapies used to treat dysfunction  -Identify targets for new therapies

-If you understand what is wrong with the patient, you can compose a  mechanism to treat them

We are trying to understand “How does the human body work?” 2. Pathophysiology vs. Physiology

Pathophysiology: functional changes associated with disease and aging

Anatomy: the branch of biology concerned with the study of the structure of  organisms and their parts.

Physiology: The branch of biology that deals with the study of organ function and  interaction. OR The branch of biology that deals with the normal functions of  living organisms and their parts.

What happens when there are different numbers of electrons between atoms of the same element?

3. Levels of organization of the human body:

a) Chemical

b) Cellular

c) Tissue

d) Organ

e) Organ system

f) System

Necessary life functions of humans:

-Maintain boundaries

-Movement (both walking and the movement of substances in the  internal environment) 

-Respond to stimuli in the environment 

-Metabolism/Digestion 

-Excretion

-Reproduction 

-Differentiation 

What is the octet rule?

-Growth 

4. HOMEOSTASIS

a) The “overall job” of every system in the body

b) Balance! If you want to learn more check out what is Internet Protocol?

“Condition of equilibrium (balance) in the body’s internal environment..” Interplay of many, many processes

Maintain certain, particular internal conditions

-Body temperature

-Blood glucose

-Internal chemical reactions operate at specific pHs (certain enzymes work best in  certain pHs. Proteins can become denatured at the wrong temperatures) Why did we watch a video about Helen Keller?  Helen Keller had scarlet fever and  was sick for more than a week, losing her sight and hearing. Because the temp was  disrupted and she therefore lost sight and hearing, it’s interesting to see the  correlation.

5. Feedback and feedback systems

a) Maintain homeostasis

In a negative feedback loop, a stimulus- a deviation from a set point- is resisted  through a physiological process that returns the body to homeostasis -A negative feedback loop has four basic parts If you want to learn more check out What is the goal of integrated marketing communications?

-Body temperature is regulated by negative feedback

stimulus, receptor, control center, and effector (four parts)

The effector brings about a change that restores the homeostasis

The response “feeds back” to affect the stimulus (hence, “feedback”)

BODY TEMPERATURE IS REGULATED BY NEGATIVE FEEDBACK Temperature Rises (stimulus)

Receptor/sensor (thermostat)

Control Center (also thermostat) Don't forget about the age old question of What is Amplitude?

Effector (AC unit)

Response (Temperature falls)

Negative feedback because the temperature is increasing, but the response is a  decrease in temperature. The stimulus and response are in opposite directions. The response negates the effect of the stimulus.

A positive feedback loop is when the stimulus is reinforced by the response- less  common in physiology because then net result is that the response pushes you  further away from that set point. Positive feedback loops are more likely to become  life threatening. (like blood clots)

NEGATIVE FEEDBACK tends to negate the effect of the stimulus (blood pressure,  blood sugar, body temperature)

POSITIVE FEEDBACK tends to reinforce the effect of the stimulus Don't forget about the age old question of What is in the reticular region of the dermis?

(understand that blood clotting is an example of a negative feedback loop) as your  blood clots, it continues to clot more and more.  

Positive feedback involves amplification and the output enhances the original  stimulus. i.e. blood loss leads to decrease in blood pressure which causes more  blood loss. Blood loss also causes blood clotting, which causes more blood clotting.Don't forget about the age old question of What is the major benefit of written vs oral communication?
We also discuss several other topics like There have been how many amendments to the U.S. Constitution?

A classic example of positive feedback loop is childbirth:

A positive feedback loop results in a change in the body’s status -The receptors would be the stretch receptors in the cervix

-The control center is the posterior pituitary of the brain

-The effectors are the uterine wall muscles contracting/the oxytocin that causes  them to do so

Chapter 2:

1. Elements, Atoms, Ions and Isotopes: Review of some basic terms and  definitions  

a) Element

b) Atom

i. Proton

ii. Neutron

iii. Electron

c) Atomic number (Z)

-Number of protons  

-Defines the element

d) Atomic Mass (mass number)

-Can differ based on number of neutrons

-The average atomic mass (calculated from isotopes) is on the periodic  table

e) What happens when there are different numbers of electrons between  atoms of the same element? (Cations-positively charged and Anions negatively charged)

f) What happens when there are different numbers of neutrons between  atoms of the same element? (Isotopes)

2. Chemical Bonds

a) The octet rule- atoms of main-group elements tend to combine in such  a way that each atom has eight electrons in its valence shell, giving it  the same electronic configuration as a noble gas.

b) Ionic bonds- transfer of valence electrons between atoms and  generally results in two oppositely charged ions.  

c) Covalent bonds (sharing electrons between atoms, within a molecule) d) Polar vs. Non-polar covalent bonds

Non-polar- equal sharing of electrons- no net dipole moment

Water molecules have unequal sharing of electrons (polar-covalent)  bonds. Therefore, it’s partially attracted to other water molecules. It’s  

an excellent polar solvent.

e) Hydrogen bonds

i. Really, these are a special case of covalent bonds

ii. These are attractions BETWEEN molecules, rather than bonds that  hold atoms together within molecules

iii. BUT they are also important WITHIN large molecules in holding  them in a particular shape

3. Chemical reactions

a) Synthesis (anabolism)

Creating something

A + B ???? AB

Reactants????Products

b) Decomposition (catabolism)

Taking something apart

AB ???? A + B

Reactants ???? Products

c) Exchange

AB + CD ???? AC + BD

Reactants ???? Products

d) Reversible

AB ???????? A + B

Forward reaction: left to right

Reverse reaction: right to left

To make reactions happen faster you can: increase temperature, have  more reactants to react with each other, or lower activation energy.

e) Catalysts

i. Often are enzymes in biological systems

-Enzymes decrease the activation energy required for a given  chemical reaction to occur (brings reactants closer together) -Most often, enzymes are proteins

-Without an enzyme, the energy input needed for a reaction to begin  is high.

-With the help of an enzyme, less energy is needed for a reaction to  begin.

Temperature and pH can affect enzyme efficiency

4. Properties of water, acids, bases, and salts

a) Water is critically important in living systems

b) Water is an excellent solvent

c) Water dissolves polar substances

Water can surround elements and cause them to separate from their ionic bonds Ionic compounds (held together with ionic bonds) dissociate into ions in water NaCl(aq) ???????? Na+(aq) + Cl-(aq)

(reassociation is possible too!)

Electricity is like movement of ions in the body- Sodium is key. Dissociation Reactions:

KI(aq) ???????? K+ + I

CaCl2(aq) ???????? Ca2+ + 2Cl

Na2So4(aq) ???????? 2Na+ + (So4)^2-

Salts and acids dissociate into ions:

CaCl2(aq) ???????? Ca2+ + 2Cl

HCl(aq) ???????? H+ + Cl

Acids dissociate into hydrogen ions

Bases dissociate into [hydroxide] ions:

Acids can donate protons, or accept electrons

Bases can accept protons, or donate electrons

Acids and bases combine to form salt and water:

Hydrogen ions combine with hydroxide ions to form water:

Water dissociates into hydrogen ions and hydroxide ions:

Only a little dissociates.

Acidic solutions:

• Higher concentrations of H+

• Greater than 1x10^-7 M of H+

• Lower concentrations of OH

Basic solutions:

• Lower concentrations of H+

• Lower than 1x10^-7 M of H+

• Higher concentrations of OH

Compounds that dissociate into ions in water are ELECTROLYTES

**Acids and bases dissociate into ions

**Hydroxide ions and hydrogen ions combine to form water

5. Hydrogen ion concentration and pH

As H+ concentration increases, the pH goes down

As the H+ concentration decreases, the pH goes up

a) Water dissociates into hydrogen ions and hydroxide ions b) Normal concentrations of H+ and OH- are equal in water

c) Acidic solutions have more H+ than normal water

d) Basic solutions have less H+ (and more OH-) than normal water e) pH is a way to express the concentration of H+ in a solution i) pH = -log[H+]

LOW pH

HIGH pH

pH of the body is 7.4

Which is more acidic (lower number on pH scale); a solution with pH =  9.82 or a solution with a pH= 9.65? The pH of 9.65

Which has a higher concentration of H+? pH of 9.65

When the body becomes more acidic, does the pH increase or  decrease? Decrease

How can stomach acid have a pH that is outside the range of pH  compatible with life and still be part of the living body?  

-It has a specialized lining

Sodium bicarbonate in alka seltzer is a base, which neutralizes the  acid in heartburn

Sphincter allows acid to splash into esophagus, which burns

Another brand uses calcium carbonate, which neutralizes the acid too An acid and a base neutralizing each other is called an exchange  reaction to make a salt and water. (Exchange reactions can be  reversible. What distinguishes them is that there’s an exchange of one  or more ionic components) (The products of an exchange reaction are  neutral and stable)

6. Buffers

a) Resist changes in pH

b) Important in maintaining the internal pH at a constant level c) Act by “tying up” excess H+ and OH-, preventing them from changing  the pH

d) Combine with both H+ and OH

e) Buffers are mixtures of weak acids or bases and their corresponding  salt

Weak acids- less dissociation into ions than strong acids

H2CO3 ???????? HCO3- + H+

Doesn’t dissociate completely^^ but very little of the parent compound itself is  left.

Strong acids and bases are more likely to completely dissociate into OH- and H+ H+ can then combine with OH- and form H2O

Provides a “handle for OH-“

So what could tie up the excess H+ ions in our weak acid example? HCO3- + H+ ???????? H2CO3-

Provides a “handle” for H+

Therefore, resists a change in pH

If we mix a strong acid and a weak base, the weak base will react with the H+  from the strong acid, forming a weak acid and buffering.

If we mix a strong base with a weak acid, the weak acid will donate its H+ to the  strong base’s OH- to form water, buffering the system.

7. Introduction to Organic Chemistry and Functional Groups

(See table 2.1 in OpenStax; table 2.5, p.42 in Tortora)

a) Organic Chemistry is the chemistry of C-containing compounds b) Functional groups give the molecule different properties  

(“personalities”)

c) Carbohydrates

i. Monosaccharides, disaccharides, and polysaccharides

We use carbohydrates for energy: sugars, starch

Dehydration synthesis means you’re losing a molecule of water

Individual molecules are synthesizing larger molecules.  

Glycogen is a starch, stored in your liver as a potential fuel source.

When glycogen is broken down, we start at the ends of the molecule (9  ends). If its more branched, you have more places to hydrolyze and it’s  faster to break it into single strands and then break it down further.

What do carbohydrates do in the body?

• Provide energy

• Act as signal molecules

• Contribute to structure and function of DNA and RNA

d) Lipids and phospholipids

If a fatty acid is saturated, all of the bonds are going to be taken up by hydrogen.  Every bond is a single bond. In palmitic acid, there is a long chain, and it’s  

saturated. You can have up to 3 fatty acids stuck to the glycerol backbone.  

Mono, di, and tri glycerides

The fatty acids do not have to be the same.  

Mono unsaturated means that there is one double bond.

All of the carbons have to be saturated to make the molecule as a whole  

“saturated. Therefore, the example above is unsaturated.

Phospholipid: phosphate group and 2 fatty acid tails- one region can interact with  water (the polar head) and one region cannot (the nonpolar tail). There is also a  

glycerol backbone. Polar and non-polar ends. The phosphate group is important  for the polarity of the head.

This is called an AMPHIPATHIC molecule^^

All of these molecules have 4 rings. Help maintain the fluidity of the cell, but also  maintains its firmness so the cell membrane doesn’t turn to mush. They’re lipid  soluble. The body needs cholesterol, because it uses it. Cholesterol has a small,  water-soluble polar region that dissolves in water (the OH), but nearly the entire  cholesterol molecule is non-polar, which will NOT dissolve in water — like oil.  This makes cholesterol an example of an amphipathic molecule — part water soluble, part water-insoluble.

e) Proteins

Amino acids together are called peptides and held together by peptide bonds. Peptide bonds are covalent bonds.

Monosaccarides forming disaccharides, fatty acids combining with glycerol, and  joining amino acids to make a peptide, are all examples of dehydration synthesis.

There are 6 amino acids in this structure, and 5 peptide bonds. They only fit  together in a chain. This is the primary structure (amino acid sequence)

Amino acids have peptide bonds and hydrogen bonds (that form the  secondary structure) 

The above picture depicts two types of secondary structures. Hydrogen bonds  are keeping the shapes of the secondary structures. In a beta-pleated sheet, the  molecule is folded. In the alpha helix, the R groups are on the outside. In the beta  pleated sheet, the H bonds are between strands. The strands can either be  parallel or anti parallel. B sheets are more stable than Alpha helixes.

Collagen- maintains tough structure in skin.  

Tertiary structure- involves the overall folding and shape of the protein. The  protein molecule will bend and twist in such a way as to achieve maximum  stability or lowest energy state

Quaternary structure- number and arrangement of multiple folded protein  subunits in a multi-subunit complex. The quaternary structure refers to how  these protein subunits interact with each other and arrange themselves to  form a larger aggregate protein complex.

Hemaglobin- transports oxygen. One hemoglobin carries 4 molecules of oxygen

f) Nucleic Acids- DNA and RNA

Nucleic acids are composed of nitrogen containing bases, 5 carbon sugars, and  phosphate groups in a ladder-like arrangement.  

a) ATP- ribose sugar, an adenine base, and three phosphate groups.  ATP is classified as a high-energy compound because the two  covalent bonds linking its three phosphates store a significant amount  of potential energy. In the body, the energy released from these high  energy bonds helps fuel the body’s activities, from muscle contraction  to the transport of substances in and out of cells to anabolic chemical  reactions. Can donate the phosphate group to other molecules  (phosphorylation). Important signaling pathways inside cells.

Monomers for carbohydrates: monosaccarides

Monomers for lipids: fatty acid chains and glycerol

Monomers for proteins: amino acids

Chapter 3:

Chart/table of organelles and their functions. We should be prepared to identify  an organelle and describe its function.

1. Generalized Cell Structure

The nucleus tells you that you’re looking at a cell and clues you in to the  type of cell and they type of tissue.

a) 3 general areas to be studied more in detail

• Nucleus

• Plasma Membrane

• Cytoplasm and associated organelles

2. Plasma Membrane

a) Lipids (mostly phospholipids) (blue and pink) (polar heads are blue and  fatty acid tails are pink) (bilayer)  

• The polar heads come into contact with the watery extracellular  environment and the watery cytosol

• The non-polar fatty-acid tails are in contact with each other.  Hydrophobic environment. This fatty layer makes the plasma  membrane such a good barrier.  

b) Proteins

• The proteins sit in and span the plasma membrane. One side on  inside, and one side on outside.

• The purple strings are structural proteins that also span the  membrane and interact with other proteins

c) Other

• The purple strings are carbohydrate molecules, either  

associated with the lipids or the proteins

• The tiny orange strings near the hydrophobic tails are  

cholesterol and contribute to the fluidity

“A sea of phospholipids”

Function of lipids

• Form barrier, form the structure or skeleton (framework) of the membrane.  The amphipathic property is very important

Functions of membrane proteins

• Transport substances across the lipid bilayer

• Enzymes (proteins are enzymes)

• Receptors for some stimulus

• Join membranes to adjacent cells

• Structure

• Cell identity markers (needs to identify, or immune system will attack)  

If plasma membranes are barriers, how do things get in/out of the cell? • Several ways, depending on the type of substance crossing • Active (requiring energy)

• Passive (no energy required)

3. Transport of substances across membranes

a) Passive processes (Do NOT require energy input by the cell) Substances move across a membrane

Substances move from an area of higher concentration to an area of  lower concentration (down the concentration gradient)

Kinetic energy is the energy of movement

Diffusion

• The movement of molecules or ions form a region of higher  concentration to a region of lower concentration

• Depends on the kinetic energy of the molecule or ion (i.e.  

heating up the system so they diffuse faster)

• Substances diffuse down their concentration gradients i) Simple diffusion- a polar molecule isn’t likely to diffuse through.  Have to be really really small and non-polar (hydrophobic) (CO2  and O2) Water has to use a channel because it has to be  regulated.  

ii) Facilitated diffusion- anything that has to use a channel to get  across, but no ATP is facilitated diffusion. “The spontaneous  passive transport of molecules or ions across a membrane via  specific transmembrane integral proteins.”

When the molecule interacts with the channel, the channel  changes shape and is let through)

(An ion channel is a different entity, and we will talk about it  later)

iii) Osmosis (special case of diffusion)

“Water moves form an area of lower solute concentration to an  area of higher solute concentration”

“Moving from where there’s more water to where there’s less  water”

The membrane is permeable to water but not to the solute. The water will move until the hydrostatic pressure (pressure  exerted by a fluid against a container, vessel) opposes it. • Movement of H2O across a membrane

• Describing the differences in solution concentrations  across a permeable membrane

a) Isotonic- surrounding medium has the SAME  

concentration of solute as cell interior

b) Hypertonic- Surrounding medium has MORE solute  than cell interior

c) Hypotonic- Surrounding medium has LESS solute  than the cell interior

If we take a cell and put it in a hypotonic solution, the cell  

will swell and burst

If we put a cell into a hypertonic solution, the cell will  

shrink (water moving from cell to environment

iv) Filtration

“The flow of liquid through a filter (or membrane that acts like a  filter) due to hydrostatic pressure

Pushing of fluid through a membrane

• Due to pressure of the fluid

b) Active processes  

• Require some sort of energy

• Energy provided by ATP OR the energy is provided  

indirectly by another process

i) Primary active transport  

• Hydrolysis of ATP provides energy to “drive” the  

mechanism

• Usually catalyzed by membrane protein “pumps”

• Can result in the formation of a concentration gradient  

across a membrane

• Na+/K+ ATPase or Na+/K+ pump is an example

• Not limited to moving substances down a concentration  gradient (very often moving against- from where there’s  

less to where there’s more)