BIOL 2160 - exam 1 notes

Physiology:

the function or what something does (ex: if you change the shape of a molecule then you will also change the function)

Anatomy:

the structure or what something is

Levels of physiological organization:

1. molecules (ATP, water, neurotransmitter receptors, etc.)

2. cells (neurons, epithelial cells, etc.)

3. tissue (nervous tissue, muscle tissue, etc.)

4. organs (heart, liver, kidneys, etc.)

5. organ systems (cardiovascular, gastrointestinal, etc.)

4 major tissue types:

1. nervous tissue

2. muscle tissue

3. epithelial tissue

4. connective tissue

Tissue:

made of similar cells performing a common function; all have some characteristics in common

Nervous tissue:

specialized for sending and receiving information - it communicates (its purpose); sending and receiving information (ex: motor neurons, cortical interneurons, etc.)

Muscle tissue

specialized for contraction - to generate movement of some kind; skeletal muscle is attached to bone and moves the skeleton (voluntary); cardiac muscle is only found in the heart; smooth muscle is found in you internal organs

Epithelial tisseu:

found in organs, glands, and lining body cavities/orifices - used for exchange and makes up the boundary between one area and another -makes up most of you skin and all of your glands (ex: intestinal epithelial cells, mouth, noes, ears, etc.)

Connective tissue:

characterized by very few cells and lots of extracellular materials like water, salta, and proteins - includes fat, bone, cartilage, blood, tendons (muscle to bone), and ligaments (bone to bone)

Endocrine glands:

secrete molecules (usually hormones) directly into the blood stream (ex: pancreatic and thymus glands) - secrete into a capillary (the bloodstream)

Exocrine glands:

utilize a duct - secrets molecules into the body cavity (stomach or mouth) or the the exterior of the body (sweat)

Homeostasis:

the ability to maintain a relatively stable internal environment despite fluctuations in the external environment (most important concept in physiology); essential for survival and function of all cells; deviation from homeostasis indicates disease; most often accomplished through negative feedback; you internal conditions are changing constantly (ex: body temperature)

Negative feedback:

involves returning conditions to a “set point”; a loop helps return internal conditions to a set point when they deviate too far outside of an acceptable range - the input and output are opposites (ex: shivering when cold makes you warmer, sweating when hot is cooling you off) - does not mean “bad” - most feedback mechanisms in the body are negative

Negative feedback involves:

• sensors - in the body to detect change and send information to integrating center

• a integrating center - assesses change around a set point; sends instructions to an effector (usually the brain but not always)

• effectors - makes the appropriate adjustments

Antagonistic effectors:

homeostasis is often maintained by opposing effectors that move condition in opposite directions - this maintains conditions within a certain normal range, or dynamic constancy - when you are hot you sweat, and when you are cold you shiver; do the exact opposite of each other but are woking together to keep conditions stable

Positve feedback:

moves conditions further away from a set point - the input and output are the same in a loop (ex: uterine contractions during child birth, and itching a bug bite) - does not mean “good”

Cell biology:

an understanding of chemistry is import because the interaction between atoms is one of the lowest levels of biological organization

Atom:

the basic unit of all forms of matter - the smallest unit of matter that retains the physical and chemical properties of the element - makes up everything living and nonliving - made up of subatomic particals

3 most stable subatomic particals:

1. neutrons

2. protons

3. electrons

Neutrons:

found in the nucleus - have no charge - all nuclei have a positive charge

Protons:

found in the nucleus - positive charge - all nuclei have a positive charge

Electrons:

have a negative charge - orbit around the nucleus - constantly in motion and are attached to the positively-charges nucleus

The electron orbitals:

the 3 dimensional space around the nucleus of an atom where an electron will be found - not a solid object - just a space occupied by electrons - space can be shared

Chemical behavior of an atom:

will be determined by the number of electrons in the outermost electron shell - an atom with an incomplete (partially full) electron shell is reactive whereas an atom with a full electron shell is inert, ot not chemically active

Reactive atom:

an atom that will try to fill the valence shell by interacting with other atoms - interaction my result in 2 atoms forming a chemical bond

Chemical bond:

an attraction that holds 2 atoms together - happens because 2 or more elements are trying to fill up their outer electron orbital

Molecule:

2 or more atoms held together by chemical bonds - the smallest unit that retains the physical and chemical properties of a compound - identical atoms/molecules/elements - different atoms/molecules/elements

Ion:

likely to be formed if an atom has an almost empty or an almost full outer electron shell - a charged atom or molecule (is charged because it has either lost or gained electrons) - formed when an atom gains or loses electrons because it no longer has the same number or slectons as protons

Anion:

a negatively charged atom or molecule - has gained an electron

Cation:

a positively charged atom or molecule - has lost an electron

Ionic bond:

a positive and negative attraction

Covalent bond:

a bond formed when 2 atoms share pairs of electrons

Non-polar covalent bond:

involves electrons being shared equally - neither atom will have a charge - a covalent bond in which the sharing of the electron pair is equal (ex: hydrogen gas)

Polar covalent bond:

a covalent bond in which the sharing of the electron pair is unequal - electrons spend more time close to one nucleus than to the other (ex: water) - strong bonds

Elecrtonegativity:

an atom’s ability to attract and hold electrons - an indication of how much [positive charge is in the nucleus - assigned a numerical value - the higher the number the more electronegative an atom is

• hydrogen: 2.2

• carbon: 2.6

• nitrogen: 3.0

• oxygen: 3.4

*HCNO - if letters are next to each other than it means it will be non-polar; if atoms are separated by at least one on this list than it means it will be polar*

Hydrogen bond:

formed by the charge attraction when a hydrogen atom which is covalently bonded to one atom is attracted to a second atom - has to be connected to at least 2 other elements - reason why water sticks to water in a river, lake or ocean - weak bonds

Hydrophilic:

the property of having an affinity for water - polar and ionic substances are easily dissolved in water - Like dissolves Like

Hydrophobic:

the property of not having an affinity for water - non-polar substances - the polarity of water molecules makes water a poor solvent for molecules which do not have charged regions - molecules clump together in water

4 basic types of biomolecuels:

1. carbohydrates

2. lipids

3. proteins

4. nucleotides

thes accomplish every physiological process in the human body

Carbohydrates - sugars

monosaccharides contains carbon, hydrogen, ans oxygen (1:2:1 ratio) - ring structure - major purpose is short-term energy - energy storage molecule in humans is glycogen, used for quick-energy and is metabolized when blood sugar levels drop - stored in the skeletal muscle and liver of humans

Carb-loading:

the process of increasing the amount of glycogen stored in the body prior to a race or competition - a 2 stage process:

1. depletion pahse: a week ot 2 prior to competition, intense exercise and a no-carb/high protein diet

2. loading phase: a couple of days before competition, no intense exercise, eating as many carbs as you can take in

Water weight:

blood glucose is metabolized first in the human body, afterwards glycogen reserves are metabolized and finally fat is burned - glycogen is polar, which means it dissolves in water, and each ounce of glycogen has as many as 4 ounces of water attached to it - fat is extremely non-polar because it has no water attached to it

Lipids - fats

hydrophobic (insoluble in water) - consist of non-polar hydrocarbon chains and rings

Saturated fat:

solid at body temperature - have no C=C bonds - saturated with hydrogens (lard, grease, fat, etc.)

Unsaturated fat:

liquid are body temperature - have at least one C=C double bond - Etc. olive oil, vegetable oil, etc. - atoms are more spaced out - way healthier for you because liquids in the bloodstream are less likely to clog your arteries than solids

Phospholipids:

2 fatty acids + phosphate group attached to glycerol backbone - dominant component of cell membranes - contains hydrophilic (polar) and hydrophobic (non-polar) regions - heads are able to dissolve in water and tails repel water

Steroids:

three 6 carbon rings + one 5 carbon ring - mostly non-polar - many function as hormones - made from cholesterol (4 rings fused together) - all have the same structure

Proteins: molecular tools

composed of multiple amine acids (amino acid polymers) - sequence of amino acids is determined by DNA through processes of transcription and translation

Amino acids:

composed of an amino group, a carboxyl group, and a functional group/R group - has 20 R groups and 20 different amino acids - R groups give amino acids different properties (ex: polar, non-polar, etc.) - each have the same general structure

Levels of protein structure:

1. primary structure - actual oder of amino acids

2. secondary structure - refers to every little coil, fold, or helix over the protein

3. tertiary structure - refers to the overall 3-D shape of the protein (a proteins tertiary structure is its function)

4. quaternary structure

structure = function - all proteins have 1-3 but only some have 4

Protein structure:

secondary, tertiary, and quaternary structure contribute to 3D shape of protein - protein 3D structure is diverse - 3D structure if protein determines function - because bonds between amino acids and peptides can be weak, proteins can be denatured (broken apart) by heat, changes in pH, etc.

Nucleotides:

composed of 5 carbon sugar (pentose), one or mroe phosphate groups, and a nitrogen base - nitrogen bases fall into 2 categories:

1. pyrimidine

2. purine

are the “letters: that make up your DNA and RNA (G, A, T, and C in DNA) - G forms hydrogen bonds with C and T forms hydrogen bonds with A

Pyrimidine:

one carbon ring (ex: cytosine (C), and thymine (T) in DNA)

Purine:

two carbon rings (ex: guanine (G), and adenine (A) in DNA)

DNA structure:

has been compared to a book - phosphate groups provide protection (front and back covers of a book) - G, A, T, and C are the nitrogenous bases that make your DNA different from everyone else (like pages of the book and where the real information is found)

What is a gene?

a length of DNA that codes for a specific person

Gene expression:

converting DNA into proteins - transcription and translation

Transcription:

• DNA → RNA

• occurs in the nucleus because thats where the DNA is

• happens FIRST

Steps:

1. RNA polymerase binds to promoter

2. RNA polymerase then unzips DNA, separates double helix

3. Free ribonucleotides bind complementary bases on DNA sense strand

4. RNA polymerase moves down DNA, new RNA molecule is synthesized

   1. G turns into C

   2. C turns into G

   3. T turns into A

   4. A turns into U - NO THYMINE IN RNA

5. product: pre-RNA transcript

Translation:

• RNA → protein

• occurs in the cytoplasm

• happens on the ribosome where the RNA copy (transcript) is used to make the protein

• 3 types of RNA:

  • mRNA (messenger RNA)

  • rRNA (ribosomal RNA)

  • tRNA (transfer RNA)

Steps:

1. initiation: tRNA, ribosome, and mRNA come together - codon on mRNA pairs with anti-codon on tRNA (always starts with AUG)

2. peptide bond forms between amino acids

3. tRNA and P site is released - tRNA at A site moves to P site - another tRNA moves into now empty A site

4. peptide bond forms between amino acids

Genes:

the human genome project revealed that most of the DNA of humans does not encode mRNAs or any other RNAs, they appear to serve no purpose in our life cycle - accounts for an astonishing ~98.5% of human chromosomal DNA - these non-coding regions are smiliar in humans, but not identical - accounts for your DNA fingerprint called mini-satellite sequences

Post-transcriptional processing:

pre-mRNA → mRNA

1. introns are removes

2. CAP is added to 5’ end of pre-mRNA

   1. pre-mRNA is made up of introns (junk) and exons (actual coding information)

3. poly-A tail is added to 3’ end of pre-mRNA

mRNA:

messenger RNA - carries genetic codes out of nucleus - made of codons (3 nucleotides in a row) and each codon codes for one specific amino acid to be added to the protein during translation

rRNA:

ribosomal RNA - forms RNA component of ribosome and allows protein assembly - ribosomes are made up of this and proteins

tRNA:

transfer RNA - allows protein assembly - does the job of reading mRNA and bringing in the correct amino acids to build the proteins during translation - where anti-codons are found and each anti-codon recognizes and binds to a specific codon in the mRNA

AUG:

human genetic code - start codon (first codon that maters) - codes for the amino acid methionine - signals for translation to begin

UAA, UGA, and UAG:

human genetic code - stop codon - does not code for an amino acid - only signal for translation to stop

Human genetic code:

64 possible codons - 4 different nucleotides (G, C, A, and T) - a codon is a combination of 3 nucleotides

• Example: ACCUACC/AUG/GGC/CCU/UAA/A

  • how many amino acids does this code for?

    • 3 - AUG, GGC, and CCU

    • UAA is a stop codon and does not code for an amino acid

• Example: CCAG/AUG/CCA/UCA/UAA/G

  • how many amino acids does this code for?

    • 3 - AUG, CCA, and UCA

    • UAA is a stop codon

Post-translational processing:

cleavage of amino acids - addition of other chemical groups (ex: addition of carbohydrates through glycosylation) - many post-translational modifications occur in the Endoplasmic reticulum and Golgi apparatus - proteins can still be changed - some proteins must be leaved (broken) to be activated - small chemical groups can also be added in the endoplasmic reticulum or the Golgi apparatus - any change tot he structure of the protein will result in a change of the function

Genome:

all the genes in a particular individual or all the genes of a particular species - researchers believe humans have about 25,000 genes

Protemone:

all the proteins that are produced from the genome - more than 150,000 proteins are produced in the human body

Bidirectional:

when the reaction proceeds in both the foward and the reverse directions at the same time

Catabolic Reaction:

the breakdown of larger molecules into smaller molecules - releases energy

Anabolic Reaction:

the production of larger molecule from smaller reactants - requires energy and builds things

1st law of thermodynamics:

energy cannot be destroyed or created, only transformed (ex: conversion of light energy into glucose by plants)

2nd law of thermodynamics:

with every transfer or transformation of energy, some useable energy is released as heat

Endergonic reactions:

chemical reactions that require an input of energy - products contain more free energy than the reactants - energetically uphill - products have more energy than the reactants, since energy cannot be created it must be added

Exergonic reaction:

chemical reactions that release energy - products will have less free energy than the reactants - energetically downhill - reactants have more energy then the products, since energy cannot be destroyed it must be released as the reactions occur

Activation energy:

the energy required for the reactants to engage in a reaction - most molecules lack this needed for a reaction to occur - all reactions require this whether they are endergonic or exergonic - can take the form ot heat (molecules colliding together) - barrier can also be surmounted through catalysts

Enzymes:

a class of proteins that serve as biological catalysts

Catalysts:

chemicals that:

• increase the rate of a reaction

• are not changed by the reaction (so can be used repeatedly)

• have no effect on free energy of reactants or products

• in enzymatic reactions, reactants are called substrates

Ligand:

receptor interactions - anything that binds to a receptor (a protein)

Affinity:

a meacure of how attracted a ligand is to a receptor - based on charge