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Lecture Exam 1 2


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Elements of nucleotides
1. Base (nitrogenous)
purines--adenine and guanine
pyrimidines--cytosine, thymine (only in DNA) and uracil (only in RNA)
2. Sugar--pentose sugar
ribose, deoxyribose
3. Phosphate group (PO4)
Is RNA single strand or double strand?
Single strand
Is DNA single strand or double strand?
Double strands joined together and twisted into helix, double helix, held together by bonds between the bases
What is complimentary binding?
Binding between bases formed by hydrogen bonds.
Complimentary binding:

adenine with ?
cytosine with ?
adenine with thymine
cytosine with guanine
Only in RNA: adenine with ?
Adenine with uracil
Types of RNA?
ribosomal RNA (rRNA)

messenger RNA (mRNA)

transfer RNA (tRNA)
What is ATP (nucleotide) made up of?
adenosine triphosphate:


(energy stored between bonds)
Cyclic AMP is made of up what?
cAMP adenosine monophosphate

used as internal signal for cells to communicate
What is used during formation of ATP, carry electrons?
List characteristics of cells.
1. taking in O2 and nutrients
2. have to assimilate O2 and nutrients from environment
3. expel O2 (eliminate) and wastes into environment
4. sense and respond to environment
5. use O2 and nutrients, perform chemical reactions to make usable energy
6. reproduce
7. synthesize proteins and other cell components
8. move material around inside of cell and/or move the whole cell
9. can mostly control movement of material across cell membrane
Plasma membrane also called?

fluid mosaic model
has phospholipid bilayer
What are integral proteins?
Proteins that are embedded in the plasma membrane
What are peripheral proteins?
Proteins that are on the surface of the plasma membrane
Where is cholesterol on plasma membrane?
Attached to outside or to phospholipid or protein
What is it called if carb attached to lipid?
What is it called when carb attached to protein?
What are carbs that stick out of plasma membrane called?
Glycocalyx--critical in communication
Define phospolipids?
determine how "fluid" membrane is--different cells have different amounts. Fluid determined by fatty acids
Characteristics of unsaturated fatty acids on membrane?
The more that are unsaturated, the more fluid the membrane
Function of phospholipids.
1. they are boundary between cell and environment.
2. provide framework that holds proteins.
3. cholesterol increases membrane flexibility.
4. cholesterol decreases membrane permeability.
Kinds of proteins.
Structural--will hold cell together and form 3-D shape of cell.

Enzymes--catalyze reaction

Receptors--part that receives faces out of cell communication
Types of transport proteins?
Channels and Carriers
Define channel proteins?
1. has hole in center of protein (water in channel)
2. can be extremely specific--letting only certain ions in
3. open channels--open all the time
4. gated channels--closed, only open in response to specifics
Define carrier proteins?
1. Will carry material across.
2. Never open at both ends at the same time.
Describe characteristics of nucleus?
1. contains genetic material
2. direct cell growth and functioning
3. double membrane (nuclear envelope)
4. nuclear pores allow material in and out, specific in what they let in and out.
What is a nucleolus?
where ribosomes are made and ribosomal RNA made (rRNA)
Define chromatin
What DNA is stretched out.
Define characteristics of DNA
1. can replicate itself
2. responsible for coding for all proteins
Two steps to forming protein:
Transcription: DNA sequence is copied into an RNA sequence

Translation: RNA sequence is translated to an amino acid sequence
Transcription Steps:
1. Enzyme binds to specific region of DNA on one strand (promotor region)

2. Enzyme locally splits double helix of DNA.

3. One strand side as template, enzyme will complimentary bind RNA nucleotides to the exposed DNA bases.

4. Enzyme link RNA nucleotides into a strand.

5. Continues down DNA until a (stop sequence) is reached.

6. RNA is released from DNA and DNA reformes into a double helix.

7. RNA strand can be processed in nucleus, cut and spliced back together.
Define introns.
When pieces of RNA are cut out.
Define exons.
When pieces of RNA are left in.
Name 3 kinds of RNA:
rRNA--holds components together and supply enzyme activity.

mRNA--brings code from DNA

tRNA--brings amino acids to ribosomes one at a time and decodes mRNA
What is a codon?
every three nucleotides on mRNA code for a single amino acid.
What is an anticodon?
On tRNA, every three nucleotides
List steps of translation:
1. mRNA combines with ribosomes--peptide bond

2. First tRNA with amino acid attached binds its anticodon to the first codon of the mRNA.

3. Second tRNA binds its anticodon to the second codon.

4. Ribosome enzymatically binds amino acid 1 to amino acid 3. Forms peptide bond.

5. First tRNA falls off and ribosome moves down the mRNA to next codon.

6. Third tRNA binds its anticodon to the third codon of the mRNA.

7. Same as setp 4, ribosome enzymatically...

(creating primary structure)

8. Process continues down RNA until STOP CODON reached and protein released.
Describe steps of tDNA replication:
1. Enzyme binds to DNA molecule and splits apart, breaking hydrogen bonds.

2. Enzyme will complimentary bind DNA nucleotides to the bases on both strands.

3. Enzyme will join DNA nucleotides into strand.

4. Process continues until you reach end of molecule; will have two strands.
What is mitosis?
Dividing of nucleus and dividing of cytoplasm
What is interphase?
The time in between cell division. Cells are growing and functioning during this time.
Describe Prophase:
--chromatin coils up into chromosomes
--nuclear envelope disappears
--centrioles move to opposite sides of cell
--mitotic spindle forms between centrioles
Describe metaphase:
--line up in middle, chromosomes line up
Describe anaphase:
-centromeres split and chromatids are pulled apart
Describe telophase:
reverse of prophase
--reform nuclear envelope from rough ER
--nucleolus reforms
--chromosomes uncoil
--mitotic spindle disappears

--have two different nuclei--exact replication
What is cytokinesis?
Dividing up cytoplasm
What is apoptosis?
Programmed cell death. Lysosomes (digestive enzymes) go to work to destruct cell
Define energy.
The ability to do work.
Name three types of energy:
Kinetic energy--movement
anything at absolute zero--atoms no longer in motion
above absolute zero--atoms in motion
higher temp., more motion

Potential energy--stored energy
ex: water behind dam

Chemical--stored energy in chemical bond
Define endergonic reactions:
Net input of energy to make reaction go.
Define exergonic reactions:
Net release of energy
Define coupled reactions:
Occur at same time so both will happen
Define hydrolysis and dehydration:
Hydrolysis is adding water to something.

Dehydration is taking water out of something.
Define phosphorylation and dephosphorylation:
Phosphorylation is adding phosphate group (PO4)

Dephosphorylation is removing phosphate group (PO4)
Define catabolism:
Break large molecule into smaller or break apart
Define anabolism:
Putting together molecules
Define oxidation and reduction:
Oxidation is losing an electron.

Reduction is gaining an electron.
Laws of Thermodynamics:
1st law: energy cannot be made or destroyed. You can convert one kind to another, but not destroy.

2nd law: everything is becoming more disorganized (entropy), more random
Define enzyme and characteristics:
-key ingredient to reactions
-catalyze reactions
-sometimes need coenzyme or cofactor to work properly
-very specific in which reactions they will catalyze
-frequently named for the reaction they catalyze

--ase always and enzyme
--ogen inactive enzyme
Define proteolytic activation:
Cutting protein piece off
Define activation energy:
How much free energy has to be added to allow the reaction to go forward. Enzymes work by reducing activation energy in a reaction.

ex: hurdle--w/o enzyme
bump--w/ enzyme
Do enzymes alter the equilibrium of reaction or direction of reaction?
Define active sites:
On surface, places where a particular molecule will bind...very specific on what molecule will bind
Define substrates:
Molecule that is going to participate in reaction...term used more frequently, reaction at one end or the other.
Steps of enzyme functioning:
1. Substrate binds to active site--specific.
2. Destabilize chemical bonds within substrates. This makes substrates more reactive.
3. Enzyme brings destabilized substrate into close contact.
4. Reaction happens very quickly.
5. Product released and enzyme ready to go again
6. Enzymes not altered by reaction.
Types of enzyme regulation:
Competitive inhibition
Allosteric inhibition
covalent modulation
Define competitive inhibition:
An inhibitor binds to the active site and prevents the substrate from binding.
Define allosteric modulation:
Some molecule will bind to enzyme away from active site and alters activity of enzyme.
--can increase how well enzyme works
--can decrease how well enzyme works
Define covalent modulation:
Covalently bond molecule to enzyme--sometimes it will turn it all, sometimes turn off. Common in phosphate groups.

No resources wasted.
Define saturated enzyme:
Reaction where all active sites are full, reaction rate will not go any faster.
Cell metabolism:
-NAD/NADH (when picked up electron and reduced)
-Coenzyme A (coA)
Define substrate phosphorylation:
take phosphate group and energy, take off one molecule to another
Glycolysis formula:
Glucose+2NAD+2ADP+2PO4-->2 pyruvic acid+2NADH+2ATP+2H+

No oxygen necessary at this time.
Where does glycolysis occur?
In cytoplasm.
What is it called when not enough oxygen in cells?
Lactic acid
Kreb's cycle (citric acid cycle)

a continuation of glycolysis
Pyruvic acid+coA+NAD-->acetyel coA+NADH+H+CO2

acetyl coA+oxaloacetic acid+3NAD+FAD+ADP+PO4+3H2O=

Kreb's cycle

oxaloacetic acid+3NADH+FADH2+3H+ATP+2CO2
How many times does Kreb's cycle happen?
Twice...each pyruvic acid
Occurs in mitochondria

form 2ATP for every glucose molecule
Electron transport and oxidative phosphorylation steps:
1. 10NADH=2FADH2 give electrons to first cytochrome
2. Passed to next cytochrome. When passing, also transporting hydrogen ion to space between membranes.
3. Take electrons, hook to O2 and make H2O.
4. Ions move through this protein/enzyme and use this movement as source of energy. Will use as kinetic energy into a chemical energy in a bond.
What is electrochemical gradient?
High concentration of hydrogen ions in intermembrane space. Wants charge to move back in because they are alike.

ex: water stored in dam

Theory called chemiosmotic theory.
Proteins are described as what?
Amino acids can feed in at glycolysis, Acetyl coA, Kreb's cycle
Where do triglycerides feed into these cycles?
At different places.
Describe extracellular environment:
fluids in body divided into compartments.

intracellular fluid---2/3 outside
extracellular fluid--1/3 inside

between these two compartments is separated by membranes
Describe semipermeable:
To move from one compartment to another.
Extracellular environment:
-has to maintain homeostasis
-in addition to water, has extracellular matrix--connective tissue
List types of connective fibers:
1. Collagen
2. Elastic
3. Reticular
Define ground substance:
gel-like, made of glycoproteins and proeoglycans (polysaccharide with lots of water attached)
Define and describe integrins:
-Embedded in membrane, molecules are glycoprotein.
-sometimes can be attached to cytoskeleton.
-can transmit signals between external and internal environment
-membrane receptors
Define physiology:
How systems work
Define mechanistic approach:
break down into small components to understand how it works
Define process:
How organs or cells work
Define evolution:
cell changes with environment, get more and more cells, more complex, multi-cellular level.
Cells and environment
all cells in contact with internal environment.

-cells in internal environment NOT in contact with external
Define membrane potentials
All cells have neurons and muscle cells. Use membrane potential to communicate or use.
Define homeostasis:
dynamic (always changing) state of equilibrium of internal environment. All of regulatory mechanisms of body--shared function

each body system is aimed at homeostasis.
Describe how body maintains internal homeostasis:
1. temperature
2. pH
3. volume and pressure
4. [nutrients]
5. [wastes]
6. [O2]
7. [CO2]
8. [salts/electrolytes]
Define negative feedback loop:
-monitors several variables at the same time
-a type of control where the feedback helps to correct an error, making the degree of error smaller.
Define positive feedback loop:
moves set point, change in variable, causes more change, move set point further away--in disease states, some are normal.

ex: oxytocin to stimulate uterine contractions
Name control systems and characteristics:
Nervous system: specific targets
-electrical and chemical signals
-response/effects very fast
-effects last brief amount of time

Endocrine system: many potential targets
-chemical signals only
-responses/effects are slower
-effects tend to last longer
List chemical properties of H2O:
-polar molecule
-good solvent
-dissolves well
-form hydration shells--water gets into the way
-once separated, they tend to stay separated
-high heat capacity--takes a lot of energy to change temp.
-good at distribution of heat
-high heat of vaporization--form liquid to gas
-high surface tension-hydrogen bonds creates it
-resistent to stretching
-reactive hydrolysis-add
dehydration--take out
Define salts/electrolytes:
-any ionic compound that contains cations (+) (except H) and anions (-) (except hydroxyl)
-can conduct electric current
Describe acids/bases:
Acid-dissociates in water to produce hydrogen ions and anions (proton donor)

Base-able to combine with or accept hydrogen ions in solution (proton acceptor)
What is pH?
measure of hydrogen ion concentration in solution

pH= log 1

pH is inversely related to [H+]
Higher concentration of H+, lower amount of pH #

ex: pH 1 more h+
pH 2 less
What is logrhythmic function:
Change 1 pH unit = 10x or tenfold

ex: from pH 5 to pH 3 = 100x change

pH 7 is neutral
Will strong acid/base dissociate in H2O?

Will weak acid/base dissociate in H2O?

Describe buffer system:
Contain weak acids and weak bases--change strong acid/base into weak acid/base.

Do not neutralize them, just change them.
ex: buffer system
HCl+ NaHCO3<-->H2CO3+NaCl
strong weak weak
acid base base
Common Functional Groups:
Hydroxyl -OH
Sulfhydryl -SH
Phosphate -HPO4-
Carboxyl -COOH
Amino -NH2
Define carbohydrate:
carbon, hydrogen and oxygen in specific ratio C:H:O
Describe functions of carbs:
-source of cellular fuel needed to make ATP.
-form structure of cells or organs
-cell recognition or communication molecules
Define monosaccharides:
Simple sugars

Define disaccharides:
2 monosaccharides

define oligosaccharides:
several monosaccharides, 2 or more
Define polysaccharides:
100s or 1000s of monosaccharides

Define lipids:
C H O (not in set ratio)
-insoluble in water
-nonpolar molecules
Describe functions of lipids:
-main componment in cell membranes
-energy storage
-chemical regulatory signals (steroids)
Define fatty acids:
-main precursor for other lipids
-long chain of carbon with carboxyl group at one end (C-C-COOH)
-length of fatty acid +16 long chain and even in #

-carbon atoms can make 4 covalent bonds
Define triglycerides:
Made by three fatty acids attached to glycerol
Define phospholipids:
main component of cell membranes.

phosphate group glycerol and two fatty acids
Define hydrophobic

Define hydrophilic

Define amphipathic
Hydrophobic--dislikes water

Hydrophilic--likes water

Amphipathic--likes and dislikes something.
Define steroids:
Rings of carbon. 4 rings, what's attached makes it different
Define eicosanoids:
20 carbon fatty acids "folded" in half, ring formed at one end.
Define characteristics of proteins:
-made from building blocks of amino acids
-20+ different types
Define essential protein:

Define non-essential protein:
Essential: must get in diet, body cannot make

Non-essential: Body can make from scratch
List levels of structure
Primary structure, secondary structure and tertiary structure.
Define primary structure

Define secondary structure
Primary--amino acid sequence of protein

Secondary--localized folding or twisting, folding is beta pleat, twisting is alpha helix
Define scientific method:
->experimentation->replication of results->theory->
Define hypothesis:
Educated gues about how something will work.
Charting dependent variable versus independent variable.
Dependent variable--what you think will change, on Y axis

Independent variable--is what experimenter can control, on X axis
Define characteristics of tertiary structure:
-not predictible, not repeating
-fibers or globs
-hydrophobic interactions
-will fold around to be next to each other
-ionic bonds
-hydrogen bonds
-disulfide bonds S-S covalent bond between 2 sulfur

ex: hair perm
Define denaturation:
Tertiary structure altered or changed,

-increase in temp.
-change in pH
-sometimes reversible
-disrupt H bonds
Define peptides, polypeptides and proteins:
peptides: small short chains-less than 10
polypeptides: 10-100 chains
proteins: more than 100 chains
Define nucleotides:
nucleotides are building blocks for nucleic acids
List elements of nucleotides:
1. Base (nitrogenous)
thymine (only in DNA)
uracil (only in RNA)

2. Sugar--pentose sugar

3. Phosphate group PO4

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