Final Review - BIOL 1306 Cheek

Hypothesis

an idea about something that can be tested

Prediction

statement about what will happen in an experiment if the hypothesis is true

Ionic Bond

- formed when electrons are transferred from one atom to another

- stronger than covalent bonds

-cation = positive charged ions

- anions = negatively charged ions

Nonpolar Covalent

- formed when atoms share valence electrons equally
- weaker than ionic bond

Polar Covalent

- formed when atoms share valence electrons unequally
- weaker than ionic bonds

Hydrogen Bonds

Very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electrostatic atom in another molecule

much weaker than covalent and true ionic bonds

What properties of water are caused by hydrogen bonds?

Cohesion
Adhesion
Surface Tension
Specific Heat
Heat of Vaporization

Cohesion

Attraction between molecules of the same substance

Adhesion

An attraction between molecules of different substances

Surface Tension

the force that acts on the surface of a liquid and that tends to minimize the area of the surface; hydrogen bonds form a lattice of water molecules which is strong and flexible

Specific Heat

the heat required to raise the temperature of the unit mass of a given substance by a given amount (usually one degree). Takes LOTS OF ENERGY

Heat of Vaporization

The amount of energy required for the liquid at its boiling point to become a gas; takes LOTS OF ENERGY

Why is water considered polar?

the polar covalent bonds (unequal sharing of electrons between atoms) and the unsymmetrical shape of the molecule means that water molecules have two poles - a positive charge at the hydrogen pole and a negative charge on the oxygen pole

Hydrophilic

"water-loving";soluble in water

Polar molecules dissolve easily in water and are hydrophilic

Hydrophobic

"Water-fearing"; pertaining to non-polar molecules (or parts of molecules) that do not dissolve in water.

Hydroxyl Group

- hydrogen atom joined to an oxygen atom by a polar covalent bond
- hydrophilic
-forming chains of sugar or fatty acids

Carbonyl Group

- a carbon atom linked by a double bond to an oxygen atom
-polar
- Hydrophilic
-Aldehydes and Ketones

Carboxyl Group

- a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group

- acidic
-polar
- hydrophilic
- components of fatty acids and amino acids

Amino Group

A functional group that consists of a nitrogen atom bonded to two hydrogen atoms

- basic

Sulfhydryl Group

A functional group consisting of a sulfur atom bonded to a hydrogen atom (—SH).

- polar
- Hydrophilic

Phosphate Group

A functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms

- acidic
- polar
-hydrophilic

Primary Protein Structure

sequence of amino acids

Secondary Protein Strucutre

Folding of the structure into alpha helices and beta pleated sheets

A-helix is coiled
B-Pleated is accordion/folded sheet

forms due to hydrogen bonding between carbonyl ) of 1 aa with amino H of another aa in another part the protein

Tertiary Protein Structure

three-dimensional folding pattern of a protein due to side chain interactions

side chain interactions caused by
- hydrogen bonds
-ionic bonds
- Van Der Waal's Interactions
-Disulfide Bridges

Quaternary Protein Structure

association between two or more polypeptide chains within one protein

Ex: insulin, collagen, hemoglobin

Prokaryotic Cells

cells without a nucleus or other membrane-bound organelles

DNA stored in the cytoplasm

Eukaryotic Cells

have a nucleus and other membrane-bound organelles

much more complex than prokaryotic cells and are multicellular

DNA stored in nucleus

Nucleus

A part of the cell containing DNA and RNA and responsible for growth and reproduction

Mitochondrion

bean-shaped organelle that supplies energy to the cell and has its own ribosomes and DNA.

Smooth Endoplasmic Reticulum

An endomembrane system where lipids are synthesized, calcium levels are regulated, and toxic substances are broken down.

Rough Endoplasmic Reticulum

An endomembrane system covered with ribosomes where many proteins production occurs - mainly transport proteins

Golgi Apparatus

A system of membranes that modifies and packages proteins for export by the cell; protein modification and export

Peroxisome

Lipid Destruction; contains oxidative enzymes

Lysosome

cell organelle filled with enzymes needed to break down proteins

Chloroplast

An organelle found in plant and algae cells where photosynthesis occurs; produces energy and oxygen releasing processes

How are proteins transported through the endomembrane system?

1. Begins in cytosol
2. Proteins are fed into the ER if they have an amino sequence called signal peptide; if they don't they stay in cytosol for rest of translation
3. The signal peptide (a series of hydrophobic amino acids) send proteins into the ER
4. in the ER, protein fold into their correct shapes and may attach to sugar groups. Most are then transported to golgi apparatus in vesicles. In the golgi, protein undergo modificiations. The final destinations includes lysosome, plasma membrane, and cell exterior

How do polar molecules cross membrane?

through active and passive transport

Hypertonic Solution

A solution in which the concentration of solutes is greater than that of the cell that resides in the solution

water will leave cell
cell will shrink

Hypotonic Solution

A solution in which the concentration of solutes is less than that of the cell that resides in the solution

- water will enter cell
- cell will swell

Isotonic solution

A solution in which the concentration of solutes is essentially equal to that of the cell which resides in the solution

- no net water movement

Active Transport

Energy-requiring process that moves material across a cell membrane AGAINST a concentration difference

REQ ATP

Cotransport

The carrier transports two substances in the same direction simultaneously, either in or out of the cell

Simple Diffusion

movement of a solute from an area of high concentration to an area of low concentration

Facilitated Diffusion

Movement of specific molecules across cell membranes through protein channels

Passive Transport

the movement of substances across a cell membrane without the use of energy by the cell

H to L

OIL RIG

oxidation is loss, reduction is gain

How does ATP couple exergonic and endergonic reactions?

AtP provides energy for both energy consuming ender rxns and energy releasing exer rxns

When the chemical bonds within ATP are broken, energy is released and can be used

ATP transfers energy to ender rxns by phosphorylating other molecules while exer rxns phosphorylate ADP to regenerate ATP

Activation Energy

the minimum amount of energy required to start a chemical reaction

Catalyst

substance that speeds up the rate of a chemical reaction

Enzyme

a biological catalyst, usually a protein, that speeds up the rate of specific biological reactions

Substrate

- the molecule upon which an enzyme acts

Enzymes catalyze the rxns involving the substrates

Active Site

a region on an enzyme that binds to a protein or other substance during a reaction.

Induced Fit

the binding of a substrate or some other molecule to an enzyme causes a change in the shape of the enzyme so as to enhance or inhibit its activity.

Competitive Inhibitor

competes with substrate for active site

Noncompetitive Inhibitor

A substance that impedes the activity of an enzyme without entering an active site. By binding elsewhere on the enzyme, a noncompetitive inhibitor changes the shape of the enzyme so that the active site no longer functions.

Allosteric Regulation

The binding of a molecule to a protein that affects the function of the protein at a different site.

Cooperativity

oxgyen binding to hemoglobin. after first oxygen molecle is bound to one heme unit, Oxygen affinity of the heme units increases to facilitate complete loading of hemoglobin with four oxygen molcules

Feedback Inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

nicotinamide adenine dinucleotide (NAD+)

conversion of NAD from NAD+ (oxidized) to NADH (reduced) and back provides the cell with a mechanism fro accepting and donating electrons

flavin adenine dinucleotide (FAD)

Oxidized form: FAD
Reduced form: FADH2

Glycolysis

- Cytoplasm
- Reactants: 1 glucose and 2 ATP
- product: 2 ATP, 2 NADH, 2 pyruvate
- G3P, NAD+, and Pi are used in later rxns
- without O2, glycolysis would still occur as it is anaerobic
- if inhibited ATP production would cease

Fermentation

- occurs in cytoplasm
- reactants: pyruvate, NADH, proton
- Products: lactate and NAD+
- fermentation replenishes NAD+ from NADH, H+ produced in glycolysis
- without O2, fermentation occurs (anaerobic)
- if inhibited, you have no method of ATP production

Pyruvate Oxidation

- occurs in mitochondrial matrix
- reactants: pyruvate, NAD+ , coenzyme A
- Products: CO2, NADH, and acetyl CoA
- pyruvate can be converted into carbohydrates, fatty acids, energy, amino acid alanine, and ethanol
- without O2, pyruvate will undergo fermentation
- if inhibited, citric acid decreases as oxaloacetate increases

Citric Acid Cycle

- occurs in Mitochondria matrix
- reactants: acetyl Coa
- products: 2 CO2, 1 ATP, NADH, FADH2 (reduced forms)
- without O2, respiratory cycle cannot function shutting down critic acid cycle (aerobic)
- if inhibited, ETC cannot occur

Electron Transport Chain

- occurs in mitochondria
- reactants: NADH, FADH2, protons, ADP, and O2
- Products: NAD+, FAD, water, protons
- without O2, electrons can't be accepted so ETC will stop and ATP will not be produced by chemiosmosis. The electrons will become backed up and eventually stop ETC. Causing products of glycolysis to go through fermentation instead of CCA
- if inhibited, there is no glycolysis so no ATP

Oxidative Phosphorylation

- occurs in mitochondria
- reactants: 8 NADH, 4FADH2, 6 O2
- products: 8 NAD+, 4 FAD+, 32 ATP, 6 H2O
- without O2, ETC does not occur so there is no proton gradient formed by electron flow. Water will not form and NAD cannot be reformed
- if inhibited, ATP cannot be produced.

Chlorophyll

Green pigment in plants that absorbs light energy used to carry out photosynthesis

Light Reactions

Input:
- water
- light
- Pi
- NADP
- ADP

Output:
- NADPH
- ATP
- Oxygen

Location: Thylkoid

Calvin Cycle

Input:
- CO2
- ATP NADH

Output:
- Pi
- ADP
- NADP+
- Sugars

Location: Stroma

How are calvin cycle and light reactions linked?

light reactions supply Calvin Cycle with CO2 to produce sugars. The Calvin Cycle supplies the light reactions with sugars to produce ATP.

Light reactions provide ATP and NADPH to Calvin Cycle and ADP, Pi, and NADP+ is returned to light reactions

Chemiosmosis in Cellular Respiration

- during ETC of cellular respiration
- in mitochondrial inner membrane
- H+ is pumped from matrix into inter-membrane space using energy derived from electron flow
- ATP synthesis occurs towards the matrix side as ATP synthase is oriented towards matrix side

chemiosmosis in photosynthesis

- occurs during light dependent reactions
- in thylakoid membrane of chloroplast
- H+ is pumped from stroma into thylakoid lumen or thylakoid space using energy derived from electron flow
- ATP synthesis occurs towards stromal side as ATP synthase is oriented towards stromal side

role of NADP+ in photosynthesis

Light rxns use energy from photons to generate high-energy electrons. These electrons are used to reduce NADP+ to NADPH - usuallly stable and can pass its H atom to other molecules

in 2nd stage of calvin cycle, AtP and NADPH are used to convert 3PGA molecules into a 3C sugar (G3P). NADPH donates electrons to a 3C intermediate to make the G3P.

Water-Soluble Hormone

-hydrophilic OR TOO large to cross membrane
- bind to extracellular membrane receptor changing the receptor intracellular domain.

Lipid Soluble Hormone

- hydrophobic
- occurs in cytoplasm
- cross membrane and bind to receptor to form hormone-receptor complex
- moves into the nuclues to bind to specific DNA sequence and begin transcription

Interphase

cell grows and makes copy of its DNA

Includes
- G1 phase
- S phase
- G2 Phase

G1 Phase

The first gap, or growth phase, of the cell cycle, consisting of the portion of interphase before DNA synthesis begins.

S phase

The synthesis phase of the cell cycle; the portion of interphase during which DNA is replicated. also duplicated the centrosome

G2 phase

The second growth phase of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs.

Mitosis (M phase)

cell division; produces 2 identical daughter cells (each with exact same content)

Ploidy Level

number of sets of chromosomes in a cell

Somatic Cells

are diploid meaning that that cell doubles its chromosomes to 4N during mitosis before dividing and resulting in daughtor cells that are 2 N

Prophase

- chromatin condenses into chromosome; each replicated chromosome appears as chromatids joined by centromeres
- mitotic spindles begin to form
- centrosomes begin to move to opposite poles (propelled by lengthening of microtubules)

Prometaphase

- nuclear envelope falls apart
- microtubules invade the nuclear and are bound to some of the chromosomes
- microtubules bind at the kinetochores

Metaphase

- centrosomes have migrated to opposite poles of the cell
- chromosomes have all lined up at the metaphase plate in middle of cell

Anaphase

- sister chromatids break apart and chromosomes begin moving to opposite ends of cell
- by end of anaphase, the 2 halves of the cell have equal # of chromosomes

Telophase

- 2 daughter nuclei form
- nuclear envelope begins to reform
- DNA begins to recondense and spindle microtubules begin to depolymerize

Cytokinesis

- division of cytoplasm
- in animals: Cleavage furrow
- in plants: cell plate

Conduction

transfer of heat from one object to another through physical contact

Convection

The transfer of thermal energy by the circulation or movement of a liquid or gas

Radiation

transfer of heat by electromagnetic waves

Evaporation

transfer of heat energy when a liquid is changed to a gas

Endotherms

-warm blooded
- use internal heat to maintain body temperatures

Ecotherms

- cold blooded
- allows body temperatures to be influenced by external environment temperatures

counter current exchange

the exchange of a substance or heat between two fluids flowing in opposite directions

Ammonia

does not required energy
but causes lots of water loss

Urea

does not lose as much water but require enzyme catalyzed reactions to convert ammonia to urea and excrete it through urination

Uric Acid

lose almost no water upon excretion but does require ATP to convert ammonia to uric acid

Tight Junctions

adjacent intestinal epithelia form tight junctions that act as a physical intestinal barrier, regulating movement of various substances across the intestinal epithelium

How does the structure of intestinal lining enhance surface area?

lining is highly folded to form microscopic finger like projections called villi which increase surface area to help with abosrption