Learning Objectives

List the organizing principles of life and relate them to the currently described domains of life.

* extract energy from environment
* replicate their genetic information in the same manner when reproducing
* have a fundamental set of genes that share structural similarites
* evolve through gradual changes in genetic info

Evaluate scientific data to support or refute a hypothesis.

observations → questions → experimentation to test a prediction → experimentation can falsify a hypothesis but cannot prove a hypothesis

What is discovery based scientific enquiry?

analye data to find a new hypothese and theories

What is hypothesis driven scientific enquiry?

emphasizing formulating and testingnew hypotheses based on observations

What are atoms?

small subdivisions of an element that retains the properties of the element

What is a molecule?

two or more atoms together

What causes Van Der Waals interactions?

movement between electrons which results in small temporary dipoles; tend to be very weak

What causes hydrophobic interactions?

two or more nonpolar molecules when they're in polar environments 

What are and what causes ionic bonds?

results from bonds between ions with opposite charges and different electronegativites

What are and what causes covalent bonds?

atoms share electrons to attain stable electron configuration, electronegativites cannot be too disimilar, typically very strong, determines properties of a molecule

What are and what causes hydrogen bonds?

slightly positive hydrogen with a slightly negative oxygen or nitrogen (bonded covalently)

Understand the energy conversions that occur during biochemical changes.

* Kinetic energy= energy of movement
* Potential energy= stored energy
* Energy conversions governed by law of thermodynamics:

1st law: energy cannot be created or destroyed

2nd law: when energy transformation occurs, there is increase in entropy.....some energy also becomes unavailable to do work

Describe the relationship between chemical bonds and energy.

Difference in bond energy and entropy change results in delta G that is either positive or negative and determines total energy change

* if deltaG is negative the reaction releases energy (exergonic ex: hydrolysis)
* if deltaG is positive the reaction requires energy to occur (endergonic ex: condensation)

Chemical reaction: when atoms combine or change their bonding partners \n Chemical transformations require activation energy because covalent bonds must first be broken

* it takes energy to break bonds
* when bonds are made energy is released
* the stronger the bond, the more energy it takes to break or more energy that is released when made

Draw the most common functional groups found on biological molecules. Hydroxyl:

end of alcohols, consist of OH which gives molecule polarity

Draw the most common functional groups found on biological molecules. Aldehyde:

contained carbonyl group, highly reactive, important in reactions

Draw the most common functional groups found on biological molecules. Keto:

contained carbonyl group in middle of carbon chain, important in energy reactions and in carbohydrates

Draw the most common functional groups found on biological molecules. Carboxyl:

end of molecules, can donate its hydrogen, at neutral pH

Draw the most common functional groups found on biological molecules. Amino:

nitrogen bonded to two hydrogen, easily accept protons and acts like a base, carry positive charge, often bonds with carboxyl groups

Draw the most common functional groups found on biological molecules. Sulfhydryl:

make up molecules known as thiols (SH)

Draw the most common functional groups found on biological molecules. Phosphate:

play critical role in energy transfer reactions, protein structure and cell membranes, important component of ATP

Define lipids based on their insolubility in water.

* insoluble with many nonpolar covalent bonds
* when close together, van der waals bonds hold them together

Identify triglycerides from their chemical structure.

three fatty acids (nonpolar carbon chain attached to a polar carboxyl group) with one glycerol (an alcohol with 3 hydroxyl groups), synthesized through 3 condensation reactions, saturated vs unsaturated(double bonds)

Identify phospholipids from their chemical structure.

two fatty acids and a phosphate compound bound to a lipid, phosphate group has negative charge so head is hydrophillic

Saturated fatty acids are

single bonds, can pack

Unsaturated fatty acids are

double bonded and kinks so it cannot pack

 Explain how saturation affects how closely they can pack together.

Saturated fatty acids tails are straight, so fat molecules with fully saturated tails can pack tightly against one another, while unsaturated can not pack closely

List some of functions of lipids.

* store energy
* structural role in membranes
* fat in animal bodies: thermal insulation

Draw the ring form of five carbon carbohydrates.

Fructose

Draw the ring form of six carbon carbohydrates

Glucose

Define monosaccarides

5 or 6 carbon rings

Define disaccharides

2 monosaccharides linked by a glycosidic bond

Define oligosaccharide

3-10 monosaccharides linked by glycosidic bonds, often bonded to proteins or lipids on cell surface, have additional functional groups

Define polysaccharide

 large polymers of monosaccharides (ex: starch, glycogen, cellulose)

Describe the functional consequences of linear versus branched polysaccharides, and how branching occurs in terms of the positional carbons involved in the bonding.

Branched more soluble in water and easier to break down \n Some rings might alternate and flip in polysaccharides

Recognized the structure of a nucleotide

a pentose (5-carbon) sugar+ N containing base + phosphate group

Mono- vs Di- vs Triphosphate in nucleotides

* Nucleoside: no phosphate group
* Monophosphate: one phosphate group
* Diphosphate: two phosphate groups
* Triphosphate: 3 phosphate groups

Complementary base pairings are

In DNA:

* A with T; purine Adenine pairs with pyrimidine Thymine
* C with G; pyrimidine Cytosine pairs with purine Guanine

In RNA:

* Adenine pairs with Uracil


* Cytosin pairs with Guanine

What are the complementary base pairing rule?

* two strands run antiparallel 5-3
* form a ladder and twists into double helix
* Base pairinf occurs between antiparallel strands

List the differences between RNA and DNA in terms of their bases, sugar, and structure.

* RNA single stranded, folds back on itself to form short double stranded regions
* DNA is double stranded, forming a helix
* DNA has a missing O
* RNA has a AU and GC pairing

Define DNA replication

Copied into a new, identical DNA molecule that can be transmitted to daughter cells/offspring

Define DNA transcription

Info encoded in DNA sequences is used to synthesize proteins (DNA to RNA)

Define DNA translation

Infromation in RNA base sequenses is used to synthesize proteins (RNA to polypeptide)

Describe how amino acids differ in their side chains (R groups).

* 20 common amino acids, have different properties based on R group
* differ in charge, shape, polarity, size and functional groups

Draw the general structure of an amino acid

amino group, carboxyl group, hydrogen on top and R group of bottom

Describe how amino acids are joined together in a peptide.

Linked by condensation

* Wgoes in order to amino-carboxyl

Describe primary structure of proteins

Amino acid monomers joined by peptide bonds, form polypeptide chains

Describe secondary structure of proteins

A helix or b pleated sheet, held together by hydrogen bonds by the amide h and the carbonyl o

Describe tertiary structure of proteins

Held together by bonds and forces between R groups or with R groups and backbone

* bonds include ionic, covalent, hydrogen, van der waals and hydrophobic

Describe quaternary structure of proteins

Ways that two or more polypeptide chains bind together and interact

* bonds include ionic, covalent, hydrogen, van der waals and hydrophobic

Define denaturation

Heat or chemicals disrupt weak interactions in a protein, destroying secondary and tertiary structure

* The protein may be able to return to normal when cooled or the chemicals are removed—all the information is contained in the primary structure.

List factors that can destabilize protein structue

* Ligand binding changes shape of the protein
* Allosteric Inhibitor can change shape of protein so ligand can no longer fit

Describe the structure of a typical biological membrane

• Give ability for cells and organelles to have own internalized environment

• Lipids and proteins move laterally through membrane

• Hydrophilic phospholipid heads on outside

• Hydrophobic tails on inside preventing polar molecules and ions from passing through

• longer the chain, the less fluidity

• more double bonds more fluidity

• fluidity decreases in cold temp.

• Membrane contains proteins

What is an integral membrane protein?

Partly embedded in the bilayer

What is an transmembrane membrane protein?

extends through the bilayer

What is an peripheral membrane protein?

only interact with the hydrophilic surface of membrane

What is an anchored membrane protein?

covalently attached to fatty acids that anchor it to the membrane

Describe how the inner and outer surfaces of a biological membrane can differ.

• inner surface: hydrophobic and tightly packed tails

• outer surface: hydrophillic with lipid heads

Explain how the temperature of the environment can affect the lipid composition of the cell membrane

The cold makes the fluidity decrease

Define a selectively permeable membrane

allow some substances to pass, but not others

What is simple diffusion?

O2, CO2 and other small nonpolar lipid soluble molecules can cross the membrane unaided

What is facilitated diffusion?

Passive transport of solutes down its concentration gradient with the help of integral transmembrane proteins

Define osmosis

• Movement of water through the membrane

• Low to high concentration

When in a hypotonic solution…

water moves into the cell making it swell and burst

When in an isotonic solution…

no net water flow in or out the cell

When in a hypertonic solution…

water would move out of the cell making it shrink

Active transport mechanism…

Energy from ATP is needed in order to move acrosses the concentration gradients

Passive transport mechanism…

Does not require metabolic energy

Polar and charged molecules use what type of membrane transport?

facilitated diffusion

Nonpolar molecules use what type of membrane transport?

simple diffusion

What is endocytosis?

• Bring macromolecules and particles INTO the cell

• Cell membrane folds around it and forms a vesicle which separates from the membrane

What is exocytosis?

Moves materials OUT of the cell

Vesicles move stuff to cell membrane and fuse with it to release it outside

What is pagocytosis?

• The cell is “eating”

• Specialized cell engulfs a large particle or another cell, forming a food vesicle (usually fuses with a lysosome)

What is pinocytosis?

• The cell is “drinking”

• smaller vesicles bring in fluids and dissolved substances

What is receptor-mediated endocytosis?

Brings specific large molecules into cell via specific receptors

Why is compartmentalization critical for normal cell function.

allows for regulation and efficiency

How do prokaryotic cells compartmentalize their cytoplasm

use protein based capsules to separate substances from each other

Purpose of the nucleus?

Store DNA

Purpose of the endoplasmic reticulum?

Modifies and synthesizes proteins, and ribosomes

Purpose of the smooth ER?

modifies and synthesizes lipids, storage of Ca for muscle contractions and is a bunch of small sheets of tubules

Purpose of the golgi apparatus?

• series flattened sacs

• modifies and processes proteins

• contains a cis, medial, and trans section

Purpose of the lysosomes?

• digests waste

• primary originates from golgi

• secondary is a vesicle from phagocytosis that has fused with a primary lysosome

Purpose of the mitochondrion?

powerhouse and site of cellular respiration

Purpose of plastids?

Circular DNA molecules and divide autonomously; chloroplasts where photosynthesis is

List the primary functions of cytoskeletal filaments.

• supports and maintains cell shape

• maintains or moves position of organelles

• interacts with extracellular structures to anchor in place

Microfilaments

• Actin polymers, attach at plus end and detach at minus end of the filament

• filaments can shorten or lengthen

• help maintain cell shape and cause localized shape changes in cell

Intermediate filaments

• tough, ropelike protein assemblages

• more permanent than other filaments

• anchor cell structures in place, resist tension maintain rigidity, in animal cells, not polymers

Microtubules

• polymers made up of the protein tubulin

• each tubulin unit has two so its called a dimer

• microtubules are tubes with hollow core and have positive and negative end

• form rigid skeleton; act as framework along with motor proteins

• can move organelles and other items

What happens in each of the three stages of cell-to-cell signaling?

1. signal is sent

2. ligand attaches to receptor

3. signal transduction (cascade of events) leads to a response

The ways in which a cell signal is different than an environmental signal.

• Environmental signal causes a change in the structure of a sensory receptor which leads to a cascade of events, its based on response signals such as touch, taste, temperature, light, magnetic fields, pH, and chemicals

• Cell signal is a ligand that is specific for a receptor (target cell). Once it reaches the receptor it causes a specific cascade of events to occur

What is juxtacrine signaling?

direct contact of two cells

What is autocrine signaling?

cell signal itself

What is paracrine?

signal diffuses to and affect nearby cells

What is endocrine signaling?

hormones are transported long distances

How do signals bind to intracellular receptors differ from those that bind to membrane receptors

• Intracellular receptors: located inside a cell so ligands must be small or nonpolar and can diffuse across membrane

• Membrane receptors: located on cell surface, cells are large and polar and cannot cross lipid bilayer, has cytosolic region that intiates signal transduction

• cytosolic region acts as an enzyme and ligand in extracellular region acts as allosteric regulator

Distinguish the three types of membrane receptors in terms of the effect of signal binding

• Ligand-gated ion channel receptors: change shape when ligand binds

• G-protein coupled receptors: ligand binding on surface exposes site on cytosolic side where a G protein can bind

• Protein kinase receptors: ligand binds and activates protein-kinase activity on cytosolic side, modifies target proteins with phosphate groups (which comes from ATP)

List three kinds of cellular responses that may occur following signal reception and transduction.

• opening ion channels

• altering enzyme activity

• altering gene expression

Define a second messenger and describe the primary benefit of incorporating a second messenger in a signal transduction pathway.

Second messenger is a nonprotein molecule that binds allosterically to an enzyme, non-specific so they can effectively distribute initial signal

Explain how a signal transduction pathway can amplify the effects of the original signal to generate a larger response.

The pathway amplifies the amount of response that occurs exponentially

Describe three ways in which a signal response can be turned off

• receptors are recycled: endocytosis of membrane receptors

• signal molecules can turn the molecules back to their inactive state

• loss of signal molecule, some molecules diffuse out of cell and get low concentrations and lose signal

Describe the effects of insulin and glucagon on glycogen synthesis and breakdown

• Glucagon is produced to pancreas and binds to G-protein coupled receptor in liver, muscle and fat cells.

• G-protein activates adenyl cyclase which catalyzes production of cAMP