Exam 1: MCB 150 Biology

Macromolecules: Carbohydrate, proteins, lipids, nucleic acids Components of a cell: prokaryote, eukaryote, organelles

What defines a Prokaryote cell? and what it contains(5)

Definiton: single celled organisms that do not have a membrane bound nucleus or internal membrane bound compartments (organelles)

-Bacteria and archaea

Contains:

-nucleoid region

-cyoplasmic membrane

-lysosomes

-ribosomes

-cell wall (not all)

Eukaryote characteristics (2) and what it contains (6)

characteristics:

-animal, yeast, fungi, plants

-has a nucleus

contains:

-mitochodria

-nucleus

-lysosomes

-golgi apparatus

-ER

-cytoplasmic membrane

What are organelles? What is the difference between them in prokaryotic and eukaryotic cells?

Organelle: a tiny specialized structure inside a cell that preforms a specific job (ex: nucleus, ribosomes)

Eukaryotic: membrane bound compartments

Prokaryotic: no membrane bound

Bacteria vs archaea vs humans

bacteria: true bacteria, found everywhere

archaea: ancient prokaryotes that are found in extreme habitats that resemble early earth (salt, heat, pressure, acids)

*archaea are more closely related to humans despite looking more like bacteria*

What is the cell theory?(3)

1. cells are the fundamental unit of life

2. all organisms are composed of one or more cells

3. all cells come from preexisting cells

cell wall

provides shape and protection in plant and most prokaryotic cells

What does the plasma membrane do for a cell? (5)

1. Every cell has a plasma membrane

2. allows cells to maintain a constant internal environment

3. acts as a selectively permeable barrier 

4. is an interface for cells where information is received from adjacent cells and extracellular signals 

5. has molecules that are responsible for binding and adhering to adjacent cells 

What happens in the nucleus?(3) What is the structure?

What occurs:

-maintenance and replication of the genome 

-transmission of genetic information (transcription)

-makes ribosomes in the nuclear region (nucleolus)

Structure:

Inner and outer membrane which makes up its nuclear envelopes

Mitochondria purpose and structure

Purpose: ATP generation 

Structure: inner and outer membrane 

Rough endoplasmic reticulum purpose? structure? (3)

Purpose: secreted proteins have their origins in the rough ER, processes proteins

Structure: 

-physically continues with the outer membrane of the nucleus 

-ribosome on top of membrane make it rough 

-lumen: inner rough ER

Smooth ER purpose (2) and structure

Purpose: 

• lipids being made 

• detoxification

Structure:

• Membrane is continuous with rough ER

• The membrane is not bumpy because it has no ribosomes (no proteins) 

Golgi apparatus purpose

Accepts proteins from the rough ER, modifies and processes proteins, sends proteins to other organelles 

Ribosomes purpose and structure

Purpose: to make proteins

Structure: 2 subunits combine during translation

What are the 2 types of ribosomes?

Free: proteins made for the cell they are in

Membrane bound: attached to rough ER, proteins synthesized for export

polysomes

Many ribosomes that are formed at the start codon during translation

What are the 4 major macromolecules and their abundance?

1. protein (most abundant)

2. Nucleic acids

3. carbohydrates/polysaccharides

4. lipids (least abundant)

monomers of the macromolecules

1. protein: amino acids

2. nucleic acids: nucleotides

3. polysacharide: monosaccharde

4. lipids: fatty acids (and usually glycerol)

condensation/dehydration synthesis

Take H2O out to form polymers

hydrolysis rxn

add H2O back to break polymers

What are Carbohydrates purpose (4)? What is the structure? What does the structure include?

Purpose:

-energy source

-structural roles (insect exoskeletons and cell walls)

-cell identification

-cell recognition  

Structure:

Carbon ring structure 

• Same amount of carbon as oxygen and half of hydrogen (ex: hexose sugar formula: C₆H₁₂O₆)

• Carbonyl group

What is a link of several monomers called?

oligosaccharide

3,5,6 carbon monosaccharide's prefix/name

3: triose

5: pentose

6: hexose

carbonyl group

carbohydrates

H-C-O

creates hydrogen bonds

what are Isomers? what are the two classifications?

Isomer: same chemical formula different structures (ex: glucose and galactose)

Classifications:

• A-glucose (alpha): hydrogen is above the ring 

• B-glucose (beta): hydrogen is below the ring

*They are isomers of each other*

What is a Aldose/aldehyde sugar? What are examples?

The carbonyl group is at carbon 1 

-The number of corners on the ring is the same number of carbons in the formula (ex: glucose, galactose, ribose)

Ketone/ketose sugar

The carbonyl group is at Carbon 2 

• The number of corners on the ring is one less than the number of carbons in the formula (ex:,fructose)

What are disaccharides? how does adding the bond affect the chemical formula?

Disaccharide: 2 monosaccharides creating a covalent glycosidic bond 

Effect on chemical formula:

For every bond, take an H2O out of the formula because of dehydration rxn

*ex: Hexose Chemical formula: C12H22O11*

How does naming bonds in a disaccharide work?

• a-1,4 glycosidic linkage 

1,4 tells us which of the carbons the bond is forming between

a (alpha) tells us that the H is above the ring 

How does bonding work in a disaccharide when the orientation of molecules is wrong?

ex: lactose

• Disaccharide of glucose and galactose 

• Galactose is turned upside down so bond can occur

Carbohydrates cell identification and recognition

When Oligosaccharides link to other macromolecules like membrane proteins or lipids, carbohydrates act as identification and recognition molecules (chemical markers) on the extracellular side of the cell membrane. 

Ex: blood types, A,AB,O marked with glycoproteins

Polysaccharides what are their purpose? What are the Glucose polysaccharides?

Purpose: serve as chemical sources of energy or structural compounds

Glucose polymers:

cellulose

starch

glycogen

Cellulose (where is it found, what is the structure, purpose, what is the bond name, what is a characteristic, branching?)

Location: Found in plant cell walls

Structure: Linear

Purpose: Structure

Bond name: Monomers covalently linked by b-1,4 glycosidic linkages 

Characteristic: The most abundant carbon-containing (i.e., organic)  compound on earth 

Branching: unbranched polymer of glucose

Where are starches found? What is the purpose? What structure does it form? What are the bonds? What is the branching?

Location: found in seeds, fruits, roots and stem of plants

Purpose: Energy Storage

Structure: Has a helical structure

Branching:

Unbranched or loosely branched polymers of glucose

• Amylose: unbranched starch

• Amylopectin: branched

Bonds:

-Monomers within chains covalently linked by a-1,4 glycosidic linkages 

-Chains branch by connecting with other chains by a-1,6 glycosidic linkages 

Glycogen (where is it found, structure, purpose, bond names, branching?)

Location: Found in muscle and liver cells of animals; energy storage

Structure: Helical

Purpose: energy storage

Branching:

Highly branched polymer of glucose

Bonds:

• Monomers with chains covalently linked by a-1,4 glycosidic 

• Chains branch by connecting with other chains by a-1,6 glycosidic 

Lipid characteristics: What is the monomer of a lipids? Polarity? Bond name? Composition? What defines a lipid? Hydrophobic or hydrophilic?

1. Monomer: glycerol (backbone) and fatty acid (tail)

2. Polarity: non polar (insoluble in water)

3. Bond: ester bond

4. Compositions: composed of mostly carbon and hydrogen with some oxygen (always even carbon)

5. defined by a physical property not a chemical structure

6. hydrophobic

Main type of lipids

1.) phospholipids (cell membrane)

2.) triglycerides (fats and oils)

3.) steroids (cholesterol)

4.) waxes

Triglycerides purpose and structure

purpose: energy storage

Structure: Composed of 3 fatty acids and glycerol 

• Glycerol:

3 carbon molecule with one hydroxyl (-OH) at each carbon

• Fatty acid:

Chain of carbons and hydrogens with a carboxyl group (-COOH) at the end 

• The bond between the glycerol’s hydroxyl and fatty acids carboxyl is an Ester bond

• The ester bond is formed from the condensation rxn. There are three ester bonds to make one triglyceride because 3 carbons in a glycerol molecule 

Saturated fatty acid vs unsaturated fatty acid

Saturated:

•  No carbon carbon double bond

• Linear chain

• Solid at room temp

Unsaturated:

• Double bonds between carbon 

• Kinked chain

• Liquid at room temperature

Phospholipid structure

• glycerol’s Hydroxyl group is linked with a phosphate group

• 2 fatty acids, glycerol, phosphate

  • Glycerol backbone(C,H,O) one carbon gets phosphate, 2 get fatty acids 

Bilayer membrane

• Phospholipids make up the bilayer cell membrane with polar heads interacting with water and non polar tails in the interior 

• Bilayers have exposed edges and will fold into liposomes 

Integral proteins (3)

Transmembrane: goes through entire cell membrane

Membrane associated: goes through half of cell membrane

Lipid linked: proteins permanently attached to the cell membrane by a covalent bond to a lipid molecule embedded in the lipid bilayer

peripheral proteins

non covalently resting on cell membrane surface

leafette

one half of the membrane (top portion vs bottom portion)

Steroid structure

• 4 fused rings of carbon 

• ampipathic

hydroxyl=hydrophilic

Everything else=hydrophobic

Steroid purpose (3)

1. Hormone production

2. Chemical signaling 

3. membrane buffer, increase/decrease fluidity: Cholesterol (only in humans)

Waxes purpose

• Barrier for water loss (non polar)

• Structural elements

Waxes structure

Contains one or more hydrocarbons and long structures that resemble a fatty acid attaches by its carboxyl group to another long hydrocarbon chain

Glycolipid composition

• Sugar, fatty acid, another group 

Bonded together makes an oligosaccharide 

Glycolipid purpose

acts as a marker for cell recognition on surface of cell membrane connecting by a covalent bond

What infuences bio membrane fluidity? How can the membrane go back to its ideal fluidity in that case?

Temperature:

• Higher temps: causes membrane to be more fluid

Solutions: Add cholesterol to decrease fluidity, make fatty acid tails longer and add more saturated fatty acids

• Lower temps: causes membrane to be more stable

Solutions: Add cholesterol to increase fluidity (only in animal cells), increase unsaturated fatty acids, shorten fatty acid tail length

What molecules can and can not move through the semi permeable membrane?

Can pass: Non polar, small molecules  

Can not pass: Charged polar molecules  

What are the 3 movements of phospholipids in the membrane

Movement: 

• rotation (rapid)

• lateral shift (rapid)

• transverse diffusion (very slow) 

-moves leaflets (does not do on own, has enzyme do it)

DNA characteristics (3)

• Store genetic information coded in the sequence of their building blocks

• Polymer 

• double stranded 

What is DNA sugar name and why? What is DNA nucleotide name and abbreviation?

• Sugar name is deoxyribose (one less oxygen than ribose, only H at c’ 2 rather than OH)

• Nucleotide name is deoxyribonucleotide triphosphate (dNTP)

What are the Nucleotide bases of DNA? Which are the purines and pyrimidines? Which bases pair with each other? How many hydrogen bonds do each pair make?

Purines: A, G (double ring of carbon and nitrogen)

pyrimidines: C,T (single carbon ring)

Pairings:

• A pairs with T (forms 2 hydrogen bonds)

• G pairs with C (forms 3 hydrogen bonds) (more stable)

*The nitrogen bases form hydrogen bonds with their complementary bases (one purine on one strand, one pyrimidine on the other) holding together the two strands of DNA*

What is the backbone of DNA? what is the difference between the 5’ and 3’ end of a DNA strand?

Backbone: Phosphate and sugar molecules are the backbone of the DNA 

5’ end:

Has an unlinked phosphate

3’ end:

has unlinked hydroxyl

RNA characteristics (4)

• Involved in decoding the genetic code into instructions for linking a specific sequence of amino acids to form a polypeptide

• Polymer 

• usually single stranded

• Polymerization of nucleic acid: condensation rxn to make phosphodiester bond (covalent bond)

RNA sugar name? Nucleotide name?

• Sugar name is ribose (OH at 2’ carbon)

• nucleotides name: ribonucleotide triphosphate (NTP)

RNA nucleotide bases pairings? What are the purines and pyrimidines?

Purines: A, G

Pyrimindine: U,C

Pairings:

• A pairs with U

• G pairs with C

What three groups make up the structure of a nucleotide?

1. Phosphate group

2. Pentose (five carbon) sugar 

3. nitrogen base

functions of membrane proteins (5)

1. Transport

2. Enzymatic activity

3. Signal transduction

4. Cell to cell recognition

5. Intercellular joining

naming nucleotides

Base and sugar: nucleoside 

1 phosphate: monophosphate

2 phosphate: diphosphate

3 phosphate: triphosphate

*ex: nucleoside monophosphate*

Proteins

A functional unit composed of one or more polypeptides that have folded and twisted into a precise three-dimensional shape (many proteins also have carbohydrates(glycoproteins) or lipids (lipoprotein) that are covalently attached to certain amino acids which creates unique functions for specific proteins) 

Protein monomer? monomer structure?

Monomer: amino acid

Structure: 

• a-carbon covalently bonds to an amino group on one side, a carboxyl group on the other, a R region on bottom, and a hydrogen on top

• The carboxyl group is negatively charged (loses H ion) while the amino is positively charged (accepts H ion) 

Only L-amino acids (isomer) are found in proteins

Protein polymer? How is it formed? What is its structure?

Polymer: polypeptide

Formation:

• Formed by covalently linking the already there carboxyl group of one amino acid to the incoming amino group of another (only way to form a peptide bond)

Structure:

• Composed of a linear sequence of amino acids 

Occurs during translation

How many amino acids are there and what causes them to be different? What are the R groups?

20 amino acids that vary by their sidechains (characterized by charge and polarity)

Amino acid R groups 

1. Uncharged but polar

2. Uncharged and non polar

3. Positively charged (Basic) full positive ions because base accepted proton

4. Negatively charged (acidic) full negative ions because acid gave up proton 

protein bond? when is it formed? what is its backbone? What is a characteristic?

Bond: peptide bond 

formed when making polypeptide chains

Characteristic: partial double bond ability-little more resistant to free rotation

Backbone: Polar (N-H is partially positive, C–O is partially negative

Functions of a protein(6)

• Movement (actin/myosin)

• Defense (antibodies)

• Structure (keratin)

• Transport (hemoglobin)

• Signaling (Glucagon)

• Catalysis/Regulation/Metabolism 

Structure of a polypeptide chain? what is the backbone?

• First amino acid specified by the mRNA: N-terminus: end of polypeptide with amino group (called this because of the nitrogen atom and has free amino group)
  

• Last amino acid specified by mRNA: C-terminus: end of polypeptide with carboxyl group (called this because of carbon atom and has a free carboxyl group)

• Backbone: carbon and nitrogen

Primary structure (proteins)

The linear sequence of amino acids is the primary structure (polypeptide)

• Primary structure is determined by genes: the genes carry information for the production of proteins with specific amino acid sequences 

Secondary structure? What are the 2 main types? what if it doesn’t fit that type? What is it stabilized by?

Folded more compact polypeptide chains between neighboring amino acids that are stabilized by relatively weak hydrogen bonds between peptide linkages  

Two basic types of secondary structure:

• a helix sheet: polypeptide backbone forms a repeating helical structure that is stabilized by hydrogen bonds along the length of backbone. The hydrogen linked to a nitrogen atom forms a hydrogen bond with an oxygen atom that is double bonded to a carbon atom.  

Usually composed of non polar amino acids to be used in a lipid rich environment like a cells plasma membrane

• B pleated sheet: regions of the polypeptide backbone lie parallel to each other.  Hydrogen bonds between a hydrogen linked to a nitrogen atom and a double bonded oxygen form between the adjacent, parallel regions.  This causes the polypeptide backbone to adopt a repeating zigzag or pleated shape. 

Contributes to strength of proteins, including keratin(hair and hooved), silk (for spiders)

not all polypeptide chains assume either of those shapes and instead are called Random Coiled Regions

What is a problem with protein folding that occurs during secondary structure? What does it lead to?

Prions:

problem: misfolded proteins which somehow induce normal versions of that protein to fold the same (incorrect) way

Results:

-misfolded proteins comes out of solution creates plaques and this causes a family of diseases called spongiform encephalitis

-In animal cells and can spread to humans and is fatal 

Tertiary Structure? What are two characteristics?

Tertiary Structure: The three dimensional shape of a single polypeptide due to interactions between R groups with each other and with backbone

• From secondary structure, polypeptide chains folds and refolds upon itself to assume a three dimensional shape

*includes all secondary structures and interactions*

Characteristics:

• Can be the final structure of a functional protein 

• Thousands of water molecules surround a protein contorting the protein so that it is hydrophilic R groups are on outside and hydrophobic R groups are on inside 

What are tertiary and quaternary structures stabilized by? (6)

Mnemonic: Hungry Hippos Invite Vegans to Dinner

• h bonds between polar side chains 

• h bonds between hydrophilic side chains and backbone 

• ionic bonds between an acidic and basic amino acid 

• hydrophobic clustering of non polar side chains

• Vander walls forces

• disulfide linkages

Relative stabilities of bimolecular forces (most stable to least stable)

Most stable

1. Disulfide linkages: covalent

2. ionic bonds (easily made and broken)

3. Hydrogen bonds and hydrophobic interactions

4. Van der Waal forces

Least stable

Exergonic and endergonic rxn

Endergonic (biosynthetic or anabolic): requires input of energy (condensation reactions) 

Exergonic(catabolic or spontaneous): output of energy (hydrolysis rxn)

Spontaneous

a reaction that releases energy, much of which is lost as heat

Denaturing protein? Can they recover?

Removal or inactivation of stabilizing forces unfolds (denatures) the protein to primary structure, but no peptide bonds are broken 

• All 2° and 3° structure is lost

• Almost always leads to loss of function

• Acids/bases, heat, detergents

If denaturing agent is removed some proteins will resume properly folded 3D structure (instructions are in primary structure)

What is an Enzyme? What do enzymes do to a reaction? why are they necessary?

Definition: Proteins that are biological catalysts and facilitate biological reaction.  Enzymes lower the activation energy required for a reaction to occur 

Why necessary: Enzymes are necessary because most cellular reactions proceed at a very slow rate 

enzymes do not cause reactions to occur that would not eventually occur anyway; only speed up existing

Active site

The spot where the enzyme binds.  Enzymes bind substrates with extremely high specificity into their active sites (usually just a few amino acids)

Induced fit

Enzymes will most likely cause some conformational change in the substrate molecule(s), but they themselves usually change shape upon binding substrate

How does substrate binding to active site decrease Ea (4)

• Acting as a template for substrate orientation

• Stressing the substrate(s) and stabilizing the transition state

• Providing a favorable microenvironment

• Participating directly in the catalytic reaction

Key characteristics of enzymes (4)

Characterisitcs:

• If an enzyme accepts a group from a substrate, it must in turn

donate that group to help form product

• Enzymes are ultimately unchanged by the reactions they catalyze

• Enzymes do not change the equilibrium of rxn 

• Enzymes have temperature and PH optima, directly related to the environment in which they function 

Enzyme inhibition Overview

Can either be Irreversible or Reversible

-Reversible inhibition can either be competitive or non competitive

Irreversible inhibitors

Permanently bind to or modify active site; changing concentration of natural substrate or inhibitor has no effect. (Ex: aspirin and neurotoxins)

• Tend to be molecules not typically encountered by that particular cell

• Demonstration that enzymes must ultimately be unchanged to be used over and over

Reversible inhibitors (2 types) and example

happens when a molecule binds temporarily to an enzyme using weak bonds and slows down its activity without permanent damage

• Competitive inhibition: the inhibitor molecule physically resembles the natural substrate, and occupies active site (ex: Sulfanilamide (antibiotic))

-inhibitor can not act as substrate so no products are formed

• Non competitive inhibition: the inhibitor molecule binds to the enzyme in a place other than the active site (allostaric site)

V Max and KM

V max: maximum amount of products per unit of time that can be formed (maximum rate)

KM: 50% substrate concentration of Vmax

Free energy and ΔG

Free energy: energy that is available and can be used to do work

ΔG: Difference in energy from reactants to products

•  -ΔG=exergonic

• +ΔG=endergonic

Sphingomyelin

provides structural support to cell membranes and acts as a source for signaling molecules

Sphingomyelin is the only major membrane phospholipid that does not have glycerol as its three-carbon backbone.

phosphatidyl ethanolamine

a vital type of lipid (fat molecule) found in the cell membranes of plants, animals, and bacteria

has a phosphate group attached to glycerol

How do high temp and low temp influence membrane? (in terms of fluidity)

High temp: increased fluidity

Low temp: decreased fluidity