Test 1 Concepts

Rank the bond energies from strongest to weakest

• C triple bonded C

• Hydrogen bonds

• C bonded to N

• C bonded to H

• C double bonded C

• C single bonded C

1. C triple bonded C

2. C double bonded C

3. C bonded to H

4. C single bonded C

5. C bonded to N

6. Hydrogen bonds

List the functional groups, their polarities, and property

• Nonpolar

  • Hydrogen/Methyl

• Polar

  • Carbonyl/Aldehyde

  • Hydroxyl

  • Sulfhydryl

  • Secondary amine

• Charge

  • Phosphoric acid (can become an anion)

  • Carboxylic acid (can become an anion)

  • Primary amine (can become a cation)

What is the monomer, monomer structure, linkage, and function of protein

• Monomer: Amino acids

• Monomer structure: Carbonyl group, hydrogen, amino group, and R-group attached to an alpha carbon

• Linkage: Peptide bonds

• Function: Cellular function

Where are amino acids connected

An oxygen from a carbonyl group on the N-terminus side hydrogen bonds to a hydrogen on the amine group on the C-terminus side

Describe the levels of protein structure and the bonds that create them

• Primary

  • Sequence of amino acids

• Secondary

  • Folded primary structure

  • alpha helix (polypeptide chain twists)

  • beta sheet (polypeptides line back and forth)

  • Connected via H-bonding

• Tertiary

  • 3D structure

  • R-groups interact with each other and/or with the peptide backbone

  • Held together by disulfide bonds, H-bonding, ionic bonds, van der Waals forces, and hydrophobic interactions

• Quaternary

  • Multiple polypeptides joined to form a final functional protein

  • Ex: hemoglobin

What is polymerization

The process of linking monomers together via condensation reactions/dehydration synthesis

• Removes a water so monomers can bond with one another

• Hydrolysis is the opposite— a water is added to break the bonds between monomers

Why do disulfide bonds only exist in organelles or extracellularly

Disulfide is oxidized while cytosol is highly reduced. Disulfide bonds break easily in cytosol

What are motifs

Short combinations of secondary structures that appear in many proteins

What are the two general structures of protein

• Fibrous (filament)

  • structural

  • Ex: keratin, collagen

  • composed of repeating amino acids

  • contain consistent secondary structure

• Globular

  • Most proteins

  • when folded into tertiary, they form big globs

  • Function: enzymes, antibodies, hemoglobin

conformation of proteins is dependent on what

pH, temperature, ion concentration, interactions with other molecules

• changing these can cause changes in function

• significant loss of structure is called denaturation

  • complete loss of function

what are chaperones

Proteins that monitor other proteins’ conformation and assist folding/refolding

What is proteolysis

A post-translational modification where portions of the peptide chain are cut off

• Can occur before or after a protein is secreted by the cell

• Ex: Insulin, digestive enzymes

• Protein needs to remain inactive until reaching destination

What is phosphorylation

A post-transitional modification where enzyme uses ATP to remove H from an OH group on an amino acid and add a phosphate

• Kinases (serine/threonine kinases + tyrosine kinases)

• Can be resersed

• Can result in activation or inactivation

• with phosphate, size increases and becomes more charged, which can change conformation

What is glycosylation

A post-translational modification where a carbohydrate group is added to an amino acid

• Occurs in the ER or Golgi apparatus

• N-linked = carbohydrate group attached to amino group (N) on Asparagine

• O-linked = carbohydrate group attached to hydroxyl group (O) on serine or threonine

what is lipid conjugation (lipid-anchor)

A post-translational modification where lipids are added to a protein

• Fatty acid chain (myritate, palmitate)

• Hydrophobic being attached to (usually) hydrophilic protein

• Adding a lipid anchors a protein to the membrane and ensures its in the right place

• Terpenes

  • Farnesyl = 3 isoprenes (15C)

  • Geranylgeranyl = 4 isoprenes (20C)

What is a disulfide bond formation

A post-translational modification where two amino acid chains form a disulfide bond

• only done inside cells

what is protein linkage

a post-translational modification where proteins covalently linked to other proteins

• misfolded proteins are linked to (tagged) with ubiquitin, a 76aa protein that is linked to one or more lysine residues in a target protein by ubiquitin ligase

  • multiple copies of ubiquitin can be linked in sequence

• Multi-ubiquitinated proteins are ‘recognized’ by the proteosome

  • Cylindrical hollow multi-protein complexes

  • Interior is lined with proteases

  • Ubiquitinated proteins enter and are broken down into short peptide fragments

What are non-covalent modifiers

A post-translational modification that is a reversible interaction with another molecule

• mediated by weak forces

• Ex: hormone/signaling molecule, cAMP, calcium ions, GTP, another protein

• Leads to changes in functions and often regulate protein activity

What is a protein domain

Stably folded region of a protein that has a specific function

• Proteins can have more than one

• Some are unique and only found in one protein, or can be common and found in many different proteins

• SH domains = Src homology domain

  • originally found in protein Src

  • SH1 = tyrosine kinase

  • SH2 = phosphotyrosine (p-Tyr binding)

  • Sh3 = proline-rich binding

What are multi-domain containing proteins, adaptor proteins, and scaffolding proteins

Proteins with multiple domains that can facilitate associations of multiple proteins into a multiprotein complex

• Called adaptor proteins when binding 2-3 proteins

• Called scaffolding proteins when binding larger # of proteins

• The portions that mediate these interactions may be:

• stably folded domains

• or intrinsically disordered regions (IDRs, have a high % of hydrophobic amino acids)

what is the monomer, linkage, general monomer structure, and function of nucleic acids

• Monomer: Nucleotides

• Monomer linkage: phosphodiester linkages at the 3’

• General monomer structure: a pentose sugar, a phosphate group attached at 5’, and a nitrogenous base attached to 1’

• Function: Genetic information

What is the difference between purines and pyrimidines

Purines have two carbon rings

• Adenine

• Guanine

Pyrimidines have one 6 carbon structure

• Thymine

• Cytosine

• Uracil

what is nucleic acid nomenclature

RNA Nucleosides: first part -dine

RNA Nucleotides: Nucleosides + monophosphate (or di, tri)

DNA nucleoside: deoxy- first part of base -sine

DNA nucleoside: Nucleosides + monophosphate (or di, tri)

what are the three common mono- and disaccharides

• α-D glucose + α-D glucose = Maltose

• β-D galactose + β-D glucose = Lactose

• α-D glucose + β-D fructose = Sucrose

Give examples of complex polysaccharides

Starch

• Used for energy storage in plants

• Made up of α-glucoses

• Amylose - unbranched helix

• Amylopectin- branched helices

Glycogen

• Used for energy storage in animals

• Made up of α-glucoses

• Highly branched helices

Cellulose

• Used for structure support in cell walls

• Made up of β-glucoses

• Parallel strands join by hydrogen bonding

Chitin

• Used for structural support in cell walls of fungi and exoskeleton of insects and crustaceans

• Made up of β-glucoses with NHCOCH₃ groups

• Parallel strands join by hydrogen bonding

Peptidoglycan

• Used for structural support in bacterial cell walls

• Made up of β-glucoses with NHCOCH₃ groups

• Parallel stranded join by peptide bonds

what is the monomer, linkage, general structure, and function of carbohydrates

• Monomers: monosaccharides

• Linkage: Glycosidic bonds

• General structure:

  • α-D glucose is a pentose sugar, the OH group attached at 1’ is facing down

  • β-D glucose is a pentose sugar, the OH group attached at 1’ is facing upward

• Function: Energy

What is the monomer, linkage, general structure, and function of lipids, and what makes them different from other bio molecules

• “Monomer” : 3 fatty acids + glycerol

• Linkage: ester linkage

• General structure: hydrophobic hydrocarbon chain

• Function: Structure and store energy

• What makes them different: Lipids do not form polymers

What are the 2 types of fatty acids

Saturated

• Linear hydrocarbon chain with a COOH group at the end

• Ex: Palmitic acid and Stearic acid

Unsaturated

• Branched hydrocarbon chain with a COOH group; branches caused by double bonds

• Ex: Oleic acid and Linoleic acid

What is the synthesis of triacylglycerol (triglyceride)

3 fatty acids + glycerol

• Major storage form of lipid

what are the 2 types of phospholipids

Phosphoglycerides

• Glycerol with a phosphate group attached

• Common R groups attached are Serine, Ethanolamine, Choline, and Inositol

• When attached to an R group, its called: Phosphotidyl + R group

Sphingolipids

• Sphingosine with a phosphate group attached

What is a glycolipid

A lipid with a sphingosine attached to a carbohydrate chain of 1 to 6 monosaccharide units

what are steroids

lipids with four-ringed hydrocarbon skeleton

• Ex: Cholesterol

what are terpenes

A lipid with an isoprene unit

• Forms Vitamin A and lipid anchors

What proves that hydrophobic amino acids and residues may be capable of very weak interactions

Aromatic rings

• p orbitals overlap and form pi orbital systems that become delocalized

• Electrons are concentrated above or below the ring

• These electrons are pushed toward the center by carbons

• This causes hydrogens to get their electrons pulled away

• A weak dipole dipole is formed, so hydrophobic molecules can form weak ionic bonds with cations (Cation-pi interactions)

• Or, interact with polar functional groups

• These contribute little to tertiary structure

What is equilibrium

When the forward rate = the reverse rate of a reaction

• it DOES NOT mean concentration of reactant = concentration of product

• Usually one side of the reaction is favored to reach equilibrium

What is Keq and what does it predict

The equilibrium constant— the ratio of product to reactant

• Keq = [P @ eq] / [R @ eq]

• predicts the favored direction of a reaction

• If Keq > 1 rxn proceeds forward

• If Keq < 1 rxn proceeds backwards

What determines equilibrium and energy in a rxn

The laws of thermodynamics

• 1st law: energy is not created nor destroyed, just changed into a different form

• 2nd law: entropy

• Thermodynamics governs IF a rxn will or will not happen (spontaneity) and the preferred direction (favorability)

• It does not determine the rate of a rxn

What is entropy

Disorder

• energy gets lost to entropy

What is Gibb’s free energy

The energy available to do work

• Keq is determined by relative free energy levels of R and P

• every chemical has inherit free energy

What are the equations and relationships relating to G

• G = H - TS, H = enthalpy, T = Temperature, S = entropy

• In a chemical rxn, Products G - Reactants G = Change in G

• If reactants G > Products G, then G is made available by the reaction (negative change in G)

• negative change in G means a rxn is exergonic and spontaneous

• If Products G > Reactants G, then G is consumed by the reactions (positive Change in G)

• Positive Change in G means a rxn is ended tonic and nonspontaneous

What is standard free energy (Go’)

Free energy at standard conditions

• used to compare change in G if different rxns and conditions

• Change in G @ 1M R and P, STP and pH 7.0

what is the equation of change in G’

G’ = Go’ + RTln[R or P]

Change in G’ = change in Go’ + RTln[P]/[R]

@ equilibrium: change in G’ = 0 = change in Go’ + RTlnK’eq

• G’ = Free energy is R or P

• Go’ = standard free energy

• R = gas constant (1.986 Kcal/mol)

• T = temperature (K) (298 K @ 25oC)

• Ln = natural log of R or P

What is the relationship between change in G and concentration of reactants and products

[R] and [P] directly impact change in G

How do cellular rxns overcome endergonic rxns

Regulate [R] and [P]

Input energy

how do you increase the rate of rxn and how can that factor be increased

Increase the frequency of molecular collisions

• increasing the concentration of reactants

• Increases chance of collisions by making it more crowded

• Increasing molecular movement (kinetic energy)

• Do this by increasing temperature

What is activation energy

The input of energy needed to pass through the transition state

• or, the energy needed to get reactants to collide with enough force to get to transition state

• Activation energy may be kinetic energy

• Kinetic energy is affected by:

• - Temperature

• - Concentration

• Cells can’t readily change these variables

What is the transition state

The structure of reactants while their chemical bonds changed

• The transition state is energetically unfavorable

How do cells reach activation energy without changing temperature or concentration

Enzymes decrease the activation energy required by directly binding to reactants (substrates)

What is the active site

A region on an enzyme where substrate fits and binds to the enzyme

What is induced fit and what does it form

Where enzymes undergo a slight conformational change as substrate binds to it

• Forms the enzyme-substrate complex

• Enzyme and substrate interact through hydrogen bonding, ionic bonding, ionic bonds, and sometimes covalent bonds

How do enzymes lower activation energy