Biology 1020- Midterm 2

polymerization

polymerization

creation of a polymer by the bonding of multiple subunits.

2 molecules with reactive functional groups: OH and H.

Each monomer in protein is an amino acid

proteins

make up 50% of body’s dry mass

multiple functions: enzymes and support

made of amino acids

amino acids structure

all have an amino group and carboxyl group

R group is attached to alpha carbon

diff. amino acids have diff. R groups- which give amnio acids diff. properties

20 diff. amino acid monomers

amino acids

nonpolar or polar?

polar: have oxygen or sulfer at terminal end

acidic or basic

acidic: donates a proton from R group (gets a negative charge)

basic: accepts proton (gets a positive charge)

how to determine a R group

check if acidic or basic (charge or not)

if neither, check for polarity (oxygen and sulfer)

nonpolar amino acids

glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline

polar amino acids

serine, threonine, cysteine, tyrosine, asparagine, glutamine

peptide bonds

links amino acids together to form proteins

proteins linked together by ribosome using mRNA

before linked by peptide bond, dehydration reaction removes water

lose water between every peptide bond

protein structure

the order (polarity) of amino acids does not matter

4 levels of structure: primary, secondary, tertiary, and quaternary

primary structure

amino acids and peptide bonds

flexible and linear chain

(amino acid) determined by gene sequence

secondary structure

shapes are formed by hydrogen bonding between atoms of a polypeptide backbone (not R groups)

many H bonds can make these stable structures

helices: alpha helix and beta pleated sheets

tertiary structure

overall 3-dimensional shape of a single polypeptide (mostly dictated by chem of R-groups)

non-polar R-groups get buried into middle of protein (excluded by water) and interacted with each other by Van Der Waals forces

polar R-groups- H bond with water and other hydrophilic R-groups at the surface

interactions between side chains- ionic bonds, covalent bonds, hydrogen bonds, Van der Waal

quaternary

interactions between multiple polypeptides, protein subunits

ex. collagen made of 3 diff. polypeptides that are intertwined together

ex. hemoglobin made from diff. polypeptide subunits that come together

protein models

ribbon model

space-filling model

wireframe model

ribbon model

just the backbone

shows secondary structures

spare-filling model

shows the electron orbit shells of each atom in the protein

hard to see where chemical interactions are occur

wireframe model

shows all of the covalent bond of backbone and r-groups

good to see how chemical interactions occur

protein interactions

specific r-groups on one protein will interact with specific r-groups on another protein

in ex. antibody will bind tightly to the flu virus protein so the immune system can destroy the virus

other protein/protein interactions are weaker and much more transitioning

enzymatic proteins

selective acceleration of chemical reactions

ex. digestive enzymes catalyze the hydrolysis of bonds on food molecules

defensive proteins

protection against disease

ex. antibodies inactivate and help destroy viruses and bacteria

storage proteins

storage of amino acids

ex. casern (protein in milk) is major source of amino acids for babies

ovalbumin is protein of egg white (used as amino acid source developing embryo)

plants has storages proteins in seeds

transport proteins

transport of substances

ex. hemoglobin, iron containing protein of vertebrae blood, transports oxygen from lungs to other parts of body

ex. cell membrane - channel and carrier proteins

hormonal proteins

coordination of an organisms activities

ex. insulin, hormone secreted by pancreas, caused other tissues to take up glucose, regulates blood sugar concentration

receptor proteins

response of cell to chemical stimuli, important for receiving info, cell communication, action potentials

contractile and motor proteins

movement

ex. motor proteins responsible for undulations of cilia and flagella

actin and myosin responsible for muscle contractions

structural proteins

support, found all throughout body (collagen)

ex. keratin is protein of hair, horns feathers, and other skin appendages

insects and spiders use silk fibers to make their cocoons and webs repetitively

collagen and elastin proteins provide fibrous network in animal connective tissue

protein coding

big consequences for changes in primary protein sequence

can cause sickle cell anemia

metabolism

organized as metabolic pathways that included multiple steps

enzymes catalyze each step

build or break down chemical to make other chemicals

liberate/store energy used to do cellular or organismal function

metabolites are the molecules in pathways

metabolic pathways

pathways involve multiple reactions

catabolic

breaks things down and releases energy

anabolic

build things up and requires energy

forms of energy

kinetic, thermal, potential, and chemical

kinetic energy

relative motion

thermal energy

kinetic energy associated with random movement

potential energy

not kinetic, static objects still have energy

(energy with no motion)

chemical energy

potential energy that is available for release

energy in covalent/peptide bonds

1st law of thermodynamics

energy cannot be created or destroyed

energy can be transformed (converted)

2nd law of thermodynamics

entropy(disorder)- increases in isolated system

transformation to energy is never 100% efficient (lose a lot of energy as heat)

quantity vs quality

free energy

G is Gibbs constant

the amount of energy in “the system”

in a chemical reaction, the system, changes (so does free energy)

reactants have initial state/energy

products have final state/energy

G = final - initial

exergonic reactions

reactants have more free energy than the products

energy is released

reaction is spontaneous, not instantanous

endergonic reactions

reactants have less free energy than the products

energy input is required

not spontaneous

ATP energy coupling

cellular work: chemical, transport, mechanical

all require energy, typically ATP

exergonic reactions can be coupled with those that are endergonic

ex. glutamine synthesis and ATP hydrolysis- adds initial and final energies to get new G.

energy barriers

spontaneous reactions are not instantaneous

transition states: intermediate state with stressed bonds

some energy must be put in

activation energy (Ea)- enzymes lower it

enzymes speed it up

add an enzyme, the reaction is catalyzed

enzymes bind to the reactant molecules very tightly and put stress in specific bonds of reactants

lowers Ea required for reaction to occur because bonds are easier to break

‘normal’ biological temperatures

no change in free energy of reaction

enzymes are specific

for specific reactants and specific products

lock and key model

very specific

relied on polarity and acidity/basicity

active site

can only fit specific molecules

induced fit models

focuses on shape enzymes and substrates are 3D compounds

shape is essential, but so are other properties

denature

change the nature of protein

changes the shape of proteins, results in it losing its function

results from bad environment for protein

environmental factors

temperature- increase breaks hydrogen bonds and desulphate bonds which change structure

pH- increase or decrease breaks ionic bonds which changes structure

competitive inhibition

slows rate of reaction

inhibitor molecules resembles substrate

binds to active site and occupies it

actual substrate cannot bind to active site

substrate inhibition is a form of competitive inhibition

blocks active site

noncompetitive inhibitor

slows down rate of reaction

does not have similar properties of substrate

inhibitor molecule does not bind to active site

changes enzyme shape

active site can’t bind to substrate

feedback inhibition is example

allosteric enzyme regulation

enzyme complex oscillating between state

reaction rate depends on proportion that is active

compounds can bind to enzymes- activators and inhibitors

activators

bind allosteric site

stabilizes active form

faster reaction rate

inhibitors

bind allosteric site

stabilize inactive form

slower reaction rate

feedback inhibition

many enzyme pathways are self-regulated

synthesis pathway with multiple enzymic reactions

final product- inhibits an enzyme

prevents further production

product used- inhibition removed and pathway proceeds

living cells

require energy from outside sources (except autotrophs)

energy flows into ecosystem in the form of sunlight and ultimately leaves as heat

photosynthesis generates organic molecules and oxygen which are used in cellular respiration

cells use chemical energy stored in organic molecules to generate ATP, which powers cellular work

yield energy by oxidizing organic fuels- electron transfer

catabolic molecules

breakdown of complex molecules (glucose) and releases energy

molecules store energy in their bonds and generates ATP for cellular work

energy is released when electrons move

reduction and oxidation reactions (redox)- catabolism and anabolism

oxidation reactions

oxidation- electron donor

becomes oxidized

reducing agent

reduction reactions

electron acceptor

becomes reduced

oxidizing agent

redox reactions

transfer of electrons during chemical reactions releases energy stored in organic molecules

this energy is use to synthesize ATP

electron shuttles

nicotinamide adenine dinucleotide (NAD+)

important oxidizing agent (electron acceptor)

shuttles electrons from ‘glucose’ to the ETC (electron transport chain)

oxidized form- NAD+

reduced form- NADH

electron transport

electrons ultimately move toward oxygen

if uncontrolled, may turn into explosive release of heat and light energy

if controlled, uses PE and gives cell time to use energy efficiently

methods of ATP production

substrate level phosphorylation

oxidative phosphorylation

substrate level phosphorylation

direct

ADP is a substrate of an enzyme

used about 10% of the time (not efficient)

oxidative phosphorylation

indirect thorough chemiosmosis

uses redox reactions of the electron transport chain

used about 90% of the time

what is metabolized?

organic substances/molecules

lipids, carbohydrates, nucleic acids, and proteins

carbohydrates

in ratio: 1 carbon, 2 hydrogens, 1 oxygen

functions: fuel (makes ATP), energy storage (stores starch or glycogen, structural component

all sugars have: a carbonyl group, other carbons with a hydroxyl group

what do different sugars differ in?

number of carbons

where carbonyl group is (isomers)

symmetry of -OH groups around the carbons (stereoisomers)

aldehyde

carbon double bonded to an oxygen (carbonyl) at the end of a sugar

ketone

carbon double bonded to an oxygen (carbonyl) in the middle of a sugar

monosaccharides

5-carbon sugars and 6-carbon sugars

5-carbon: ribose and ribulose

isomers- same chemical formula, different structure or arrangment

6-carbon: glucose, galactose, and fructose

stereoisomers- function groups can be on either side of carbon

can be linear or a ring

glycosidic linkages

join 2 simple sugars together

dehydration reaction forms either alpha or beta linkages (requires energy)

dehydration reactions

chemical reactions in which water molecules are removed from a compound or a mixture

These reactions typically involve the loss of a water molecule (H2O) from a larger molecule

alpha linkages (glycosidic)

all hydroxyl groups are on the same side

below carbon 1 (plane)

storage carbs

beta linkage (glycosidic)

hydroxyl groups are alternating sides

above plane

structural carbs

storage carbs

all alpha form

allows them to tightly pack together (because hydroxyl us below plane)

starch storage- alpha glucose

structural carbohydrates

OH is on opposite sides they’re paired to (beta)

has hydrogen bonding

forms matrix and strong support

glucose in beta form

not linear

disaccharides

2 monosaccharides put together

ex. sucrose = glucose + fructose (linkage is 1-2 glycosidic linkages)

ex. lactose = galactose + glucose (linkage is beta 1-4 linkage- not linear)

ex. maltose = made of 2 glucose (linkage alpha 1-4 linkages), storage carb- linear, alpha

polysaccharides

100-1000s of repeating subunits

ex. amylose- very linear, alpha chain, storage, 1 branch

ex. amylopectin- linear, alpha chain, storage, slightly branched

ex. glycogen- linear, alpha chain, very branched, found in animals

ex. cellulose- not linear, beta chains, structural, found in plants

glycosidic linkage make structural polymers

glycosidic linkages of cellulose differ from those of starch because the ring of glucose in the 2 polymers are slightly different

cellulose contains beta glucose

starch contains alpha glucose

structural carbs

chitin- animal, glucose with extra functional group that contains nitrogen

monomer- N-acetyl-glucosamine (NAG)

used to make arthropod exoskeletons and fungi cell walls

lots of H-bonding between parallel strands gives a strong material thats further hardened by proteins

evolution of pathways

glycolysis was likely one of the first pathways - due to not using oxygen (3.5 billion years old)

early atmosphere was anaerobic (no oxygen)

fermentation- simple, cycles protein

‘anaerobic respiration- complex, more efficient

aerobic respiration- was a relatively easy change from anaerobic respiration, oxygenation of atmosphere (2.7 billion years ago),

glycolysis

cells used glucose as energy source (not just glucose, other molecules can be broken down in different pathways that connect)

earliest pathway

involves 10 enzymic reactions including: phosphorylation (substrate level ATP synthesis), redox reactions, isomerization

glycolysis- overall reaction

1 glucose (6C) —→ 2 pyruvate

energy investment- 2 ATP

energy payoff- 4 ATP and 2 NAD+ reduced to NADH

substrate level phosphorylation (ATP synthesis in glycolysis)

reactant: substrate + ADP + P

product: ATP

fermentation

organisms surviving without atmospheric oxygen

organisms without the electon transport chain

organisms must regenerate NAD+

available organic molecules can act as oxidizing agents (several diff. pathways), typically toxic end products (waste)

glycolysis can still function

Ethanol fermentation

glycolysis produces 2 ATP, 2 NADH, 2 pyruvate

pyruvate decarboxylation- liberation of CO2- produced acetaldehyde

acetaldehyde accepts electrons from NADH, regenerates NAD+ and forms ethanol

yeast, some bacteria

step 1. remove carbon

step 2. NADH donates electrons to acetydehyde

lactic acid fermentation

glycolysis produces: 2 ATP, 2 NADH, 2 pyruvate

pyruvate-accepts electrons from NADH (recycles NAD+ and forms lactate)

lactic acid bacteria

in humans- ‘anaerobic exercise’

what processes evolved after fermentation?

pyruvate oxidation into Acetyl-CoA- energy from pyruvate

Citric Acid Cycle- energy from pyruvate

the electron transport chain- harnesses energy from NADH e-

pyruvate oxidation

acetyl CoA (2C) production

pyruvate is transported to mitochondrial matrix

3 step reaction:

1. liberation of CO2 (removal)

2. reduction of NAD+

3. addition of coenzyme A (CoA)

makes 2 NADH

citric acid cycle

occurs within mitochondrial matrix

cycle series of 8 enzymatic reactions

acetyl-CoA (2C) + oxaloacetate —→ citrate

products (per acetyl-CoA)- 1 CoA, 2 CO2, 3 NADH, 1 ATP, 1 FADH2

used substrate level phosphorylation

electron transport chain

series of electron carries that NADH and FADH2 donate electrons o

occurs in plasma membrane of prokaryotes and mitochondria in eukaryotes (between intermembrane space and mitochondrial matrix)

first ETC was in bacteria

involved in both aerobic and anaerobic respiration

what reactions occur in the electron transport chain?

sequential redox reactions

multiple small changes in free energy (G < 0)

energy released is coupled with moving protons against their gradient (energy used for PMF)

bacteria: from intracellular to extracellular

eukaryotes: to intermembrane space from mitochondrial matrix

*gradient is from proton motive force (H+)

possible final anaerobic electron acceptors

ferric iron (Fe3+)- pumps most protons

nitrate (NO2-)- pumps mid amount of protons

sulphate (SO 2-)- pumps least amount of protons

*fewer protons pumped, lower proton motive force, and less ATP by ATP synthesis = small difference in free energy

ATP synthase

a proton channel on the inner membrane (enzyme)

4 H+ moving through —> produced 1 ATP

occurs after ETC

chemiosmosis

movement of H+ down its concentration gradient

energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane

energy from gradient comes from exergonic redox reactions

in photosynthesis: products of light reactions go to the calvin cycle (ATP and NADPH)

anaerobic respiration

with no O2, some bacteria can use alternative final electron acceptors

this pathway involves: glycolysis, pyruvate oxidation and citric acid cycle, the electron transport chain

ATP is produced by: substrate level phosphorylation and proton motive force and ATP synthase

*efficiency of ATP production depends on final electron acceptor

photosynthesis

provides energy for life

converts light energy into chemical energy

evolved about 3 billion years ago (started among bacteria)

creates all O2 in the air

an anabolic pathway

dependance on photosynthesis in organisms

direct: autotrophs- uses photosynthesis to convert light energy

indirect: heterotrophs- can’t take sunlight and make it into energy