HL Bio Proteins, Water, Carbs, Muscle, Lipids and Enzymes

Bio HL 2024 curriculum

Amino Acids: Function and Structure

Building blocks of protein

Central atom is called the ALPHA atom

can bond to 4 other atoms

One is a nitrogen from a amine group

Another is Carbon from a carboxyl group

Carboxyl group

A functional groups, -COOH

Acidic since it wants to donate a proton

Amine group

A functional group -NH2

Basic because it wants to receive a proton

Alpha carbon atom

Contains a covalent bond to an H

Other covalent bond links the alpha carbon to a side chain called the R-group

R-group

Varies between 20 standard amino chains

Affects the specific acids of the amino acids such a polar, non-polar, acidic and basic.

some hydrophobic other hydrophillic

determine chemical charactersitics

Forming a Dipeptide DRAW

2 amino acids are joined by a condensation reaction

Water us generated as a product

• OH on one end and H on the other

• amino acid+amino acid= dipeptide+ water

Amino Acids bonds

Carbon and Nitrogen bonds

Catalyzed by ribosomes

Directional process

amine group of a free amino acid

linked to a carboxyl group at end of a chain

Dietary Requirements

20 different amino acids

PLants gain from synthesis

Animals from diets

Essential and Non-essential amino acids

11 can be synthesized by the body, during metabolic process

9 are essential

Polypeptides

Infinite variety of possible peptide chains

Ribosomes link amino acids one by one

Ribosomes receive instructions from genetic code to create sequences

20^n combinations possible

Denaturation

change in conformation of a protein

Bonds are week between R-groups

Permanent

Maintaining the tertiary structure

Effect of pH and Heat on Proteins

Heat- due to vibrations emitted that break those bonds

pH- extreme positive or negative charges change R-group configurations

• breaks and creates ionic bonds

Denaturation on solubility of proteins

Soluble often become insoluble or precipitate

• hydrophobic r-groups in the center becoming exposed to water 

Polypeptides structures DRAW

On one end is carboxyl COOH and other amine group NH2

hydrogen attached to the alpha carbon

Primary structure DRAW

linear sequence of amino acids

• c-c-n-c(a)-c-n-c(a)

There can only be rotation in alpha carbon and adjacent nitrogen and carbon

allows folding

Secondary Structure

C=O and N-H  are what remain from the functional gorups

H slightly + O slightly -

Many weak h bonds form due to frequency of C=O and N-H

• stabilize structures

A-helix draw w bonds

polupeptides wound into helix

Hbonds betweeen adjacent truns of the helix H to the floating 0

B- pleated Sheet

two or more sections of polypeptides are arranged parallel with hydrogen in between

sections must run in opposite directions forming pleats

Tertiary Structure (draw)

Interactions between R groups

Ionic Bonds- positive and negatively charged R-groups

• amine get proton

• carboxyl give proton

Hydrogen bonds- between polar R-groups

• two electronegative atoms

• Covalently bonded to O or N

• makes slightly positive attreact to the slightly negative

Disulfide Bond- between pairs of cysteins

• covalent bonds

Synthesized by a ribosome and with a chaperone protein present

super secondary structure

various combinations of a and b secondary structures

makes bundles

Polar Amino Acids

hydrophillic carry actions out in cytoplasm

Non-polar Amino Acids

Hydrophobic, in the center water is excluded

hydrogen bonding between exterior allowing for protection

Integral Proteins

non-polar in the center in contact with hydrocarbon tails

polar on outside

stabilizes the protein

tunnel is lioned wiht hydrophillic amino acids

Non conjugated Quaternary Structure

2 or more polypeptides

only p[olypeptide subunits

ex. insuling, two polypeptides are linked

Conjugated Quaternary structure

1 or more non-polypeptide bonds

ex. haaemoglobin, has one haem to allow oxygen tobind to

Globular Proteins

rounded shape folding

bonds between folded amino acids

Fibrous Proteins

elongated proteins

lacking folds like tertiary structures

do not develop secondary structures

developed by linking unit fiber like structures or filaments with hydrogen bonds

ex. collagen

Two types of movement

Locomotion- one place to another

within the body, persistalisis

Parts of the muscle

multi nucleate

large number of mitochondria

Sarcoplasmic reticulm

Tubular myofibrils (action and myosin)

sarcolemma

why multu nucleate

since the cells are very big

why multiple mitochondria

high energy demand

sarocplasmic reticulum

smooth endoplasmic reticulum in muscle cells that stores and releases calcium ions to trigger muscle contraction.

Myofibrils

series of sarcomeres linked end-to-end at z-dscs

light bands at bonth ends

relaxed muscle

light bands are wider

z-dscs are further apart

sarcomere is longer

Actin

thin attached to z-discs at one end

Myosin

Thick at the center of the sarcomere, interlock with actin, surrounded by 6 actin

contraction

1. myosins have heads that bind together at regular intervals in the actin, at binding sites

2. cross brigdes exert force in ATP

3. pushing the actintowards the center of sarcomere, causing more overlap

exerting force

when myosin heads bind they swivel exerting force that pushes the actin filaments short distance, towards center

head detach then swivel back to next binding site on the actin

features of Titin

titin is elastic

biggest protein in the body

stores potential energy

releases enrgy when it recoils

connect z-dscs to myosin

Role of titin

keeps myosin in place in the center

preventents over stretching of the sarcomere

adds to the force of the contraction and releases energy as it recoils

Antagonistc Muscles

working as a pair

one relaxes other contracts

• titin energy is exerted when contraction need another muscle to provide the energy 

Striated muscle fibers

contract when stimulated by motor neuron

passed through synapse using acetylcholine

neurons have branches to multiple fibers

Role of ATP

Hydrolysis of ATP ( breaking off the phosphate) and cross bridge formation are necessary for filaments to slide

• ATP binds to myosin heads causing them to break cross-bridges by detaching from actin binding site

  • causes myosin heads to change their angle, becoming cokced

• Heads attach to new binding site further from center of sarcomere

• Energy is stored in the cocked heads

• This is continued until motor neuron stops signals to muscle fibre and calcium ions are pumped back to SR

muscle contraction in depth

Calcium ion and the protein tropomyosin and troponin control muscle contraction

• When muscle is relaxed tropomyosin blocks binding sites on actin

When signal to muscle is absent, sarcoplasmic reticulums releases CA+ ions

These ions bind to proteins troponin which causes tropomyosin to move

• exposes actin binding site

Skeletons as levers

origin (fulcrum), the pivot point is fixed

insertion, contraction causes movement

Distance vs force

closer to the pivot point the more force but less distance

further from pivot point the less force but more distance

Fulcrum

bone meets bone

Effort

By muscles via tendon

Joints

move in relation to each other, called articulation

Bones

anchorage for muscles and ligaments

allows certain movement depending on shape

Cartillage

covers bone at the joint

prevents friction and wear and tear

absorbs shock

Synnovial Fluid

fills joint cavity

between cartillage and bone

prevents friction

Ligaments

cords of tissue

prevents wrong movement

covers the joint

holds in the fluid

Tendons

tissue with collagen

high tensile stretch

attaches muscle to bone

Ball socket

allows all movement but sliding ( hip)

Plane joints

allows for sliding (wrist)

Hinge joint

flexion and extension (knee elbow)

Saddle Joint

Permits same movement as condyloid joints and combine to form compound joints

Pivot joint

allows for roation on anothe rbone (neck)

Condyloid Joints

abduction, adduction, flexion and extension

Inter and external intercostal muscles

muscles between the ribs

antagonistic

moves ribcage in different direction

External Intercostal Muscles- Contract

expands ribcage

inhalation

stretches internal

stores potantial energy in the titin

Internal Intercostal Muscles -Contract

Exhalation

stretches the external

Adaptations for Marine Animals

Streamlining- shape teardrop reduce resitance

Flipper- reduce drag

Smooth body no hair

Locomotion in Marine Animals

Flippers to steer

Blubber for buoyancy

Flukes- increase thrust

Dorsal fin- stability

Enzymes as catalyst

catalyst speed up reaction

catalyst are not used up, can catalyze reaction many times

less catalyst needed than reactants

Enzymes

converts substances to product

catalyze on reaction

• benefits controls ammount of metabolism

Enzymes in Metabolsim

complex network of interdependent reactions

• form pathways

• small steps

Anabolic

simple molecule to complex molecule, requires energy

macromoners made from monomers

• condensation reaction

Protein or DNA synthesis

Endergonic reaction- takes in energy

more energy than reactants

Catabolic

breaks down larger molecules

• releases energy

digestion, cell respiration

exoergonic- releases energy

less energy than reactants

Enzymes as Globular proteins

Shape and chemical properties match

-allows specifity

Enzymes substrate complex

substrate is bound to active site

substrate is raised to higer energy transition state

substrate undoes anabolic or catabolic reaction

product form and detaches (unchanged enzyme)

Active sites may only be made from a few amino acids, but the proper shapes give the active site the ability for catalysis

Interaction between substrate and active site

enzyme emits forces that attract the substrate, unitl then movement is random

Induced fit binding

bond angles and shapes are altered (allows for transition to higher energy level)

arrangement of amino acids will match the group of the substrate (enzyme substrate complex)

Substrate collision

Higher kinetic energy more chance for substrate enzyme collision to occur

proper collision they are aligned

Chemical properties of enzymes and how they affect substrates

some chemical properties attract substrater

adjust their orientation

only for shirt distances

Variations in Enzymes

reactions occur in cytoplasm

substrates are smaller so they move more

embedded enzymes let the substrate come to them (intracellular)

Extracellular Enzymes

exported from cells

placed into vessicles nad secreted by endocytosis

• synthesised by ribosomes on outside of reticulum

Immobilized Enzymes

immobilized on membrane

allows more convenient catalysis

more stable than free enzymes

easily separated

used in food processing such as lactose free milk

Enzymes specifity

chemical properties and shape

protease have broad specifity

glucose only substrate that binds to glucoskinase

Denaturation

Weak interactions between amino acids

• hydrophobic and hydrogen bonds

Heat and acidity affect these bonds

Effects on temperature on enzymes

when heated particles move

increase chance of collision = higher increase in enzyme activity

more vibrations= higher chance of bonds breaking, changing shape and denaturatioton

Effect of pH on Enzymes

higher acidity= higher hydrogen bonds= lower pH

ionic bonds break when too high or too low

Effect of substrate concentration

increase substrates more collision occuring 

more active sites occupied

will plateau at one point

Metabolic efficiency

w/o constant body temp enzymes would denature

too much activity, sweat to regualte

not enough activity, muscle contractions (shivers)

many mammals have brown adipose fat tissue, this tissue ewhat many mitochondria which generate heat instead or ATP.

Activation energy

energy needed to bring an enzyme to an activation state

Intracellular enzymes

worki on the inside of cells

synthesized by free ribosomes in cytoplasm

Non-competitive inhibitors

Bind to allosteric sites, a different biding spot

• allows sites to be regualted

changes the shape

Competitive inhibitors

Go to active binding site

• inhibitors have simmilar structures

do not make products

fight by increasing substance concentration

end-product inhibition

end product binds to allosteric site

• changing shape

prevents too much to be made

Isoleucine Synthesis

• threonine is converted to isoleucine

• end product and would inhibit the first enzymes

• non-competitive

Mechanism Based inhibition

All other inhibition are reversible these are not

Heavy metals irreversibly bond to -SH altering the structure

• bond covalently

inhibitors might kill organisms