BIO - Unit 2

Proteins - building block

amino acids

↪ NH₂ - CH(R) - COOH

Proteins - primary structure

amino acid chain

Proteins - primary structure - terminus

N-terminus: amino group (NH₂) → start of protein

C-terminus: carboxyl group (COOH) → end of protein

Proteins - primary structure - bonds

Peptide bonds between amino acids

Proteins - secondary structure

interactions of nearby amino acids

Proteins - secondary structure - types

α-helix: SAME polypeptide chain

β-pleated sheets: TWO polypeptide chains

β-sheets types

Antiparallel: opposite ways (horizontal lines)

Parallel: same ways (zigzag lines)

Mixed: combination of both

Proteins - secondary structure - bonds

H-bonds between H of NH₂ and O of COOH

Proteins - tertiary structure

interactions between R-groups of the same polypeptide chain

Most proteins only have ___ structures

tertiary

Proteins - tertiary structure - bonds

• H-bonds

• ionic bonds

• hydrophobic interactions

• disulfide bonds (S-S)

Proteins - quaternary structure

interactions between polypeptide chains

Common examples of quaternary structure

• hemoglobin

• DNA polymerase

Denaturation

change in temp or pH of environment → primary structure is only intact one

Colloid behavior

diffuse slowly & scatter light when in water

Buffering capacity of proteins

can resist changes in pH → because of their groups that can accept/donate H⁺

Amphoteric behavior

something can act as both an acid and a base depending on the situation

Different types of protein shapes

Fibrous: support tissues

Globular: transport, enzymes, and regulation

Different types of protein composition

Simple: just amino acids

Conjugated

Conjugated protein terminology

Apoprotein: protein part of conjugated protein

Holoprotein: apoprotein & prosthetic group

Prosthetic group: non-protein component → permanently attached → necessary for protein function

Common eg of conjugated protein

Hemoglobin:

• heme: prosthetic group

• globin: apoprotein

Different types of protein functions

• enzymatic

• structural

• transport

• storage

• defense

• hormonal/signaling

• receptors

• regulator (control cellular processes)

Solubility of different protein shapes

Globular: more soluble

Fibrous: less soluble

Allostery

when a molecule binds to a protein at a site that’s NOT the active site

Allosteric enzymes

enzymes that are able to change between T and R states

T and R states of allosteric enzymes

T: tense, active site is not super open → binding is difficult

R: relaxed, configuration of enzyme makes easy binding

Different types of models for allosteric enzymes

Concerted model: specific ratio (ie 90T:10R) that must be continued so enzymes change from T to R and then at the end R to T to keep the ratio the same

Sequential model: 100% T at the beginning → substrate builds up until forcibly binds to T protein → enzyme actually has 3 subunits! As one substrate binds, second subunit becomes R, then third subunit becomes R → entire protein is R

Enzymes

Biological catalysts → lower activation energy requried

Categories of enzymes

Intracellular: inside cells

Extracellular: outside cells (ie in mouth or small intestine)

Structure of enzymes

Globular protein

Models of enzymes

Lock and key: substrate fits perfectly to active site

Induced fit: substrate doesn’t fit perfectly but active site conforms (more evidence)

Types of inhibitors

Competitive: compete with substrate for active site

Noncompetitive/allosteric: bind to enzyme at an allosteric site and change enzyme shape so substrate can’t bind to active site

Strengths of inhibitors

Reversible: weak bonds, can detach and allow enzyme to work again

Irreversible: strong bonds, permanently stop enzyme from working

Covalent modification

regulation of enzymes by covalently adding/removing chemical groups

Types of covalent modification

Phosphorylation: adding PO₄ → using enzyme kinase → usually turns enzyme ON → phosphorylated enzyme

Dephosphorylation: removing PO₄ → using enzyme phosphatase → usually turns enzymes OFF

Common examples of monosaccharides

• glucose

• fructose

• galactose

• mannose

• ribose

• deoxyribose

Monosaccharides

C_n(H₂O)_n → n = num from 3-7

Types of glucose

α-glucose: OH on C^1’ on bottom

β-glucose: OH on C^1’ on top

Anomeric carbon

only carbon where if OH is on top/bottom it changes whether carbohydrate is α or β

Glucose

• bonds store lots of energy → major cellular fuel

• blood sugar → glucose traveling through blood

• building block of starch, glycogen & cellulose

Fructose

• sugar in fruits and honey

• component of sucrose

Types of fructose

D-fructose: found in nature

L-fructose: exists in laboratories

Difference between D- and L- carbohydrates

Two different forms that are mirrored images of one another (flipped horizontally)

Galactose

• component of lactose

• provides cellular energy

• building block for tissues, brain, and immune system

Difference between glucose and galactose

Galactose has OH of C^4’ on top instead of on the bottom (where glucose OH is)

Glucose molecule

C₆H₁₂O₆

Galactose molecule

C₆H₁₂O₆

Fructose molecule

C₆H₁₂O₆

Mannose molecule

C₆H₁₂O₆

Ribose molecule

C₅H₁₀C₅

Deoxyribose molecule

⁠C₅H₁₀O₄

Mannose

• helps build proteins → glycosylation

• stops bacteria (mainly E. coli) from sticking to urinary tract → offered as a supplement to prevent urinary infections

Types of mannose

α-mannose: OH on C^1’ is on the bottom

β-mannose: OH on C^1’ is on top

Ribose

• present in RNA, ATP and NAD⁺

• important for cellular energy, genetic material and metabolic cofactors

Deoxyribose

• forms backbone of DNA

• without the hydroxyl group on C^2’, it’s more stable than RNA → better for long-term storage

Oligosaccharides

3-10 sugar units → most are disaccharides (2 sugar units)

Succrose/sacchrase

• table sugar

• energy storage/transport in plants

• energy source in humans

Succrose/sacchrase make-up

glucose + fructose

Lactose

• milk sugar

• helps body absorb important minerals

• supports healthy gut bacteria

Lactose make-up

galactose + glucose

Maltose

• produced during starch digestion

Maltose make-up

glucose + glucose

Common examples of oligosaccharides

• succrose/sacchrase

• lactose

• maltose

Polysaccharides

more than 10 sugar units

Common examples of polysaccharides

• starch

• glycogen

• cellulose

• chitin

Amylopectin branch frequency

every 20 subunits

Bond formation in amylopectin

α(1→4) in chains & α(1→6) in branch points

Types of starch

amylopectin: branched

amylose: not branched

Bond formation in amylose

α(1→4)

Starch

• energy storage in plants

• dietary energy in animals

Bond formation in glycogen

α(1→6) at branch points

Glycogen

• short-term energy storage in animals and funghi

• stored in liver and muscle cells

Glycogen branch frequency

every 10 subunits

Cellulose

• gives support to plants

• insoluble fibers in humans → adds bulk to stool

• primary nutrient for cows and horses

Bond formation in cellulose

β(1→4)

Chitin

• forms exoskeletons

• tight hydrogen make it very strong

Chitin make-up

N-acetylglucosamine

Chemically modified carbohydrates change

Phosphorylation: addition of a phosphate group - PO₄

Glycosidation: replacement of hydroxyl group with an alcohol or amine

Phosphorylation function

increases reactivity and traps molecule inside cell membrane

Glycosidation function

removes reducing properties and forms stable glycosides or nucleotides

Glycoproteins

carbohydrate + protein (main component)

Glycoprotein function

• cell recognition

• cell receptors

• immune functions

Glycosylation

covalent attachment of carbohydrate chains to proteins

Types of glycoproteins

O-linked glycoproteins: carbohydrate attached to O of hydroxyl group of serine (Ser) or threonine (Thr).

N-linked glycoproteins: carbohydrate attached to N of amino acid → usually asparagine (Asn)

Proteoglycans

carbohydrates + protein

Proteoglycan functions

• structure

• hydration

• joint cushioning

• cell signaling

• extra-cellular matrix

Glycosaminoglycan (GAG) chains

unbranched complex carbohydrates made of repeating disaccharide units