AP Bio Unit 1

What is life?

Life is a self-sustained chemical system capable of undergoing Darwinian evolution

Functions of lipids

Structural function as waterproof barriers in cell membranes, signaling and control function as steroids

Enzymatic proteins

Selective acceleration of chemical reactions

Defense proteins

protection against disease

storage proteins

storage of amino acids

transport proteins

transport of substances

hormonal proteins

coordination of an organism’s activities

receptor proteins

response of cell to chemical stimuli

contractile and motor proteins

“walk” to transport substances

structural proteins

support

Functions of carbohydrates

Structural function as cell wall and backbone of DNA

Functions of nucleic acids

Structural function as ribosomes, signaling and control function as DNA, chemical work function as ribozymes, coenzymes, ATP

Eubacteria cells

Oldest, prokaryotic, with DNA and proteins in a membrane

Archaea

Prokaryotic, complex biomolecules and processes

Eukarya

Has internal membrane structures, complex biomolecules and processes

Genome

Made up of all the protein and RNA encoding genes

Proteome

Made up of all the proteins encoded by genes

Catalytic proteins vs catalytic RNAs

Enzymes vs ribozymes

LUCA tree

LUCA (3.8 bya) split into eubacteria and archea, eukarya branched off from archea 1.2 bya

Elements common to life

C, H, O, N, P, S, (as ions - Ca, Na, Cl, K, Fe, Mg)

What makes an isoptope radioactive

Unstable nuclei (too much mass) causes stabilization by destroying or ejecting protons or neutrons with enough energy to destroy biomolecules

Ions

Metals can be oxidized by losing electrons, nonmetals can be reduced by gaining electrons, ions are more stable and have different chemical behavior

Van der Waals Forces

Weak IMFs/LDFs

When is water most dense

At 4 degrees celsius, any higher and the energy would cause the molecules to spread out, any lower and the hydrogen bonds would lock the molecules in place

What are the benefits of water’s high specific heat capacity

Reduces temperature stress on organisms that sweat by absorbing body heat and evaporating

Capillary action

Ability to defy gravity with cohesion and adhesion working together, vital to plant circulatory systems

Surface tension

Measure of difficulty to break the surface of a liquid due to cohesion

Buffers

A weak base/acid and its conjugate acid/base that neutralize slight changes in pH by accepting/donating H⁺ as they are gained/lost, blood pH is maintained by carbonic acid and its conjugate base (H₂CO₃ and HCO₃^-)

What is organic chemistry

The study of carbon compounds associated with life (often containing carbon and hydrogen)

Types of isomers

Structural isomer is simplest and results in a different shape, geometric isomer has a different shape due to varying multi-bond position, chiral/handed isomer/enantiomers have different mirrored shapes

Methyl group

-CH₃, hydrophobic, no effect on pH

Carbonyl group

-C=O, hydrophilic, whole molecule is a ketone if within a carbon chain, aldehyde if at an end

Alcohol/hydroxyl group

-OH, hydrophilic, no effect on pH, can make three methyl groups dissolve in water

Thiol/sulfhydral group

-SH, hydrophilic, plays a role in stabilizing tertiary structure of proteins by covalently bonding to another of itself to form disulfide bridges

Carboxyl group

-COOH (one O double bound), hydrophilic, acidic due to double bond O attracting electrons so strongly that the H splits off

Phosphate group

-OPOO₂H₂^- (one O double bound), hydrophilic, acidic due to double bound oxygen attracting electrons so strongly that ONE H splits off, found in DNA

Amino group

-NH₂, hydrophilic, basic due to lone pair sucking up H⁺

Monomers and polymers

Monomers are small molecules that build polymers, polymers are a long molecule of many monomers bound together

Dehydration synthesis

Binds two monomers together by the enzyme polymerase breaking off an OH^- on one end and an H⁺ on the other, with the two molecules fusing at the remaining O and the OH^- and H⁺ forming H₂O

Hydrolysis

Breaks down polymers by an enzyme/hydrolase binding to the polymer and adding water to break a covalent bond between monomers

Lipids (fats)

Monomers are fatty acids (-oic acid), hydrophobic, dangerous to use because they can clog blood vessels due to being hydrophobic

Triglycerides (lipid)

energy storage lipid for animals

Phospholipids (lipid)

structural lipids found in the cell membrane bilayer, hydrophilic head with hydrophobic fatty acid tails

Cholesterol (lipid)

Keeps membrane intact in varying temperatures and is only found in animals

Steroids (lipid)

A product of cholesterol that function as messengers that go straight through the cell membrane due to being lipids

Carbohydrates (sugars)

Monomers are monosaccharides or simple sugars like glucose and ribose, often end in -ose, usually pentagonal or hexagonal but can be in chain form (a ketone)

Cellulose (carbohydrate)

makes up the cell wall of plants, is only digestible by prokaryotes, and is an alternating chain of glucose monomers

Chitin (carbohydrate)

Makes up the cell wall of fungi and exoskeleton of arthropods

Starch (carbohydrate)

energy storage carbohydrate for plants, structure is a chain of symmetrical glucose monomers

Glycogen (carbohydrate)

energy storage carbohydrate for animals

Nucleic acids

Monomers are nucleotides composed of a five carbon sugar (a pentose), a phosphate group on the 5’ carbon, a nitrogenous base on the 1’ carbon (glycosidic bond),

DNA vs RNA

DNA is an anti parallel double helix and uses deoxyribose (-OH on 2’ carbon), while RNA is a single strand (final form can differ) and uses ribose (-H on 2’ carbon)

Types of RNA

mRNA temporarily stores DNA information, coenzymes (help enzymes), ribozymes (act as enzymes)

Proteins (polypeptides)

monomers are amino acids composed of an amino group bonded to a C-H which is then bonded to a carboxyl group, often end in -in, pept means related to proteins

Protein structure

unique shapes that are vital to functions, described in primary, secondary, tertiary, and quaternary structure

Primary structure

the sequential order of amino acids in a protein, determined by nucleotide sequence in DNA, ends are the N terminal and C terminal domains

Secondary structure

local regions of a polypeptide chain that are formed into structures like alpha helices and beta pleated sheets due to the hydrogen bonds between the backbone, some sections only exist as filler with no shape

Tertiary structure

The overall 3D shape of the polypeptide that is the result of secondary structure, hydrophobic interactions, van der waals interactions, hydrogen bonds, disulfide bridges , and ionic attractions between the side chains

Quaternary structure

When multiple proteins/polypeptides bind together to form a complex machine that performs its function, not always found in proteins

Biomolecule bonds

glycosidic linkages for carbohydrates to another molecule, ester linkages connect glycerol to fatty acids in lipids, peptide bonds bind amino acids together, phosphodiester linkage connecting a pentoses to a phosphate group in nucleic acids

Cis vs trans isomers

cis isomers are very polar and have the molecules on the same side of a carbon double bond, while trans isomers are nonpolar and have the same molecules on opposite sides of a carbon double bond, caused by the lack of flexibility of double bonds

What are chaperonins

Barrel shaped proteins that help proteins fold/refold into their shape

What is denaturation

Disruption of secondary, tertiary, and quaternary structure by a change in temperature, pH, salt concentration, or an attack by toxins

How does a temperature change cause denaturation

When temperature is too high, the protein’s side chains vibrate faster and push further apart, causing the hydrogen bonds to break, and when temperature is too low, the hydrogen bonds are locked into place, preventing them from breathing apart and fixing their shape if misfolded

How does a change in pH or salt concentration cause denaturation

increase leads to excess ions that interfere with the hydrogen bonds by attracting to the opposite charges, decrease leads to too few ions that prevent the hydrogen bonds from breathing apart and making it difficult for them to reshape if misfolded

Pyrimidines

C, U, T

Purines

A, G

How do RNA molecules synthesize proteins

mRNA bound by tRNA and processed by rRNA in ribosomes