Introduction to Biology and Cellular Structures

These flashcards cover key concepts in biology, including the structure and function of macromolecules, cell theory, protein synthesis, and elements of cellular biology.

Biology

The study of organisms and the processes that make life.

Homeostasis

The regulation of internal environments in living organisms.

Macromolecules

Large complex molecules essential for life, including proteins, nucleic acids, carbohydrates, and lipids.

Hydrophilic

Having an affinity for water; being attracted to water.

Macromolecule Function

Dependent on the properties of their functional groups.

Proteins

Polymers made from amino acids, serving various functions such as catalyzing biochemical reactions.

RNA World Hypothesis

Theory suggesting that RNA molecules were the first catalysts for biological processes.

Cell Theory

All living organisms are composed of cells, which are the fundamental unit of life.

Phospholipid Bilayer

Structure that makes up cell membranes, consisting of hydrophobic tail regions and hydrophilic head regions.

Nucleotides

The monomers of nucleic acids, which consist of a nitrogenous base, a sugar, and a phosphate group.

Peptide Bond

A covalent bond formed between two amino acids in a protein.

Protocells

Simple cell-like structures that may have been precursors to living cells.

Condensation Reaction

A chemical process where two molecules combine, releasing water.

Hydrolysis Reaction

A chemical process that breaks down macromolecules by adding water.

Electron Configuration

The arrangement of electrons in an atom's orbitals.

Catalyst

A substance that speeds up chemical reactions.

Chaperone proteins

Proteins that assist other proteins in folding into their proper shapes.

Cell Fractionation

A technique used to separate cellular components by size and density.

Flagella

Long, whip-like structures used for locomotion in some prokaryotes.

Saturated Fatty Acids

Fatty acids that have no double bonds and are saturated with hydrogen atoms.

Unsaturated Fatty Acids

Fatty acids that contain one or more double bonds.

Gene

A sequence of DNA that encodes instructions for building proteins.

living organisms have these common traits

1. Made of a common set of chemical compounds (carbon-based)

2. Made up of cells

3. Use molecules from the environment to synthesize new molecules

4. Extract energy from the environment and use it do work

5. Regulate their internal environments (homeostasis)

6. Contain genetic information that enables them to develop, function, and reproduce

7. Use a universal genetic code to build proteins

8. Exist in populations that evolve over time 

Electrons (e-), mass and charge?

• Mass: 0

• Charge: -1

neutrons (n0) mass and charge?

• mass: 1

• charge: 0

protons (p+) mass and charge?

mass: 1

charge: +1

where is the nucleus

middle of the cell

atomic number

number of protons

atomic charge

protons and electrons

mass number

protons and neutrons

Hydrogen: the first element 

• Atomic number: 1= 1 proton

• Atomic charge: 0, 1 proton + 1 electron, cancels out

• Atomic mass {if 0 nu}: 1proton = 1

Orbitals fill in a specific sequence

• Electron shells: energy levels around the nucleus 

• Shells closer to the nucleus are typically low energy, shells further away are usually higher energy.

• 1st shell: 1 orbital = 2 electrons (e-)

• 2nd shell: 4 orbitals = 8 electrons (e-)

• The outermost shell of electrons dictates the chemical reactivity of an element 

  • Valence shell (outermost shell for a particular atom)

The octet rule dictates how atoms form bonds

• The tendency of atoms to form bonds to create a full valence

• Reactive atoms have unpaired valence electrons 

• Atoms with a full valence shell are stable 

Hydrogen bond 

• Interaction between two molecules, always a partially positive hydrogen, and a partially negative atom, usually oxygen but not always 

Polar covalent bond

• Hydrogen positive, nitrogen negatively charged.

Living organisms are made of macromolecules

• 70%water

• Some ions and small molecules

• About ¼ macromolecules 

Macromolecules 

• Proteins (most)

• Nucleic acids

• Carbohydrates 

• Lipids 

Macromolecule function is dependent on the properties of their functional groups 

• Polar vs. nonpolar covalent bonds

• Ability to hydrogen bond

• Ability to form ions

• Ability tonact as weak acids or bases

• Chemical reactivity 

• High vs low energy bonds

Hydroxyl

• when u have an OH (oxygen and hydrogen bound together) and r (means it bound to something else)

• Polar, partially positive hydrogen, partially negative oxygen.

• Ability to hydrogen bond 

• Involved in condensation reactions 

keto

• a carbon that has a double bond to an oxygen something bond on either isde

• Polar 

• Ability to hydrogen bond

Aldehyde, has a carbon double bonded to an oxygen but one side is bond to a hydrogen

• Polar

• Ability to hydrogen bond 

• Very reactive 

carboxyl

• no hydrogen, hydroxyl instead

• Polar

• Ability to hydrogen bond 

• Charged and acidic acids: lonizes to -COO + H+

• Involved in condensation reactions

Sulfhydryl R-SH

• Polar

• Can form covalent bond with another– SH

Phosphate 

• Nonpolar due to shape

• Ability to hydrogen bond 

• Charged and acidic: P-OH – P-O + H+

• Involved in condensation reactions 

• High energy bonds  

amino

• Polar 

• Ability to hydrogen bond 

• Charged and basic: -NH2 + H+ – NH3

• Involved in condensation reactions 

Methyl

• Nonpolar 

• Involved in hydrophobic interactions

protiens

a monomer of amino acids

carbs

monosacchrides

nucleic acids

nucleotides

lipds

not a polymer

energy

reactant

• Hydrolysis reaction: breaking down macromolecules, the exact opposite of a condensation reaction; instead of forming water, we need water.

  - H2O: reactent

  -energy: product

Monomers

 monosaccharides, a single sugar (simple sugar)

       Disaccharide, 2 simple sugars, less common

       Oligosaccharide, a few, 3-20 simple sugars 

       Polysaccharide, poly meaning many, 100+ sugars bonded together

Alpha orientation-

 hydroxyl group points down from carbon one

Beta orientation

when the hydroxyl group points up

when the hydroxyl group points up…

• Sugars are bonded together throught glycosidc bond (bond between sugars)

• The way theyre catagorized is based on the orientation and number of carbons involved in the bond

Energy

 transport of energy/storage, short term, transporting in the form of bonds from one location in the organism to another

Glucose

how to transfer energy in the blood

Energy

medium to long-term storage

•  Starch (plants) long-term 

• Glycogen  (animals) is primarily stored in the liver/ medium storage

Structure

 using sugars as a carbon skeleton for other molecules

Cellular structure

 larger molecules (cellulose, plant wall of plant cells)

Polysaccharides may be branched 

• Linear (cellulose) - Parallel cellulose molecules form hydrogen bonds, resulting in thin fibrils (insoluble in water)

• Branched (starch). Branching limits the number of hydrogen bonds that can form in starch molecules, making starch less compact than cellulose (not close enough to hydrogen bond)(soluble, able to dissolve in water)

• Highly branched (glycogen), the high amount of branching in glycogen makes it solid deposits more compact than starch (all sugars have hydroxyl groups and are close enough to hydrogen bond. Also, another insoluble polysaccharide.

• Non-polar hydrocarbons

• Van der Waals forces (occur with all molecules, more important here bc they cannot hydrogen bond)

• Hydrophobic

• lipids are insoluble in water

fats and oils

• Storage of energy

• thermal/electrical insulation

• Repel water or prevent evaporation

• Phosphilipds

• Form membranes

• Steroids

• Multiple rings that share carbons 

• Hormones

• Vitamins 

• Carotenoids and chlorophylls

• Pigments and plants

• Capture light energy in photosynthesis

Fats and oils are made of triglycerides 

• Fats: 

  • Solid at room tempo

• Oils:

  • Liquid at room temp

Triglycerides have two main components 

• Glycerol 

  • 3 carbon carbohydrate 

• Fatty acids

  • Hydrocarbon chain with a hydroxyl group

  • Can vary with structures, classify with how carbons are bonded together

    • Saturated with hydrogens, no double bonds, saturated with hydrogens, have max hydrogens they can.

  • Unsaturated fatty acids have 1+ double bonds

    • Not fully saturated with hydrogens, packed together loosely, bends in fatty acids, cant pack as tighyly, lots of movements, not as wander los forces keeping togethor, liquid at room temp

good to know

Polyunsaturated fatty acids have 2+ double bonds 

Cis vc trans unsaturated fatty acids 

• Cis: has hydrogens on the same side of the carbons participating in double bond 

  • Having a large bend, bc of orentation, loosely packed found in oil liquid at room temp

• Trans: opposite sides

  • Going in a straight line, tightly packed solid at room temp\

Ester

carbon double-bonded to an oxygen, the carbon will also be bonded to an oxygen that is not attached to a hydrogen

Phospholipids are modified triglycerides 

• Glycerol

• 2 fatty acids 

• 1 phosphate-containing molecule

• Fatty parts are moostly non polar, hydrophobic

Amphipathic

• Tails: hydrophobic

• Heads: hydrophilic 

• Phophilipds aggregate in water 

The phospholipid bilayer 

• makes up the cell membranes.

• two layers,

• makes up to be favorable for hydrogen bonding in water. 

• Hydrocarbon chains are internal to the membrane, interacting with other hydrocarbons 

Phospholipid heads

hydrophilic, hydrogen bond, and interact with water

Amino acids with electrically charged hydrophilic side chains are positive 

• Positive (basic)

  • Arginine

  • Histidine

  • Lysine 

• Negative (acidic) 

  • Aspartic acid/aspartate 

  • Glutamic acid/glutamate

Amino acids with polar but uncharged side chains (hydrophilic) 

• Serine

• Threonine

• Asparagine (keto amino groups)

• Glutamine (keto amino groups)

• Tyrosine

Amino acids with nonpolar side chains 

• Alanine (smallest, methal as R group)

• Isoleucine

• Leucine (split or branched)

• Methionine

• Phenylalanine

• Tryptophan

• Valine (split or branched)

Special cases 

• Cysteine (polar), the solvate group that it contains

• Glycine (nonpolar) bonds to two hydrogens 

• Proline (nonpolar) side chain bonds back to the amino portion of the amino acids

Automatic

6-sided ring with alternating double bonds

Alypathic

 any amino acids with a chain R group

A polypeptide is a polymer of amino acids 

• Proteins are made up of one or more polypeptide chains 

• Folded into a 3d shape

  • Up to 4 levels of structure 

The sequence of amino acids makes up the primary structure of a polypeptide 

Interaction between individual amino acid monomers 

• Peptide bonds form from condensation reactions

• Main backbone, carbons in nitrogens 

• Polarity of the backbone, alpha-carbon, attached to the R group

The hydrogen bonds that occur between the backbone atoms of a polypeptide

• Alpha (helix), no R groups in center, if divided in half, one side polar, another side non-polar 

• Beta pleated sheet, some R groups pointing up, some down. Generally, more space for r groups. If they have very large side chains its more commonly beta than alpha

The 3-dimensional structure of a polypeptide is the tertiary (3’) structure.

• Determined by both 1’ and 2’ structures 

• Determined by the order of amino acids

Tertiary (3’) structure is dependent on r groups 

• Disulfide bridges 

  • Covalent bond occurs berween two solfide bonds

• H-bonds between r groups 

  • Occur between r groups

• Hydrophobic interactions 

  • Occur between non polar amino acids

• Ionic bonds between r groups (salt bridges)

  • Several amino acids have a neg or pos charge

Cysteine can form a disulfide bridge with another cysteine

• Disulfide bond (bridge), the only example that isa covalent bond

  • Covalent bond

  • Has to occur between two cysteine 

  • Not all cysteine will form these bonds 

Protien folding is influenced by the solubility of amino acids

• Water dictates how protein folds 

• Water will want to interact with certain molecules 

• Hydrophilic side chains will be on the outside of a protein and interact with water

Proteins with 2+ polypeptide chains have quaternary (4’) structure 

• Each polypeptide chain = a subunit 

• Each subunit has its own 3’ structure 

• Subunits interact via the same interaction as 3’ structure

Enzymes

catalyze (speed up) biochemical reactions 

Structural proteins

provide physical stability and movement  

Defensive proteins

recognize and respond to nonself substances 

Signaling proteins control physiological processes

Membrane transporters

regulate the passage of substances across the cell

Storage proteins

store amino acids for later use 

Transport proteins

bind and carry substances within

What properties of proteins contribute to their function?

Protein shape and active site go hand in hand, closely related, so there is a proper fit.

Interactions with other molecules can alter protien shape 

• Conformational shape change 

• Binding molecules 

• Cobvaklent modifications 

Environmental changes can affect protein structure (and prob function)

• Function of a protein is dictated by shape,

  • Optimal temp for two enzymes 

  • Optimal ph for two enzymes 

Denatured proteins lose their structure 

• Loss of a protiens native confirmation

  • Native: more compact structure, one shape, can be modified 

• Various factors will cause a protein to denature 

• Affects 2’-4’ structure 

• nonfunctional

Several conditions can denature protiens 

• Heat

  • Disrupts H-bonds 

• Ph 

  • Changes in charge → change in interaction

• Reducing agents 

  • Break disulfide bridges 

Denaturation is sometimes reversible 

• Some proteins can renature on their own 

  • Occurs when the denaturing condition is reversed 

• Some proteins need help to renature 

  • Require chaperone proteins

• Some proteins are permanently denatured 

Chaperons help proteins fold properly 

Two different scenarios u will see them in the most 

• A denatured protein binds to HSP60 and enters it 

• The inside of the structure has hydrophobic amino acids that bind to hydrophobic amino acids on the target protein 

• A lid seals the cage 

• The protein folds into its appropriate shape and is released 

How did life originate on earth 

• Spontaneous generation.. 1700’s things just started to pop up mysteriously..

• Chemical evolution 

  • Atmospheric experiments (Miller and Urey)

  • Primordial soup hypothesis

    • Life might have begun in oceans from simple gases and lightning sparks

• Brought from space on meteorites