Unit 1 - Chemistry of Life Flashcards
what does all life on earth have in common?
made up of organic molecules
ionic bonding
bond in which an element transfers an electron to another element
- this results in ions
cations
positive ions
anions
negative ions
covalent bonding
a bond that involves the sharing of electrons
what does covalent bonding result in
stable configurations
nonpolar covalent bonds
- electrons are shared equally
- hydrophobic
electronegativity
when an atom is considered “electronegative”, it means it is one with a strong pull on electrons towards its nucleus
- results in partial charges
polar covalent bonds
- one atom pulls electrons towards its nucleus
- hydrophilic
ex: H2O
how do we know if a molecule is polar?
- P, O, N, S, etc. cause that region of the molecule to be polar (hydrophilic) due to the high EN of those elements
- N (nitrogen) means polar and basic
- once you see charges, you know its polar
explain the covalent bonding in water
- oxygen, which is highly electronegative, pulls on the hydrogens electrons
- the bonds between the H and O within the molecule are POLAR COVALENT BONDS
how do we know if a molecule is nonpolar?
- long chains of carbons and ringed carbon structures are nonpolar (hydrophobic)
- symmetrical compounds are nonpolar
hydrogen bonds
- a WEAK attraction between a hydrogen atom and a highly electronegative atom (ex: H2O)
hydrophilic
- mix with water
- polar
hydrophobic
- will NOT mix with water
- nonpolar
water’s 7 properties
- cohesion
- adhesion
- high heat capacity + heat of vaporization
- transpiration
- surface tension
- liquid water vs ice
- water as a solvent
cohesion
- waters ability to stick to itself
- due to hydrogen bonding
adhesion
- water’s ability to stick to polar molecules
heat capacity
- the amount of energy needed to change the temperature of water
- water has a high heat capacity
**this is why organisms can live in aquatic environments
heat of vaporization
**thermoregulation
- water, in the form of sweat, will absorb heat energy
- this reduces body temperature
transpiration
evaporation of water through the leaves of a plant
- water will stick together (cohesion) and stick to the xylem (adhesion)
- this prevents the backflow of water
- pulled up the plant as water evaporates from the leaves
surface tension
- intermolecular forces at the top are stronger than below
- extreme due to cohesion and adhesion forces; why certain insects can walk on water bc the interaction btw their bodies and water is weaker than the Hydrogen bonds between H2O
liquid water vs ice
ice is less dense than H2O therefore ice floats and aquatic organisms can survive in the cold
water as a solvent
water will dissolve ionic and polar compounds
carbon
- has 4 valence electrons
- forms 4 covalent bonds with other elements which causes diff molecular shapes - found in ALL organic compounds
- used to make macromolecules
4 major organic molecules (macromolecules)
- carbohydrates
- lipids
- amino acids / proteins
- nucleic acids
carbohydrates
- polar
- made up of C, H, O
function of carbohydrates
- energy
- makes up the cell walls of plants and prokaryotes
lipids
- nonpolar
- made up of C, H, O
function of lipids
- energy source
- make up the cell membrane
amino acids / proteins
- polar
nucleic acids
- polar
monomers
single molecule
polymers
many molecules put together
how are monomers and polymers synthesized?
- dehydration synthesis
- hydrolysis
dehydration synthesis
- linking monomers together to form polymers
- H2O is removed
hydrolysis
- adding H2O to break polymers into monomers
hydroxyl
- polar
- “OH”
- alcohol
carboxyl
- polar
- “COOH”
- carboxylic acids
phosphate
- polar
- organic phosphates
carbonyl
- polar
- think ketones and aldehydes!!
amino
- polar
- amines
sulfhydryl
- polar
- “-SH”
- thiols
methyl
- nonpolar
- “CH3”
what is the importance of functional groups
they influence how molecules behave in reactions and with H2O
description of carbohydrates
- C, H, O
- the monomer is known as monosaccharide
- drawn as hexagon, number 1-6 starting from right middle
monosaccharides
ex: glucose, fructose, galactose
ex: deoxyribose, ribose
hexose sugars
- glucose, fructose, galactose
pentose sugars
- deoxyribose, ribose
alpha glucose
- the 2 hydroxyl groups (OH) are faced down
beta glucose
- the left hydroxyl (OH) is faced down while the right is faced up
what is the difference between alpha glucose and beta glucose
the position of the hydroxyl (OH)
disaccharides
- 2 monosaccharides linked together (via dehydration synthesis)
- glucose + glucose -> maltose
- glucose + fructose -> sucrose
- glucose + galactose -> lactose
maltose
- disaccharide
- glucose + glucose -> maltose
sucrose
- disaccharide
- glucose + fructose -> sucrose
lactose
- disaccharide
- glucose + galactose -> lactose
glycosidic bonds
bond that links carbohydrates
polysaccarides
- starch
- cellulose
- glycogen
- chitin
starch
stored sugar in plants
- alpha glycosidic linkage
chitin
makes up the exoskeleton of insects
glycogen
stored sugar in mammals
- alpha glycosidic linkage
cellulose
- (fiber)
- makes up the cell walls of plant cells
- made up of beta glucose molecules which we CANNOT digest (we lack the proper enzymes)
function of carbs
- major energy source
- make up cell walls
elements of lipids
- C, H, O
are lipids polar/nonpolar generally?
they are nonpolar, hydrophobic (phospholipids are both)
triglycerides
- formed by combining a glycerol molecule (3 C sugar) and 3 fatty acids
- saturated vs unsaturated fatty acids
saturated fatty acids
- saturated fats: no double bonds, solid at room temperature
unsaturated fatty acids
- unsaturated fats: 1 or more double bonds, “liquid at room temp”
- nonpolar, hydrophobic
what type of bonds are in triglycerides
ester bonds
ester bond
links a glycerol and 3 fatty acids
trans fats
- stay straight so it can stack, unhealthy
phospholipids
- made up of a phosphate group (head), glycerol (3 C sugar), 2 fatty acids (tails)
- the head is polar, tail is nonpolar
- make up the cell membrane (phospholipid bilayer)
amphipathic
- contains both polar and nonpolar regions
why are the tails of a phospholipid drawn differently
they are drawn differently to show saturated (straight) and unsaturated (squiggle)
sterols/steroids
- 4 fused carbon rings with attached functional groups
- found in cell membranes (cholesterol) & signaling molecules/hormones ( testosterone, estrogen )
functions of lipids
- protection (of organs)
- temperature regulation/insulation
- **makes up the cell membrane
- **can be used for energy
protein’s elements
C, H, O, N and sometimes S
protein’s monomer
amino acid
protein’s polymer
polypeptide
protein’s bond
peptide bond
what determines proteins function
the shape
amino acids - buffer
- amino acid is a buffer (regulates pH)
- buffer can accept/donate hydrogen
- contains a variable side chain which is responsible for the properties of polypeptides
primary structure of protein
- the sequence of amino acids (coded for by DNA)
- amino acid has directionality; from the n-terminus to c-terminus
- peptide bonds
secondary structure of protein
- 2 types of folding: alpha helix and beta pleated sheet
- **the structure is formed from the hydrogen bonding of the polypeptide backbone
tertiary structure of protein
- 3D structure when alpha helixes & beta sheets fold further due to r-group interactions
- folds are due to the R-group interactions
- hydrogen bonding
- ionic bonds
- covalent bonds “S-S” -> disulfide bonds, very strong
- hydrophobic and hydrophilic interactions
how do R-group properties determine how a protein folds?
- hydrogen bonds -> hydrophobic vs hydrophilic
- hydrophobic will tend to come inwards
quaternary structure
- 2 or more polypeptides combined
protein functions
- make up the muscles
- antigens, antibodies
- involved in transport; receptors
- CTFR (cystic fibrosis)
- enzymes (catalysts - speed up chemical rxns)
mutations in proteins
- DNA codes for the production of proteins
- a change in the DNA can lead to a change in an amino acid -> changes R-group interactions
what causes the partial charges in H2O
- oxygen is more EN, therefore it has a stronger pull on the shared electrons w hydrogen
- causes O to have partial “-“
- causes H to have partial “+”
- this uneven distribution of charge causes H2O to be polar
what is the universal solvent
water
what are waters properties attributed to
its polarity and ability to form hydrogen bonds
hydrogen bonds: boils
- when water boils, hydrogen bonds are breaking to cause H2O molecules to move rapidly (high specific heat)
hydrogen bonds: freezes
- when water freezes, H2O molecules get pushed apart therefore less dense; ice floats on water
metabolism
- sum of all chemical reactions that take place within an organism
- catabolic: bond breaking
- anabolic: bond forming
proteins
- they are polymers formed from amino acid monomers
amino acids
- made up of one central carbon covalently bonded to 4 things: hydrogen, acidic carboxyl groups, amino group, “R group”
what gives amino acids their unique properties
the r-group which subs for different side chains that give amino acids their unique chemical properties
when amino acids link together, what happens
dehydration synthesis occurs between amino group and carboxyl group
- known as a peptide bond
polypeptide chains
primary structure of proteins which is formed during the process of translation at the ribosome
protein stuctures
there are 4 levels of structure as it bends and folds upon itself; one wrong amino acid and folding will be incorrect
the structure of each protein is dependent on
- the chemical properties of the R-group & can be influenced by envi. factors
ex: R-group side chains that are hydrophobic will face inwards, away from aqueous environment
carbohydrates: H to O ratio
always 2:1
main difference in polysaccarides
- glycosidic linkages, branching patterns, and functions
- glucose, fructose, and galactose are isomers!!
starch and glycogen linkage + monomer
- monomer: alpha glucose
- linkage: 1-4 alpha glycosidic linkage
cellulose monomer + linkage
- monomer: beta glucose
- linkage: 1-4 beta glycosidic linkage
lipids
diverse group of hydrophobic molecules that are nonpolar due to their hydrocarbon chains`
lipids: H to O ratio
- much larger than carbohydrate’s ratio (fewer O)
fats / triglycerides
- made up of glycerol molecule and 3 fatty acids held together by ester bonds
types of proteins
- globular proteins
- fibrous proteins
globular proteins
- the do”ers”
- carry out chemical reactions
- ex: enzymes
fibrous proteins
- provide structural support
- ex: collagen, cytoskeleton components
do enzymes change during the chemical reaction?
no
enzyme
catalyst; speeds up chemical reaction
substrate
what the enzyme “works” on/binds to
enzyme substrate complex
substrate bound to enzymes active site
active site
where the substrate binds to the enzyme
lock and key
specific substrate shape fits into ONE specific enzyme
induced fit
enzyme changes shape to fit substrate
competitive inhabition
- a molecule that’s similarly shaped to the substrate fits into the active site of enzyme and blocks the substrate
allosteric inhabition
- allosteric receptor away from the active site
- inhibitor binds -> the enzyme active site changes shape. substrate cannot bind
- “non competitive inhibition”
what factors affect enzyme activity
- temperature
- pH
- substrate or enzyme concentration
how does temperature affect enzyme activity
- as temperature increases, enzyme activity increases to optimal temperature; then, enzyme activity decreases
- the enzyme denatures: bonds start to break in tertiary and secondary structure
**as long as primary structure is not altered
the polypeptide could be restored
how does pH affect enzyme activity?
- pH is a measure of how acidic or basic something is
enzyme/substrate concentration effect on enzyme activity
- as substance concentration increases, enzyme activity increases and then levels off
function of nucleic acids
- stores hereditary information (this is the code for proteins)
- transmit hereditary information (express the protein)
- “codes for the production of proteins”
elements of nucleic acids
- C, H, O, N, P
monomer of nucleic acids
- nucleotides
polymer of nucleic acids
- nucleic acid, DNA, RNA
nucleotide composition
- phosphate group; “-“ charge
- pentose sugar
- nitrogenous base
- phophodiester bonds link nucleotides together
phophodiester bonds
- covalent
- link nucleotides together
pyrimidine
- C, T; cytosine and thymine
- shorter structure
purine
- A, G; adenine and guanine
- longer structure
what are pyrimidine and purine subgroups of
- these are nitrogenous bases that make up different nucleotides in DNA and RNA
DNA
- double stranded
- thymine
- deoxyribose
- antiparallel
RNA
- single stranded
- uracil
- ribose sugar
what do DNA and RNA have in common
- sugar phosphate backbone
- 5’ -> 3’
- both are made up of nucleotides
complementary base pairing and bonding: A-T
- Adenine and Thymine = 2 Hydrogen Bonds
complementary base pairing and bonding: C-G
- Cytosine and Guanine = 3 Hydrogen Bonds
DNA is antiparallel
- DNA always runs 5’ -> 3’; it has a 5’ end and 3’ end
central dogma: DNA
- DNA is going to transcribe itself into mRNA -> proteins
- DNA codes for the production of proteins
hydrolysis
breaks down polymers to form monomers with the addition of a water molecule
dehydration synthesis
joins monomers to form polymers with the removal of a water molecule (anabolic process)
why can’t animals digest cellulose
we lack the enzyme to break down beta glycosidic linkage
are lipids polymers
NO
- u cannot keeping add onto triglycerides; u can add monosaccharides to polysaccharides to extend it (glycogen). amino acids are continuously attached to the end of a growing chain
steroids examples
- hormones (estrogen and testosterone)
- cholesterol (in cell membrane)
are proteins a primary source of energy
NO
proteins are involved in
- structure (growth and repair)
- enzymes
- cell signaling (hormones)
- transport of other molecules
- storage
- immune system (antibodies)
a protein consists of…
- one or more polypeptide chains folded into a unique shape that determines it’s function
DNA into amino acids:
- DNA directs the order of amino acids in protein
- this sequence is transcribed into mRNA
- this is translated and forms a polypeptide
secondary structure
the folding of a protein due to the formation of hydrogen bonds along the backbone of the polypeptide
what is the backbone of a polypeptide
everything aside from the r-groups
tertiary structure
- 3D shape due to bonding between R-groups that give each protein a unique specificity
- the bonds formed between these groups can be hydrogen bonds, ionic, hydrophobic/hydrophilic interactions, van der walls forces, or disulfide bonds
quaternary structure
- occurs in proteins only if there are multiple polypeptide chains
- interaction between the chains
proteins have an ideal environment for functioning
- if a protein is exposed to something outside its ideal temp or pH range, you can disrupt the interactions between the secondary and tertiary structure levels, denaturing the protein which disrupts its shape; this prevents it from functioning properly
why is the proper folding of a protein so crucial to its function?
- a protein’s specific conformation determines its function to recognize and bind to some other molecule
protein denaturation
- change in a protein’s configuration
- disruption of tertiary structure
- due to alterations in temp, pH
- once the tertiary structure is altered, the protein no longer has the correct shape to carry out its function
explain the effect of increased temperature on the structure and function of a protein
as you increase temperature, molecules will move faster and break apart with increasing speeds, breaking the tertiary structure. since the structure is broken, the protein cannot function
the effect of mutations on protein structure and function
- a change in a single base pair can alter the entire structure
- DNA is changed which changes the primary structure of the protein. as a result, the secondary and tertiary folding will differ.
- the protein resulting from the mutated DNA will have a different shape and will most likely not carry out its function
does a mutation resulting in an amino acid always cause the protein to be nonfunctional?
no, if the phillic/phobic property is not changed between the proteins, the function may be possible
2 types of nucleic acids
- DNA
- RNA
DNA -> RNA
DNA gives the code to RNA which gives the order of amino acids
chemical structure of nucleotide
- a nucleic acid (polymer) is composed of monomers called nucleotides
- each nucleotide contains a sugar, a phosphate, and a nitrogenous base
- contains C, H, O, N, P
DNA - double stranded
- DNA is a double stranded nucleic acid
- the two antiparallel strands are connected by hydrogen bonds
RNA
- single stranded
- ribose is the sugar
- T of DNA is replaced by U in RNA
- the original hereditary molecule
enzymes
- are proteins
- names end in “-ase”
- act as catalysts
- speed up a reaction by lowering the activation energy
- speed up the making/breaking of chemical bonds
induced fit model
- when the substrate binds to the active site with weak bonds, the enzyme changes shape slightly, leading to (inducing) a tighter fit between the substrate and the active site. this further speeds up the reaction
cofactor
inorganic substance that aids an enzyme in binding substrate
coenzyme
organic substance that aids an enzyme in binding substrate
why is it important that the bonds between the substrate and active site are weak bonds?
to allow the substrate to be released and for another to go in
denaturation of enzymes
- a change in the tertiary or secondary structure of a protein leads to a change in shape of the active site which leads to a nonfunctional enzyme
- caused by high temp, change in pH, amt of material
negative feedback inhibition
- the end product of a metabolic reaction inhibits an initial enzyme via competitive or noncompetitive inhibition and slows down the reaction
positive feedback
- the product of a reaction causes the reaction to occur producing even more product
- this is NOT a common mechanism
negative feedback
- when a product inhibits the activity of an enzyme earlier in the pathway
- when there is an abundance of product, that product inhibits an enzyme earlier in the pathway to slow down the reaction so less product is made
noncompetitive inihibition
- when the product binds to a spot remote from the active site, causing the enzyme to change the conformation of its active site so it does not bind substrate -> reaction slows down
inhibition
means to slow down or prevent
what makes alpha glycosidic linkage easy to break down?
the identical orientations of the glucose monomers in starch create a polysaccharide with alpha bonds that is easy to break down into glucose for energy use. The alternating orientations of the glucose monomers in cellulose create beta bonds that produce a rigid polymer that is difficult to digest for energy use.
cohesion
Water molecules are attracted to each other due to hydrogen bonding, leading to high surface tension. This allows for phenomena like water droplets forming beads on surfaces and insects walking on water.
high specific heat
Water has a high specific heat, meaning it can absorb or release a large amount of heat with only a slight change in its temperature. This property stabilizes temperatures in environments, making aquatic ecosystems more stable and helping organisms maintain homeostasis.
high heat of vaporization
Water requires a significant amount of energy to change from a liquid to a gas. This property is important in regulating temperature through evaporative cooling, as seen in sweating in humans and transpiration in plants.
water as ice
Unlike most substances, water expands and becomes less dense when it freezes. This property ensures that ice floats on water, insulating the liquid water below and protecting aquatic life in cold environments.
water as a solvent
Water’s polarity makes it an excellent solvent, capable of dissolving a wide variety of solutes. This is essential for life because it allows for the transport of nutrients, waste products, and gases in organisms. It also facilitates chemical reactions within cells.
