Chapter 3: The Chemical Building Blocks of Life Flashcards
What are the four types of organic molecules?
carbohydrates, lipids, proteins, nucleic acids
How many atoms can carbon bond to? What kinds of bonds can it form?
4, single, double, triple, quadruple
How many valence electrons does carbon have?
4
What is the backbone of biological molecules?
carbon
Hydrocarbons
molecules consisting of ONLY carbon and hydrogen
Where are many hydrocarbons found?
in many of a cell’s organic molecules
Isomers
molecules with the same molecular formula but different structures and properties
What are the three types of isomers?
- structural
- geometric
- enantiomers
Structural isomers
- isomers with differences in actual structure of their carbon skeletons
- ex) glucose and fructose
Geometric (stereoisomers) isomers
have same carbon skeleton, but differ in how the groups are attached to the skeleton
Enantiomers
- mirror images of each other
- important in pharmaceutical industry
What are functional groups and their purpose?
- parts of molecule involved in chemical reactions
- chemically reactive groups of atoms within an organic molecule
- give organic molecules distinct chemical properties
What are the 6 functional groups important to life?
- hydroxyl
- carbonyl
- carboxyl
- amino
- sulfhydryl
- phosphate
Hydroxyl group
hydrogen atom bonded to oxygen atom; this is bonded to the carbon skeleton
Carbonyl group
carbon atom double bonded to oxygen atom
Carboxyl group
oxygen atom is double bonded to a carbon atom, which is also bonded to a hydroxyl group (COOH)
Amino group
nitrogen bonded to two hydrogen atoms and to the carbon skeleton
Sulfhydryl group
sulfur atom bonded to hydrogen atom
Phosphate group
phosphorus atom bonded to four oxygen atoms; one oxygen bonded to carbon skeleton
Ketones
carbonyl group is within carbon skeleton
Aldehydes
carbonyl group at the end of the carbon skeleton
What type of bonds are the subunits of macromolecules joined by?
covalent bonds
Dehydration Synthesis
- one molecule of water (H2O) is removed as subunits are linked with a bond
- water is produced
- anabolic (build up)
- requires input of energy
- enzymes carry out the breaking of bonds
Hydrolysis
- molecule can be broken down into subunits as water is added
- water is needed
- catabolic
- energy released
- enzymes needed
Monomers
simplest unit of macromolecules
Polymer
large molecule made of repeating monomers
What are carbohydrates?
“sugars” and “starches”
What elements are found in carbs?
C, H, O
Ratio of C:H:O in carbs
1:2:1
Function of carbs
- short term energy storage
- structure
Examples of carbohydrate isomers
glucose, fructose, galactose
What kind of isomers are glucose and fructose
structural isomers, double bonded O is attached to diff carbons
What kind of isomers are glucose and galactose
stereoisomers, diff orientation of -OH groups
What are the most famous monosaccharides?
hexose sugars
How are disaccharides formed
2 monosaccharides connected by a covalent bond
Glucose + Glucose
Maltose
Glucose + Fructose
Sucrose
Glucose + Galactose
Lactose
What are big polymers of sugar called?
Polysaccharides
Function of glucose polymers
- energy storage
- structural support
Amylose (starch)
- used for energy storage in plants
- alpha linked
Glycogen
used for energy storage in animals, stored in liver and muscles
Cellulose
- major component of plant-like cell walls
- beta linked
Pectin
branched chains with short linear amylose branches found in plants
Why is cellulose difficult to digets?
orientation of glucose subunits (CH2OH) are on opposite sides, so it is hard to break the bonds
Chitin
- structural support in fungi cell walls
- exoskeleton of insects
- dissolving stiches
- modified polysaccharide
How do herbivores digest cellulose?
cows have bacteria that can break down cellulose
Peptidoglycan
- in bacterial cell walls
- modified peptidoglycan
What are the 3 ways that carbohydrates are used in organisms?
1.) kept as glucose/immediate energy
2.) converted to transport disaccharides
3.) converted to starch, glycogen, or fat, and used in the future
What are common lipids?
fats, oils, waxes
What elements are found in lipids?
C, H, O
Ratio of H:O in lipids
greater than a 2:1 ratio
Function of lipids
- long term energy storage
- insulation
Unique characteristic of lipids
insoluble in water - expose hydrophilic (polar) parts in water, but protect their hydrophobic (nonpolar) parts
What are the three major groups of lipids?
- triglycerides
- phospholipids
- steroids
What are triglycerides made of?
3 fatty acids and 1 glycerol
What are triglycerides connected by?
- dehydration synthesis
- ester bonds
Saturated triglyceride
- no double bonds between carbons
- saturated with hydrogen
Unsaturated triglyceride
- at least one double bond
- often liquid at room temperature because the double bond creates a bend in the tail that prevents the tight packing of molecules
What do phospholipids make up?
the cell membrane
What makes up a phospholipid?
a glycerol, 2-fatty acids, and a phosphate group
Phospholipid nickname
modified triglyceride
What kind of molecule is a phospholipid?
amphipathic
Glycerol
3 carbon alcohol molecule that forms backbone of phospholipids
2 Fatty Acids in phospholipids
long hydrocarbon chains ending in a carboxyl group
Where is the phosphate group of a phospholipid attached to?
attached to one end of the glycerol
How are the layers of phospholipids forms?
tails point towards each other
What is responsible for the ability of fats to store energy for long periods?
energy is stored in the C-H bonds, which are harder to break down because they are nonpolar
More than one double/triple bond in a fat is considered…
polyunsaturated
How many water molecules are lost in the synthesis of 1 fatty acid? How many bonds are formed?
- 3 water molecules lost
- 3 bonds formed
Are plant fats usually liquid or solid at room temp?
liquid
Are animal fats usually liquid or solid at room temp?
solid
How can oil be converted into a solid?
Add hydrogen (hydrogenated)
Terpenes
- long chain lipids that make up many pigments (chlorophyll, retinal)
- ex) rubber
Steroids
- 1 class of hormones and cholesterol
- 4 carbon rings
Where is cholesterol found?
in the cell membrane
Examples of hormones
- testosterone
- estrogen
What is responsible for the different functions of steroids?
different functional groups
Prostaglandin
- a group of 20 lipids that are modified fatty acids
- help communicate between cells
- aspirin holds back prostaglandin to reduce pain
Are carbs or fats more efficient for energy storage and why?
- fats because they contain over 40 carbon atoms
- fats yield 9 kcal of energy/gram vs cabrs yeild 4 kcal of energy/gram
Elements in proteins
C, H, O, N, sometimes S
Why are proteins the most complex biological molecule?
because of all the possible amino acid sequences
What determines a proteins function?
specific amino acid sequence
What are proteins made of?
polymers of amino acids monomers
What kind of bonds connect amino acids
peptide (covalent) bonds
Globular proteins
- ex) enzymes, antibodies, transport proteins
Fibrous proteins
- for structure and support
- keratin, actin & myosin, collagen
Peptides
- hormones, intercellular messengers
How many known amino acids are there?
21
Structure of an amino acid
- amino group (NH2) and carboxyl group (COOH) bonded to a central alpha carbon
- R side chain varies and determines the solubility and identity of the amino acid
Directionality in amino acids
- N-terminus is the amino end
- C-terminus is the carboxyl end
What are the 5 classes of amino acids based on their R groups?
- nonpolar
- polar (uncharged)
- ionizable
- aromatic
- special function
Nonpolar amino acids
R groups have CH2 or CH3
Polar (uncharged) amino acids
R groups have only H or OH
Ionizable amino acids
R groups have acids/bases
Aromatic amino acids
R groups have an organic ring with an alternating single/double bond
Special function amino acids
- specific properties
- methionine = initiates protein synthesis
- proline = caused kinks in chain
- cysteine - links chains together
Dipeptide
2 amino acids joined to make a molecule
Polypeptide
chain of amino acid sequence
What determines a protein’s function?
its shape
What can be used to determine a protein’s shape?
x-ray diffraction
What are the 4 levels of protein structure?
1.) Primary structure
2.) Secondary structure
3.) Tertiary structure
4.) Quaternary structure
Primary structure of a protein
- the sequence of amino acids in one polypeptide chain
- peptide (covalent) bonds between amino acids
Secondary structure of a protein
- regular, repeating 3D structures found in all polypeptide chains
- alpha helix
- beta sheet
- folds are called motifs
- hydrogen bonding within the primary chain between the C double bonded to O and H of NH
Tertiary structure of a protein
- final folded shape of a specific polypeptide chain
- bonds are between the R groups (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions)
- driven by hydrophobic interactions
Domains
sections of the tertiary structure with different functions
Quaternary structure of a protein
- the specific 3D shape of a protein that is made of more than one polypeptide chain (each with own tertiary structure)
- only “optional” level of structure
- happens from the overall structure when multiple chains form a functional protein
- bonds are between the R groups (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions)
What are the 8 different types of proteins?
- storage
- structural
- transport
- contractile/motor
- hormonal
- defensive
- receptor
- enzymatic
What are proteins responsible for?
all life activities of the cell
Sickle cell anemia
- results from valine (hydrophobic) replacing glutamic acid (hydrophilic) in beta chains of hemoglobin
What does hemoglobin do?
it carries oxygen in red blood cells
Chaperone proteins
help new proteins fold correctly
Denaturation
- if a protein’s environment is altered
- most of the time cannot be reversed
- denaturation = change in structure of a protein; inactive
- protein shape changes, but bonds do not
What conditions can denature proteins?
pH, temperature, concentration
Renaturation
the ability of a small protein to spontaneously refold into its original shape with the normal environment is established - shows relation of primary and tertiary structure
Nucleic Acids function
information storage for biological systems
What elements are nucleic acids made of?
C, H, O, N, P
What are nucleic acids polymers of?
nucleotides
What are polymers of nucleotides linked by?
phosphodiester bonds (btwn phosphate of one nucleotide and sugar of next nucleotide)
Nucleotide structure
- phosphate
- pentose sugar
- nitrogenous base
DNA function
- stores info about primary structure of proteins and sequences of RNA molecules
- heritable
- encodes info
RNA function
- reads info and directs protein synthesis
- transmits and translates DNA info into protein
- many enzymatic and regulatory functions
- 15 known types of RNA
What are the three types of RNA?
- messenger
- transfer
- ribosomal
DNA characteristics
- deoxyribose sugar
- bases: adenine, thymine, guanine, cytosine
- double helix
- 2 chains of covalently bonded nucleotides
- chains are bonded to each other by hydrogen bonds between the nitrogenous bases
RNA characteristics
- ribose sugar
- bases: adenine, uracil, guanine, cytosine
- single strand
- less stable than DNA
Polynucleotides different ends
- phosphate on one end (5’) and an OH from a sugar on the other end (3’)
- numbers come from carbon numbering of the sugar
Who discovered DNA structure?
- Watson and Crick published the paper
- Wilkins and Franklin did the X-ray diffraction
- won the Nobel prize for it in 1962
Purines
- large double ring molecules
- adenine and guanine
Pyrimidines
- smaller, single-ring molecules
- cytosine, thymine, uracil
What nucleotides are used as electron carriers?
- nicotinamide adenine dinucleotide
- flavin adenine dinucleotide
How does information travel?
- info stored in DNA goes to RNA before some of the info is used to direct the construction of proteins - “Central Dogma” of molecular biology
What is ATP?
- the energy currency of the cell
- adenosine triphosphate
- high energy molecule produced as a result of respiration
- contains the nucleotide base adenine
