Chapter 5 - The Structure and Function of Large Biological Molecules Flashcards
what are the 4 macromolecules?
carbohydrates, lipids, proteins, nucleic acid
what are polymers? which macromolecules are polymers?
a long molecule consisting of many similar or identical building blocks linked by covalent bonds
carbohydrates, proteins, and nucleic acids
what kinds of bonds link polymers?
covalent
what are the building blocks of polymers?
monomers
what are enzymes? what do they do?
specialized macromolecules that speed up chemical reactions
help with making/breaking polymers
what is a dehydration reaction?
when monomers are connected by a reaction in which two molecules are covalently bonded to each other with the LOSS of a water molecule
each monomer contributes part of the water molecule that is released during the reaction (-OH from one, -H from the other)
what is hydrolysis?
polymers are disassembled into monomers by hydrolysis: the bond between monomers is broken by the ADDITION of a water molecule
what are examples of carbohydrates?
sugars: glucose, fructose, etc.
starch, cellulose
what are the monomers of carbohydrates?
monosaccharides (simple sugars)
what is the molecular formula of a carbohydrate? what functional groups does it contain?
multiple of the unit CH2O (H-C-OH)
carbonyl group (CHO) and hydroxyl groups (OH)
how many carbons are usually in a carbohydrate?
3-7 carbons in a chain
what is the function of carbohydrates?
major energy source for the cell!
they are storage structures structures for storing sugar in the cell
major nutrients/energy for cells (cellular respiration)
what are disaccharides?
double sugars linked by glycosidic linkage
what types of bonds link disaccharides? what are they?
a covalent bond between monosaccharides by dehydration
what are carbohydrate polymers called? what are they?
polysaccharides: polymers made of monosaccharides joined by glycosidic linkages
in what form do carbohydrates usually exist?
rings in aqueous solutions
what is the molecular formula for a molecule made by linking three glucose molecules together by dehydration?
C6H12O6 —> C18H32O16
because there’s only 2 places where water is released
what shape is starch?
helical
what shape is cellulose?
straight, never branched, OH groups can bond with other cellulose, most animals don’t have the enzyme to break it down
how is the function of polysaccharides determined?
determined by monomers and position of glycosidic linkage
what are the function of polysaccharides?
1) storage polysaccharides
2) structural polysaccharides
3) modification of proteins and phospholipids
4) glycosylation
what are storage polysaccharides?
- plants store starch: made of glucose monomers (amylose, unbranched, simplest form)
- animals store glycogen (amylopectin form, branched)
what are structural polysaccharides? examples?
organisms build strong materials from structural polysaccharides
- cellulose (polymer of glycose) is a component of the tough walls that enclose plant cells, insoluble fibers that surround the cell
- chitin is used by insects to build exoskeletons
- area that exists outside the cell is made of polysaccharides
what is glycosylation? what does it help with?
modification of protein and phospholipids by carbohydrates –> increases chemical diversity
what does gycosylation help with?
1) cell recognition:
important for immune system for recognition of cells
2) protein function/stability:
function/stability can rely on if it gets glycosylation
3) protein folding:
folding can depend on if it receives glycosylation
4) important for secreted proteins:
proteins that get made in the cell that need to be on the outside of the cell/are on the outside and it serves as a zipcode to let the cell know where it needs to go
are lipids polymers?
no, they aren’t big enough
are lipids hydrophobic or hydrophilic?
hydrophobic
lipids mix poorly, if at all, with water because mostly hydrocarbons and not very polar - water molecules hydrogen bond to each other and exclude the fats
3 types of lipids?
steroids, fats, phospholipids
what are fats constructed from? what kind of macromolecule are they?
they are lipids
a fat is constructed from two smaller molecules: glycerol and fatty acids
glycerol is an alcohol
hydrophobic!
what is a fatty acid?
a fatty acid has a long carbon skeleton (16-18 carbons)
COOH group
how is a fat made?
to make a fat: THREE fatty acids are joined to glycerol by an ester linkage (dehydration reaction between hydroxyl and carboxyl) = triacylglycerol
C-OH + CO-OH –> C-O-C=O bond it formed from the dehydration
C-O-C=O is the ester bond: 3 are formed, one for each dehydration!
look at the picture, it helps
what is a saturated fat?
no double bonds
as many hydrogen atoms as possible are bonded to the carbon skeleton = saturated!
makes uniform straight chain = stacks closely = solids at room temp
usually found in animals
what are unsaturated fats?
has one or more double bonds
almost all naturally occurring fatty acids have cis double bonds = kink in the chain –> don’t stack = liquid
usually found in plants
what do cis double bonds cause in fats (lipid)?
a kink in the chain = prevents them from stacking = liquid at room temperature
what is a hydrogenated fat?
means that the unsaturated fat has synthetically been converted to a saturated fat by adding hydrogen
recent studies have shown that this produces saturated fats and unsaturated fats with trans double bonds (trans fats)
what kind of fat causes health risks?
saturated fats!
what is a trans fat?
the result of partially hydrogenation
cis C = C bond are converted to trans C = C so the fat behaves like a saturated fats (solid at room temperatures)
what is the function of fats?
1) storage of energy (animals use adipose cells)
2) insulates body
what is a phospholipid?
only has TWO fatty acids attached to glycerol rather than three
the third hydroxyl group of glycerol is joined to a polar phosphate group
what does the third hydroxyl group of a glycerol bond to in a phospholipid?
a polar phosphate group
how does the behavior of the two heads of a phospholipid differ?
the hydrocarbon tails are hydrophobic and are excluded from water
the phosphate group attached to the head is hydrophilic —> when added to water they form bilayers
hydrophobic tails are turned in to each other to exclude water
polar heads are on outside of membrane towards water b/c they interact w/ H2O
what is the function of phospholipids?
important for membrane structure
phospholipids make up the aqueous side of the cell membrane
what are steroids?
steroids are lipids characterized by a carbon skeleton consisting of four fused rings
how are steroids distinguishable from one another?
by the chemical groups attached to the rings
what are examples of steroids?
signaling hormones
vitamins
cholesterol
what is cholesterol?
a steroid (lipid)
a crucial molecule in animals, common component of animal cell membranes, precursor from which other steroids are synthesized
what is the monomer of a protein?
amino acid
what is the polymer of a protein?
polypeptide
what descriptions of the function of proteins?
1) help make up membranes
2) structural: for support (keratin is the protein of hair or collagen in connective tissues)
3) hormone receptors: response of cell to chemical stimuli (receptors built into membrane of a nerve detect signaling molecules released by other nerve cells)
4) hormonal: coordination of an organism’s activities (insulin is secreted by pancreas and causes other tissues to take up glucose which regulates blood sugar)
5) catalysts: speed chemical reactions (enzymes: lactase is the enzyme that speeds up hydrolysis of lactose)
6) defense: protect against disease (antibodies are proteins that destroy viruses/bacteria)
7) storage: storage of amino acids: plants have storage proteins in seeds
8) transport: proteins can bond inside phosolipid bilayer and form a channel for molecules to get in and out of cell - proteins can be part of plasma membrane (hemoglobin transports oxygen)
9) motor: movement - undulations of cilia and flagella, myosin/actin in muscles
what are the functions of proteins?
functions of proteins are emergent properties!
1) speed up chemical reactions
2) defense
3) storage
4) transport
5) cellular communication
6) movement
7) structural support
examples of proteins?
enzymes, antibodies
how many amino acids are there?
20
what are the bonds between amino acids?
peptide bonds
what is an amino acid?
an organic molecule with both an amino group (NH2) and a carboxyl group (COOH)
what is an asymmetric carbon?
has four different functional groups
basic vs. acidic amino acids?
acidic amino acids have side chains w/ negative charge (COOH)
basic amino acids have side chains w/ positive charge
(both hydrophilic b/c charged)
what is a peptide bond?
when carboxylic group of one amino acid is adjacent with the amino group of the other then they can become joined through dehydration = peptide bond
O=C-OH + H-N-H –> H2O + O=C-N-H
polypeptide back bone?
after many dehydrations a polypeptide back bone forms which has different R groups extending from it
one end of the chain has a free amino group (N-terminus) while the other has a free carboxyl group (C-terminus)
side chains outnumber the terminal groups so the chemical nature of the molecule as a whole is determined by the kind and sequence of the side chains
what is a functional protein?
not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape
what determines the 3D structure of a protein?
the amino acid sequence of each polypeptide
folding is driven and reinforced by the formation of various bonds between parts of the chain (which depends on amino acid sequence)
what are the two shapes of proteins?
globular proteins: roughly spherical
fibrous proteins: shaped like long fibers
what does the function of a protein depend on?
a proteins structure determines its function –> the function of a protein depends on its ability to recognize and bind to some other molecule
what are endorphins?
natural signaling molecules called endorphins bind to specific receptor proteins on the surface of the brain = euphoria/pain relief
where are proteins made?
ribosomes
how are proteins made?
DNA –> transcription –> mRNA –> translation –> chain of amino acids –> protein folding –> protein
what are the 4 different levels of structure that occur in proteins?
primary, secondary, tertiary, and quaternary
when will a protein have quaternary structure?
when a protein has of two or more polypeptide chains
what is the primary structure of a protein?
the primary structure of a protein is its sequence of amino acids, like the order of letters in a very long word
held together by peptide bonds
determined by inherited genetic information
primary structure dictates secondary and tertiary structure
what is the primary structure of a protein held together by?
peptide bonds
what is the secondary structure of a protein?
most proteins have segments of their polypeptide chains repeatedly folded in pattern that contribute to the proteins overall shape - the coils and folds are collectively referred to as secondary structure
they are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone
what are the two types of secondary structures of proteins?
alpha helix and beta pleated
what is alpha helix?
a delicate coil held together by hydrogen bonding between every fourth amino acid
type of secondary structure of proteins - form coil like a telephone cord
what is beta pleated structure?
type of secondary structure of proteins - looks like loose ribbon
structure where two or more segments of polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel segments of the polypeptide backbone
make up the core of many globular proteins and dominate some fibrous proteins
what is the tertiary structure of a protein?
the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids (when the substructures interact with each other - if two alpha helix interact with each other or a beta pleated sheet)
due to weak intermolecular interactions like from the hydrogen bonds
what is quaternary structure of a protein?
two separate polypeptide chains which are already folded bind together to form an even larger structure
what type of interaction contributes to tertiary structure?
hydrophobic interaction:
as polypeptide folds into its function shape, amino acids with hydrophobic non polar side chains usually end up in a cluster at the core of the protein out of contact with water - van der Waal s interaction help hold non polar amino acid side chains together
hydrogen bonds between polar side chains also help stabilize tertiary structure
what can reinforce the shape of a protein?
covalent bonds called disulfide bridge can further reinforce the shape of a protein - they form where two cysteine monomers (with -SH groups on side chain)are brought close together by the folding of the protein: S-S bond forms
what are some examples of proteins with quaternary structure?
1) collagen: fibrous protein that has three identical helical polypeptides intertwined into a larger triple helix
2) hemoglobin is a globular protein with four polypeptide subunits (two α and two B) - each subunit has nonpolypeptide component called heme, with an iron atom that binds oxygen
what is sickle cell disease?
an inherited blood disorder that is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin - the protein that carries oxygen in red blood cells
normal hemoglobin proteins don’t associate with one another but hydrophobic interactions between sick-cell hemoglobin proteins lead to their aggregation into a giver which blocks tiny vessels and impedes blood flow
what does a proteins structure depend on ?
protein structure also depends on physical and chemical conditions of the protein’s environment: pH, salt concentration, temperature alteration can cause the interactions within a protein to be destroyed and cause the protein to unravel = denaturation
what is denaturation?
when a protein unravels
causes the protein to be biologically inactive
ex. if a protein is transferred from aqueous environment to a non polar solvent the polypeptide chain refolds so the hydrophobic regions face outward towards the solvent
what are chaperonins?
(chaperone proteins) are protein molecules that assist in the proper folding of other proteins
don’t specify the final structure of a polypeptide, they just keep the new polypeptide segregated from disruptive chemical conditions in the cytoplasmic environment while it folds spontaneously
what are the diseases associated with misfiled proteins?
cystic fibrosis, Alzheimer’s, Parkinson’s and mad cow disease
what tool is used to determine the 3D structure of proteins?
X-ray crystallography
which structure determines the shape of a protein?
primary structure
what is a gene?
genes consist of DNA which belongs to a class of compounds called nucleic acids
what kind of macromolecule is DNA?
nucleic acid
what encodes the amino acid sequence of a polypeptide?
genes (nucleic acid!)
nucleic acid monomer?
nucleotides
nucleic acid polymer?
polynucleotides
what kind of backbones do nucleic acids have?
sugar-phosphate backbone
what are the nucleic acids in DNA and RNA, respectively?
thymine and uracil
what is mRNA?
messenger RNA which interacts with the cell’s protein synthesizing machinery to direct production of a polypeptide which folds into all or part of a protein
mRNA convert genetic instructions for building proteins from the DNA in the nucleus to ribosomes in the cytoplasm
where are proteins made?
ribosomes
what are ribosomes?
reside in the region between the plasma membrane and nucleus in eukaryotic cells = cytoplasm
where does DNA reside in eukaryotic cells?
nucleus
how do prokaryotic cells transcribe proteins?
prokaryotic cells lack a nucleus but still use mRNA to convey message from DNA to ribosome
do prokaryotic cells have a nucleus?
no
what does a nucleotide consist of? aka what do you need to build a nucleotide?
a nucleotide consists of:
1) a five-carbon sugar (pentose)
2) a nitrogen-containing base (nitrogenous)
3) one or more phosphate groups (PO4-)
structure: phosphate - sugar - nitrogenous base
what is a nucleoside?
each nucleotide has only one phosphate group and the portion without any phosphate groups (nitrogenous base and pentose part) is called a nucleoside
what are the two families of nitrogenous bases in nucleic acids?
pyrimidines and purines
what is pyrimidine? what are members of this group?
one of the two families of nitrogenous bases in nucleic acids
has one six membered ring of carbon and nitrogen atoms
members are cytosine, thymine, and uracil
what are purines?
one of the two families of nitrogenous bases in nucleic acids
larger with a six membered ring fused to a five-membered ring: members are adenine and guanine
which nitrogenous bases are found both in DNA and RNA?
adenine, guanin, cytosine = found in both DNA and RNA
thymine is only in DNA
uracil is only RNA
what is the sugar found in DNA and RNA respectively?
DNA: deoxyribose (lacks an oxygen atom on second carbon in ring)
RNA: ribose
how are adjacent nucleotides linked?
adjacent nucleotides are joined by a phosphodiester linkage which consists of a phosphate group that links the sugars of two nucleotide –> results in sugar-phosphate backbone (nitrogenous base not part of it)
what are the two different ends of the sugar-phosphate backbone of a nucleic acid?
one end has a phosphate attached to a 5’ carbon and the other end has a hydroxyl group on a 3’ carbon
5’ end and 3’ end
what is the structure of DNA?
double helix
antiparallel: the two sugar-phosphate backbones run in opposite 5’—> 3’ direction from each other (one from 5’ to 3’ and the other is 3’ to 5’)
backbones are on the outside of the helix and the nitrogenous bases are paired in the interior of the helix - the two strands are held together by hydrogen bonds
what holds the two strands of DNA together?
hydrogen bonds
which nitrogenous bases pair up when the double helix of DNA forms?
adenine and thymine pair up
guanine and cytosine pair up
what is the complimentary DNA sequence to 5’-ATCGGAGATT - 3’?
3’ - TAGCCTCTAA - 5’
what is the structure of RNA?
RNA exist as single strands
complementary base pairing can occur between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule = allows it to take on 3D shape necessary for function
adenine pairs with URACIL thymine isn’t present
what does tRNA do?
brings amino acids to the ribosome during synthesis of polypeptide
what is the function of nucleic acids?
1) genetic information
2) gene expression: DNA is the code, mRNA is transcribed
3) gene regulation,
what are polymerases?
the enzymes responsible for replicating DNA or making mRNA - they get their names b/c they’re responsible for making polymers of nucleic acids
what are ribozymes?
enzymes made up of RNA instead of protein
