bio ch 1: molecules and fundamentals of biology Flashcards
matter
anything that takes up space and has mass
element
a pure substance that has specific physical/chemical properties and can’t be broken down into a simpler substance
atom
the smallest unit of matter that still retains the chemical properties of the element
molecule
two or more atoms joined together
intramolecular forces
attractive forces that act on atoms within a molecule
intermolecular forces
forces that exist between molecules and affect physical properties of the substance
monomers
single molecules that can potentially polymerize
polymers
substances made up of many monomers joined together in chains
polymerization
any process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule
carbohydrates
contains carbon, hydrogen, and oxygen atoms (CHO)
- comes in the form of monosaccharides, disaccharides, and polysaccharides
monosaccharides
carbohydrate monomers with an empirical formula of (CH2O)n
- “n” represents the number of carbons
ribose
five carbon monosaccharide
fructose
six carbon monosaccharide
glucose
six carbon monosaccharide
relationship between fructose and glucose
isomers- same chemical formula, different arrangement of atoms
disaccharides
contain two monosaccharides joined together by a glycosidic bond
glycosidic bond
a type of covalent bond that joins a carbohydrate (sugar) molecule to another group
- the result of a dehydration (condensation) reaction
dehydration (condensation) reaction
reaction where a water molecule leaves and a covalent bond forms
hydrolysis reaction
a covalent bond is broken by the addition of water
sucrose
disaccharide made of glucose + fructose
lactose
disaccharide made of galactose + glucose
maltose
disaccharide made of glucose + glucose
polysaccharides
contain multiple monosaccharides connected by glycosidic bonds to form long polymers
starch
form of energy storage for plans and is an alpha bonded polysaccharide
amylose
linear form of starch
amylopectin
branched form of starch
mnemonic to remember amylose vs amylopectin
amylopectin has more branching letters (y, l, p, t) than amylose (y, l)
- making amylopectin the more branched form
glycogen
form of energy storage in animals
- alpha bonded polysaccharide
- has more branching between starch
bonds found in both starch and glycogen
a-1,4-glycosidic bonds
a-1,6-glycosidic bonds
cellulose
structural component in plant cell walls
- beta bonded polysaccharide
- linear strands are packed rigidly in parallel
chitin
structural component in fungi cell walls and insect exoskeletons
- beta bonded polysaccharide with nitrogen added to each monomer
proteins
contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON)
amino acids
the monomers of proteins
- formed from carbon, hydrogen, oxygen, and nitrogen atoms
- twenty different kinds, each having a different r-group
structure of a.a.
- amino group
- hydrogen
- carboxyl group
- r-group (varies)
polypeptides (proteins)
polymers of amino acids, joined by peptide bonds
- done through dehydration (condensation reactions)
- hydrolysis reactions break peptide bonds, polypeptide becomes an amino acid chain that contains two end terminals on opposite sides (N and C)
proteome
refers to all the proteins expressed by one type of cell under one set of conditions
N-terminus (amino terminal)
the side of a polypeptide that is the side that ends with the last amino acid’s amino group
C-terminus (carboxyl terminal)
the side of a polypeptide that is the side that ends with the last amino acid’s carboxyl group
conjugated proteins
proteins that are composed of amino acids and non-protein components
- examples: metalloproteins, glycoprotein
metalloproteins
proteins that contain a metal ion cofactor
- e.g. hemoglobin
glycoprotein
proteins that contain a carbohydrate group
- e.g. mucin
primary structure of a protein
sequence of amino acids connected through peptide bonds
secondary structure of a protein
intermolecular forces between the polypeptide backbone (not R-groups) due to hydrogen bonding
- forms alpha helices or beta pleated sheets
tertiary structure of a protein
3D structure due to interactions between R-groups
- can create hydrophobic interactions based on the R-groups
- hydrogen bonding and and ionic bonding between R groups also hold together the tertiary structure
disulfide bonds
part of tertiary structure
- created by covalent bonding between the R-groups of two cysteine amino acids
quaternary structure
multiple polypeptide chains come together to form one protein
protein denaturation
describes the loss of protein function and higher order structures
- only the primary structure is unaffected
causes for protein denaturation
- high or low temperatures
- pH changes
- salt concentrations
ex: cooking an egg in egg in high heat will disrupt the intermolecular forces in the egg’s proteins, causing it to coagulate
protein function: storage
reserve of amino acids
protein function: hormones
signaling molecules that regulate physiological processes
protein function: receptors
proteins in cell membranes which bind to signal molecules
protein function: structure
provide strength and support to tissues (hair, spider silk)
protein function: immunity
antibodies that protect against foreign substances
protein function: enzymes
regulate rate of chemical reactions
catalysts
increase reaction rates by lowering the activation energy of a reaction
- reduces the energy of the transition state
- does not shift a chemical reaction or affect spontaneity
transition state
the unstable conformation between the reactants and the products
enzymes
act as biological catalysts by binding to substrates (reactants) an converting them into product
- binds at active sites of substrates, these active sites are specific for the substrate that it acts upon
- most enzymes are proteins
- protein enzymes are susceptible to denaturation, they require optimal temperatures and pH for function
specificity constant
measures how efficient an enzyme is at binding to the substrate and converting it to a product
induced fit theory
describes how the active site molds itself and changes shape to fit the substrate when it binds
- outdated theory: “lock and key” model
ribozyme
RNA molecule that can act as an enzyme (a non-protein enzyme)
cofactor
non-protein molecule that helps enzymes preform reactions
coenzyme
organic cofactor (i.e. vitamins)
- inorganic cofactors are usually metal ions
holoenzymes
enzymes that are bound to their cofactors
apoenzymes
enzymes that are not bound to their cofactors
prosthetic groups
cofactors that are tightly or covalently bonded to their enzymes
ways that enzymes catalyze reactions (4):
- conformational changes that bring reactive groups closer
- the presence of acidic or basic groups
- induced fit of the enzyme-substrate complex
- electrostatic attractions between the enzyme and substrate
phosphatase
cleaves a phosphate group off of a substrate molecule
phosphorylase
directly adds a phosphate group to a substrate molecule by breaking bonds within a substrate molecule
kinasse
indirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from an ATP molecule
- these enzymes do not break bonds to add the phosphate group
feedback regulation of enzymes
the end product of an enzyme-catalyzed reaction inhibits the enzyme’s activity by binding to an allosteric site
competitive inhibition
occurs when a competitive inhibitor competes directly with the substrate for active site binding.
- in competitive inhibition, adding more substrate can increase enzyme action
noncompetitive inhibition
occurs when the noncompetitive inhibitor binds to an allosteric site that modifies the active site
- in noncompetitive inhibition, the rate of enzyme action cannot be increased by adding more substrate
allosteric site
a location on an enzyme that is different from the active site
enzyme kinetics plot
used to visualize how inhibitors affect enzymes
1. x-axis represents substrate concentration [X], while the y-axis represents reaction rate or velocity (V)
2. Vmax is the maximum reaction velocity
3. Michaelis Constant (Km) is the substrate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax)
4. saturation occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus)
competitive inhibition (on enzyme kinetics plot)
- Km increases
- Vmax stays the same
noncompetitive inhibition (on enzyme kinetics plot)
- Km stays the same
- Vmax decreases
lipids
contains carbon, hydrogen, and oxygen atoms (CHO)
- similar to carbohydrates
- have long hydrocarbon tails that make them very hydrophobic
triacylglycerol (triglyceride)
lipid molecule with a glycerol backbone (three carbons and three hydroxyl groups) and three fatty acids (long hydrocarbon tails)
what are glycerol and the three fatty acids connected by in triglyceride
ester linkages
saturated fatty acids
have no double bonds and as a result pack tightly (solid at room temp)
unsaturated fatty acids
have double bonds
- can be divided into monounsaturated fatty acids (one double bond) and polyunsaturated fatty acids (two or more double bonds)
cis-unsaturated fatty acids
have kinks that cause the hydrocarbon tails to bend
- as a result they do not pack tightly
trans-unsaturated fatty acids
have straighter hydrocarbon tails
- as a result they pack tightly
phospholipids
lipid molecules that have a glycerol backbone, one phosphate group, and two fatty acid tails
- the phosphate group is polar, while the fatty acid tails are nonpolar
- they are amphipathic
- can spontaneously assemble to form lipid bilayers
amphipathic
both hydrophobic and hydrophilic
cholesterol
an amphipathic lipid molecule that is a component of the cell membranes
- most common precursor to steroid hormones (lipids with four hydrocarbon rings)
- starting material for vitamin D and bile acids)
factors that influence membrane fluidity
- temperature: an increase in temperature increases fluidity, a decrease in temperature decreases fluidity
- cholesterol: holds membrane together at high temperatures and keeps membrane fluid at low temperatures
- degrees of unsaturation: saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinks
lipoproteins
allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins
low-density lipoproteins (LDLs)
have low protein density and work to deliver cholesterol to peripheral tissues
- sometimes considered “bad cholesterol” because it can cause vessel blockage and heart disease
high-density lipoproteins (HDLs)
have high protein density and take cholesterol away from peripheral tissues
- considered “good cholesterol” because they deliver cholesterol to the liver to make bile (reduces blood lipid levels)
waxes
simple lipids with long fatty acid chains connected to monohydroxy alcohols (contain a single hydroxyl group) through ester linkages
- used mainly as hydrophobic protective coatings
carotenoids
lipid derivatives containing long carbon chains with conjugated double bonds and six-membered rings at each end
- functions mainly as pigments
sphingolipids
- have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognition
glycolipids
lipids found in the cell membrane with a carbohydrate group attached instead of a phosphate group in phospholipids
- like phospholipids, they are amphipathic and contain a polar head and a fatty acid chain
nucleic acids
contains carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms (CHONP)
- contains nucleotide monomers that build into DNA and RNA polymers
nucleosides
contain a five-carbon sugar and a nitrogenous base
nucleotides
contain a five-carbon sugar, a nitrogenous base, and a phosphate group
deoxyribose sugars
found in DNA have a hydrogen at the 2’ carbon while ribose five-carbon sugars (in RNA) have a hydroxyl group at the 2’ carbon
nitrogenous bases found in DNA
(A) adenine
(T) thymine
(C) cytosine
(G) guanine
what nucleotide replaces thymine in RNA
uracil (U)
what nitrogenous bases are purines
A and G
- they have a two-ringed structure
what nitrogenous bases are pyrimidines
C, U, and T
- they have a one-ringed structure
PUR As Gold
PURines are Adenine and Guanine
CUT the PY
Cytosine, Uracil, and Thymine are PYrimidines
phosphodiester bonds
formed through a condensation reaction where the phosphate group of one nucleotide (at the 5’ carbon) connects to the hydroxyl group of another nucleotide (at the 3’ carbon) and releases a water molecule as a by-product
what creates the sugar-phosphate backbone
a series of phosphodiester bonds
- with a 5’ end (free phosphate) and a 3’ end (free hydroxyl)
nucleic acid polymerization proceeds as nucleoside triphosphates are added to the 3’ end of the sugar-phosphate backbone
antiparallel double helix
two complementary strands with opposite directionalities (positioning of 5’ ends and 3’ ends) twist around each other
nitrogenous bases and H-bonding
- adenine can only H-bond to thymine (using two hydrogen bonds)
- guanine can only H-bond to cytosine (using three hydrogen bonds)
mRNA
messenger RNA
- single stranded after being copied from DNA during transcription
- in RNA, uracil binds to adenine, replacing thymine
miRNA
micro DNA
- small RNA molecules that can silence gene expression by base pairing to complementary sequences in mRNA
rRNA
ribosomal RNA
- formed in the nucleolus of the cell and helps ribosomes translate mRNA
dsRNA
double stranded RNA
- some viruses carry their code as double stranded RNA
- dsRNA must pair its nucleotides, so it must have equal amounts of A/U and C/G
tRNA
transfer RNA
- small RNA molecule that participates in protein synthesis
modern cell theory (7 points)
- all lifeforms have one or more cells
- the cell is the basic structural, functional, and organizational unit of life
- all cells come from other cells (cell division)
- genetic information is stored and passed down through DNA
- an organism’s activity is dependent on the total activity of its independent cells
- metabolism and biochemistry (energy flow) occurs within cells
- all cells have the same chemical composition within organisms of similar species
central dogma of genetics
information is passed from DNA –> RNA –> proteins
- there are a few exceptions to this (e.g. reverse transcriptase and prions)
each cell consists of what
- nucleic acids
- cytoplasm
- cell membrane
specialized organelles
organelles that have specific functions within the cell
- mitochondria
- chloroplasts
