First Exam Flashcards
form covalent bonds with carbon
- other carbons
- oxygen
- hydrogen
- nitrogen
- sulfur
special arrangements of atoms within a biomolecule
functional group
support life as we know it
acid and bases
- have hydrophobic properties that help form the cell membrane
- is a selectively permeable barrier between what is inside and outside the cell
hydrocarbons
important component of cell membranes
stearic acid H3C(CH2)16COOH
a biologically important hydrocarbon containing 4 rings
cholesterol
- forms the hard exoskeleton of arthropods
- composed entirely of N- acetylglucosamine units
N-acetylglucosamine/ chitin
when 4 different atoms are bonded to a single carbon, there are 2 different spatial configurations possible
stereoisomers
four broad biomolecular classes
carbohydrates, nucleic acids, proteins, and lipids
will not assume their biologically functional conformations in the absence of water
proteins
will not come together to form a cell membrane when no water is present
lipids
cannot be made soluble in a non-aqueous solvent and hence will not enter glycolysis
glucose
water properties
- functions as the universal solvent in biological systems
- compromises 75-85% of a cell’s weight
- makes up extracellular environment
three properties of water which are critical to supporting life
- cohesiveness
- temperature- stabilization
- capacity to function as a solvent
cohesiveness
- water molecules form hydrogen bonds that join themselves to one another
- one H can form one H bond with one oxygen, one oxygen can form TWO H bonds with TWO h atoms
- water molecules form 3.5 H bonds in an instant
water’s cohesive properties
- high boiling point: water can absorb high levels of heat without damaging the cell
- high specific heat: enables water to heat and cool slowly
- high heat of evaporation: amount of heat energy needed to change water from a liquid to a gaseous state
water solvent properties
the most critical property that contributes to its supporting life
- water creates a strong attraction, enough to break ionic bonds
- function as a shield that reduces the formation of ionic compounds
- maintain ionic substances in a solubilized state
spheres of hydration
substances that are ionic at a neutral pH
carboxyl, phosphate, and amino groups
cannot solubilize in water
hydrophobic molecules
[H+]=10^-4 has a pH value of
4
a ____ pH value corresponds with a _____ [H+] and hence a _____ acidity
higher; lower; lower
substances that DONATE protons
acids
have less capacity to donate protons
weak acids
substances that ACCEPT protons
bases
most acids and bases of living cells are
weak
necessity for preserving cellular homeostasis
maintenance of pH within narrow limits
deviations from normal pH levels result in
inefficient to nonfunctional enzymes
In multicellular organisms it is necessary to maintain both
intracellular and extracellular pH levels
help to maintain the proper pH of both intracellular and extracellular fluids in multicellular organisms
buffer systems
contain both acid to neutralize added base and base to neutralize added acid
buffers
strong buffering systems are made up of
weak acids and their corresponding salts
Effective buffer systems of living systems consists of
bicarbonates and phosphates
the cell membrane is a
- selectively permeable structure
- bilayer structure
primarily hydrophobic structure composed of lipids proteins, and carbohydrates
cell membrane
contain both hydrophobic and hydrophilic regions
amphipathic
the amphipathic character of ______ is foundational to forming the cell membrane
phospholipids
consists of a glycerol backbone attached, via an ester or ether linkage, to a fatty acyl group
phospholipid
attached to the phosphate and amino containing group
phospholipid fatty acyl tails
represents the lowest possible energy conformation by which the phospholipids can occur in the presence of water molecules
formation of the phospholipid bilayer spherical structure
associate with the neutrally chawed interior of the membrane
hydrophobic regions
project out into the aqueous environments located on either side of the membrane
hydrophilic regions
all membrane proteins can be classified as one of the following
- integral
- peripheral
- lipid- anchored
- amphipathic
- the hydrophobic portion of the integral membrane protein anchors it in the interior of the lipid bilayer
- the protein is not easily moved
integral membrane proteins
types of integral membrane proteins
- transmembrane
- monotypic
- characterized by traversing the membrane from one side to the other
- two types: single and multipass
transmembrane protein
a single hydrophobic region crosses the membrane only once
single pass
multiple hydrophobic regions cross the membrane two or more times
multipass
- embedded in only one side of the membrane (usually the intracellular side)
monotypic proteins
- lack hydrophobic regions that function to anchor the protein in the membrane bilayer
- bound to the membrane surface through weak electrical forces and H bonding with hydrophilic regions of integral proteins
peripheral membrane proteins
occur on the surface of one of the membrane bilayer sides and are covalently bonded to lipid molecules of the bilayer
lipid anchored membrane proteins
composed of subunits that are brought together via a general process referred to as polymerization
macromolecules
smaller, hydrophilic subunits arranged in a linear manner
monomers
sub cellular structures such as chromosomes, ribosomes, cilia, flagella, and membranes are made up of
macromolecules
monomers
level 1
macromolecules
level 2
supramolecular structures
level 3
organelles
level 4
cell
level 5
includes nucleic acids and proteins
- the order is non- random, genetically determined and carries information that determines the function of the macromolecules
informational macromolecules
the information contained in the nucleotide sequences determines the amino acid sequence of a particular protein
nucleic acids
the information contained in the amino acid sequence determines the three dimensional structure of the protein and hence its function
proteins
most are composed either entirely of as single repeated monomer, or two monomers that strictly alternate one another
storage and structural macromolecules
- examples of storage macromolecules because they function as a reservoir of energy within the cell
- made up of the single repeated monomer: glucose
starch and glycogen
- macromolecules produced through the joining of similar or identical monomers to one another
- condensation reaction
- in order for a condensation reaction to proceed, monomers to be joined must exit in an activated state
- monomer activation
- ATP provides the energy needed to join the carrier molecule to the monomer
- macromolecules are assembled from monomers such that there is a definite directionality to he resulting macromolecule
polymerization of monomers
elements of water are collectively removed from monomers when one is joined to another
condensation reaction
generally achieved through joining that monomer to a carrier molecule
monomer activation
provides the energy needed to join the carrier molecule to the monomer
ATP (adenosine triphosphate)
- small and large ribosomal units come
self assembly
all cells are made up of approximately ___ different molecules
30
these include: _ common amino acids, _ nucleic acids, _ forms of lipids’ and _ forms of carbs
20; 5; 3; 2
- represent the most structurally and functionally diverse of all biomolecules
- they are made up of 20 different monomers: the amino acids
proteins
- enzyme
- structural
- motility
- regulatory
- transport
- hormones
- receptors
- defense
- storage
protein types
catalyze a specific chemical reaction
enzyme protein
provide a foundation for cellular components
structural protein
control cellular processes
regulatory proteins
move substances in and out of the cell
transport proteins
cell to cell communicatory molecules; can send messages considerable distances
hormones protein
enable cells to react to chemical stimuli
receptor proteins
protect from agents of disease
defense proteins
maintenance of amino acids for future utilization
storage proteins
- monomers that make up proteins
- smallest biochemical units we can find
amino acids
all amino acids start with
alpha carbons
8 of the 20 common amino acids are
hydrophobic
amino acids with hydrophobic R- groups tend to be located in the
interior of a protein
amino acids with hydrophilic R- groups tend to be located in the
protein’s surface
usually 7.0 inside the cell
pH considerations of amino acids
the joining of amino acids to one another to form protein macromolecules requires
a condensation reaction
the immediate product of translation
polypeptide
biologically active protein made up of a single polypeptide chain
monomeric
proteins made up of two or more polypeptide chains
multimeric
hydrogen bonds: weak, attractive interactions that form between an electronegative atom and a H atom that is covalently bonded to another electronegative atom
ionic bonds: bonds formed through electrical attraction between substances of oppositely charged ions
van der Waals interactions: result from dipole separations in both atoms
hydrophobic interactions: non polar substances that interact with one another and thereby have minimal contact with water molecules
types of bonds
- most common covalent bonds
- form between 2 cysteine groups
- can only be broken through reducing processes
- cysteine that form a disulfide bond are often part of the same polypeptide molecule
disulfide bonds
- adds stability
- form between amino acids that are either far apart from each other or from two entirely separate polypeptide chains
- a single hydrogen bond is weak, many hydrogen bonds are stable
hydrogen bonds
- form between oppositely charged R groups within a protein
- have about 3.0 kcal/mol strength
- unlike covalent bonds, ionic bonds do not require specific bond angle alignments
- pH changes can greatly disrupt ionic bonds
ionic bonds
- occur when two molecules are very close to one another and have fleeting dipoles between them
van der Waals interactions
- greater density of electrons in one area of the molecule rather than the other
dipole
- tend to be located in the proteins interior where water concentration is much lower
hydrophobic interactions
- amino acid sequence from one end to the other
- the three higher levels of protein structure are derived from this structure
primary structure
the amino acids that become protein components
residue
results from hydrogen bonding that occurs between atoms making up the peptide bonds of a polypeptide chain
secondary structure
a spiral made up of a peptide chain with the R- groups protruding outward
- there are 3.6 complete turns of alpha helix
- the peptide bonds of every 4th amino acid form hydrogen bonds between the amino group “above it” and the carbonyl group “beneath it”
alpha helix
result from H bonds forming between all amino and carbonyl groups of two polypeptide chains that are next to each other
B sheets
within the same polypeptide
intramolecular
between two different polypeptides
intermolecular
more stable
antiparralel
results from interaction among R groups of a polypeptide
tertiary structure
result from interactions between two or more polypeptide chains that make up an individual protein molecule
quaternary structures
tend to be FIBROUS OUTSIDE OF CELLS while those INSIDE of cells tend to be globular
structural cells
RNA and DNA
- encode genetic info
- order of nucleotides is genetically determined
nucleic acids
Though RNA is single stranded, a single strand sequence _____ pair with other portions of itself and from various double- stranded structures
may
- Molecules of the general formula (CH2O)n
- include monosaccharides and polysaccharides
Carbohydrates
- macromolecules composed of sugars or single substances called monosaccharides
- most are made up of a single type of monosaccharide or two forms that alternate sequence
- unlike proteins and nucleic acids, polysaccharides do not contain information
- play roles in either structure or storage
- the most common storage form for plants is starch while for animals, glycogen
- made up of D- glucose units joined together by glycosidic bonds
Polysaccharides
- either Aldo or keto sugars
- Aldo sugars have a terminal carbonyl group
- keto sugars have an internal carbonyl group
most sugars contain from 3 to 7 carbons - covalently bonded to each other by condensation reactions
monosaccharides
- biomolecules not made of monomers that are classified according to their inability to solubilize in aqueous polar solvents
- not synthesized as polymers
- hydrophobic
- helps with communication between cells
lipids
- triacylglycerols
- phospholipids
- glycolipids
- steroids
- terpenes
types of lipids
- most are 16 to 18 carbons long
- long unbranched hydrocarbon chain
- saturated fatty acids contain no double bonds
- monounsaturated fatty acids contain 1 double bond
- polyunsaturated fatty acids contain two or more double bonds
fatty acids
- glycerol molecules with one fatty acid joined to each of the three glycerol carbons via ester linkages
triacylglycerols
- most important lipids making up cell membranes
because their hydrophilic head group and hydrophobic fatty acid tail groups cause them to form, the lipid bilayer component of the cell membrane - phoshpoglycerides and sphingolipids
- common phospholipids are:
phosphatidyl choline
phosphadityl serine
phosphadityl ethanolmine
phosphadityl inositol
phospholipids
- are less common forms of membrane lipids
- form glycolipids when having a carbohydrate group substitute a phosphate group
sphingolipids
- lipid molecules formed from four ringed hydrocarbons
- only occur in eukaryotic cells
- cholesterol is the main animal steroid
steroids
- occur in globular proteins
- compacted region containing an alpha and beta sheet, that has a particular function
domains
DNA
- purines: adenine and guanine
- pyrimidines: cytosine and thymine
A-T= 2 H bonds
G-C= 3 H bonds
RNA:
- purines: adenine and guanine
- pyrimidines; cytosine and uracil
nucleotides
- 5 carbon sugar
- PO4^2- group (joined by a phosphodiester bond)
- nitrogen- containing aromatic base
nucleotide components
when a nucleotide loses its PO4^2- gtroup
nucleoside
smallest units of life
share the following features with one another:
- enclosed by a membrane
- obtain substances from the environment
- have the capacity to convert energy into ATP
- posses mechanisms of energy conversion that are basically similar, can regulate their activities
- can control structures
cells
archea, eubacteria, and eukaryotes
- archea and eubacteria are referred as “prokaryotes”
three basic types of cells
- nucleus
- organelles
- microtubules
- microfilaments
- intermediate filaments
- capacity to perform -endo and exocytosis
characteristics of eukaryotes
most cells are from 1 to 10 micrometers long (eubacteria and archea) or 10 to 30 micrometers long (eukaryotes)
small sizes ensure that:
1. diffusion can play a significant role in physiological/biochemical processes
2. surface to volume ratio will remain sufficiently high to enable effective passage of substances into and out of the cell
3. concentration of substances will remain sufficiently high to support life
cell size
the interior of the eukaryotic cell is divided up into smaller compartments by intracellular membranes
endoplasmic reticulum
makes up areas of protein synthesis
- contains many ribosomes hence appears rough
rough endoplasmic reticulum
largely an area of lipid synthesis
- lacks ribosomes hence appears soft
smooth endoplasmic reticulum
extend from the extracellular to the intracellular membrane side
receptor proteins
move substances from one side of the membrane to the other
transport proteins
in eukaryotes, most DNA transcription occurs ___ the cell
inside
- contains most of a eukaryotic cell’s DNA
- where the majority of transcription occurs
- information center
- bounded by a membrane bilayer called the nuclear envelope
nucleus
chloroplasts
convert light into useful chemical energy
- contains own DNA and ribosomes
- organelle that processes and packages membrane and secretory proteins
- produces complex polysaccharides
- series of stacked, flattened, disk-like structures
Golgi apparatus
manufacture and degrade hydrogen (H2O2)
- its enzyme catalase breaks down very toxic H2O2
- perform a detoxification function
Peroxisomes
used for temporary storage or transport
vacuoles
protein and nucleic acid complexes that manufacture protein
ribosomes
made up of microfilaments, intermediate filaments, and microtubules
cytoskeleton
give cells a rigid structure
extracellular matrix and cell wall
- produced during cell division
- flexible and enables cells to grow
primary cell wall
characteristic of mature plant cells and is a thicker, more rigid structure
secondary cell wall
enables material from the cytosol of one cell to pass to the cytosol of an adjacent plant cell
plasmodesmata
a molecule’s diffusion rate is ____ to its size
inversely proportional
DNA contained within a protein matrix
- form chromatin within the fluid environment
chromosomes
forms within the cell a vesicle containing what were formerly extracellular substances
endocytosis
substances are taken out of the cell by intracellular vesicles joining to the cell membrane
exocytosis
plasma membranes that have carbohydrates attached to the extracellular protruding portion of the protein
glycoproteins
membrane proteins usually contain at least one _____ region that traverses the bilayer
hydrophobic
a single eukaryotic cell may contain hundreds of
- has an inner and outer membrane
mitochondria
foldings of the inner mitochondrial membrane
cristae
located in the mitochondria
Citric acid cycle/ Krebs cycle and chain/oxidative phosphorylation
flattened disks
- reactions requiring solar energy occur here
thylakoids
tubular- shaped membrane structures occupying the chloroplast interior
- reactions requiring conversion of carbon dioxide into organic molecules occur here
stroma
flattened sacks
cisternae
