Molecular and Cellular Exam 1 Flashcards
What is a hydroxyl group?
A standard molecular bonded to oxygen.
The oxygen bonded to hydrogen
Polar
What is a methyl group?
A standard molecule bonded to CH3
Nonpolar
What is a carbonyl group?
Two standard molecules bonded to carbon
Carbon double bonded to oxygen
Polar
What is a carboxyl group?
A standard molecule bonded to carbon
Carbon bounded to OH and double bounded to oxygen
Charged and ionizes to release H+. Acidic
What is an amino group?
A standard molecule bonded to nitrogen
Nitrogen bonded to two hydrogen atoms
Charged, accepts H+ to create ammonia (NH3+). Basic
What is a sulfhydryl group?
A standard molecule bonded to sulfur
Sulfur bonding to hydrogen
Polar
What is a phosphate group?
A standard molecule bonded to phosphate
Phosphate bonded to oxygen, two OH and double bonded to one oxygen
Charged, ionizes to release H+. Acidic
What is the unique property of liquid water?
Hydrogen bonds are constantly made, broken and remade
What is the unique property of gaseous water?
Water is heated the increased kinetic energy of water causes hydrogen bonds to break and water molecules escape into air as gas
What is the unique property of solid water?
Temperature is lowered and a crystalline structure is maintained
Why does solid water float on liquid water?
Hydrogen bonding in water causes solids to be less dense than liquids
What is the specific heat capacity of water?
Specific heat capacity refers to the amount of heat one gram of a substance must absorb in order to raise its temperature one degree Celsius
What is the heat of vaporization in regards to water?
The amount of energy required to change one gram of a liquid substance to gas
What is cohesion in water?
Water molecules at the liquid-gas interface stick together due to hydrogen bonding
What is surface tension in water?
Capacity of a substance to withstand being ruptured when placed under tension or stress
How does capillary action work?
Capillary action in a glass tube is caused by the adhesive forces exerted by the internal surface of the glass exceeding the cohesive forces between the water molecules themselves.
What is adhesion?
It is an attraction between water molecules and other molecules
What are the four macromolecules?
- Lipids
- Carbohydrates
- Proteins
- Amino Acids
What element is essential to life and macromolecules?
Carbon
Why is carbon unique?
It can form covalent bonds with up to four different atoms
This allows it to serve as the “backbone” for the macromolecules
Each carbon has four electrons in the outer shell
It forms four covalent bonds to “fill” the outer shell
This allows it to achieve the “octet rule”
What is CH4?
Methane
What affects the function of molecules?
The shape or the geometry!
What are hydrocarbon rings?
Molecules with 5-6 carbon atoms that are single or double bonded to each other that form a ring
**Nitrogen can replace carbon
What are isomers?
Molecules that have the same chemical formula but differ in placement/arrangement of atoms or types of bonds between atoms
What are the three types of isomers?
Structural
Geometric
Enantiomers
What are structural isomers?
They are isomers that have a different covalent arrangement of atoms.
What are geometric isomers?
They are isomers that have a different arrangement of atoms around a double bond
What are enantiomers?
They are molecules that share chemical formula and bonds but differ in 3D placement of atoms; mirror images
What are unsaturated hydrocarbons?
They are fatty acids made up of carbons with at least one double bond
What are saturated hydrocarbons?
They are fatty acids made up of carbons with no double bonds
What is a trans fatty acid?
A fatty acid with carbons are on opposite sides of double bond so a molecule chain remains straight
What is a cis fatty acid?
A fatty acid with carbons on the same side of a double bond so a molecule chain is bent
What molecules can dissolve in water?
Ions and polar molecules can dissolve in water
What is a hydrogen bond?
Interaction between the δ+ of hydrogen and the δ- of a more electronegative atom on another molecule – often occurs between water molecules
What are van der Waals interactions?
Weak attractions or interactions between two or more molecules (in close proximity) due to changes in electron density
What are ionic bonds?
Metals lose electrons and nonmetals gain electrons to achieve an octet when bonding
What is a chemical bond?
The attractive force that links atoms together to form molecules
What is a covalent bond?
Two or more atoms may bond with each other to form a molecule by sharing electrons
What is a polar covalent bond?
Electrons are unequally shared by the atoms and attracted more to one nucleus than the other
What is electronegativity?
The ability to attract and gain electrons
Four major macromolecules
Lipids
Carbohydrates
Proteins
Nucleic acids
Macromolecules consisting of individual subunits
Monomers
Monomers linked together by covalent bonds
Polymers
Monosaccharides
Simple sugars and the most basic units from which all carbohydrates are built
Three requirements of a monosaccharide
-3-7 carbons
-End with the suffix –ose
-Contain a carbonyl group C=O
Five types of monosaccharides
-Aldoses
-Ketoses
-Trioses
-Pentoses
-Hexoses
Aldoses
Carbonyl group at the end of the carbon chain
Ketoses
Carbonyl group in the middle of the carbon chain
Trioses
Three carbons
Pentoses
Five carbons
Hexoses
Six carbons
Dehydration synthesis
Two monosaccharides bonded together by a covalent bond and releasing a water molecule
Hydrolysis (Dehydration reaction)
Water reacts with polymers to break them down into individual monomers
Enzymes
Biological molecules that speed up or catalyze reactions like hydrolysis or dehydration synthesis
Monosaccharides exist in this form in aqueous solutions
5-6 carbon ring between ring and linear in equilibrium, creating alpha and beta sides
Glycosidic bond
The bond between two monosaccharide monomers forming a covalent glycosidic linkage
Polysaccharides
A long chain of monomers bonded by glycosidic linkages
Potential characteristics of polysaccharides
-May be branched or unbranched
-May consist of multiple types of monosaccharides
-Molecular weight could be > 10,000 daltons
-May be distinguished by the formation of the bonds
Cellulose
A polysaccharide found in the cell wall of plants and made of unbranched chains of glucose monomers
Lipids
-Diverse group of non-polar hydrocarbons which are hydrophobic
-Includes fats and oils
Two components of fats
- Glycerol
- Fatty acids
Triacylglycerol and bond type
Formed by bonding three fatty acids to a glycerol backbone via an ester linkage
Three water molecules are released
Stearic acid
A common saturated fatty acid (solids at room temperature like meat, butter, etc.)
Oleic acid
A common unsaturated fatty acid (liquid at room temperature like oils)
Phospholipids
Two fatty acids and a phosphate group bonded to a bonded to a glycerol backbone
The structure of a phospholipid
Two layers of phospholipids with the phosphate hydrophilic heads protecting the fatty acid hydrophobic tails
A common function of phospholipids
They contribute to the dynamic nature of plasma membranes
The macromolecule category of steroids
Lipids
The main features of steroids
- Hydrophobic
- Insoluble in water
- Typically a ring shaped molecule with four linked carbon rings with unique short tails
The most common steriod
Cholesterol
Amino acids
Monomers that make up proteins
The 5 fundamental features of amino acids
- Central carbon atom
- Amino group (-NH2)
- Carboxyl group (-COOH)
- Hydrogen
- Side chain
How are amino acids commonly written?
Amino acids are represented by a single upper case letter or three letters
Essential amino acids
Leucine
Isoleucine
Cysteine
Peptide bond formations
After a dehydration synthesis reaction, amino acid monomers are linked together through peptide bond formations
Polypeptide
A chain of amino acid monomers linked together through peptide linkages
Protein
One or many polypeptides
Often combined with non-peptide prosthetic groups
Has a unique structure and function
Many proteins are modified following translation
Translation
Process of creating a new protein
The four levels of the protein structure
- Primary
- Secondary
- Tertiary
- Quanternary
Primary level of a protein structure
The unique sequence of amino acids in a polypeptide
Amino acid sequence is based upon gene encoding that protein. If the sequence changes, so could the amino acid and function
Secondary level of a protein structure
Local folding of the polypeptide
Tertiary level of a protein structure
The unique 3-D structure of a polypeptide due to sequence of helixes and sheets
Determined by chemical reactions (hydrophobic interactions, ionic bonding, hydrogen bonding, disulfide linkages)
Quaternary level of a protein structure
Interactions between several polypeptides that make up a protein
Weak interactions between subunits help stabilize the structure
The specific structure of α-helix of a protein structure
Formed by hydrogen bond between oxygen in carbonyl group and an amino acid 4 positions down the chain
β-pleated sheet
Hydrogen bonding between atoms on the backbone of the polypeptide chain
Denaturation
Changes in protein structure that leads to changes in function
Nucleic acids definition
Constitute the genetics material of living organisms
Two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
The 4 locations of nucleic acids
-Nucleus of eukaryotic cells
-Mitochondria
-Chloroplasts
-Prokaryotic cells (not membrane enclosed)
Nucleotides are monomers in DNA and RNA that have what three things
What monomers in DNA and RNA that have:
-Nitrogenous base
-Pentose sugar
-One or more phosphate groups
Two types of nucleotide nitrogenous bases
Pyrimidines – cytosine, thymine, uracil
Purines – Adenine, guanine
The type of pentose sugar found in DNA
Deoxyribose
The type of pentose sugar found in RNA
Ribose
The bonds between nucleotides
Phosphodiester bonds
Base pairing in DNA and its bond
The two strands run antiparallel to one another. one strand runs 5′ to 3′ the other 3′ to 5′
Bonds with phosphodiester bonds
Base pair adenine forms with?
Base pair thymine forms with?
Base pair guanine forms with?
Base pair cytosine forms with?
The number of hydrogen bonds with A=T
2 hydrogen bonds for this base pair bond
The number of hydrogen bonds with G=C
3 hydrogen bonds for this base pair bond
DNA features
- Carries genetic information
2 .Remains in the nucleus - Double helix
- Deoxyribose sugar
- Pyrimidines: Cytosine, thymine
- Purines: Adenine, guanine
RNA features
- Involved in protein synthesis
- Leaves the nucleus
- Usually single-stranded
- Ribose
- Pyrimidines: Cytosine, uracil
- Purines: Adenine, guanine
Ester bond and linkage
The type of connection between glycerol molecules and fatty acids to create a triacylglycerol
Peptide bond and linkage
Amino acid monomers
Nucleotide connections
Phosphodiester linkages and bonds
An underlying principle of biology
Cells are basic units of life
All living organisms made of cells
All cells come from preexisting cells
Cells have 4 common components
-An enclosing plasma membrane which separates the cell’s interior from the environment
-Cytoplasm made of cytosol in which other components of the cell are found
-DNA: the genetic material of the cell
-Ribosomes which synthesize proteins
Generalized structure of a prokaryotic cell
-Chromosomal DNA is localized in a nucleoid
-Ribosomes are in the cytoplasm
-The cell membrane is surrounded by a cell wall
-The other structures shown may be present in some, but not all, bacteria
Region between the plasma membrane and the nuclear envelope
70-80% of THIS is water but it has semi-solid consistency due to proteins within it.
Cytoplasm
Nucleus
-Usually only one per cell
-Usually the largest organelle
-Bigger itself than most prokaryotic cells
-Separates DNA from cytoplasm
-Separates transcription from translation
-Nuclear pores perforate this membrane to allow molecules through
Nuclear Envelope
Nucleolus
A region inside nucleus where ribosomes are assembled from RNA & proteins
-Made of two different-sized subunits
Slightly larger in eukaryotes
-Made of special RNA (rRNA) and proteins
-During protein synthesis, THEY assemble amino acids into proteins
Ribosomes
Mitochondrion (purpose and parts)
-Site for conversion of stored energy (macromolecule molecular bonds) to more useful form (ATP)
-Inner membrane is folded
-Folds are called cristae
-Area enclosed is the mitochondrial matrix
Cell division (in animals?). Two centrioles that lie at right angles to each other, microtubules and nontubulin proteins
Centrosome
Plant Cell Walls
A rigid protective structure external to the plasma membrane made of cellulose
-Double membraned organelles with their own DNA and ribosomes
-The site of photosynthesis
Chloroplasts
Endomembrane System and what it does
Consists of internal membranes and organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins.
-Cells in animals that contain digestive enzymes
-These breakdown large biomolecules and even worn-out organelles
Lysosomes
Endoplasmic reticulum (ER)
Interconnected membranous sacs and tubules for nutrient storage, synthesis and metabolism
-Ribosomes attached to the cytoplasmic surface manufacture proteins
-Modifies proteins
-Phospholipid, enzymes and protein hormone creation
Rough ER
Smooth ER
-Synthesizes lipids, carbs and steroid hormones
-The SER is continuous with the RER but has few or no ribosomes on its cytoplasmic surface.
-Detoxification of medications and poisons
-Storage of Ca++
The hollow portion of the ER tubules
Lumen or cisternal space
Nuclear envelope
The membrane of the ER is continuous
Lipids or proteins within transport vesicles still need to be sorted, packaged, and tagged so that get to the right place
Golgi Apparatus
Cis Face Golgi Apparatus
This face transport vesicles from the ER fuse and empty their contents into the lumen of the Golgi apparatus.
THIS sorts proteins, lipids, lysosomes and more
Trans Face Golgi Apparatus
Cytoskeleton
-A network of protein fibers with several functions
-It helps maintain the shape of the cell;
-Hold some organelles in specific positions
-Allows movement of cytoplasm and vesicles within the cell:
-Enables cells within multicellular organisms to move
-Microfilaments
-Intermediate filaments
-Microtubules
Three Components of Cytoskeleton
Microfilaments
-ACTIN
-Involved in movement
-Whole cell or internal parts
-Determine & stabilize shape
-Made from actin monomers
-Form rigid internal skeleton for some cells
-Provide framework for motor proteins to move structures within cell
-Made of tubulin dimers
13 chains of dimers surround the central cavity
Microtubules
Cilia & Flagella
Ultrastructure
Same 9+2 array of microtubules
9 doublets on outside
2 unfused in center
Spokes connect doublets to middle
Cilia shorter and more numerous
Beating patterns differ
-Support
-Barrier to infection
-Plasmodesmata transport and communication cells
Plant cell wall
What the extracellular matrix in animals are made of
Collagens & other fibrous proteins
Glycoproteins called proteoglycans
Linking proteins
Provide direct channels of communication between cells
Plants and animals do this differently
Intercellular Junctions
Plasmodesmata
Plasmodesmata are channels that pass between cell walls in plants to connect cytoplasm and allow materials to move from cell to cell
-Watertight seals between animal cells that prevent materials from leaking between cells
-These are found in epithelial cells that internal organs and cavities.
Tight Junctions
Desmosomes
-Short proteins in the plasma membrane (cadherins) that act as spot welds
-These join adjacent cells in tissues that stretch (eg. heart, lungs, muscles)
-Only present animals
They form channels that allow ions, nutrients and other material to move between cells in animal cells
Gap Junctions
The partial negative charge in a molecule of water occurs because _____.
the electrons shared between the oxygen and hydrogen atoms spend more time around the oxygen atom nucleus than around the hydrogen atom nucleus
A lake heats up more slowly than the air around it.
Which of the following can be attributed to water’s high specific heat?
Water has many exceptional and useful properties. Which is the rarest property among compounds?
Solid water is less dense than liquid water.
The partial negative charge at one end of a water molecule is attracted to the partial positive charge of another water molecule. What is this attraction called?
A hydrogen bond and it’s attraction on water
Which of the following is a property of liquid water? Liquid water _____.
has a heat of vaporization that is higher than that for most other substances
A carbon atom is most likely to form what kind of bond(s) with other atoms?
covalent
A hydrocarbon skeleton is covalently bonded to an amino group at one end and a carboxyl group at the other end. When placed in water this molecule would function _____.
An acid and a base
The complexity and variety of organic molecules is due to _____.
the chemical versatility of carbon atoms
Why is carbon so important in biology?
It can form a variety of carbon skeletons and host functional groups.
What determines whether a carbon atom’s covalent bonds to other atoms are in a tetrahedral configuration or a planar configuration?
the presence or absence of double bonds between the carbon atom and other atoms
Differences among organisms are caused by differences in the _____.
types and relative amounts of organic molecules synthesized by each organism
Which of the following best summarizes the relationship between dehydration reactions and hydrolysis?
Dehydration reactions assemble polymers; hydrolysis reactions break polymers apart.
Which polysaccharide is an important component in the structure of many animals and fungi?
Chitin
What is the major structural difference between starch and glycogen?
the amount of branching that occurs in the molecule
Starch and cellulose _____.
are polymers of glucose
Humans can digest starch but not cellulose because _____.
humans have enzymes that can hydrolyze the α-glycosidic linkages of starch but not the β-glycosidic linkages of cellulose
What does the term insoluble fiber refer to on food packages?
cellulose
Phospholipids and triglycerides both _____.
have a glycerol backbone
Which of the following is the best explanation for why vegetable oil is a liquid at room temperature while animal fats are solid?
Vegetable oil has more double bonds than animal fats.
You have just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at regular intervals. What is the significance of this finding?
Cysteine residues are involved in disulfide bridges that help form tertiary structure.
The R-group, or side chain, of the amino acid serine is -CH2-OH. The R-group, or side chain, of the amino acid leucine is -CH2-CH-(CH3)2. Where would you expect to find these amino acids in a globular protein in aqueous solution?
Leucine would be in the interior, and serine would be on the exterior of the globular protein.
Normal hemoglobin is a tetramer, consisting of two molecules of β hemoglobin and two molecules of α hemoglobin. In sickle-cell disease, as a result of a single amino acid change, the mutant hemoglobin tetramers associate with each other and assemble into large fibers. Based on this information alone, we can conclude that sickle-cell hemoglobin exhibits what protein structure changes?
altered primary structure and altered quaternary structure; the secondary and tertiary structures may or may not be altered
Which of the following statements about the 5’ end of a polynucleotide strand of RNA is correct?
The 5’ end has a phosphate group attached to the number 5 carbon of ribose.
Nucleic acids are polymers made up of which of the following monomers?
nucleotides
If 14C-labeled uracil is added to the growth medium of cells, what macromolecules will be labeled?
RNA
When nucleotides polymerize to form a nucleic acid what bonds form between what?
a covalent bond forms between the sugar of one nucleotide and the phosphate of a second
The advantage of light microscopy over electron microscopy is that _____.
light microscopy allows one to view dynamic processes in living cells
In the fractionation of homogenized cells using centrifugation, the primary factor that determines whether a specific cellular component ends up in the supernatant or the pellet is the _____.
size and weight of the component
What technique would be most appropriate to use to observe the movements of condensed chromosomes during cell division?
standard light microscopy
What is the reason that a modern transmission electron microscope (TEM) can resolve biological images to the subnanometer level, as opposed to tens of nanometers achievable for the best super-resolution light microscope?
Electron beams have much shorter wavelengths than visible light.
In a bacterium, we will find DNA in _____.
Nucleotide
In a plant cell, DNA may be found _____.
in the nucleus, mitochondria, and chloroplasts
The evolution of eukaryotic cells most likely involved _____.
endosymbiosis of an aerobic bacterium in a larger host cell—the endosymbiont evolved into mitochondria
Which organelle often takes up much of the volume of a plant cell?
vacuole
Golgi Apparatus three functions
ALL:
-Transport vesicles fuse with one side of the Golgi and leave from the opposite side.
-Proteins in the membrane of the Golgi may be sorted and modified as they move from one side of the Golgi to the other.
-Lipids in the membrane of the Golgi may be sorted and modified as they move from one side of the Golgi to the other.
The liver is involved in detoxification of many poisons and drugs. What part of a cell is important for this?
Smooth ER
Tay-Sachs disease is a human genetic abnormality that results in cells accumulating and becoming clogged with very large, complex, undigested lipids. Which cellular organelle must be involved in this condition?
Lysosome
The difference in lipid and protein composition between the membranes of the endomembrane system is largely determined by the _____.
function of the Golgi apparatus in sorting and directing membrane components
A cell with an extensive area of smooth endoplasmic reticulum is specialized to _____.
synthesize large quantities of lipids
Which of the following produces and modifies polysaccharides that will be secreted?
Golgi apparatus
Motor proteins provide for molecular motion in cells by interacting with what types of cellular structures?
components of the cytoskeleton
How do cilia and flagella move?
Movement of cilia and flagella is the result of motor proteins causing microtubules to move relative to each other.
Cells require which of the following to form cilia or flagella?
Tubulin
Cytochalasin D is a drug that prevents actin polymerization. A cell treated with cytochalasin D will still be able to _____.
move vesicles within a cell
Researchers tried to explain how vesicular transport occurs in cells by attempting to assemble the transport components. They set up microtubular tracks along which vesicles could be transported, and they added vesicles and ATP (because they knew the transport process requires energy). Yet, when they put everything together, there was no movement or transport of vesicles. What were they missing?
Motor proteins
