GCU BIO 333 EXAM 1
structural proteins
provide mechanical support to cells and tissues
what are the names of the two different nitrogenous bases? how do you differentiate between them?
purines- larger pyrimidines- smaller
what is a mole?
the relative formula mass of a substance in grams
There are 61 mRNA codons that specify an amino acid, but only 45 tRNAs. This is best explained by the fact that
the rules for base pairing between third base of a codon and tRNA are flexible.
what is a substrate?
the substance on which an enzyme acts
what is molecular weight?
the sum of the atomic weights of all the atoms in a molecule
What is protein denaturation?
the unfolding and disorganization of a proteins structure
Isotopes
there protons stay the same but there neutrons can change
why are genomes useful to compare species?
to see genes from different organisms have very similar nucleotide sequences and they might descend from a common ancestral gene to loo for homologies to look for where everything started
why are fies and zebrafish used as model organisms?
to study genetics and development
the protein product of the lacl gene is best classified as what type of molecule?
transcription factor
what does the following compounds fall under: serine C-carbohydrates P-protein L- lipids N- nucleci acids
N
what is a polypeptide backbone
N-C-C-N-C-C
what size is larger? 10nm or 0.1um
0.1 um
you need to make a 0.5 M solution of NaCl in 100 mL. Calculate how muh NaCl (in grams) needs to be dissolved in 100 ml.
0.5M= 0.5M/1L x 58g/1 mole x 0.1 liters= 2.9 g NaCl
What are the 3 differences between DNA nucleotides and RNA nucleotides?
1. different sugars ribose vs. deoxyribose 2. different base uracil vs. thymine 3. double stranded vs single stranded
what are the three ways enzymes can encourage a reaction?
1. holding reacting substrates together in a precise alignment. 2. rearranging the distribution of charge in a reaction intermediate. 3. altering bond angles in the substrate to increase the rate of a particular reaction.
How common are intrinsically disordered sequences?
1/3 of call eukaryotic proteins also posses longer, unstructured regions in their polypeptide chains
What size is larger? 100um or 1nm
100um
what size is larger? 10mm or 0.001m
10mm
What is Avogadro's number?
6.02 x 10^23
calculate the molecular weight of sodium chloride
Na:23 Cl: 35 =58 daltons
What is an ionic bond?
A chemical bond that's formed when an atom transfers and electron to another Atom
What is a polypeptide chain?
Another word for protein
what does the following compounds fall under: glycogen C-carbohydrates P-protein L- lipids N- nucleci acids
C
what does the following compounds fall under: sucrose C-carbohydrates P-protein L- lipids N- nucleci acids
C
enzymes
protein catalysts
shared components of eukaryotes and prokaryotes.
DNA, RNA, protein, ribosomes, membrane
T/F: mitochondria are not found in plants
F
T/F: at a pH of 8 the hydrogen ion concentration is higher than the hydroxide concentration
F: -OH is higher than H+
T/F: DNA can only be found in the nucleus
F: DNA is in the cytoplasm of prokaryotic cells
T/F: cell recieve nutrients by exocytosis
F: endocytosis
T/F: an acidic solution has a high hydroxide in concentration
F: high proton concentration
T/F: mujscle cells are likely to have a very smooth endoplasmic reticulum
F: liver cells
T/F: actin filaments are responsible for pulling apart sister chromatids during mitosis.
F: microtubules
T/F: acidic solutions are considered to be alkaline
F: pH below 7
T/F: bases minimize hydroxide ions in solutions
F: protons
T/F: Cholorplast are responsible for pulling apart sister chromatids during mitosis
F: they convert solar energy into sugar
what kind of bond holds two DNA strands together?
Hydrogen
what is the function of the release factor (RF)?
It binds to the stop codon in the A site in place of a tRNA.
What is a phospholipid?
It is a lipid that has a phosphate group attached to the glycerol and only two fatty acid chains.
What is lysozyme and what does it do?
It is an enzyme that severs the polysaccharide chains that form the cell walls of bacteria: gound in many selections including saliva and tears, where it serves as an antibiotic.
what does the following compounds fall under: GTP C-carbohydrates P-protein L- lipids N- nucleci acids
N
what does the following compounds fall under: adenine C-carbohydrates P-protein L- lipids N- nucleci acids
N
what does the following compounds fall under: SOAP C-carbohydrates P-protein L- lipids N- nucleci acids
L
what does the following compounds fall under: butter C-carbohydrates P-protein L- lipids N- nucleci acids
L
what does the following compounds fall under: fatty acid C-carbohydrates P-protein L- lipids N- nucleci acids
L
what does the following compounds fall under: phophatidylcholine C-carbohydrates P-protein L- lipids N- nucleci acids
L
what does the following compounds fall under: ribose C-carbohydrates P-protein L- lipids N- nucleci acids
N
What are chaperone proteins?
proteins that assist in the proper folding of proteins
What is a peptide bond?
O, C, N, H
what are different types of nucleotides?
RNA or DNA
definition of atom
Smallest form of an element that maintains distinct chemical properties.
components of the golgi apparatus
Stack of flattened membrane-enclosed sacs, modifies and packages molecules made in the ER
T/F: bacterial DNA is found in the cytoplasm
T
T/F: muscle cells ar elikely to have an increased concentration of mitchondria.
T
T/F: the double membrane found in cholorplasts and mitochondria are thought to be formed by an exosymbiont theory.
T
T/F:a hydronium ion and a hydrogen ion are considered the same in solution
T
what is the active site?
The active site is the region on the enzyme where the substrate binds.
what does hydrophobic mean
Water fearing
what are bases?
proton acceptors
Definition of genome
The whole of the genetic information of an organism
A particular triplet of bases in the coding sequence of DNA is AAA. The anticodon on the tRNA that binds the mRNA codon is
UUU
what are tertiary structures?
complete three-dimensional structure of a fully folded protein
which subatomic particles determine the atomic #?
protons
What are subatomic particles?
protons, neutrons, electrons
What are covalent bonds?
a chemical bond that involves the sharing of electron pairs between atoms
what is a protein family?
a group of proteins that share a common evolutionary origin, reflected by their related functions and similarities in sequence or structure
What is a triacylglycerol?
a lipid made with three fatty acids and glycerol
What is the pH scale?
a measure of how many free H+ ions there are in a solution
what is a dimer?
a molecule or molecular complex consisting of two identical molecules linked together.
What are monomers?
a molecule that can be bonded to other identical molecules to form a polymer.
which of the following does not occur in prokaryotic gene expression, but does in eukaryotic gen expression?
a poly-A tail is added to the 3' end of an mRNA and a cap is added to the 5' end
what is a trimer?
a polymer comprising three monomer units.
What is a beta sheet?
a secondary structure of a protein that is formed by a hydrogen bond of the atoms in a peptide bond that lie within linear regions of polypeptide, chain may run in same direction (parallel) or opposite direction (anti parallel), also can turn and fold back on itself
What is an alpha helix?
a secondary structure of a protein that is formed with a hydrogen bond between carboxyl oxygen of one amino acid and an amide nitrogen of another amino acid
Definition of conformation?
a single-chain macromolecule to adopt an almost unlimited # of shapes
what is an enzyme?
a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction.
What is a hydrogen bond?
a weak bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other.
Describe the size of a cell:
abojut 20 um, light microscope, 25 times smaller than the width of a human hair
components of the cytoskeleton
actin- thinnest-muscle contractions microtubules- thickest- pyull duplicated chromosomes apart intermediate filaments-thinner- strengthens most animal cells these are all proteins filaments
albumin is a larger protein which circulates freely in human plasma. Another type of protein, called aquaporins, act as a channel for water to enter and exit the cell, and are located within the lipis bilayer of a cell's plasma membrane. Based ont heir physiological locations, how would the tertiary structure of these two proteins most likely compare?
albumin has a more nonpolar core with a polar out layer, while aquaporins have a more polar core with a nonpolar outer layer
in the lac operon, the repressor protein exerts a negative effect on the expression of the structural genes in the absence of the inducer molecule. In the case of the lac operon, what is the inducer molecule?
allolactose
the interaction betweenlactose and the lacl repressor protein is an example of what biochemical process?
allosteric regulation
what are secondary structures?
alpha helices and beta sheets
what is a protein subunit?
amino acid
what is the n-terminus?
amino group end
what functional groups are found at the N and C terminus of all proteins, respectively?
amino, carboxyl
what is a ribozyme?
an RNA with enzymatic activity
what are electron shells?
an energy level of electrons at a characteristic average distance from the nucleus of an atom
what can be found in the genome
ancestral history, DNA, gene activity
What is a ligand?
any molecule that binds specifically to a receptor site of another molecule
what is a protein domain?
any segment of a polypeptide chain that can fold independently into a compact, stable structure
In an alpha helix, the R groups on the amino acid residues:
are found on the outside of the helix spiral
What are coiled coil structures?
are stable, rodlike protein structures ormed when two or more alpha-helices twist repeatedly around each other.
what are acids?
are substances that release protons when they dissolve in water
The term denaturation, when used in connection with nucleic acids or proteins refers to a change in structural characteristics due to a. The disruption of covalent bonds b. The disruption of non-covalent bonds c. The binding of toxic compounds d. Changes in primary structure
b
a coiled peptide chain held in place by hrydrogen bonding between peptide bonds in the same chain is a. primary structure b. alpha-helix c. beta-pleated sheet d. tertiary structure
b
a new drug is developed which selectivelly cleaves bonds between two sulfur atoms of non-adjacent amino acids in a polypeptide chain. Which level of protein sturcute in affected molecu;es would most directly affected by the drug? a. secondary structure b. tertiart stucture c. primary structure d. quaternary structure
b
what is the main function of cytoplasm in the cell? a. synthesizing proteins in the cell b. suspending cellular structures and providing a place for cellular functions to take place c. regulating the transport of molecules into and out of the cell d. packaging and sending out proteins and lipids
b
which of the following scenarios occur when lactose is present as the sole energy source? a. production of the repressor protein is increased b. the enzyme for lactose metabolism are produced c. the repressor protein binds to the operator d. the lac operon genes are not transcribed.
b
what is the correct sequence of proteins found in the lac operon?
beta-galactosidase, permease, transacetylase
transcription regulators
bind to DNA and switch genes on and off
What is the enzyme-substrate complex?
binding of the enzyme and the substrate, which then speeds up the chemical reaction by lowering the activation energy
Accuracy in the translation of mRNA into the primary structure of a polypeptide depends on specificity in the
bonding of the anticodon to the codon and the attachment of amino acids to tRNAs.
if a soljution is said to be a buffer which of the following statements is true? a. the solution is at a pH of 7 b. the solution has a high hydrogen ion concentration c. the solutions pH will have a little chang when exposed to a acid or a base d. the solutions pH will have a drastic change when exposed to ana cid or a base
c
which of the following statements is NOT true regarding the comparison of the alpha-helix structure to the beta-sheet structure in proteins? a. each is stabilized by inter-chain hydrogen bonds b. each is an example of secondary structure c. all possible hydrogen bonds between the peptide carbonyl oxygen (C=O) and the amide hydrogen (N-H) are formed in each d. each may occur in typical globular proteins
c
which of the following statements is most likely to be true of nonpolar R groups in aqueous solution? a. they are hydrophilic and found buried within proteins b. they are hydrophilic and found on protein surfaces c. they are hydrophobic and found buried within proteins d. they are hydrophobic and found on protein surfaces
c
which of the following structures is found in all proaryotes? a nucleus b. flagellum c. ribosomes d. mitochondria
c
what re the components of the chloroplasts?
captures energy from sunlikght, converts it to ATP, photosynthesis, CO2 to glucose
What is the C-terminus?
carboxyl end
What is a fatty acid?
carboxylic acid consists of hydrocarbon chain and terminal carboxyl groups
signal proteins
carry extracellular signals from cell to cell
transport proteins
carry small molecules or ions
What are quaternary structures?
complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule.
the substration of water is
condenstation
what type of bond links nucleotides in the same strand?
covalent bonds
what is macromolecule assemble
covalent bonds allow organic molecules to join together to form macromolecules, which can assemble into large macromolecular complexes via non covalent bonds
where in the eukaryotic cell does translantion occur?
cytoplasm
where in the prokaryotic cell does replication occur?
cytoplasm
where in the prokaryotic cell does transcription occur?
cytoplasm
where in the prokaryotic cell does translation occur?
cytoplasm
A single prokaryotic cell can divide several times in a hour. Most eukaryotic cells cannot divide this quickly. Which of the statements best explains this difference? a. eukaryotic cells are smaller than prokaryotic cells b. eukaryotic cells have less DNA than prokaryotic cells c. prokaryotic organisms are typically multicellular while eukaryotic organism are unicellular. d. eukaryotic cells are more structurally complex than prokaryotic cells
d
all of the following are considered "weak" interactions in proteins, expect: a. hydrogen bonds b. hydrophobic interactions c. ionic bonds d. peptide bonds e. van der waals forces
d
which of the following nucleotide triplets best represents a codon? a. a triplet separated spatially from other triplets b. a triplet at the opposite end of tRNA from the attachment site of the amino acid c. a triplet at the opposite end of tRNA from the attachment site of the amino acid d. a triplet in the same reading frame as an upstream AUG e. a sequence in tRNA at the 3' end
d
receptor proteins
detect signals and transmit them to the cell's response machinery
What are some model species?
escherichia coli (bacteria), saccharomyces cerevisiae, arabidopsis thaliana (plant), drosphila melanogaster (fly), caenorhabditis elegans, zebrafish, mus musculus (mouse).
Put in order from largest to smallest. bacterial cell ribosome nucleus o2 eukaryotic cell
eukaryotic cell bacterial cell nucleus ribosome O2
what are human cells used for?
fibroblasts, neurons, epithelial cells, embroynic heart muscle cells
components of the marcomolecule: proteins
monomer: amino acid polymer: polypeptide linakge: peptide bond
motor proteins
generate movement in cells and tissues
Components of a eukayote.
have organelles, membrane bound nucleus, 24hrs. to divid, epitheal cells, multicellular, 185 rRNA,unicellular, larger, and about 5-50um
special purpose proteins
highly variable
what are the components of the nucleus?
holds dna in the form of chromosmes, molecules of dna- long polymers that encodes the genetic information
what are three types of noncovalent bonds that help fold proteins
hydrogen bonds, electrostatic attractions, and van der waals
the addition of H20 is
hydrolysis
components of the endoplasmic reticulum
irregular maze of interconnected spaces enclosed by a membrane, membrane components made, secretion of proteins
components of the marcomolecule: lipids
monomer: fatty acid polhymer: tricylgycerol phospholipid linkage: ester bond
components of the marcomolecule: carbohydrates
monomer: momosaccharide polymer: polysaccharide linkage: glyosidic bond
components of the marcomolecule: nucleic acids
monomer: nucleotide polymer: DNA or RNA linkage: phospodiester bond
What are side chains?
portions of an amino acid not involved in forming a peptide bonds; its chemical identity gives each amino acid unique properties.
What are cations?
positively charged ions
Why is Arabidopsis Thaliana a model organism?
it is a plant that is a model for other plants
what are the components of the cytosol?
liquid of the cell, pH of 7.4, where most proteins are made by ribosomes
What is a polypeptide?
long chain of amino acids
What are polymers?
long chains of monomers
which of the following molecules are required for the process of translation?
mRNA, tRNA, and rRNA
what are the general distributions of macromolecules in cells?
macromolecules are constructed simply by covalently linking small organic monomers or subunits, into long chains or polymers
what is the structure of a protein
made of amino acids (20 different ones), held together by peptide bonds making polypeptide chains
what are the components of the mitochondria?
makes ATP, tri-carboxyl cycle
components of the cytoplasm
metobolism, things brought in and out of cell
evolution of mitochondria and cholorplast
mitochondria evolved from aerobic bacteria that were engulfed by an archaea-derived, early anaeorbic eukaryotic cell and survived inside it
What are organic molecules?
molecules that contain carbon
what is a subunit?
monomer
What are anions?
negatively charged ions
What is a nucleotide composed of?
nitrogenous base, five carbon sugar, phosphate group
components of a prokaryote
no membrane bound nucleus, 20 min. to divid, unicellular, cell wall, 165 rRNA, binary fission, smaller, about 0.2-2 um.
What are inorganic molecules?
non-carbon based molecules
Where in the eukaryotic cell does transcription occur?
nucleus
where in the eukaryotic cell does replication occur?
nucleus
what does the following compounds fall under: glutamine C-carbohydrates P-protein L- lipids N- nucleci acids
p
identify the three components of all nucleotides
phosphate- sugar - base
why does e.coli have polycistronic messages?
polycistronic messages allow the bacteria to regulate several functionally related genes at the same time.
what is a enzyme product complex?
rapidally dissociates, releasing the product and leaving the enzyme free to act on another substrate molecule.
What is protein renaturation?
refolding
what are intrinsically disordered sequences?
region in a polypeptide chain that lacks a definite structure
what is an example of a protein family?
serine protease
definition of cell:
small, membrane- enclosed units filled eith a concentrated aqueous solution of chemicals and enduced with the ability to create copies of themeselves by grounding and dividing.
storage proteins
store of amino acids or ions
what are the four major families of small molecules?
sugars, fatty acids, amino acids, nucleotides
what are primary structures?
the amino acid sequences of a protein
what is atomic weight?
the atomic weight of an element reflects the number of grams per mole (g/mol) of the element. the atomic weight is usually derived from a weighted average of the naturally occurring isotopes of the element
what is the benefit of the repressor being constitutively produced?
the bacteria does not want to expend energy creating lactose metabolizing enzymes if lactose is not available.
What is the transition state?
the complex formed as covalent bonds are being broken and re-formed during a reaction
why are valence electron shells important?
the fewer valence electrons the less stable the atom becomes
Why e.coli and important model orgaism
useful to study genetics
what does hydrophilic mean
water loving
what are buffers
weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH
