Test 1 Review Flashcards
How many different amino acids are there?
20
Long chains of amino acids are called?
Polypeptides because they are held together by peptide bonds
What is a structural protein?
A protein providing the cell with shape and structure
tubulin and actin are examples
What do enzymes do?
Catalyze covalent bond formation or breakage
Transport molecules do what?
Carry other molecules or ions
What do motor proteins do?
Generates movement in cells and tissues
myosin is example
What do storage proteins do?
store small molecules or ions
What do signal proteins do?
Store small molecules or ions
insulin-glucose levels
What do receptor proteins do?
detect signals and transmit them to the cells resonse machinery
insulin receptor
what do gene regulatory proteins do?
Binds to DNA to switch genes on or off
Latose repressor is example
What is a peptide bond?
Covalent bond formed when carbon atom from carboxyl group shares and electron from amino group of 2nd amino acid
What type of reaction is a peptide bond?
A condensation reaction because a molecule of water is eliminated during bond formation
What is a polypeptide backbone?
Repeating sequence of core atoms N (-N-C-C), and each end is different
The C-terminus contains?
The free carboxyl group
The N-terminus contains?
Amino group with nitrogen
When hearing the term R-group, what should you think of?
R Groups=Side chain
What do the N-terminus and C-terminus provide?
directionality and polarity to the polypeptide chain, but R-groups give protein distinct characterstics
The conformation of a protein is?
It’s final folded structure
What are the 3 types of covalent bonds?
Electrostatic interactions
Hydrogen bonds
Van der Waals Attraction
What do hydrophobic interactions do?
help proteins fold into small, compact conformations because the non-polar side chains tend to be forced together to minimize disruption of hydrogen bonded network
If the factor that caused the protein to become denatured is removed the protein does what?
can refold (re-nature) itself back to to it’s stable conformation
Prion diseases are caused by?
misfolded protein aggregates.
They occur through rare conformational changes where proteins fold abnormally
What is the abnormally folded proteins (of prions) called?
PrP
What is a dimer?
Two proteins bound to one another
What are chaprone proteins?
Proteins that assist partially folded chains and help them fold along most energy favored pathway.
They also can form isolation chambers that allow single polypeptides to fold without risk of forming aggregates
Protein aggregates are called?
Amyloid fibers
A-Helix and B-Sheets are formed using what type of bonds?
hydrogen bonds
In an A-helix structure, the N-H pf peptide bond is bonded to the?
C=O
When A-helices interact and intertwine with each other it is referred to as a?
coiled-coiled interaction
B-sheets allow what?
amyloid fibrils and they use them for structural purposes
In parallel B-sheets, how do the polypeptides run?
N-terminus to C-terminus
What is a protein domain
any segment of a polypeptide that can fold into a compact structure
Primary structure refers to?
The linear amino acid
Secondary structure refers to?
an organization that forms within certain segments of the polypeptide chain
ex. a-helcies and B-sheets
Tertiary Structure refers to?
the full, three dimensional confomation of the entire polypeptide
Quaternary Structure refers to?
a complex of more than one polypeptide joined together
Dimers are an example
What are the three different protein domains/motifs?
a) all alpha helices
b) mixture of alpha helices and beta sheets
c) all beta sheets
What are protein families?
they consist of proteins that have amino acid sequences and 3-D confomation that closely resemble each other
Proteins that contain multiple copies of a single protein subunit are considered ________ and can interact through?
symmetrical and can interact through two identical binding or form multiple copies of a single polypeptide chain
Globular proteins are?
polypeptide chains fold into compact shape like a ball with irregular surface
Proteins can assemble into?
filaments, sheets, or spheres
Protein orientations are affected by?
the number of binding sites
If a protein has one binding site?
it can form a dimer with another identical protein
Identical proteins with 2 binding sites will often form?
a long helical filament
If two identical protein binding sites are oriented properly, the proteins can also form?
a sphere or ring like structure
Fibrous proteins are?
proteins requiring them to span a large distance
Collagen forms what protein shape?
a triple helix
What are the most common covalent cross-link proteins?
sulfer-sulfer bonds
disulfide bonds
How do disulfide bonds help proteins?
they stabilize a favored protein conformation and acts as a “staple” to reinforce the most favored conformation
What is a ligand?
any substance that is bond by a protein
The ability of a protein to bound to bind selectively and with high affinity is due to what?
The formation of noncovalent bonds
If the binding of the protein and ligand is unfavored what do the molecules do?
dissasociate
The folding of a polypeptide chain creates a __________ in the protein which allows what to interact with it?
cavity; the ligands to interact and bind with it
All proteins must bind with _______ to carry out a specific function.
ligand
What do antibodies do? What do they bind with?
Antibodies are Y shaped and have two binding sites for the antigen. They bind extremely tightly with the target molecule and mark it, inactivate it or mark it for distruction
What is the active site?
the bonding site on the the surface substrate molecule on which an enzyme acts
How do enzymes encourage catalysis?
A) holding substrates in a precise alignment
B) stablizing charges of substrates
C) alterins bind angles to force into a favorable reaction
What is feedback inhibition?
an enzyme early in the rxn pathway is inhibited by a late product in that pathway. When large quantites of the final product build up, later producrs bind to earlier enzymes
What type of regulation is feedback inhibition?
negative
What does feedback inhibition trigger?
a conformational change
What is allosteric inhibition?
can adopt two or more slightly different conformations and activity can be regulated by a shift from one to another.
Basically, each ligand will stablize the confirmation that it binds most strongly to in an effort to switch the protein to its most active form
What is protein phosphorylation?
addition and removal of phosphate groups from specific proteins often occur in response to signals that specify some change in a cell’s state
What is the enzyme that is responsible for the addition of the phosphate group?
kinase
What is the enzyme involved in the reverse process (removal of a phosphate group)?
phosphatase
GTP binding proteins form?
molecular switches, in that the protein is in its active form when GTP is bound, and becomes inactive when GTP hydrolyzes itself into GDP, switching to the inactive conformation
Changing __________ conformation of the motor protein to push the protein forward
allosteric
What is protein phosphorylation?
involved the enzyme catalzed transfer of the terminal phosphate group of ATP to the Hydroxyl group on a serine, threonine, or tyrosine chain of a protein
What does protein phosphatase do?
removes the phosphate group or is responsible for dephosphorylation
How can a protein’s structure be determined?
by x-ray crystallography
Describe “cell line” and explain what that means
Cell line refers to cells that are monoculture and are immortal as long as they have specific nutrients
“in vitro” comes from?
the fact cell culture experiments are not taking place in the whole living organism
What does Affinity chromatography can be used to?
isolate the binding partners of a protein of interest
A deoxyribonucleic acid is defined as?
a molecule consisting of two long polynucleotide chains
In what year was DNA recognized as the possible carrier of the genetic informaiton?
1940
How did Rosaline Franklin discover the double helix?
she discovered it using X-ray diffraction patterns of crystalline B-form DNA
Shortly describe Griffith’s experiment?
Living S strain=mouse dead
Living R strain=mouse lived
Heat-killed S strain=mouse lived
Live R strain + Heat-killed S strain=mouse died
Live S strain material was found in the dead mouse upon autopsy, and a year later it was discovered that the main component of the purified substance was DNA
Describe the building blocks of DNA-
Phosphate + sugar = sugar-phosphate
sugar-phosphate+ nitrogenous base=nucleotide
nucleotide + hydrogen bonded base pairs=DNA
Thread-like structures in the eukaryotic cell nucleus that becomes visible as the cell divides…
Describes?
Chromosomes
The covalent linkage b/w the sugar phosphate backbone forms a?
phosphodiester bond
Nucleotide=
sugar-phosphate covalently linked to a base
Nucleoside=
sugar covalently linked to a base (no phosphate group)
A & G are?
What is their structure like?
Purines ***** KNOW THIS JACKI
double ring nitrogenous bases
C & T are?
What is their structure like?
pyrumidines**KNOW THIS JACKI
single ring nitrogenous bases
The 5’ and 3’ positions help provide?
directionality and polarity to the polynucleotide chain
How many _______ bonds hold together A & T?
How many hold together C & G?
hydrogen
A&T=2 bonds
C&G=3 Bonds
Why is the 3’ end called 3’?
Because the 3’ end carried an unlinked -OH group attachde to the 3’ position of the sugar ring
Why is the 5’ end called 5’?
the 5’ end carries a free phosphate group attached to the 5’ position on sugar ring
DNA is always read in the _____ direction?
DNA is always read in the _____ direction?
The DNA double helix is _______ handed?
right
Hershey and Chase-
What was the DNA labelled with?
What did the experiment conclude?
p^32
Protein was labelled with S^35 but only DNA p32 entered bacterial cells
What is the central dogma of molecular biology?
DNA->RNA->PROTEINS
A genome contains?
The complete set of information in an organisms DNA
What is Chromatin?
complex of DNA and Protein, total genetic info carried by all chromosomes in a cell or organism
How does Chromosome painting work?
exposing the chromatin to a collection of fluorescent dye-labeled DNA
Ataxia is a mutaion in what chromosome?
What occurs to the chromosome?
Chromosome 12
and one chromosome is longer with additional material from chromosome 4
What occurs to the chromosomes during interphase?
cell is actively expressing its genes and the DNA is replicated
What occurs to the chromosomes during mitosis?
chromosomes condense, gene expression laregely ceases, and the mitotic spindle forms from microtubules
condensed chromosomes are captured by mitotic spindle and one set of chromosomes is pulled to each end of cell
nuclear envelope forms around each chromosome and cell divides to form two daughter cells
How many DNA sequence elements are required for chromosome replication?
3
Each chromosome has ______________, ______________, and ____________.
Each chromosome has multiple origins of replication, one centromere, and two telomeres
What occurs during the M phase?
centromere attaches the duplicated chromosomes to the mitotic spindle so that one copy/chromosome is distributed to each daughter cells
What is a nucleolus?
Non-membrane bound structure composed of proteins and nucleic acids found within the nucleus
Most prominate structure in the interphase nucleus
Where is heterochromatin located?
mainly around the periphery, immediatly under the nuclear envelope.
What do nucleosomes contain?
DNA wrapped around the core of eight histone molecules
What is contained in an INDIVIDUAL nucleosome CORE particle?
8 histones-2 molecules each histone H2A, H2b, H3, and H4
The double stranded DNA-147 nucleotide pairs long that winds around this histone octomer
What just an overal nucleosome?
A nucleosome core particle plus one of its adjacent DNA linders
How many times is the 147 nucleotide pairs of DNA wrapped around the nucleosome core?
1.7 turns
DNA PACKING-
A linker histone (H1) do what?
pull nucleosome particles together into the 30-nm fiber
DNA PACKING-
Chromatin isolated from interphase nucleus appears as?
threats 30-nm thick
DNA PACKING-
Histone H1 consists of a globular region plus?
a pair of long tails at its C-terminal and N00termainla ends
DNA PACKING-
The globular region contrains?
an additional 20 base pairs of the DNA where it exits from the nucleosome core
Heterochromatin are?
More condensed than Euchromatin
Protein machines that use the energy of ATP hydrolyisis to change the postion of the DNA wrapped around nucleosome are?
Chromatin-remolding complexes
How do Chromatin-remoldeling complexes work?
by pushing tightly bound DNA as they move along, they loosen underlying DNA, allowing it to become accessible to other proteins
What continues (repeating) allows Chromatin-remodeling complexes to loosen nucleosome DNA by pushing it along the histone core?
ATP Hydrolysis
___________ of nucleosome sliding can decondense (loosen) chromatin.
Multiple rounds
The __________ ____ __________ of histone tails can dictate how a stretch of chromatin is treated by cells.
pattern of modification
Each histone cane be modified by the covalent attatchment of a number of different chemical groups including:
an acetyl group, a methyl group, or a phosphate
Epigenetic modifications are?
covalent attachments of different chem. groups that act on chromatin structure, but DO NOT change genetic sequence
Where do most modifications occur on histones?
the N-terminal tails
____________ modifications to the histone tails can attract heterochromatic-specific proteins that preoduce the smae modifications of neighboring protiens.
Repressive
Repressive modifications allow heterochromatin to spread until it encounters?
a DNA barrier sequence that prevent heterochromatin spread
Expression of a gene can be altered by?
moving it to another location in the genome
What is position effect?
the activity of a gene depends on its position along a chromosome
An ______ chromosome can be inactivated by heterochromatin formation
X chromosome
Semiconservative replication refers to?
each parental strand serves as the template for one new strand, therefore each daughter double helix is composed of of the original strands plus a completely new strand
How is the process of DNA replication started?
By initiator proteins that bind to the two specific DNA sequences called replication origins.
How do initiator proteins begin?
by prying/pulling apart the two strands of the double helix by breaking the hydrogen
The addition of a deoxyribonucleotide to the _____ end of a polynucleotide chaing is the fundamental reaction by which DNA is synthesixed
addition of a deoxyribonucleotide to the 3’ hydroxyl end
DNA is synthesized in the _____ direction
5’ to 3’ direction
How do nucelotides enter the reaction?
as nucleoside triphoshates (5-C sugar attached to nitrogenous base and 3 phosphate group
What enzyme catalyzes addition of nuceotides to the free 3’ hydroxyl on growing DNA strand
DNA polymerase
What bond breakage provides a large amount of energy for the polymerization reaction?
the phosphoanhydride bond on incoming nucleoside triphosphate
At the replication fork, the two newly synthesized strands are of?
opposite polarities
DNA polymerase can only catalyze the addition of incoming nuclleotides in what direction?
the 5’ to 3’ direction adding nucleosides to 3’ end
Initially the lagging strand is made of?
short DNA strands called Okazaki fragments
If an incorrect nucleotide is added to a growing strand what will DNA polymerase do?
cleave it from the strand and replace it with the correct nucleotide before continuing
What are the Steps of DNA polymerase’s catalyzation of of nuceotides?
First, it monitors the base-pairing and only when match is correct does it catalyze the nucelotide addition reaction.
Second, when it does make a mistake, it fixes it through proofreading
DNA polymerase contains two sites, what are they fore?
It has two seperate sites for DNA synthesis and proofreading
Why exactly is DNA only synthesized in the 5’ to 3’ direction?
A need for proofreading
If it was synthesized in the other direction removal of a incorrect nucleotide would block the addition of the correct nucleotide and prevent further elongation
DNA polymerase cannot-
Start a completly new DNA strand
Primase is a
RNA polymerase
How long are RNA Primers
10 nucleotides
