PdBio midterm 2 Flashcards
molecule
2+ atoms held together b y various forces or bonds
Types of bonding
covalent, ionic, hydrogen
covalent bonds
sharing of electrons between 2 nonmetal atoms
ionic bonds
transferring electrons between metal and nonmetal atoms (ex: NaCl)
hydrogen bonds
H partial positive charge bonding with an electronegative atom such as N, O, or F
4 types of macromolecules
carbohydrates, lipids, proteins, nucleic acids
monomers
many small molecules linked together to form polymers
monomer: simple subunit (mono=1)
polymer: longer chain (poly=many)
polymer formation done by…
dehydration
dehydration
removes a water molecule (needs energy/enzymes to help)
polymer breakdown done by…
hydrolysis
hydrolysis
water added back in each time a monomer is released (enzyme used to catalyze the breakdown)
Carbohydrates
- monomer?
- function?
- composition?
- bonds used:
- monomer = monosaccharide sugar subunit
- function: store energy & aid in cell recognition
- composition: C,H,O atoms
- bonds used: covalent
Lipids -monomer? -function? -composition? bonds used:
- monomer = glycerol & fatty acids
- function: store energy & add structure/protection
- composition: C & H atoms, clumped together
- bonds used: covalent no H bonds
Which macromolecule is non polar and insoluble in H2O?
Lipids
Proteins -monomer? -function? composition? bonds used:
- monomer = amino acids
- function: provide structure & communicate
- composition: C,H,O,N,S atoms
- 20 different amino acids with a different R group
- changing R group also changes pH and charge
-bonds used: depends on the structure
What does the R group of an amino acid determine
chemical characteristics > pH and charge
Nucleic Acids
- monomer?
- function?
- composition?
- bonds used?
- monomer = nucleotide
- function: storage, expression, transmission of genetic info
- composition: phosphate group, 5C sugar, and a base (C,U,T,A,G)
- bonds used: covalent & hydrogen
purines in DNA
Adenine (A) and Guanine (G)
pyrimidines in DNA
Cytosine (C) and Thymine (T)
Base pairs in DNA - which bases pair with each other?
A&T pair together
C&G pair together
Things to remember about DNA structure (3)
base pairing (ATCG) double helix - anti-parallel no hydroxyl group on 2'
purines in RNA
Adenine (A) and Guanine (G)
pyrimidines in RNA
Cytosine (C) and Uracil (U)
Base pairs in RNA - which bases pair with each other?
A & U pair together
C & G pair together
Things to remember about RNA structure (3)
base pairing (AUCG)
single strand
hydroxyl group on 2’
DNA stands for
Deoxyribonucleic Acid
RNA stands for
Ribonucleic Acid
General process of the Central Dogma
DNA transcribed to RNA translated to Proteins
Why is DNA replication necessary?
It is necessary because cells divide and they need double the amount of DNA so the resulting daughter cells will contain the correct amount of DNA
Types of DNA replication (3)
- conservative
- semi-conservative
- dispersive replication
What is the most common/popular type of replication? Explain it.
Semi-conservative = DNA replication produces DNA molecules with 1 parental strand and 1 newly made daughter strand
Where does replication begin?
Origin of replication - provides an opening called a replication bubble that forms two replication forks
How many origins of replication are found in eukaryotes and prokaryotes?
- eukaryotes may have multiple origins of replication
- prokaryotes (bacteria) only have 1 origin of replication
Where does DNA replication happen in a cell and in which way does it proceed?
DNA replication happens in the nucleus. It proceeds outward from the forks.
What is the direction of DNA replication?
5’ to 3’ direction in the primary structure of nucleic acids
What is the composition of nucleic acids (in more detail)?
- the 5’ end has the free phosphate attached to the 5’ carbon
- the 3’ end has an OH group attached to the 3’ carbon
- 2’ end has either (H) for DNA or (OH) for RNA
- Nitrogen base attached to 1’C on sugar (ATCG)
- nucleic acids are sequenced from 5’ to 3’
Directions of the leading and lagging strands?
- leading strand is moving TOWARD the replication fork in 5’ to 3’ direction
- lagging strand is moving AWAY from the replication fork in 5’ to 3’ direction
Players in DNA replication (7)
- helicase
- single strand binding proteins (SSBP)
- topoisomerase
- primase
- DNA polymerase III
- DNA polymerase I
- Ligase
Function of helicase
“unzips” DNA strands
Function f single strand binding protein (SSBP)
keeps the strands separated
Function of topoisomerase
loosens the tension to prevent supercoiling in the rest of the DNA strand
Function of primase
makes RNA primer so that the enzymes know where to start building
Function of DNA polymerase III
builds the new base (5’ to 3’)
Function of DNA polymerase I
removes RNA primers (Okazaki fragments)
Function of ligase
links the bases together
DNA replication accuracy based off of 3 things
1) Hydrogen bonding between A & T and between G & C is more stable than mismatched combinations
2) Active site of DNA polymerase is unlikely to form bonds if pairs are mismatched
3) DNA polymerase can proofread to remove mismatched pairs (DNA polymerase backs up and digests linkages)
DNA replication accuracy based off of 3 things
1) Hydrogen bonding between A & T and between G & C is more stable than mismatched combinations
2) Active site of DNA polymerase is unlikely to form bonds if pairs are mismatched
3) DNA polymerase can proofread to remove mismatched pairs (DNA polymerase backs up and digests linkages)
Griffith experiment
experiment with rough/smooth strains of streptococcus and mice
-process of “heat killing” bacteria denatures the proteins, but DNA is still intact
Hershey-Chase
experiment - infection, blending, centrifuge (heavy bacteria pellets at bottom)
-conclusion: DNA was injected into bacteria, not protein. DNA is the genetic material
Beadle & Tatum
Hypothesize one gene codes for one enzyme/protein
-mutated the DNA one enzyme at a time
Variations/exceptions to the Central Dogma
- the genetic code is not really universal
- mitochondria usually have their own genetic code different from the code that governs the nuclear genome.
What bonds link amino acids together in proteins?
peptide bonds
In what direction are amino acids built?
N - C direction
What is polymerization and what does it require?
the binding together of monomers
-requires 1+ enzymes and energy to form
What are the 4 levels of structure in proteins (describe)?
- primary: the sequence of amino acids (covalent peptide bonds) form a linear string of peptide bonds in the N to C direction
- secondary: hydrogen bonds form alpha helices and beta pleated sheets (2 STRUCTURES HERE)
- tertiary: secondary structures and other regions fold into 3D shapes to become functional (all kinds of bonds)
- quaternary: two or more polypeptides join together to form a functional protein (all kinds of bonds)
What are the two classes of nucleic acids?
DNA (stores genetic info encoded in the sequence of nucleotide monomers)
RNA (decodes DNA into instructions for linking together a specific sequence of amino acids)
How can you tell if a nucleic acid has DNA or RNA?
look at the 2’ carbon
- if hydrogen (H) is present it is DNA
- if oxygen (OH) is present it is RNA
What is an element found in all organic molecules?
Carbon
Meselson & Stahl
Proved that DNA replication occurs through semi-conservative replication
DNA has to be made in the _______ direction so you must add to the _____ end every time.
DNA has to be made in the 5’ to 3’ direction so you must add to the 3’ end every time
What is the difference between purines and pyrimidines?
Purines have a double ring structure and pyrimidines have a single ring structure
The double helix structure of DNA was proposed by who?
Watson and Crick
The ability to predict the DNA sequence in one strand based on the sequence of another strand is referred to as what?
complementarity
During DNA replication, the lagging strand is synthesized as a series of small fragments called
Okazaki fragments
A DNA polymerase can detect a mismatched nucleotide and remove it from the daughter strand. It does so by digesting the linkages in the 3’ to 5’ direction to remove the incorrect base and then changing direction to synthesize again in the 5’ to 3’ direction. This process is called…?
Proofreading
Synthesis is ______
bidirectional
Helices breaks _____ bonds between nucleotides to open the replication fork
hydrogen
synthesis of the leading strand - direction and process?
synthesizes in the 5’ to 3’ direction TOWARD the replication fork.
The DNA polymerase III recognizes the location of the primer sequence and clamps hold of the DNA at that location. It then creates a copy of the leading strand as it travels toward the replication fork.
synthesis of the lagging strand - direction and process?
synthesis in the 5’ to 3’ direction AWAY from the replication fork.
DNA polymerase III would synthesize short fragments (Okazaki fragments) of DNA along the lagging strand that later are linked together to form a continuous strand of DNA. DNA polymerase I comes in and removes the RNA primer and synthesizes DNA in its place. DNA ligase joins the Okazaki fragment with a phosphodiester bond.
Where does RNA transcription occur in prokaryotes and eukaryotes?
In the cytoplasm in prokaryotes and the nucleus in eukaryotes
The mRNA strand that is synthesized with a DNA strand serving as a template is referred to as ______ to the DNA strand.
complementary
example of DNA template strand sequence to mRNA sequence:
GAATCT»_space;>
CUUAGA
Which strand of DNA serves as the template for mRNA?
The 3’ to 5’ strand
- non-coding strand
- template strand
Which strand of DNA does NOT serve as the template for mRNA?
The 5’ to 3’ strand
- coding strand
- the gene
- non-template strand
In which direction does mRNA synthesize?
5’ to 3’ direction
Which enzyme transcribes the template strand of DNA to mRNA?
RNA polymerase
Steps of transcription
Initiation
-Sigma, a protein subunit, must bind to the DNA
Elongation
-Sigma and RNA polymerase together form a holoenzyme
-The sigma guides the RNA polymerase to specific PROMOTER sequences on the DNA template strand
What is a holoenzyme and what creates it?
A holoenzyme is an enzyme made up of core enzymes and other required proteins
It’s created by a sigma and RNA polymerase
How to know if it is a bacterial promoter?
- 10 box: 10 bases upstream during transcription is the sequence TATAAT
- 35 box: consisting of the sequence TTGACA is 35 bases upstream
- all bacterial promotes have a -10 box and a -35 box
How to know if it is a eukaryotic promoter?
- more complex series of promoters than prokaryotes
- many eukaryotic promoters include a unique sequence called the TATA box centered about 30 base pairs upstream
RNA processing in eukaryotes
- introns
- exons
- snRNPs (“snurps”)
- capping
- poly A tail
What are introns?
intervening noncoding sequences transcribed but not translated
What are exons?
exons are coding regions of eukaryotic genes that are found in mature mRNA
What is required to make a functional mRNA?
the introns (noncoding regions) must be removed through splicing
What is the removal of introns called and what enzyme carries out this function?
Splicing.
snRNPs (“snurps”) remove the introns
-look at notes for pictures
What is capping?
a cap is added to the 5’ end of the mRNA (called 5’ cap)
-necessary for mRNA to exit nucleus and prevent degradation
What is the poly A tail?
many A in sequence added to the 3’ end (called poly A tail)
- aids in the export mRNA from nucleus
- increases stability and lifespan
Where does RNA translation occur?
translation happens in ribosomes in the cytosol or rough ER
If a codon in a strand of mRNA is UCG (5’ to 3’ direction), what is the anticodon?
AGC (3’ to 5’) direction
What does tRNA do?
carries the amino acid.
-the anticodon part of the tRNA molecule allows binding between the tRNA and mRNA codon
What is aminoacyl-tRNA synthetase?
catalyzes attachment of amino acids to tRNA (one for each of 20 different amino acids)
-results in tRNA with amino acid attached
When is the tRNA charged?
When it carries an amino acid
Ribosomes can be separated into two subunits:
- the small subunit - holds the mRNA in place during translation
- the large subunit - where peptide bonds form
During translation ___ tRNAs line up within the ribosome.
3
Process of translation (general)
- initiation - mRNA binds to small subunit off ribosome in 5’ to 3’ direction
- ribosome looks for AUG start codon (anticodon UAC)
- large subunit of ribosome binds
- peptide bond formation
- continues until stop codon
- polypeptide relaxed with release factors and mRNA chain released and ribosome breaks apart
What allows the polypeptide to be released?
release factors
What is the function of telomerase?
makes extra DNA on 3’ overhangs
What is the function of the sigma in transcription?
Searches for the promoters
What are the promoters?
sequence of DNA
in prokaryotes -35 and -10 boxes
in eukaryotes TATA
What is the terminator?
Sequence of DNA that indicates the finish of transcription
What does the splicosome do?
w/ snRNPs that cuts out introns and it adds a cap to the 5’ end and a poly A tail to the 3’ end
Players in Transcription? (5)
- sigma
- promoter
- RNA polymerase
- terminator sequence
- splicosome
Players in translation?
- codon on mRNA 5’ to 3’
- anticodon on tRNA 3’ to 5’
- tRNA synthetase
- look for AUG start codon
- until stop codon
What is the start codon?
AUG
3 Stages of transcription?
initiation, elongation, termination
Transcription results in…
1) mRNA that encodes a polypeptide
2) rRNA that’ll be incorporated in a ribosome
3) tRNA that’ll be used to translate an mRNA
Transcription units are called _____
genes
In transcription in eukaryotes, ______ are used instead off the sigma protein that is used during transcription in prokaryotes
transcription factors that detect recognition sites in the eukaryotic promoter regions
binds too the TATA box at -30
What are the 3 different kinds of RNA polymerases?
I: makes large rRNA transcripts
II: makes mRNA transcripts
III: makes tRNA and small rRNA transcripts
Why does the final product of transcription result in mRNA that is different in length from the original gene sequence? (2)
1) Because of splicing and introns being taken out by snRNPs and only exons staying.
2) The addition of the 5’ cap and the 3’ poly A tail
In ______, the mRNA must be completely transcribed and processed before it leaves the nucleus to be translated by the ribosome machinery
eukaryotes
3 steps of translation?
1) initiation
- the mRNA has a ribosome-winding site and initiation factors to help temporarily bind the mRNA to the small ribosomal subunit. This allows aminoacyl tRNA to bind to the start codon which allows the large ribosomal subunit to bind to the RNA complex
2) elongation
- appropriate aminoacyl tRNAs bind to specific locations in the mRNA complex which initiates movement of the tRNAs in the active sites and movement of ribosome along the mRNA so that the A-site becomes open for the next appropriate aminoacyl tRNA
- growing polypeptide attached to the tRNA in the P-site and the go methionine residues detached from the tRNA that’s still attached to the start codon in the E-site
3) termination
- a tRNA that lacks an amino acid comes to occupy the A-site and is complimentary to the termination codon
- the last amino acids in the chain detach from their respective tRNAs, the polypeptide has nothing holding it in place, so it detaches from the ribosomal complex
- mRNA is now free to combine with another ribosome and produce more polypeptide products
An tRNA is ______ when an amino acid is attached by the aminoacyl-tRNA synthetase
charged
Ribosomes contain ____ and _____.
protetins
rRNA
