PoB 1 Midterm 2

origin of replication

special sequence where DNA strands first separated - moves outward once triggered, forming a replication bubble. has special types of enzymes to do this

replication fork

y shaped structure that forms in a DNA double helix during replication

helicase

enzyme responsible for unzipping DNA. works as a wedge sliding on only one strand, not on both.

ssDNA binding proteins

stabilize the DNA, prevent it from folding back on itself while separated into two single strands

DNA polymerase

catalyzes addition of nucleotides to the DNA strand. makes the dna polymer

two types of bonds formed by DNA polymerase

hydrogen bonds: to template strand

covalent phosphodiester bond: to previous nucleotide

removing phosphates from dNTP/incoming nucleotide

powers the phosphodiester bond formation (endergonic reaction)

DNA polymerase requirement

3’ OH on previous nucleotide

dna primase

type of RNA polymerase that makes a primer (short single-stranded strand of nucleotides. DNA polymerase cannot start a new strand from scratch

dNTP

a deoxygenated f nucleotide with three phosphates

5’ to 3’

the direction in which polymerases move on the strand they are synthesizig

leading strand

the strand in which DNA synthesis is continuous

lagging strand

the strand in which DNA synthesis has to keep getting started

okazaki fragments

the fragments of DNA synthesized on the lagging strand

DNA ligase

enzyme that synthesizes pieces of the lagging strand together. fills in the missing bond with ATP

DNA polymerase

gets rid of RNA pieces in DNA new strands by displacing

topoisomerase

cuts and rejoins DNA to alleviate twists during replication. on the front of the replication fork and untwists it. targeted in antibiotic and cancer drugs

telomeres

repetitive sequences on he ends of eukaryotic DNA that cells can afford to waste.

telomerase

prevents degradation of telomere that would otherwise become shorter and shorter with each cell replication.

proofreading

DNA polymerase itself can fix a lot of its mistakes - recognizes when the wrong base has been added and can remove the last nucleotide then try again. gets error down to 1/10^6

mismatch repair

special enzymes recognize misshapen DNA, cut it out, and replace it. reduces error rate to 1/10^9

PCNA

clamp protein; DNA polymerase falls off of DNA easily, this clamp keeps it on and speeds up replication.

sequence-specific

being able to choose what DNA sequences get copied

polymerase chain reaction (PCR)

method of making many copies of a chosen region from a single DNA molecule. makes analysis much easier

synthetic DNA primers

about 20 bases long. if complimentary to a specific sequence, they will bind there. need to be next to the strand we want to copy with the 3’ ends facing inwards.

DNA, DNA polymerase, DNA primers, dNTPs, buffers

what is added to the PCR test tubes? (5)

denaturation, annealing, extension

3 chronological steps of PCR - will be repeated 30 times

denaturation

1st stage of PCR; high temps used to break hydrogen bonds, separating the strands of DNA

annealing

2nd stage of PCR; lower temps allowing for primers to bind to the template DNA

extension

3rd stage of PCR; intermediate temps to optimize DNA polymerase activity

negative

charge of DNA in water due to phosphate groups

gel electrophoresis

allows for the size separation of DNA. electric current moves through gel, and DNA moved towards the cathode

cathode

negatively charged electrode

anode

positively charged electrode

agarose gel

contains + separates DNA by size. made of polymerized agarose sugars witha mesh-like structure of pores

loading dye

moves ahead of the DNA molecules, allowing you to track its movement without stopping the process

DNA ladder

mixtures of DNA of known size, used as a standard ruler for comparison

DNA stains

fluorescent molecules that bind to DNA so that it can be visualized

glycerol

increases the density of the DNA sample

dNTP

deoxyribonucleic acids (-OH on 3’ carbon)

ddNTP

dideoxynucleotides - no reaction -OH group on 3’ carbon

1/1000

number of errors in replication based only on bonding errors

1/10^6

number of errors in replication with proofreading only

1/10^9

number of errors in replication with proofreading and mismatch repair

1

how many primers does sanger sequencing use

2

how many primers does PCR typically use

new techniques for genome sequencing

what came out of the human genome project?

gene

stored in DNA, information in code form. used to make a product that performs a function in a cell

mRNA

what acts as a temporary message to transmit info because DNA cannot leave the nucleus

alleles

different versions of the same gene

transcription

the process of changing information in DNA form to mRNA form. the sequence of DNA bases acts as a template for the synthesis of an RNA molecule

RNA polymerase

enzyme responsible for transcription - catalyzes formation of phosphodiester bonds between RNA monomers

translation

the process of a ribosome building a protein using the information from mRNA

tRNA

the type of RNA responsible for bringing amino acids to the ribosome during translation. they are also created during transcription

spontaneous

is translation spontaneous or nonspontaneous - (NTPS have high potential energy)

rRNA

major component of multimolecular ribosome - where protein synthesis takes place

promoter

site on DNA where RNA polymerase can bind and start transcription. initiation complex binds to DNA at this site and opens it

upstream

the part of the gene that RNA polymerase has already transcribed

template strand

the strand of DNA that is “read” by RNA polymerase during transcription

coding strand

strand of DNA that matches the sequence of bases in the RNA product of transcription, except t is now u

codon

group of 3 nucleotides in mRNA that are read to make a specific amino acid

initiation, elongation, termination

3 steps of transcription

initiation

the stage of transcription in which RNA polymerase binds to a specific DNA sequence (promoter)

higher

is free energy higher or lower when electrons are perfectly shared in covalent bonds?

acceptor

NAD+ is an electron….

donor

NADH is an electron. . .

2 ATP, glucose, 2 NAD+

inputs of glycolysis (3)

4 ATP, 2 NADH, 2H+, 2 pyruvate, 2 H2O

outputs of glycolysis (5)

3

how many carbons does pyruvate have

6

how many carbons does glucose have

fermentation

anaerobic respiration using H+ and NADH to covert pyruvate to NAD+

ethanol + CO2, lactic acid

what are the two options for fermentation waste

alcohol and lactic acid

2 types of fermentation

-686 kcal/mol

what is the change in free energy of glucose oxidation

-7.3 kcal/mol

what is the change in free energy of ATP hydrolysis

ethanol

is lactic acid or ethanol more reduced

glucose to pyruvate to CO2

carbon respiration pipeline

glycolysis, pyruvate oxidation, citric acid cycle, oxidatibe phosphorylation

4 major steps of cell respiration in order

NAD+ and FAD reduction

main point of the citric acid cycle

a hydride ion - one hydrogen and two electrons

what is added to NAD+ to make NADH (and define that)

substrate-level phosphorylation

type of ATP production that makes a small amount of ATP - not in the ETC

50 kcal/mol

what is the change in free energy of reducing NADH and FADH2

outer membrane, intermembrane space, matrix, inner membrane

4 parts of the mitochondria

H+

what ion does ATP synthase use as potential energy

the electron moving down a molecule in the ETC

what reaction is the H+ proton pump (endergonic) against the gradient in the ETC coupled with

CO2

where do plants get their mass

light energy + H2O = O2 + ATP + NADPH

light reaction equation of photosynthesis

ATP + NADPH + CO2 = C6H12O6

dark reaction equation of photosynthesis

water

where do electrons come from in the photosynthesis ETC

highly exergonic

is added H+ to O2 exergonic or endergonic, and to what extent

thylakoids

where does the light reaction take place

endergonic

is breaking apart water exergonic or endergonic

excitement of electrons in PSII

what is the splitting of water coupled with in photosynthesis

long term energy and cell wall

what is the dark reaction/calvin cycle responsible for making (2)

Rubisco

worst enzyme of all time that combines RuBP with CO2 for carbon fixation in photosynthesis

it adds O2 instead of CO2 to RuBP

why is rubisco so ass

short

what wavelength has high energy (short or long)

violet, blue, and red

what 3 wavelengths does chlorophyll use/absorb

NADPH production, ATP production

what are the two uses for light in the light reaction

P680

another name for chlorophyll