Review Bio Final

Eukaryotic cell

a cell that contains a nucleus

Rough ER

membrane bound space, studded with ribosomes, synthesis of proteins

Golgi apparatus

completes protein packages and ships proteins, stores protein

smooth ER

no ribosomes, synthesize lipids, stores calcium

lysosomes

cellular digestive system

peroxisomes

converts reactive oxygen species

centrioles

organizes microtubules

cytoskeleton

gives our cell their shape

endosymbiotic theory

How eukaryotic cell came to be
- one cell engulfed another
- plant cell engulfed another cell which was good at getting energy from the sun (chloroplasts)

eukaryotic picture

cell membrane

fluid mosaic model- within the membrane there is lipids and proteins

integral membrane protein

spans entire membrane, embedded in the membrane

peripheral membrane proteins

no exposed hydrophobic amino acid protein, on outer part of membrane

anchored proteins

tends to have a hydrophobic molecules covalently attached, anchored to membrane

structure of a phospholipid

How does enzymes lower activation energy

1. orient substrates
2. induce physical strain
3. alter chemical charge of a substrate

orient substrate

putting molecules in the right position to bond them
ex: bonding two amino acids to form a peptide bond

induce physical strain

stretching bonds to be a able to produce chemical reactions

environmental enzyme regulation

temperature, pH

factors enzyme regulation

- inorganic ions
- co-enzymes- carbon containing molecule (ATP)
- prosthetic- permanently bound (heme)

inhibitors

a molecule that binds to an enzyme and blocks its activity

irreversible inhibitors

covalent bond with enzyme and shut off activity

competitive reversible inhibitors

compete for the same active site with a substrate

non-competitive reversible inhibitors

binds somewhere other than the active site and can change the shape of the active site

cellular respiration equation

C6H12O6 + 6O2 → 6CO2 + 6H2O

oxidation

loss of an electron

reduction

gain of an electron

how to enzymes help with energy release

energy is lost more slowly to heat (stair step method) each step is another enzyme and chemical reaction

two co-enzymes

-NAD+ -----> NADH
-FAD+ --------> FADH2

cellular respiration

glucose + O2 ------> CO2 + H2O

steps of cellular respiration

1. glycolysis
2. pyruvate processing
3. krebs cycle
4. electron transport chain

glycolysis energy investment phase

glucose is oxidized and an investment of two ATP molecules to result in 2 glyceraldehyd 3-phosphate and 2 ADP

glycolysis energy harvesting

4 ADP+ NAD+ (reduced)+ 2G3P ---> 2 pyruvate + 4 ATP + 2 ADP

ATP yielded from glycolysis

2 ATP

substrate level phosphorylation

taking a phosphate and adding it to something else (G3P--->ADP= ATP)

pyruvate processing

2 Pyruvate + 2 NAD+ + 2 CoA → 2 Acetyl-CoA + 2 NADH + 2CO2
-NAD+ is reduced to NADH

krebs cycle

2acetylCoA + 6NAD+ + 2FAD + 2ADP --> 4Co2 + 6NADH + 2FADH2 + 2ATP

What does the Krebs cycle produce

4 ATP and lots of NADH

electron transport chain

a series of four protein complexes that couple redox reactions, creating an electrochemical gradient that leads to the creation of ATP in a complete system named oxidative phosphorylation.

ATP synthase

a system that pumps hydrogen back into the cell through an ion gradient to create ATP from ADP+ Pi

how much ATP is yielded from electron transport chain

32 ATP

ATP yielded from cellular respiration

about 36 ATP
32 ATP from electron transport chain, 4 ATP from glycolysis

lactic acid fermentation

pyruvate converted to lactate (cheese, yogurt, buttermilk, sour cream)

alchohol fermentation

Pyruvate converted to acetaldehyde by pyruvate dehydrogenase
acetaldehyde converted to ethanol by alcohol dehydrogenase
occurs in some bacteria and fungi
loses CO2

fermentation vs respiration

goal: covert glucose into energy
respiration: 32 ATP, needs oxygen
fermentation: 2 ATP, occurs when there is a lack of oxygen

photosynthesis equations

light energy + 6CO2 + 6H2O → C6H12O6 + 6O2

light reactions

converts light energy into usable energy (ATP+ NADPH)
happens in the inner membrane of the chloroplasts in the stroma

light independent reactions

uses ATP and NADPH and CO2 from light reactions to make carbohydrates

chloroplasts

where photosynthesis occurs, 2 membranes and has its own DNA

Non- cyclic electron transport chain

-occurs in the inner membrane of the chloroplast
- photosystem II absorbs so much light it gives electrons to another molecule (oxidizing agent) takes e- from H2O to make O2
- then given to photosystem I which is also absorbing light
- electron is eventually sent to where NADP+ is reduced to NADPH
- hydrogen is pumped back in through ATP synthase to produce ATP

cyclic transport chain

- only uses photosystem I
- e- always goes back to photosystem I
- can only produce ATP
- ATP synthase can still pump H+ back in to produce ATP

mitosis

cell division resulting in two daughter cells with the same DNA as the parent cell

Mitosis steps

1. prophase
2. metaphase
3. anaphase
4. telophase
5. cytokinesis

prophase

microtubules spindles form and nuclear membranes breaks down

metaphase

chromosomes line up at the metaphase plate

anaphase

separating sister chromatids, separates cleaves the proteins that hold the sister chromatids together

telophase

nuclear envelope reforms, chromosomes recodenses, triggers cytokinesis

cytokinesis

pulls membranes together to split, uses myosin and actin filaments

meiosis

cells are not identical to the parent cell, generate gametes (egg or sperm cell)

meiosis I

separates homologs (2n---> 1n)

meiosis II

separates sister chromatids

Prophase I (meiosis I)

homologous chromosomes pair up
crossing over occurs

metaphase I (meiosis I)

chromosomes line up at metaphase plates
where independent assortment occurs

Anaphase I (meiosis I)

pull homologous chromosomes apart- separating one from mom and one from dad

telophase I/ cytokinesis (meiosis I)

separates the cell to make 2 different cells

meiosis II

separates sister chromatids (similar steps to mitosis)

central dogma

DNA---> RNA---> protein

essential characteristics of DNA

1. stores genetic information
2. genetic material is subject to mutations
3. genetic material is precisely replicated in cell division
4. genetic material is expressed as a phenotype

gel electrophoresis

- grew bacteria in heavy nitrogen
- take DNA in gel and run electricity through it so it runs down through the gel
- DNA has a negative charge so it wants to move towards positive pols
- how it was discovered that DNA uses a semi conservative method in replication

steps of DNA replication

1. unwind parental DNA (separate the two strands)
2. add new nucleotides by complimentary base pairing

helicase

unwinds and separates the two strands of DNA

DNA polymerase

synthesizes DNA in the 5'-3' direction

primer

made by primase
RNA sequence to start the replication
can't add DNA from nothing so it needs a 3' hydroxyl

single stranded binding proteins

holds DNA strands apart

topoisomerase

relieves supercoiling tension

DNA ligase

seals nicks left by Pol I

telomerase

extends the ends of chromosomes

PCR

- replicates DNA in lab
1) heat run to 95C
2) cool to allow primer to bind
3) maintain temp to taq polymerase
4) repeat

mRNA

messenger
carries of copy of gene sequences to ribosomes

rRNA

- ribosomal
- provides structure and framework of ribosomes
- catalyzes formation of a peptide bond

tRNA

- transfer RNA
- carry an amino acid to ribosomes

transcription steps

1. initiation
2. elongation
3. termination

initiation (transcription)

promoter binds an directs RNA polymerase

elongation (transcription)

RNA polymerase unwinds DNA about 10 BP at a time
- 5'-3' direction

termination (transcription)

happens via unique sequence of DNA

initiation (translation)

- the start codon initiates an amino acid to bind
the tRNA with an amino enters through the A site

elongation (translation)

amino acids build on each-other as the ribosome moves through down the RNA strand

termination (translation)

protein enters the A site and H2O attaches to break off the aa chain

gene transformation in bacteria

2 strands- Smooth and rough
smooth- virulent causes you to get sick
rough- non virulent, don't get sick

heat s strain- not virulent
heat killed s stain + R strain= virulent

R stain was transformed- discovered that DNA is what is transformed

restriction digest

endonuclease recognizes certain sequences of nucleotide and cleaves them at a certain point
when there is a change that does not match the specific recognized sequence then it will not cut it

the fragments will show up on a gel electrophoresis and help us differentiate the DNA

primary structure

chain of amino acids

secondary structure

chain of aa start to fold on themselves to form hydrogen bond and form alpha helix and beta pleated sheet

tertiary structure

interaction between alpha helix and beta pleated sheet- bonds between these two forms
- give the basic shape of the protein