Bis 2A

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How does electronegativity predict bonds

* if electronegitivity below .4 it is = non polar covalen
* Bean .5 and 2 = polar covalent
* Above 2= ionic

Condensation

Water is released ‘

Protein

Series of amino acids (amino group and carbonyl groups)

Carbonyardes

C -h2-c

* long chain of Monomers-and polymers

Nucleic acids

Phosphate group WTH nitrogen and Pentose sugar (deoxiribose)

Hydroxyl functional group

OH

Carboxyl functional group

O= C - OH

Phosphate functional

P and 4 O

Aldehyde functional group

O=c-h

Ketone functional group

0=c with two carbons

Amino functional group

N-2H

Sylfhydral functional group

S-H

Deoxiribose vs ribose

* C2-H = deoxiribose
* C2-OH= ribose

Count where carbonyl starts

Steroids

* ring structure
* 4 linked carbon
* Tail
* Lipids
* Some have OH (STEROLS ALCOHOL CLASSIFICATION)

Unsaturated

\-Double bonds present

\-kinks

\-Liquid and not lightly packed

Saturated

* long chain of singlebonds
* No kinks
* Stacked
* \

Explain structure of phospholipid

* Phosphate group polar
* Glycerol
* Two non polar fatty acid l
* Make Micelle structure

Define pKa

The quantative measure of how readily acid donates H+

( when ph increases the more the acid will become depronated)

Primary structure protein

Series of amino. Acids. Held by peptide Bonds

\

Secondary structure protein

* localized structure within primary Structure (intra)
* Held by hydrogen Bonds ( btwn carbonyl O and H of two amino acid)
* Folding bc hydrogen bonds

Tertiary structure

* held together by everything But non covalent bonds
* Shaped bcc of side chain interactions

Quaternary structure

Peptide bonds

* protein-consists of more than one amino acid

Describe interaction between amino acids during protein folding of 1,2,3,4)

Drives the folding and intramdecular bonding of the linear amino acid chain

How do differences in lipid composition affect the fluidity of different membranes?

Lipids that can pack more tightly make membranes more rigid and stronger but less fluid

Cell membrane

Protects cell from surrounding

Nucleus

Control Center of cell

Endoplesmic rectum

* folding of protein molecules
* Transport of proteins to Golgi apparatus

Golgi apparatus

* modifying and sorting of proteins
* Transport lipids
* Creation of lysosomes

Lysosomes

* contain digestive enzymes
* Engulf viruses or bacteria

Vacuole =

Maintains proper pressure

* provide structure and support for growing plants

Chloroplasts

Convert light into sugars

Explain how water moves in and out of cell

Osmosis

* low to high

Passive transport

High to low

\-down concentration gradient

Facilitated transport

* move molecules WTH membrane proteins
* \

Active transport

* move molecules against concentration gradient
* Use ATP

First law of thermodynamics

* energy is conserved
* Neither destroyed or created

Second law of thermodynamics

After energy transformation some energy is no longer usable

What makes a reaction spontaneous

delta G

What makes a reaction nonspontancus

Delta G >0

Endorganic

Now ATP hydrolysis can be coupled to endorgenic beatin

ATP drives endorganic reactions bY phosphorylation

* transferring a phosphate group

What happens during glycolysis

Glucose broken down into pyruvate and energy

* 2 ATPDerived
* Cytoplasm
* Catabolic
* Exorgenic

\

Substrate level of phosphorylation

* phosphoryl group transferred from substrate to ADP
* Forms ATP which releases energy

Fermentation explain

Anaerobic pathway breaking down glucose

* glycolysis is the only energy extraction
* Absent oxygen

Oxidative phosPhoralyation VS fermentation

\
fermentation

* produces little ATP
* Does not need O2 l ‘‘
* Evolved first
* final e acceptor is pyruvate

Oxidati ve

* mass amounts of ATP
* Needs O2
* Evolved after fermentation
* Final E accepter O2

\

Glucogenesis

Produces glucose

* occurs in mitochondria and cytoplasma
* Anabolic
* Endorgenic

Pentose phosphate pathucy

* glucose 6 phosphate denhydrogenesis
* ATP synthesis and NADPH
* CO2 releases during oxidation

Calvin Cycle

* enzyme is rubisco
* CO2 fixation
* Produce NADPH
* CO2 is fixed in the environment
* Use products of Light dependent reactions

Ether functional group

* central oxygen bonded to two Carbons

Esterbonds

* Central carbon bonded to oxygen

Glucose vs galactose

\-Direr at position c4

\-aldose

Fructose

* divers at C 1 and C2
* Ketone

Nome of biomolecule

Chosteral

* lipid molecule
* \

Name molecule

Cortisol

A vs B glucose

* differ at C1
* H top = A
* \

Cellulose structure

1-4 b linkages glucose

Components of membrane

_Proteins

* lipids
* Carbonyardes

Integral membrane proteins

* integrates completely into membrane structure
* Can stretch from one side to another

Photo phosphorylation

* transfer of energy from eight
* Creat PMF
* Nadph
* ATP

DNA helices

* couples ex hydrolysis of ATP to unwind DNA

Telomerase

* fixes overhang of RNA using DNA
* RNA dependent polymerase
* Contains RNA primer

DNA polymerase 1

\-Proofreads DNA

* removes incorrect sequence
* Adds correct base

Direct chemical reversal

* No excision of backbone
* Removes mismatched pair

Base excision repair

\-Excision of DNA backbone

* damage ATP
* Glycolsylase detects and removes it
* End nuclease removes site
* Poly/ligase fill gap

Nucleotide excision repair

* involves THYMINE DIMER
* Damaged region cut cut
* Gap filled in

What are the challenges of replicating the ends of linear chromosome and how telomerase solved this?

The DNA in end can not be fully replicated. Resulting in shorter chromosome which telomerase helps

What is the central dogma?

DNA to RNA to protein

RNA polymerase

5 to 3’

\-Unwinds DNA (transcription

* does not proofread and correct mistakes

Eukaryotic mRNA

* splicing and capping occur in nucleus
* Introns degraded in nucleus into nueleuides
* Leaves to cytoplasma

Gram negative

* ping (spaced)
* Outer membrane and space

Gram positive

\-Purple

\- pep layer

* plasma membrane

Endoplasmic reticulum

* Folding protein
* Transport proteins to Golgi apparatus

Lysosomes

* contain digestive enzyme
* Digest excess
* Engulf

Vacuole

* maintains pressure
* Provide structure

Peroxisome

* breaks down toxic materials
* Metabolic activity

How can surface area be increased?

* Can increase protein receptors
* Increase membrane
* \

Microfilements

* composed of actin
* Bound to ATP
* Thicken cortex
* \

Microtubules

* maintain cell shape
* GTP BOND
* Creates GDP

Intermediate filaments

\-Holds organelles in place

\

Moter proteins

* converts energy from ATP hydrolysis to walk along microtubule

Dynein

Moves from (+ to-)

kinesins

Moves from ( - to+ )

What is the consequences of not having nad+?

Glycolysis would not continue

No ATP formed

\#Of hyorgenbonds stun adenine and thymine

2

. in DNA

Ump

Reverse transpitase

DNA copy from RNA

Promoter

DNA element

* instructs RNA polymerase where to bird

When does saturation Occur

When a group of carrier proteins is operating at max

Silent mutation

Negligible reject

of ligase

Joins 3 hydroxyl and 5 phosphate

Overview of transcription

Intiation

Elongation

\
Termination

Sites on DNA required for transcription

Promoter

* transcription start
* Termination site

Sigma factor

RNA polymerase

_Recognizes promoter

\-Tatta box

Transcription

5 to 3

\-RNA polymerase (unwinds DNA)

’

Eukaryotic transcription

5 cap modified

Poly A tail added

’

Translation initiation and stop codons

Start: Aug

_Ribosome chooses start

Stop: USA, UAG,UGA

tRNA

Translates code

Aminoacyl tRNA

Charges TRNA with correct amino acid

ATP required

Overview of translation initiation

* ribosome around mRNA
* TRNA with codon
* 5cap mRNA REQ

Translation elongation

TRNA transfers amino acid to the next trna

Translation translocation

Ribosome moves to the next mRNA codoln