exam 2 - bio 107

carbohydrates

one of the three major classes of biological molecules; most abundant of the three

• general formula: C_n(H₂O)

functions of carbohydrates

nutritional:

• energy storage

• fuels

• metabolic intermediates

structural:

• components of nucleotides, plant, and bacteria cell walls, arthropod exoskeletons, animal connective tissue

specialized functions:

• informational (cell surface of eukaryotes— molecular recognition, cell-cell communication)

• osmotic pressure regulation (bacteria)

monosaccharides

one unit of carbohydrate

• used for energy

disaccharides 

two units of carbohydrate

• used for energy

oligosaccharides

3-10 monosaccharide units

• used for structure

polysaccharides

100s of monosaccharide units

• used for structure

glycolipids

carbohydrates combined with lipids

• found in cell membrane

glycoprotiens

carbohydrates combined with proteins

• found in cell membrane

isomers

molecules that have the same molecular formula but have different arrangements of atoms in space (different structure) 

ex. glucose, fructose, galactose, mannose all have formula C₆H₁₂O₆

epimers

sugars that differ in configuration at ONLY 1 POSITION (specific type of isomer)

ex. D-glucose & D-galactose (epimeric @ C4)

D-glucose & D-mannose (epimeric @ C2)

D-idose & L-glucose (epimeric @ C5)

enantiomers

molecules that are complete mirror images of one another (non-superimposable)

• differ in configuration at EVERY chiral center

ex. D-glucose & L-glucose

chiral center

an atom that has four different groups bonded to it in such a matter that it has a non-superimposable mirror image

cyclization of sugars

less than 1% of CHO exist in an open chain form

they’re predominantly found in ring form

• two types:

  • pyranoses - 6 membered ring structures

  • furanoses - 5 membered ring structures

pyranoses

6 membered ring structures

furanoses

5 membered ring structures

mutarotation

the process by which a carbohydrate is dissolved and water and it’s able to change in configuration by undergoing a slow and reversible conversion between two cyclic forms of the sugar (alpha and beta)

ex. when pure alpha-glucose or beta-glucose is dissolved in water, it converts between the two forms

stereoisomer

molecules that have the same molecular formula and connectivity but have a different arrangement in space

homopolysaccharies

polysaccharides that are made up of only one type of monomer

ex. glycogen, starch, cellulose, chitin

heteropolysaccharies

polysaccharides that are made up of multiple different types of monomers

ex. peptidoglycans, glycosaminoglycans

functions of polysaccharides

• glucose storage (glycogen in animals & bacteria; starch in plants)

• structure (cellulose, chitin, peptidoglycans, glycosaminoglycans)

• information (cell surface oligosaccharides and polysaccharides, on proteins/glycoprotiens and on lipids/glycolipids)

  • acts like a signaling molecule

• osmotic regulation

where are peptidoglycans found?

in cell wall of bacteria 

reducing sugar

sugars in which the oxygen of the anomeric carbon is free and not attached to any other structure; such sugars can act as reducing agents

oxidation

loss of electrons

reduction

gain of electrons

nucleic acids

• polymeric macromolecules essential for all known forms of life

• made of monomers called nucleotides

deoxyribonucleic acid (DNA)

• polymer of deoxyribonucleotide triphosphate (dNTP)

• 4 types of dNTP (ATP, CTP, TTP, GTP)

ribonucleic acid (RNA)

• polymer of ribonucleotide triphosphate (NTP)

• 2 types of NTP (ATP, CTP, UTP, GTP)

nucleotides

include a pentose sugar, nitrogenous base, and one or more phosphates

phosphate group

important because they link the sugar on one nucleotide to the phosphate of the next nucleotide to make a polynucleotide

pentose sugars

deoxyribose: a sugar with 5 carbons, has one less oxygen 

ribose: a sugar with 5 carbons, as an oxygen

nitrogenous bases

DNA:

• thymine

• adenine

• cytosine

• guanine

RNA:

• uracil

• adenine

• cytosine

• guanine

purines

have two rings

• adenine

• guanine

pyrimidines

have one ring

• uracil

• thymine

• cytosine

nucleoside

a nucleotide that doesn’t have a phosphate group

conformations of ribose

in a solution, the straight-chain (aldehyde) and ring (-furanose) forms of free ribose are in equilibrium

phosphodiester bonds

successive nucleotides of both RNA and DNA are covalently linked through phosphate-group “bridges”

• 5’-phosphate group if one nucleotide is joined to the 3’-hydroxyl group of the next nucleotide

• covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and nitrogenous bases may be regarded as side groups

• backbones of DNA and RNA are hydrophilic

• 5’ end of a nucleic acid strand lacks a nucleotide at the 5’ position and 3’ end lacks a nucleotide at the 3’ position

complementary pairing

in DNA, adenine = thymine; guanine = cytosine

chargaff’s rules:

• bases pair w/ other bases

• space b/t chains is limited

• purines pair w/ pyrimidines

• complementary pairing is vital for use and storage of genetic info

• interaction is stabilized by hydrogen bonds

A-T/ A-U are double bonded (easier to break)

C-G are triple bonded (harder to break)

distance of one complete turn of DNA?

34 armstrongs

distance between base pairs?

3.4 armstrongs

number of base pairs in each complete turn?

10

number of base pairs per helical turn in an aqueous solution?

10.5

DNA structure

• DNA strands run antiparallel

• double helix is held together by hydrogen bonding b/t base pairs and base-staking interactions

• complementarity b/t strands attributed to hydrogen bonding b/t base pairs

• base-stacking interactions make major contribution to stability of double helix

length of eukaryotic DNA

~2 meters long

diameter of nucleus

~6 micrometers

DNA packaging step 1 - DNA double helix

fundamental structure of DNA is the right-handed double helix, consisting of:

• 2 strands of nucleotides running antiparallel

• base pairing stabilized by hydrogen bonds

• major and minor grooves, which serve as binding sites for proteins

• 2nm diameter

DNA packaging step 2 - formation of nucleosomes

formation of nucleosomes, the fundamental unit of chromatin structure

nucleosome structure

• core histone octamer, composed of 8 histone proteins (H2A, H2B, H3, H4 —> 2 copies of each)

• histones are basic, allowing tight binding to negatively charged (acidic) DNA

• 146 base pairs of DNA wrapped around the histone core (1.7 turns of a left-handed supercoil)

• linker DNA (~20-60 bps) connects adjacent nucleosomes 

histone H1 & higher order folding

• histone H1 (linker histone) binds to the outside of the nucleosome

• it stabilizes nucleosomes and promotes higher-order chromatin folding

• at this stage, chromatin appears as “beads on a string” in an electron microscope

DNA packaging step 3 - formation of 30nm fiber

• nucleosomes further fold into a more compact 30 nm fiber

• involves interactions between adjacent nucleosomes, stabilized by histone H1 and other factors

2 proposed models:

• solenoid model— nucleosomes form a spiral-like helix

• zigzag model— nucleosomes alterate in a zigzag pattern

  • this compaction reduces DNA length by ~50 fold

DNA packing Step 4 - Chromatin Looping

• 30 nm fiber is further organized into chromatin loops, anchored to a scaffold of non-histone proteins

• loops contain active genes and are arranged for accessibility

  • loops go through scaffold; unnecessary DNA located in scaffold, less accessible

• scaffold consists of SMC proteins (structural maintenance of chromosomes)

• this step compacts DNA by ~1,000 fold

final step for cells that aren’t actively dividing

DNA packaging step 5 - metaphase chromosome

during mitosis, chromatin undergoes final level of condensation:

• chromatin loops coil into a tightly packed structure (~700 nm per chromatid)

• condensation is caused by proteins like condensins and cohesins

• at metaphase, chromosomes become visible as highly condensed structures ready for segregtion

• final stage reduces DNA length by ~10,000 fold

nuclear envelope

double membrane structure that encloses nucleus in eukaryotic cells, separating the nuclear contents from the cytoplasm

• plays crucial role in regulating material exchange and maintaining nuclear integrity

nuclear envelope double membrane

composed of an inner an outer membrane, each with distinct functions

nucleoporines

proteins that line the inner layer of pore of nuclear envelope

perinuclear space

space (~20-40 nm wide) between the inner and outer membranes, continuous with the lumen of the ER

outer membrane of nuclear envelope

continuous with the rough ER and may have ribosomes attached, contributing to protein synthesis

inner membrane of nuclear envelope

contains specific proteins that interact with the nuclear lamina and chromatin to provide structural support

nuclear lamina

a fibrous network of intermediate filaments (lamins) underlying the inner membrane, essential for nuclear shape and chromatin organization

central dogma

a theory stating that genetic information flows only in one direction, from DNA to RNA to protein, or RNA directly to protein

amino acids

molecules that combine to form proteins (monomers of proteins)

consists of: an amino group, carboxyl group, side chain, and alpha carbon

• more than 300 amino acids found in nature

• proteins are synthesized from just 20 amino acids

peptide

multiple amino acids joined by peptide bonds

• <50 amino acids

polypeptide

multiple peptides joined together; a polypeptide will then fold into a specific conformation depending on the interactions b/t its amino acid side chains

• <50 amino acids

amino acid residue

describes an amino acid that is bound to others by peptide bonds; can no longer be called an amino acid bc it has lost a molecule of water

acidic amino acids

amino acids in which the R-group is acidic or negatively charged

ex. Glutamic acid, Aspartic acid

basic amino acids

amino acids in which the R-group is basic or positively charged

ex. Lysine, Arginine, Histidine

amino acids w/ non-polar side chain

amino acids that have a side chain that does NOT bind of give off protons or participates in hydrogen or ionic bonds; can be thought of as “oily” or lipid-like

ex. Alanine, Valine, Leucine, Isoleucine, Phenylalaine, Tryptophan, Proline

amino acids w/ polar but uncharged side chains

amino acids that are uncharged at neutral pH, though side chains of Tyrosine and Cysteine can lose a proton at an alkaline pH

• Serine, Threonine, and Tyrosine each have a polar hydroxyl group that can participate in hydrogen bond formation

• side chains of Asparagine and Glutamine contain a carbonyl group and amide group, they can also participate in hydrogen bond formation

ex. Glycine, Serine, Threonine, Tyrosine, Cysteine, Asparagine, Glutamine

amino acids w/ + charged side chain

the basic amino acids: Lysine, Arginine, Histidine

amino acids w/ - charged side chain

the acidic amino acids: Glutamic acid and Aspartic acid

• hydrophilic in nature

aromatic amino acids

have aromatic side chains, relatively nonpolar, can participate in hydrophobic interactions

ex. Phenylalaine, Tyrosine, Tryptophan

essential amino acids

amino acids that cannot be synthesized in the body and have to be present essentially in the diet

ex. Valine, Isoleucine, Leucine, Lysine, Threonine, Tryptophan, Phenylalanine

semi-essential amino acids

amino acids that can be synthesized in the body but the rate of synthesis is lesser than the requirement (during growth, repair, or pregnancy)

ex. Glycine, Alanine, and other remaining amino acids

proteins

polymers of amino acids

• # of amino acids may range from 2-thousands 

• contain N, C, H, and O

primary structure

sequence of amino acids in a polypeptide chain

secondary structure

coiling of the peptide chain due to hydrogen bonding; may acquire spiral or zigzag shape

tertiary structure

further twisting/folding of polypeptide chain

quaternary structure

arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex

DNA replication

biological process of producing 2 identical replicas of DNA from 1 original DNA molecule; occurs in all living organisms acting as most essential part of biological inheritance

• 3 steps: initiation, elongation, termination

semiconservative replication

each DNA strand serves as a template for the synthesis of a new strand, producing 2 new DNA molecules, each w/ 1 new strand and 1 old strand 

function of DnaA

DnaA protein binds to DNA replication origin forms initial complex

helicase

unwinds double helix in advance of replication fork

• helicase is a hexameric protein; needs external energy of ATP hydrolysis to unwind DNA

• moves directionally

single stranded binding proteins (SSB)

stabilize single-stranded DNA prior to replication

• SSB binds to ssDNA w/out and sequence specificity 

• ssDNA held in an elongated state by SSB

supercoiling

when unwinding of DNA helix causes helix to become twisted/tangled

topoisomerase

removes supercoils produced by DNA unwinding at the replication fork

• in front of replication fork becomes increasingly positive supercoiled (energetically unfavorable to DNA unwinding)

• DNA link must be removed every 10 base pairs of DNA unwound

• “linking number” of DNA describes the number of times one strand winds around the other in a double helix

replication fork

both strands of DNA synthesized together at replication fork

RNA primers

initiation of new strand of DNA requires RNA primer

• 5-10 nucleotides long

• synthesized by primase

mechanism of DNA polymerase

DNA poly uses a single active site to catalyze DNA synthesis

• performs template-dependent synthesis

• distinguishes b/t ribo- and deoxyribonucleotide triphosphate (important bc in a cell NTP concentration is 10-fold higher than dNTP)

• moniters ability of incoming nucleotide to form a watson-crick base pair

polymerase proofreading strategy 1

when an incorrect nucleotide is incorporated by mistake, elongation of newly synthesized strand slows down; allows incorrect nucleotide to dissociate and correct nucleotide to bind

• error rate of ~10^-5

polymerase proofreading strategy 2

if incorrect nucleotide doesn’t dissociate, 3’ end of synthesizing strand is moved from polymerase active site to exonuclease active site

• exonuclease activity removes the nucleotide

how many base pairs can DNA poly synthesize alone?

10-100 (before dissociating from template)

how many base pairs can DNA poly synthesize w/ clamps?

100-1000

sliding clamps

clamps associate w/ DNA poly to prevent it from diffusing away from DNA (DNA poly still disengages its active site from DNA strand frequently)

• associate w/ clamp increases processivity

• clamps in eukaryotes are made of PCNA and are trimers

speed of DNA synthesis by DNA poly?

~1,000 nucleotides/sec

processivity

average # of nucleotides added each time the enzyme binds to a primer

• can range from a few bases to >50,000

speed of DNA synthesis vs. binding of strands?

DNA synthesis is much faster than that of binding of 2 strands of DNA

speed of replication fork limited by what?

limited by helicase’s activity 

• DNA poly needs to wait for helicase to separate a small section of DNA before it can synthesize the new strand

polymerase alpha

involved in synthesis of RNA/DNA primer

• 50-100 nucleotides

polymerase beta

primarily responsible for DNA repair & synthesizing the leading strand

polymerase y

mitochondrial enzyme responsible for replicating and repairing the DNA

polymerase d

primarily responsible for synthesizing the lagging strand & plays are role in repairing DNA