Intro to Bio exam 2

how is energy in sugars used

sugars’ carbon backbone are broken down, which drives ATP synthesis

the two main mechanisms b ywhich organisms break down sugars into ATP

aerobic respiration and fermentation

aerobic respiration

requires O2 to break down sugars into ATP. main energy-releasing pathway in almost all eukaryotes and some bacteria

the stages of aerobic respiration and how many ATP are produced

Gycolysis:2, Krebs cycle:2, and ETC:~32, ~36 total

fermentation

sugar breakdown into ATP not requiring O2. begins with glycolysis. occurs entirely in cytoplasm. net yield of 2 ATP. 2 pathways: alcoholic or lactate.

alcoholic fermentation

anaerobic sugar breakdown pathway that produces ATP, CO2, and ethanol.

• pyruvate split into CO2 and acetaldehyde

• e- and H+ transferred from NADH to acetaldehyde, forming NAD+ and ethanol

lactate fermentation

anaerobic sugar breakdown pathway that produces ATP and lactate. white muscle fibers primarily produce ATP by this.

• e- and H+ carried by NADH transferred to pyruvate

• pyruvate converted directly to lactate

• NADh converted to NAD+

red muscle fibers

many mitochondria and myoglobin. produce ATP mainly by aerobic respiration. sustains prolonged activity

white muscle fibers

contain few mitochondria and no myoglobin. produce ATP mainly by lactate fermentation. useful for quick, strenuous activities

fermentation steps

• pyruvate not fully broken down into CO2

• e- dont move through ETC so no ATP formed

• NAD+ regenerated allowing glycolysis to continue, Net 2 ATP

• 
  

energy-releasing pathway evolved

first cell appeared 3.4 billion years ago and didnt use sunlight. photosynthesis evntually evolved since sunlight offered unlimited energy. H2O split into H2 and O2. O2 spread in the atmosphere and ocean. Originally lead to pollution. Few lineages persisted, aerobic organisms. Organisms used O2 in pathways.

glycolysis

phase 1 of aerobic respiration. occurs in cytoplasm. 10 steps where glucose is broken down into two pyruvate molecules. net 2 ATP.

glycolysis steps

• phosphate group is transferred from ATP to glucose forming glucose-6-phosphate

• glucose-6-phosphate accepts a phosphate group from another ATP forming two phosphoglyceraldehyde (PGAL)

• each PGAL receives a 2nd phosphate, gives up 2 e-, and gives up a H+ which NAD+ will accept to form NADH. phosphoglycerate (PGA) will form

• a Pi is transferred from each PGA to ADP to form 2 ATP.

• ends with 2 ATP formed (NET 2 ATP) by substrate-level phosphorylation and 2 pyruvate molecules

substrate-level phosphorylation

direct transfer of a Pi from a substrate to ADP

Citric acid cycle

stage 2. occurs in mitochondrial matrix. complete breakdown of pyruvate. includes acetyl-CoA formation and Krebs cycle. all C released as CO2. Net 6 CO2, 2 ATP, 8 NADH, and 2 FADH2.

acetyl-CoA formation

pyruvate transported to mitochondrial matrix. split into CO2 and 2 acetyl groups (-COCH3). CO2 diffues from cell and acetyl binds with coenzyme A (CoA).

actiavted carrier molecules

NADH and FADH2. exist in oxidized or reduced forms. reduced form carries high energy e- that can be transferred to other molecules.

krebs cycle steps

• acetyl-CoA are transferred to oxaloactetate to form citrate, 2 CO2 depart, 2 NADH are formed

• ATP formed by substrate-level phosphorylation, FAD and NAD+ are reduced, oxaloacetate is regenerated

• Net 6 CO2, 2 ATP, 8 NADH, and 2 FADH2 (will provide e- for 3rd stage)

oxidative phosphorylation

stage 3. occurs in mitochondrial inner membrane. 2 stages: creation of proton (H+) gradient across mitochondrial membrane and use of the gradient to power ATP synthesis.

oxidative phosphorylation steps

• NADH and FADH2 deliver e- and H+ to ETC.

• e- give up energy little by little as they move through the gradient.

• H+ ions actively transported across membrane. resulting H= gradient allows ions to flow through ATP synthase driving ATP formation

• O2 final acceptor. H2O formed as by product. ~30-34 ATP formed. fueled by 12 coenzymes reduced.

organic molecules used for energy from the body

dietary molecules: aerobic respiration makes ATPby oxidizing glucose , dismantling Cs. can dismantle other organic molecules by oxidation. carbohydrates, fats, and proteins in food can be converted into molecules that enter glycolysis or krebs

carbohydrates

broken down into monosaccharides. sugars converted to glucose-6-phosphate fro glycolysis. high ATP levels cause glucose-6-phosphate to divert from glycolysis and into glycogen

fats

dismantled by breaking bonds connecting faty caid tails to glycerol heads. free fats are oxidized by splitting backbones into 2 C parts, these parts are converted into acetyl-CoA. glycerol converts to PGAL.

proteins

split into amino acid subunits. NH3 formed as waste product, eliminated in urine, and very toxic to cell. backbone split into acetyl-CoA, pyruvate, or intermediates. enter aerobic respiration

mitochondrial malfunction

• O2 can exit ETC as a free radical which can cause damage by oxidizing biological molecules and break C backbones. antioxidants in cytoplasm detoxify free radicals.

• genetic disorders/encounters with toxin can result in a missing antioxidant/defective ETC. associated with hundreds of incurable disorders: cancer, HTN, alzheimers, Parkinson, etc.

• free radicals accumulate and destry mitochondrial function, then cell. tissue damage is oxidative stress

discovery of DNAs function

many experiments. DNA discovered in 1869 by Johannes Miescher: nuclei are rich in acidic compound high in N and Ph. Frederick Griffith in 1920s uncovered clues about DNAs function: smooth adn rough strains of bacteria

DNA as genetic material

Avery and McCarty in 1940 idenitfied “transforming principle” as DNA. s cell extract treated with protein and lipid destroying enzymes dont block the s cells transformation of R cells. DNA degrading enzymes prevented transformation

DNA structure

building blocks. a polymer of nucleotides. 4 bases. Jmes Watson and Francis Crick suspect DNA is a helix. Rosalind Franklin made first clear x-ray diffraction image of DNA in cells. non covalent bonds holds both strands together.

Chargaff’s rules

erwin chargaff discovered A=T and G=C (1:1) and proportions of A and G differ in DNA of different species

variations in base sequences (genetic variation)

source of lifes diversity

length of DNA molecules

hundreds of millions nucelotides long, 3×10^9 BP/ 6x10^9

~6 ft long in a cell

so they can encode massive amount of information

histone

a protein that structurally organizes eukaryotic chromosomes

chromosomes

consist of 1 DNA molecule most of its life, DNA replication duplicates them in preparation to divide, after replication each chromosome consists of sister chromatids (2 DNA) that attach at a centromere

mitotic chromosome

duplicated with filaments in “X” shape and the copies stay attached after replication until mitosis

diploid

cells have 2 of each type of chromosome (2n), humans have 23n (1 maternal and 1 paternal)

haploid

gametes, 1n

karyotypes

an image of an individuals diploid set of chromsomes

autosomal chromosomes

same in males and females. 2 autosomes of a pair have same length, shape, centromere location, and hold same info about traits

sex chromosomes

differ between males and females: determine sex. females=XX males=XY

sex determination in humans

1 sex chromsome from mom and 1 from dad.

DNA replication

a cell copies its chromosomes to contain two sets, an exact copy for each daughter. DNA is its own template. multiple steps with activity of a few enzymes, DNA polymerase

DNA polymerase

creates new DNA strand by assembling proper nucleotides. attach to hybridized primers to begin DNA synthesis. catalyzes formation of sugar-p bond. proofread their own work. attach to 3’ end

DNA is antiparallel

helicase

replication begins when it breaks hydrogen bonds holding the double helix together

primase

constructs primers

primers

short single strands of nucleotides. serve as attachment points for DNA polymerase. base pairs with complementary strand of DNA

nucleic acid hybridization

establishment of base pairing between two DNA strands. spontaneous, driven by H bonds between bases of the complementary strands. nucleotides provides energy for its attachment

DNA ligase

seals nicks from DNA polymerase so the strand is continuous

DNA repair mechanisms

corrects mismatches by reversing synthesis reaction to remove a mismatched nucleotide then resuming synthesis.

mutations

errors after proofreading and repair mechanism fail. permanent change in DNA sequence of a cells chromosome. if occuring during egg/sperm formation can be passed to offspring

semiconservative replication

produces 2 copies of DNA molecule where one strand is new and the other is parental. both copied at the same time

mutations causes

• ionizing radiation from x-rays, UV light, gamma rays

• can form in any type of cell

• mutations altering DNAs instructions may have harmful/lethal outcome, like cancer

• some give rise to variation=not harmful

transcription

DNA —> RNA. part of one DNA strand is used as template to assemble an RNA strand with RNA polymerase. eukaryotes=nucleus, prokaryotes=cytoplasm

gene

part of a DNA base sequence. specifies mRNA, tRNA, and rRNA

information carried in DNA

the instructions for building RNA or protein products. the DNA subset that specifies a certain RNA

gene expression

converting information encoded by a gene to a product. begins by transcription (RNA synthesis). transcription and translation. DNA—> RNA—> protein.

RNA

ribonucleic acid, single stranded, (A,U,G,C). sugar=ribose.

DNA

deoxyribonucleic acid. deoxyribose. (A,G,C,T). double stranded

ribosomal RNA (rRNA)

main part of ribosomes, which assemle AA into polypeptide chains. have enzymatic activity

transfer RNA (tRNA)

delivers AA to a ribosome during protein synthesis. recognizes base pairs with rRNA and delivers correct AA

messenger RNA (mRNA)

contain protein building message. specifies AA order sequence

translation

RNA —> protein. mRNAs message encoded by sets of three nucleotides. the protein building information in an mRNA is translated into AA sequence. results in polypeptide chain twisting and folding into a protein.

RNA polymerase

adds nucleotides to the end of growing RNA. transcription begins when this and regulatory proteins attach to a promoter on DNA. when it reaches the end of a gene region it releases DNA and RNA. can transcribe many at a time

RNA splicing

remove introns to stay in the nucleus.

introns

intervening sequences. removed from newly transcribed RNA before leaving the nucleus. dont have protein coding information.

exons

sequences that stay in RNA

post-transcriptional cap

a modified guanine cap is added to 5’ end to help mRNA bind ribosomes

post-transcriptional polA-tail

many adenine nucleotides are added to 3’ end to enable exportation from the nucleus

codon

an mRNA nucleotide base triplet that codes for an amino acid or stop signal. occur one after another along th elength of mRNA. the order of codons determine the order of AA

start codon

AUG= methionine!

stop codons

UGA, UAA, UAG

tRNA

deliver AA to ribosomes in the specified order by mRNA. have two attachment sites: anticodon and AA attachment site

ribosomes as translator molecules

contain rRNA and structural proteins. interact with tRNA to translate mRNA. bind mRNA and interact with tRNA to allow codon base pairing. have a large and small subunit. subunits converge during translation as an intact ribosome on mRNA. prokaryotic and eukaryotic differ in size

rRNA

catalyzes formation of the peptide bond between AA. is catalytic

anticodon

a triplet of nucelotides that base pairs with an mRNA nucleotide

translation: initiation

• a initiator is pre-loaded on small subunit

• mRNA is bound and 1st AUG pairs with initiator

• large subunit joins small one and the ribosome begins assembling a polypeptide chain moving along mRNA

initiator

special tRNA. carry methionine.

translation: elongation

• another tRNA joins joins when anticodon pairs with 2nd codon

• ribosome catalyzes formation of a peptide bond between AA

• as ribosome moves to next codon it releases 1st tRNA

translation: termination

• continuation of AA chain until the ribosome reaches a stop codon and mRNA, polypeptide releases

mutation types

• silent: CCU → CCC

• missense: CCU → CUU

• nonsense: make stop codons?

frameshift mutations

insertion/deletions (often in DNA rep). ex: beta thalassemia

gene control

typical cell uses 10% of genes at one time. genes can affect structure and metabolic pathways and others can only be expressed by cell subsets

what turn a gene on or off

molecules or processes that trigger or inhibit the individual steps of its expression

transcription factors

bidn directly to DNA and affect whether and how fast a gene is transcribed

repressors

bind to operators or silencers to shut off or slow down transcription.

operators

prokaryoptic silencers (DNA)

activators

recruit RNA polymerase to a promoter region to enhance transcription. enhancers

enhancer

distant DNA binding site (far from RNA polymerase binding site) for eukaryotic activators

histone

proteins that wrap and condense DNA. relatively unwound ones are accesible to RNA polymerase. modified ones may be more/less accessible to RNA polymerase

microRNAs

small noncoding RNA. can shut down translation of a particular mRNA. can destruct all mRNA complementary to i tby RNA interference

post-translational modifications

inhibit, activate, or stabilize many molecules. “many newly synthesized polypeptide chains must be modified before they become functional”

master genes

products of this affect the expression of other genes

differentiation

process by which cells become visually distinct and specialized in th erole in the organism. occurs as cells express different subsets of their genes making different cell lineages

genes controlling development in animals

• nucleus turns on master genes based on their position relative to the protein gradient

master genes

products form gradients which further infleunce which master genes the nucleus will turn on. eventually cause undifferentiated cells to differentiate and formation of specialized cells. sffect other genes expression

homeotic gene

encode transcription factors with a home-domain. type of master gene. its expression control formation of specific body parts during development. often named for what happens when a mutatino alters their function. evolved in the most ancient eukaryotic cells

homeodomain

a region of about sixty AA that can bind to regulatory sequences. often differ among species only in conservative substitutions

barr bodes

an X chromosome in each cell tightly condensed. most genes not expressed (X inactivation)

x chromsome inactivation

ensures only 1/2 X chromosome in a female is active

dosage compensation

mechanisms where X chromsome inactivation equalizes gene expression between males and females. there is random inactivation of mom and dad X chromsomes in each cell